Starting phenix.real_space_refine on Wed Mar 4 02:05:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qew_13943/03_2026/7qew_13943.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qew_13943/03_2026/7qew_13943.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7qew_13943/03_2026/7qew_13943.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qew_13943/03_2026/7qew_13943.map" model { file = "/net/cci-nas-00/data/ceres_data/7qew_13943/03_2026/7qew_13943.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qew_13943/03_2026/7qew_13943.cif" } resolution = 2.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 84 5.16 5 C 6384 2.51 5 N 1476 2.21 5 O 1758 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9702 Number of models: 1 Model: "" Number of chains: 18 Chain: "G" Number of atoms: 1530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1530 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 181} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "H" Number of atoms: 1530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1530 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 181} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "I" Number of atoms: 1530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1530 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 181} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "J" Number of atoms: 1530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1530 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 181} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "K" Number of atoms: 1530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1530 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 181} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "L" Number of atoms: 1530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1530 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 181} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "G" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 48 Unusual residues: {'LMT': 4, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 256 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "H" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 48 Unusual residues: {'LMT': 4, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 256 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "I" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 48 Unusual residues: {'LMT': 4, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 256 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "J" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 48 Unusual residues: {'LMT': 4, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 256 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "K" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 48 Unusual residues: {'LMT': 4, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 256 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "L" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 48 Unusual residues: {'LMT': 4, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 256 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "G" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 42 Classifications: {'water': 42} Link IDs: {None: 41} Chain: "H" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 40 Classifications: {'water': 40} Link IDs: {None: 39} Chain: "I" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "J" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "K" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 40 Classifications: {'water': 40} Link IDs: {None: 39} Chain: "L" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 36 Classifications: {'water': 36} Link IDs: {None: 35} Time building chain proxies: 2.43, per 1000 atoms: 0.25 Number of scatterers: 9702 At special positions: 0 Unit cell: (96.9, 107.95, 89.25, 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 84 16.00 O 1758 8.00 N 1476 7.00 C 6384 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS G 53 " - pdb=" SG CYS G 180 " distance=2.03 Simple disulfide: pdb=" SG CYS G 60 " - pdb=" SG CYS G 174 " distance=2.03 Simple disulfide: pdb=" SG CYS G 64 " - pdb=" SG CYS G 169 " distance=2.03 Simple disulfide: pdb=" SG CYS H 53 " - pdb=" SG CYS H 180 " distance=2.03 Simple disulfide: pdb=" SG CYS H 60 " - pdb=" SG CYS H 174 " distance=2.03 Simple disulfide: pdb=" SG CYS H 64 " - pdb=" SG CYS H 169 " distance=2.03 Simple disulfide: pdb=" SG CYS I 53 " - pdb=" SG CYS I 180 " distance=2.03 Simple disulfide: pdb=" SG CYS I 60 " - pdb=" SG CYS I 174 " distance=2.03 Simple disulfide: pdb=" SG CYS I 64 " - pdb=" SG CYS I 169 " distance=2.03 Simple disulfide: pdb=" SG CYS J 53 " - pdb=" SG CYS J 180 " distance=2.03 Simple disulfide: pdb=" SG CYS J 60 " - pdb=" SG CYS J 174 " distance=2.03 Simple disulfide: pdb=" SG CYS J 64 " - pdb=" SG CYS J 169 " distance=2.03 Simple disulfide: pdb=" SG CYS K 53 " - pdb=" SG CYS K 180 " distance=2.03 Simple disulfide: pdb=" SG CYS K 60 " - pdb=" SG CYS K 174 " distance=2.03 Simple disulfide: pdb=" SG CYS K 64 " - pdb=" SG CYS K 169 " distance=2.03 Simple disulfide: pdb=" SG CYS L 53 " - pdb=" SG CYS L 180 " distance=2.03 Simple disulfide: pdb=" SG CYS L 60 " - pdb=" SG CYS L 174 " distance=2.03 Simple disulfide: pdb=" SG CYS L 64 " - pdb=" SG CYS L 169 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.77 Conformation dependent library (CDL) restraints added in 354.4 milliseconds 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2148 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 6 sheets defined 72.3% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'G' and resid 7 through 15 removed outlier: 4.092A pdb=" N LYS G 15 " --> pdb=" O GLY G 11 " (cutoff:3.500A) Processing helix chain 'G' and resid 23 through 39 removed outlier: 3.606A pdb=" N PHE G 29 " --> pdb=" O LEU G 25 " (cutoff:3.500A) Processing helix chain 'G' and resid 39 through 44 removed outlier: 3.834A pdb=" N VAL G 43 " --> pdb=" O ALA G 39 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N TRP G 44 " --> pdb=" O ALA G 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 39 through 44' Processing helix chain 'G' and resid 59 through 69 Processing helix chain 'G' and resid 72 through 100 Proline residue: G 87 - end of helix removed outlier: 3.944A pdb=" N ALA G 96 " --> pdb=" O ALA G 92 " (cutoff:3.500A) Processing helix chain 'G' and resid 130 through 159 removed outlier: 3.586A pdb=" N ILE G 140 " --> pdb=" O TYR G 136 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE G 141 " --> pdb=" O THR G 137 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL G 144 " --> pdb=" O ILE G 140 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE G 145 " --> pdb=" O PHE G 141 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR G 158 " --> pdb=" O PHE G 154 " (cutoff:3.500A) Processing helix chain 'G' and resid 184 through 217 removed outlier: 3.696A pdb=" N ARG G 216 " --> pdb=" O TYR G 212 " (cutoff:3.500A) Processing helix chain 'H' and resid 7 through 15 removed outlier: 4.092A pdb=" N LYS H 15 " --> pdb=" O GLY H 11 " (cutoff:3.500A) Processing helix chain 'H' and resid 23 through 39 removed outlier: 3.607A pdb=" N PHE H 29 " --> pdb=" O LEU H 25 " (cutoff:3.500A) Processing helix chain 'H' and resid 39 through 44 removed outlier: 3.833A pdb=" N VAL H 43 " --> pdb=" O ALA H 39 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N TRP H 44 " --> pdb=" O ALA H 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 39 through 44' Processing helix chain 'H' and resid 59 through 69 Processing helix chain 'H' and resid 72 through 100 Proline residue: H 87 - end of helix removed outlier: 3.944A pdb=" N ALA H 96 " --> pdb=" O ALA H 92 " (cutoff:3.500A) Processing helix chain 'H' and resid 130 through 159 removed outlier: 3.586A pdb=" N ILE H 140 " --> pdb=" O TYR H 136 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE H 141 " --> pdb=" O THR H 137 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL H 144 " --> pdb=" O ILE H 140 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE H 145 " --> pdb=" O PHE H 141 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR H 158 " --> pdb=" O PHE H 154 " (cutoff:3.500A) Processing helix chain 'H' and resid 184 through 217 removed outlier: 3.696A pdb=" N ARG H 216 " --> pdb=" O TYR H 212 " (cutoff:3.500A) Processing helix chain 'I' and resid 7 through 15 removed outlier: 4.091A pdb=" N LYS I 15 " --> pdb=" O GLY I 11 " (cutoff:3.500A) Processing helix chain 'I' and resid 23 through 39 removed outlier: 3.607A pdb=" N PHE I 29 " --> pdb=" O LEU I 25 " (cutoff:3.500A) Processing helix chain 'I' and resid 39 through 44 removed outlier: 3.833A pdb=" N VAL I 43 " --> pdb=" O ALA I 39 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N TRP I 44 " --> pdb=" O ALA I 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 39 through 44' Processing helix chain 'I' and resid 59 through 69 Processing helix chain 'I' and resid 72 through 100 Proline residue: I 87 - end of helix removed outlier: 3.944A pdb=" N ALA I 96 " --> pdb=" O ALA I 92 " (cutoff:3.500A) Processing helix chain 'I' and resid 130 through 159 removed outlier: 3.587A pdb=" N ILE I 140 " --> pdb=" O TYR I 136 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE I 141 " --> pdb=" O THR I 137 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL I 144 " --> pdb=" O ILE I 140 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE I 145 " --> pdb=" O PHE I 141 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR I 158 " --> pdb=" O PHE I 154 " (cutoff:3.500A) Processing helix chain 'I' and resid 184 through 217 removed outlier: 3.696A pdb=" N ARG I 216 " --> pdb=" O TYR I 212 " (cutoff:3.500A) Processing helix chain 'J' and resid 7 through 15 removed outlier: 4.092A pdb=" N LYS J 15 " --> pdb=" O GLY J 11 " (cutoff:3.500A) Processing helix chain 'J' and resid 23 through 39 removed outlier: 3.607A pdb=" N PHE J 29 " --> pdb=" O LEU J 25 " (cutoff:3.500A) Processing helix chain 'J' and resid 39 through 44 removed outlier: 3.834A pdb=" N VAL J 43 " --> pdb=" O ALA J 39 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N TRP J 44 " --> pdb=" O ALA J 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 39 through 44' Processing helix chain 'J' and resid 59 through 69 Processing helix chain 'J' and resid 72 through 100 Proline residue: J 87 - end of helix removed outlier: 3.944A pdb=" N ALA J 96 " --> pdb=" O ALA J 92 " (cutoff:3.500A) Processing helix chain 'J' and resid 130 through 159 removed outlier: 3.586A pdb=" N ILE J 140 " --> pdb=" O TYR J 136 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE J 141 " --> pdb=" O THR J 137 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL J 144 " --> pdb=" O ILE J 140 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE J 145 " --> pdb=" O PHE J 141 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR J 158 " --> pdb=" O PHE J 154 " (cutoff:3.500A) Processing helix chain 'J' and resid 184 through 217 removed outlier: 3.696A pdb=" N ARG J 216 " --> pdb=" O TYR J 212 " (cutoff:3.500A) Processing helix chain 'K' and resid 7 through 15 removed outlier: 4.091A pdb=" N LYS K 15 " --> pdb=" O GLY K 11 " (cutoff:3.500A) Processing helix chain 'K' and resid 23 through 39 removed outlier: 3.607A pdb=" N PHE K 29 " --> pdb=" O LEU K 25 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 44 removed outlier: 3.833A pdb=" N VAL K 43 " --> pdb=" O ALA K 39 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N TRP K 44 " --> pdb=" O ALA K 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 39 through 44' Processing helix chain 'K' and resid 59 through 69 Processing helix chain 'K' and resid 72 through 100 Proline residue: K 87 - end of helix removed outlier: 3.944A pdb=" N ALA K 96 " --> pdb=" O ALA K 92 " (cutoff:3.500A) Processing helix chain 'K' and resid 130 through 159 removed outlier: 3.587A pdb=" N ILE K 140 " --> pdb=" O TYR K 136 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE K 141 " --> pdb=" O THR K 137 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL K 144 " --> pdb=" O ILE K 140 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE K 145 " --> pdb=" O PHE K 141 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR K 158 " --> pdb=" O PHE K 154 " (cutoff:3.500A) Processing helix chain 'K' and resid 184 through 217 removed outlier: 3.696A pdb=" N ARG K 216 " --> pdb=" O TYR K 212 " (cutoff:3.500A) Processing helix chain 'L' and resid 7 through 15 removed outlier: 4.092A pdb=" N LYS L 15 " --> pdb=" O GLY L 11 " (cutoff:3.500A) Processing helix chain 'L' and resid 23 through 39 removed outlier: 3.607A pdb=" N PHE L 29 " --> pdb=" O LEU L 25 " (cutoff:3.500A) Processing helix chain 'L' and resid 39 through 44 removed outlier: 3.834A pdb=" N VAL L 43 " --> pdb=" O ALA L 39 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N TRP L 44 " --> pdb=" O ALA L 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 39 through 44' Processing helix chain 'L' and resid 59 through 69 Processing helix chain 'L' and resid 72 through 100 Proline residue: L 87 - end of helix removed outlier: 3.944A pdb=" N ALA L 96 " --> pdb=" O ALA L 92 " (cutoff:3.500A) Processing helix chain 'L' and resid 130 through 159 removed outlier: 3.586A pdb=" N ILE L 140 " --> pdb=" O TYR L 136 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE L 141 " --> pdb=" O THR L 137 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL L 144 " --> pdb=" O ILE L 140 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE L 145 " --> pdb=" O PHE L 141 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N TYR L 158 " --> pdb=" O PHE L 154 " (cutoff:3.500A) Processing helix chain 'L' and resid 184 through 217 removed outlier: 3.696A pdb=" N ARG L 216 " --> pdb=" O TYR L 212 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 52 through 53 Processing sheet with id=AA2, first strand: chain 'H' and resid 52 through 53 Processing sheet with id=AA3, first strand: chain 'I' and resid 52 through 53 Processing sheet with id=AA4, first strand: chain 'J' and resid 52 through 53 Processing sheet with id=AA5, first strand: chain 'K' and resid 52 through 53 Processing sheet with id=AA6, first strand: chain 'L' and resid 52 through 53 600 hydrogen bonds defined for protein. 1764 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.33 Time building geometry restraints manager: 1.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2718 1.35 - 1.46: 2633 1.46 - 1.58: 4237 1.58 - 1.70: 0 1.70 - 1.81: 120 Bond restraints: 9708 Sorted by residual: bond pdb=" C1 LMT H 303 " pdb=" C2 LMT H 303 " ideal model delta sigma weight residual 1.516 1.566 -0.050 2.00e-02 2.50e+03 6.17e+00 bond pdb=" C1 LMT L 303 " pdb=" C2 LMT L 303 " ideal model delta sigma weight residual 1.516 1.565 -0.049 2.00e-02 2.50e+03 6.11e+00 bond pdb=" C1 LMT G 303 " pdb=" C2 LMT G 303 " ideal model delta sigma weight residual 1.516 1.565 -0.049 2.00e-02 2.50e+03 6.07e+00 bond pdb=" C1 LMT J 305 " pdb=" C2 LMT J 305 " ideal model delta sigma weight residual 1.516 1.565 -0.049 2.00e-02 2.50e+03 6.06e+00 bond pdb=" C1 LMT J 303 " pdb=" C2 LMT J 303 " ideal model delta sigma weight residual 1.516 1.565 -0.049 2.00e-02 2.50e+03 6.05e+00 ... (remaining 9703 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 12723 1.61 - 3.21: 153 3.21 - 4.82: 63 4.82 - 6.42: 99 6.42 - 8.03: 60 Bond angle restraints: 13098 Sorted by residual: angle pdb=" C6 LMT H 305 " pdb=" C7 LMT H 305 " pdb=" C8 LMT H 305 " ideal model delta sigma weight residual 117.26 109.23 8.03 3.00e+00 1.11e-01 7.17e+00 angle pdb=" C6 LMT I 305 " pdb=" C7 LMT I 305 " pdb=" C8 LMT I 305 " ideal model delta sigma weight residual 117.26 109.27 7.99 3.00e+00 1.11e-01 7.10e+00 angle pdb=" C6 LMT J 305 " pdb=" C7 LMT J 305 " pdb=" C8 LMT J 305 " ideal model delta sigma weight residual 117.26 109.28 7.98 3.00e+00 1.11e-01 7.08e+00 angle pdb=" C6 LMT K 305 " pdb=" C7 LMT K 305 " pdb=" C8 LMT K 305 " ideal model delta sigma weight residual 117.26 109.30 7.96 3.00e+00 1.11e-01 7.04e+00 angle pdb=" C6 LMT L 303 " pdb=" C7 LMT L 303 " pdb=" C8 LMT L 303 " ideal model delta sigma weight residual 117.26 109.31 7.95 3.00e+00 1.11e-01 7.03e+00 ... (remaining 13093 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.92: 5056 11.92 - 23.85: 344 23.85 - 35.77: 144 35.77 - 47.70: 42 47.70 - 59.62: 30 Dihedral angle restraints: 5616 sinusoidal: 2298 harmonic: 3318 Sorted by residual: dihedral pdb=" CA ILE J 23 " pdb=" C ILE J 23 " pdb=" N TRP J 24 " pdb=" CA TRP J 24 " ideal model delta harmonic sigma weight residual -180.00 -165.41 -14.59 0 5.00e+00 4.00e-02 8.51e+00 dihedral pdb=" CA ILE I 23 " pdb=" C ILE I 23 " pdb=" N TRP I 24 " pdb=" CA TRP I 24 " ideal model delta harmonic sigma weight residual -180.00 -165.43 -14.57 0 5.00e+00 4.00e-02 8.49e+00 dihedral pdb=" CA ILE H 23 " pdb=" C ILE H 23 " pdb=" N TRP H 24 " pdb=" CA TRP H 24 " ideal model delta harmonic sigma weight residual -180.00 -165.45 -14.55 0 5.00e+00 4.00e-02 8.47e+00 ... (remaining 5613 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.021: 764 0.021 - 0.042: 395 0.042 - 0.063: 209 0.063 - 0.084: 51 0.084 - 0.105: 51 Chirality restraints: 1470 Sorted by residual: chirality pdb=" CA ILE H 71 " pdb=" N ILE H 71 " pdb=" C ILE H 71 " pdb=" CB ILE H 71 " both_signs ideal model delta sigma weight residual False 2.43 2.54 -0.11 2.00e-01 2.50e+01 2.76e-01 chirality pdb=" CA PRO J 185 " pdb=" N PRO J 185 " pdb=" C PRO J 185 " pdb=" CB PRO J 185 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.10 2.00e-01 2.50e+01 2.70e-01 chirality pdb=" CA PRO H 185 " pdb=" N PRO H 185 " pdb=" C PRO H 185 " pdb=" CB PRO H 185 " both_signs ideal model delta sigma weight residual False 2.72 2.62 0.10 2.00e-01 2.50e+01 2.61e-01 ... (remaining 1467 not shown) Planarity restraints: 1542 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP I 172 " -0.016 5.00e-02 4.00e+02 2.49e-02 9.90e-01 pdb=" N PRO I 173 " 0.043 5.00e-02 4.00e+02 pdb=" CA PRO I 173 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO I 173 " -0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP L 172 " 0.016 5.00e-02 4.00e+02 2.49e-02 9.89e-01 pdb=" N PRO L 173 " -0.043 5.00e-02 4.00e+02 pdb=" CA PRO L 173 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO L 173 " 0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP G 172 " -0.016 5.00e-02 4.00e+02 2.49e-02 9.89e-01 pdb=" N PRO G 173 " 0.043 5.00e-02 4.00e+02 pdb=" CA PRO G 173 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO G 173 " -0.012 5.00e-02 4.00e+02 ... (remaining 1539 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 455 2.73 - 3.27: 9822 3.27 - 3.82: 15831 3.82 - 4.36: 18958 4.36 - 4.90: 32012 Nonbonded interactions: 77078 Sorted by model distance: nonbonded pdb=" O ILE J 71 " pdb=" OH TYR J 158 " model vdw 2.191 3.040 nonbonded pdb=" O ILE I 71 " pdb=" OH TYR I 158 " model vdw 2.191 3.040 nonbonded pdb=" O ILE L 71 " pdb=" OH TYR L 158 " model vdw 2.191 3.040 nonbonded pdb=" O ILE K 71 " pdb=" OH TYR K 158 " model vdw 2.192 3.040 nonbonded pdb=" O ILE G 71 " pdb=" OH TYR G 158 " model vdw 2.192 3.040 ... (remaining 77073 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: 0.02 Found NCS groups: ncs_group { reference = (chain 'G' and (resid 2 through 301 or resid 303 through 304)) selection = (chain 'H' and (resid 2 through 301 or resid 303 through 304)) selection = (chain 'I' and (resid 2 through 301 or resid 303 through 304)) selection = (chain 'J' and (resid 2 through 301 or resid 303 through 304)) selection = (chain 'K' and (resid 2 through 301 or resid 303 through 304)) selection = (chain 'L' and (resid 2 through 217 or (resid 301 and (name C2 or name C3 or nam \ e C4 or name C5 or name C6 or name C7 or name C8 )) or resid 303 through 304)) } 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 individual isotropic 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: 5.530 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.590 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.010 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:6.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 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 : 0.005 0.050 9726 Z= 0.233 Angle : 0.862 8.031 13134 Z= 0.353 Chirality : 0.035 0.105 1470 Planarity : 0.002 0.025 1542 Dihedral : 11.152 59.620 3414 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.18 % Allowed : 5.36 % Favored : 92.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.25), residues: 1104 helix: 1.43 (0.18), residues: 714 sheet: 4.08 (0.68), residues: 66 loop : -1.08 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG L 143 TYR 0.004 0.001 TYR L 217 PHE 0.006 0.001 PHE I 51 TRP 0.005 0.001 TRP K 24 HIS 0.001 0.000 HIS H 16 Details of bonding type rmsd covalent geometry : bond 0.00463 ( 9708) covalent geometry : angle 0.86266 (13098) SS BOND : bond 0.00143 ( 18) SS BOND : angle 0.79270 ( 36) hydrogen bonds : bond 0.23950 ( 600) hydrogen bonds : angle 6.52537 ( 1764) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 239 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 134 TRP cc_start: 0.8079 (m100) cc_final: 0.7759 (m100) REVERT: J 41 LYS cc_start: 0.8219 (tttt) cc_final: 0.7960 (tttp) REVERT: K 41 LYS cc_start: 0.8293 (tttt) cc_final: 0.8012 (tttp) outliers start: 22 outliers final: 1 residues processed: 250 average time/residue: 0.4556 time to fit residues: 123.5870 Evaluate side-chains 193 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 192 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 14 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 106 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.125731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.082046 restraints weight = 14680.865| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 1.80 r_work: 0.2912 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2803 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9020 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9726 Z= 0.165 Angle : 0.648 8.684 13134 Z= 0.341 Chirality : 0.042 0.132 1470 Planarity : 0.004 0.030 1542 Dihedral : 9.037 59.295 1400 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.38 % Allowed : 13.29 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.35 (0.25), residues: 1104 helix: 2.41 (0.18), residues: 732 sheet: 3.38 (0.61), residues: 66 loop : -1.10 (0.35), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG I 216 TYR 0.015 0.002 TYR J 65 PHE 0.014 0.002 PHE K 31 TRP 0.017 0.001 TRP H 133 HIS 0.005 0.001 HIS G 73 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 9708) covalent geometry : angle 0.64615 (13098) SS BOND : bond 0.00217 ( 18) SS BOND : angle 1.12448 ( 36) hydrogen bonds : bond 0.07607 ( 600) hydrogen bonds : angle 4.41950 ( 1764) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 206 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 19 SER cc_start: 0.8655 (p) cc_final: 0.8400 (t) REVERT: H 134 TRP cc_start: 0.8152 (m100) cc_final: 0.7821 (m-10) REVERT: I 216 ARG cc_start: 0.7564 (ttp80) cc_final: 0.7361 (tmm-80) REVERT: K 41 LYS cc_start: 0.8833 (tttt) cc_final: 0.8587 (tttp) outliers start: 24 outliers final: 5 residues processed: 213 average time/residue: 0.4409 time to fit residues: 101.8371 Evaluate side-chains 201 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 196 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 93 MET Chi-restraints excluded: chain I residue 41 LYS Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain K residue 85 SER Chi-restraints excluded: chain L residue 42 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 8 optimal weight: 1.9990 chunk 102 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 86 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 101 optimal weight: 0.8980 chunk 90 optimal weight: 10.0000 chunk 16 optimal weight: 0.9990 chunk 54 optimal weight: 8.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.124609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.080328 restraints weight = 14646.620| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 1.80 r_work: 0.2880 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9044 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 9726 Z= 0.171 Angle : 0.622 7.933 13134 Z= 0.328 Chirality : 0.044 0.146 1470 Planarity : 0.003 0.022 1542 Dihedral : 8.627 59.771 1398 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.67 % Allowed : 12.80 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.54 (0.25), residues: 1104 helix: 2.61 (0.18), residues: 738 sheet: 2.96 (0.56), residues: 66 loop : -1.16 (0.35), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 216 TYR 0.013 0.002 TYR J 65 PHE 0.017 0.002 PHE L 29 TRP 0.011 0.001 TRP H 133 HIS 0.006 0.001 HIS J 73 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 9708) covalent geometry : angle 0.61993 (13098) SS BOND : bond 0.00291 ( 18) SS BOND : angle 1.12194 ( 36) hydrogen bonds : bond 0.06821 ( 600) hydrogen bonds : angle 4.20152 ( 1764) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 201 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 216 ARG cc_start: 0.8190 (ttp80) cc_final: 0.7748 (tmm-80) REVERT: H 19 SER cc_start: 0.8610 (p) cc_final: 0.8379 (t) REVERT: H 134 TRP cc_start: 0.8113 (m100) cc_final: 0.7782 (m-10) REVERT: I 216 ARG cc_start: 0.7655 (ttp80) cc_final: 0.7443 (tmm-80) REVERT: K 41 LYS cc_start: 0.8871 (tttt) cc_final: 0.8650 (tttp) REVERT: K 42 GLU cc_start: 0.8331 (pt0) cc_final: 0.8100 (pm20) REVERT: L 22 LYS cc_start: 0.7757 (mtmp) cc_final: 0.7490 (mttp) outliers start: 37 outliers final: 15 residues processed: 217 average time/residue: 0.4859 time to fit residues: 113.7357 Evaluate side-chains 197 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 182 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 34 MET Chi-restraints excluded: chain G residue 199 SER Chi-restraints excluded: chain G residue 210 LEU Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain I residue 23 ILE Chi-restraints excluded: chain I residue 34 MET Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain J residue 23 ILE Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain K residue 23 ILE Chi-restraints excluded: chain K residue 85 SER Chi-restraints excluded: chain L residue 42 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 39 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 55 optimal weight: 0.3980 chunk 59 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 24 optimal weight: 0.5980 chunk 49 optimal weight: 0.0980 chunk 67 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.125428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.081683 restraints weight = 14875.439| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 1.76 r_work: 0.2908 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9021 moved from start: 0.3122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9726 Z= 0.136 Angle : 0.603 8.581 13134 Z= 0.308 Chirality : 0.042 0.138 1470 Planarity : 0.003 0.031 1542 Dihedral : 8.122 58.882 1398 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.17 % Allowed : 14.19 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.74 (0.25), residues: 1104 helix: 2.84 (0.18), residues: 738 sheet: 2.77 (0.54), residues: 66 loop : -1.23 (0.35), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J 216 TYR 0.009 0.001 TYR L 65 PHE 0.020 0.001 PHE G 29 TRP 0.010 0.001 TRP I 133 HIS 0.004 0.001 HIS G 73 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 9708) covalent geometry : angle 0.60187 (13098) SS BOND : bond 0.00218 ( 18) SS BOND : angle 0.95047 ( 36) hydrogen bonds : bond 0.05810 ( 600) hydrogen bonds : angle 3.95775 ( 1764) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 191 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 216 ARG cc_start: 0.8207 (ttp80) cc_final: 0.7840 (tmm-80) REVERT: H 134 TRP cc_start: 0.8064 (m100) cc_final: 0.7753 (m-10) REVERT: J 134 TRP cc_start: 0.6965 (OUTLIER) cc_final: 0.6652 (m-10) REVERT: J 216 ARG cc_start: 0.7810 (ttp80) cc_final: 0.7435 (tmm-80) REVERT: K 41 LYS cc_start: 0.8826 (tttt) cc_final: 0.8611 (tttp) REVERT: K 42 GLU cc_start: 0.8328 (pt0) cc_final: 0.8104 (pm20) REVERT: K 216 ARG cc_start: 0.7943 (ttp80) cc_final: 0.7564 (tmm-80) REVERT: L 93 MET cc_start: 0.8063 (mmp) cc_final: 0.7435 (tmm) REVERT: L 216 ARG cc_start: 0.8143 (ttp80) cc_final: 0.7773 (tmm-80) outliers start: 32 outliers final: 19 residues processed: 205 average time/residue: 0.4877 time to fit residues: 108.1568 Evaluate side-chains 206 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 186 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 16 HIS Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 210 LEU Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain I residue 23 ILE Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 34 MET Chi-restraints excluded: chain J residue 16 HIS Chi-restraints excluded: chain J residue 23 ILE Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain J residue 134 TRP Chi-restraints excluded: chain J residue 210 LEU Chi-restraints excluded: chain K residue 23 ILE Chi-restraints excluded: chain K residue 85 SER Chi-restraints excluded: chain L residue 16 HIS Chi-restraints excluded: chain L residue 25 LEU Chi-restraints excluded: chain L residue 42 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 4 optimal weight: 1.9990 chunk 73 optimal weight: 0.2980 chunk 86 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 95 optimal weight: 0.8980 chunk 46 optimal weight: 0.1980 chunk 63 optimal weight: 0.9980 chunk 106 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 1 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.124639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.081074 restraints weight = 14820.978| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 1.77 r_work: 0.2894 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2787 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9028 moved from start: 0.3260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9726 Z= 0.146 Angle : 0.598 8.017 13134 Z= 0.312 Chirality : 0.042 0.137 1470 Planarity : 0.003 0.025 1542 Dihedral : 7.871 59.897 1398 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.97 % Allowed : 14.58 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.94 (0.25), residues: 1104 helix: 3.03 (0.18), residues: 738 sheet: 2.68 (0.55), residues: 66 loop : -1.21 (0.35), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 216 TYR 0.011 0.002 TYR J 65 PHE 0.014 0.002 PHE K 31 TRP 0.008 0.001 TRP H 133 HIS 0.005 0.001 HIS G 73 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 9708) covalent geometry : angle 0.59645 (13098) SS BOND : bond 0.00269 ( 18) SS BOND : angle 1.02108 ( 36) hydrogen bonds : bond 0.05791 ( 600) hydrogen bonds : angle 3.90398 ( 1764) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 192 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 216 ARG cc_start: 0.8205 (ttp80) cc_final: 0.7883 (tmm-80) REVERT: H 134 TRP cc_start: 0.8055 (m100) cc_final: 0.7772 (m-10) REVERT: J 216 ARG cc_start: 0.7838 (ttp80) cc_final: 0.7490 (tmm-80) REVERT: K 41 LYS cc_start: 0.8842 (tttt) cc_final: 0.8616 (tttp) REVERT: K 216 ARG cc_start: 0.7992 (ttp80) cc_final: 0.7622 (tmm-80) REVERT: L 93 MET cc_start: 0.7988 (OUTLIER) cc_final: 0.7366 (tmm) REVERT: L 216 ARG cc_start: 0.8108 (ttp80) cc_final: 0.7734 (tmm-80) outliers start: 40 outliers final: 20 residues processed: 207 average time/residue: 0.4760 time to fit residues: 106.3763 Evaluate side-chains 204 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 183 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 210 LEU Chi-restraints excluded: chain H residue 34 MET Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain I residue 23 ILE Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 42 GLU Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain J residue 16 HIS Chi-restraints excluded: chain J residue 23 ILE Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain J residue 210 LEU Chi-restraints excluded: chain K residue 16 HIS Chi-restraints excluded: chain K residue 25 LEU Chi-restraints excluded: chain K residue 85 SER Chi-restraints excluded: chain L residue 25 LEU Chi-restraints excluded: chain L residue 42 GLU Chi-restraints excluded: chain L residue 93 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 79 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 56 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 86 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 67 optimal weight: 0.0770 chunk 61 optimal weight: 0.9980 chunk 106 optimal weight: 0.5980 chunk 36 optimal weight: 0.2980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.125239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.081098 restraints weight = 14864.200| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 1.80 r_work: 0.2906 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9023 moved from start: 0.3423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9726 Z= 0.136 Angle : 0.615 8.960 13134 Z= 0.314 Chirality : 0.042 0.142 1470 Planarity : 0.003 0.033 1542 Dihedral : 7.597 59.101 1398 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.17 % Allowed : 16.37 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.00 (0.25), residues: 1104 helix: 3.11 (0.18), residues: 738 sheet: 2.66 (0.55), residues: 66 loop : -1.29 (0.35), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG I 216 TYR 0.010 0.001 TYR H 68 PHE 0.022 0.001 PHE G 29 TRP 0.007 0.001 TRP H 133 HIS 0.004 0.001 HIS G 73 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 9708) covalent geometry : angle 0.61378 (13098) SS BOND : bond 0.00241 ( 18) SS BOND : angle 0.93505 ( 36) hydrogen bonds : bond 0.05450 ( 600) hydrogen bonds : angle 3.79706 ( 1764) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 185 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 216 ARG cc_start: 0.8224 (ttp80) cc_final: 0.7941 (tmm-80) REVERT: H 134 TRP cc_start: 0.8076 (m100) cc_final: 0.7802 (m-10) REVERT: J 216 ARG cc_start: 0.7880 (ttp80) cc_final: 0.7549 (tmm-80) REVERT: K 41 LYS cc_start: 0.8800 (tttt) cc_final: 0.8572 (tttp) REVERT: K 216 ARG cc_start: 0.7966 (ttp80) cc_final: 0.7623 (tmm-80) REVERT: L 22 LYS cc_start: 0.7792 (mttp) cc_final: 0.7584 (mttp) REVERT: L 93 MET cc_start: 0.8076 (OUTLIER) cc_final: 0.7364 (tmm) REVERT: L 216 ARG cc_start: 0.8028 (ttp80) cc_final: 0.7809 (tmm-80) outliers start: 32 outliers final: 16 residues processed: 201 average time/residue: 0.4962 time to fit residues: 107.5729 Evaluate side-chains 197 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 180 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 16 HIS Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 213 LEU Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 42 GLU Chi-restraints excluded: chain J residue 16 HIS Chi-restraints excluded: chain J residue 23 ILE Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 210 LEU Chi-restraints excluded: chain K residue 23 ILE Chi-restraints excluded: chain K residue 25 LEU Chi-restraints excluded: chain K residue 85 SER Chi-restraints excluded: chain L residue 25 LEU Chi-restraints excluded: chain L residue 42 GLU Chi-restraints excluded: chain L residue 93 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.0870 chunk 75 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 86 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 63 optimal weight: 0.6980 chunk 85 optimal weight: 1.9990 chunk 6 optimal weight: 0.3980 chunk 41 optimal weight: 0.7980 chunk 76 optimal weight: 0.5980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.125740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.082029 restraints weight = 14685.289| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 1.80 r_work: 0.2916 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9014 moved from start: 0.3501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9726 Z= 0.131 Angle : 0.603 9.643 13134 Z= 0.312 Chirality : 0.041 0.146 1470 Planarity : 0.003 0.019 1542 Dihedral : 7.312 57.733 1398 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.47 % Allowed : 16.27 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.08 (0.25), residues: 1104 helix: 3.20 (0.18), residues: 738 sheet: 2.61 (0.55), residues: 66 loop : -1.30 (0.35), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 216 TYR 0.010 0.001 TYR H 68 PHE 0.013 0.001 PHE K 29 TRP 0.006 0.001 TRP H 133 HIS 0.003 0.000 HIS G 73 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 9708) covalent geometry : angle 0.60242 (13098) SS BOND : bond 0.00219 ( 18) SS BOND : angle 0.90591 ( 36) hydrogen bonds : bond 0.05204 ( 600) hydrogen bonds : angle 3.76025 ( 1764) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 190 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 216 ARG cc_start: 0.8250 (ttp80) cc_final: 0.7913 (tmm-80) REVERT: H 93 MET cc_start: 0.7991 (OUTLIER) cc_final: 0.7639 (pp-130) REVERT: H 134 TRP cc_start: 0.8087 (m100) cc_final: 0.7807 (m-10) REVERT: H 216 ARG cc_start: 0.7770 (tmm-80) cc_final: 0.7499 (tmm-80) REVERT: J 216 ARG cc_start: 0.7919 (ttp80) cc_final: 0.7609 (tmm-80) REVERT: K 41 LYS cc_start: 0.8764 (tttt) cc_final: 0.8539 (tttp) REVERT: K 216 ARG cc_start: 0.7909 (ttp80) cc_final: 0.7542 (tmm-80) REVERT: L 93 MET cc_start: 0.8007 (mmp) cc_final: 0.7397 (tmm) outliers start: 35 outliers final: 19 residues processed: 209 average time/residue: 0.4716 time to fit residues: 106.4054 Evaluate side-chains 202 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 182 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 93 MET Chi-restraints excluded: chain I residue 16 HIS Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 42 GLU Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain J residue 23 ILE Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain K residue 16 HIS Chi-restraints excluded: chain K residue 23 ILE Chi-restraints excluded: chain K residue 25 LEU Chi-restraints excluded: chain K residue 85 SER Chi-restraints excluded: chain K residue 213 LEU Chi-restraints excluded: chain L residue 16 HIS Chi-restraints excluded: chain L residue 25 LEU Chi-restraints excluded: chain L residue 42 GLU Chi-restraints excluded: chain L residue 213 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 0 optimal weight: 10.0000 chunk 48 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 94 optimal weight: 0.9990 chunk 78 optimal weight: 0.6980 chunk 107 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.124226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.079945 restraints weight = 14749.274| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 1.80 r_work: 0.2879 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9044 moved from start: 0.3544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9726 Z= 0.172 Angle : 0.656 10.400 13134 Z= 0.343 Chirality : 0.044 0.160 1470 Planarity : 0.003 0.019 1542 Dihedral : 7.435 59.443 1398 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.28 % Allowed : 17.46 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.07 (0.25), residues: 1104 helix: 3.16 (0.18), residues: 738 sheet: 2.63 (0.56), residues: 66 loop : -1.24 (0.35), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG K 216 TYR 0.013 0.002 TYR H 68 PHE 0.025 0.002 PHE L 29 TRP 0.005 0.001 TRP I 133 HIS 0.004 0.001 HIS J 73 Details of bonding type rmsd covalent geometry : bond 0.00394 ( 9708) covalent geometry : angle 0.65459 (13098) SS BOND : bond 0.00313 ( 18) SS BOND : angle 1.12661 ( 36) hydrogen bonds : bond 0.05773 ( 600) hydrogen bonds : angle 3.86455 ( 1764) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 188 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 216 ARG cc_start: 0.8306 (ttp80) cc_final: 0.7914 (tmm-80) REVERT: H 93 MET cc_start: 0.7946 (OUTLIER) cc_final: 0.7608 (pp-130) REVERT: H 134 TRP cc_start: 0.8089 (m100) cc_final: 0.7829 (m-10) REVERT: H 216 ARG cc_start: 0.7795 (tmm-80) cc_final: 0.7555 (tmm-80) REVERT: J 93 MET cc_start: 0.7789 (ptp) cc_final: 0.7467 (pp-130) REVERT: J 216 ARG cc_start: 0.7933 (ttp80) cc_final: 0.7630 (tmm-80) REVERT: K 41 LYS cc_start: 0.8794 (tttt) cc_final: 0.8571 (tttp) REVERT: K 216 ARG cc_start: 0.7973 (ttp80) cc_final: 0.7542 (tmm-80) REVERT: L 93 MET cc_start: 0.8110 (OUTLIER) cc_final: 0.7321 (tmm) outliers start: 23 outliers final: 18 residues processed: 202 average time/residue: 0.4669 time to fit residues: 102.0059 Evaluate side-chains 207 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 187 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain H residue 16 HIS Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 93 MET Chi-restraints excluded: chain H residue 213 LEU Chi-restraints excluded: chain I residue 16 HIS Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 42 GLU Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain J residue 23 ILE Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain K residue 25 LEU Chi-restraints excluded: chain K residue 85 SER Chi-restraints excluded: chain K residue 213 LEU Chi-restraints excluded: chain L residue 16 HIS Chi-restraints excluded: chain L residue 25 LEU Chi-restraints excluded: chain L residue 42 GLU Chi-restraints excluded: chain L residue 93 MET Chi-restraints excluded: chain L residue 213 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 0.0770 chunk 68 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 85 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 10 optimal weight: 0.0770 chunk 75 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 overall best weight: 0.4496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.125772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.082052 restraints weight = 14513.208| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 1.80 r_work: 0.2920 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9012 moved from start: 0.3610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9726 Z= 0.131 Angle : 0.626 11.158 13134 Z= 0.324 Chirality : 0.042 0.161 1470 Planarity : 0.003 0.019 1542 Dihedral : 7.100 58.734 1398 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.08 % Allowed : 17.76 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.06 (0.25), residues: 1104 helix: 3.21 (0.17), residues: 738 sheet: 2.57 (0.55), residues: 66 loop : -1.37 (0.34), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 216 TYR 0.009 0.001 TYR H 68 PHE 0.030 0.001 PHE G 29 TRP 0.006 0.001 TRP H 133 HIS 0.003 0.000 HIS J 73 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 9708) covalent geometry : angle 0.62545 (13098) SS BOND : bond 0.00215 ( 18) SS BOND : angle 0.89357 ( 36) hydrogen bonds : bond 0.05045 ( 600) hydrogen bonds : angle 3.72613 ( 1764) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 189 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 216 ARG cc_start: 0.8290 (ttp80) cc_final: 0.7890 (tmm-80) REVERT: H 93 MET cc_start: 0.7958 (OUTLIER) cc_final: 0.7636 (pp-130) REVERT: H 134 TRP cc_start: 0.8060 (m100) cc_final: 0.7795 (m-10) REVERT: J 93 MET cc_start: 0.7816 (ptp) cc_final: 0.7497 (pp-130) REVERT: J 216 ARG cc_start: 0.7934 (ttp80) cc_final: 0.7506 (tmm-80) REVERT: K 41 LYS cc_start: 0.8769 (tttt) cc_final: 0.8544 (tttp) REVERT: K 216 ARG cc_start: 0.8007 (ttp80) cc_final: 0.7679 (tmm-80) REVERT: L 93 MET cc_start: 0.7968 (mmp) cc_final: 0.7316 (tmm) outliers start: 21 outliers final: 12 residues processed: 203 average time/residue: 0.4666 time to fit residues: 102.1579 Evaluate side-chains 194 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 181 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 93 MET Chi-restraints excluded: chain I residue 16 HIS Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 42 GLU Chi-restraints excluded: chain J residue 23 ILE Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain K residue 25 LEU Chi-restraints excluded: chain K residue 85 SER Chi-restraints excluded: chain L residue 25 LEU Chi-restraints excluded: chain L residue 213 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 14 optimal weight: 0.7980 chunk 54 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 70 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 74 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.124444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.080307 restraints weight = 14683.452| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 1.79 r_work: 0.2886 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9038 moved from start: 0.3645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9726 Z= 0.165 Angle : 0.673 11.738 13134 Z= 0.350 Chirality : 0.044 0.173 1470 Planarity : 0.003 0.018 1542 Dihedral : 7.163 59.095 1398 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.49 % Allowed : 19.15 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.04 (0.25), residues: 1104 helix: 3.16 (0.18), residues: 738 sheet: 2.61 (0.56), residues: 66 loop : -1.30 (0.34), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG K 216 TYR 0.013 0.002 TYR H 68 PHE 0.025 0.002 PHE L 29 TRP 0.005 0.001 TRP H 133 HIS 0.003 0.001 HIS J 73 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 9708) covalent geometry : angle 0.67146 (13098) SS BOND : bond 0.00290 ( 18) SS BOND : angle 1.07585 ( 36) hydrogen bonds : bond 0.05603 ( 600) hydrogen bonds : angle 3.83033 ( 1764) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 187 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 216 ARG cc_start: 0.8242 (ttp80) cc_final: 0.7874 (tmm-80) REVERT: H 93 MET cc_start: 0.7972 (OUTLIER) cc_final: 0.7633 (pp-130) REVERT: H 134 TRP cc_start: 0.8091 (m100) cc_final: 0.7859 (m-10) REVERT: J 93 MET cc_start: 0.7824 (ptp) cc_final: 0.7475 (pp-130) REVERT: J 216 ARG cc_start: 0.7979 (ttp80) cc_final: 0.7555 (tmm-80) REVERT: K 41 LYS cc_start: 0.8771 (tttt) cc_final: 0.8549 (tttp) REVERT: K 216 ARG cc_start: 0.8031 (ttp80) cc_final: 0.7615 (tmm-80) REVERT: L 41 LYS cc_start: 0.8745 (tttt) cc_final: 0.8515 (tttp) REVERT: L 93 MET cc_start: 0.8078 (OUTLIER) cc_final: 0.7309 (tmm) outliers start: 15 outliers final: 12 residues processed: 198 average time/residue: 0.5218 time to fit residues: 111.1236 Evaluate side-chains 197 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 183 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 16 HIS Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 93 MET Chi-restraints excluded: chain I residue 16 HIS Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain J residue 23 ILE Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain K residue 25 LEU Chi-restraints excluded: chain K residue 85 SER Chi-restraints excluded: chain L residue 25 LEU Chi-restraints excluded: chain L residue 93 MET Chi-restraints excluded: chain L residue 213 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 0.8980 chunk 103 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 94 optimal weight: 0.9980 chunk 49 optimal weight: 0.0980 chunk 14 optimal weight: 0.6980 chunk 104 optimal weight: 0.6980 chunk 59 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 77 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.124862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.081129 restraints weight = 14707.181| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 1.79 r_work: 0.2901 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9024 moved from start: 0.3697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9726 Z= 0.143 Angle : 0.657 12.217 13134 Z= 0.339 Chirality : 0.043 0.169 1470 Planarity : 0.003 0.019 1542 Dihedral : 7.007 58.867 1398 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.39 % Allowed : 18.95 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.01 (0.25), residues: 1104 helix: 3.16 (0.17), residues: 738 sheet: 2.63 (0.56), residues: 66 loop : -1.40 (0.34), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 216 TYR 0.010 0.001 TYR H 68 PHE 0.031 0.002 PHE G 29 TRP 0.006 0.001 TRP H 133 HIS 0.004 0.001 HIS G 73 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 9708) covalent geometry : angle 0.65567 (13098) SS BOND : bond 0.00244 ( 18) SS BOND : angle 0.95886 ( 36) hydrogen bonds : bond 0.05253 ( 600) hydrogen bonds : angle 3.75582 ( 1764) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5603.77 seconds wall clock time: 95 minutes 29.98 seconds (5729.98 seconds total)