Starting phenix.real_space_refine on Sun Jun 8 23:37:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qew_13943/06_2025/7qew_13943.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qew_13943/06_2025/7qew_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_13943/06_2025/7qew_13943.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qew_13943/06_2025/7qew_13943.map" model { file = "/net/cci-nas-00/data/ceres_data/7qew_13943/06_2025/7qew_13943.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qew_13943/06_2025/7qew_13943.cif" } resolution = 2.1 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 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 8.94, per 1000 atoms: 0.92 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: 2.66 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 0.96 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: 2.79 Time building geometry restraints manager: 3.29 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: 0.08 Found NCS groups: ncs_group { reference = (chain 'G' and (resid 2 through 217 or resid 301 or resid 303 through 304)) selection = (chain 'H' and (resid 2 through 217 or resid 301 or resid 303 through 304)) selection = (chain 'I' and (resid 2 through 217 or resid 301 or resid 303 through 304)) selection = (chain 'J' and (resid 2 through 217 or resid 301 or resid 303 through 304)) selection = (chain 'K' and (resid 2 through 217 or resid 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: 6.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 29.890 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.140 ------------------------------------------------------------------------------- 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 : 3.73 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 (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: 1.32 (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 TRP 0.005 0.001 TRP K 24 HIS 0.001 0.000 HIS H 16 PHE 0.006 0.001 PHE I 51 TYR 0.004 0.001 TYR L 217 ARG 0.001 0.000 ARG L 143 Details of bonding type rmsd hydrogen bonds : bond 0.23950 ( 600) hydrogen bonds : angle 6.52537 ( 1764) SS BOND : bond 0.00143 ( 18) SS BOND : angle 0.79270 ( 36) covalent geometry : bond 0.00463 ( 9708) covalent geometry : angle 0.86266 (13098) *********************** 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 : 1.417 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: 0.9599 time to fit residues: 261.5069 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 : 1.158 ------------------------------------------------------------------------------- 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 91 optimal weight: 0.4980 chunk 81 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 84 optimal weight: 0.5980 chunk 32 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.3845 r_free = 0.3845 target = 0.124739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.080845 restraints weight = 14667.131| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 1.78 r_work: 0.2888 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9038 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9726 Z= 0.186 Angle : 0.677 8.682 13134 Z= 0.359 Chirality : 0.044 0.136 1470 Planarity : 0.004 0.026 1542 Dihedral : 9.176 59.766 1400 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.88 % Allowed : 12.60 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.34 (0.25), residues: 1104 helix: 2.40 (0.18), residues: 732 sheet: 3.23 (0.60), residues: 66 loop : -1.05 (0.35), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 133 HIS 0.006 0.001 HIS G 73 PHE 0.015 0.002 PHE K 31 TYR 0.017 0.002 TYR J 65 ARG 0.010 0.001 ARG I 216 Details of bonding type rmsd hydrogen bonds : bond 0.07411 ( 600) hydrogen bonds : angle 4.41702 ( 1764) SS BOND : bond 0.00296 ( 18) SS BOND : angle 1.21048 ( 36) covalent geometry : bond 0.00408 ( 9708) covalent geometry : angle 0.67468 (13098) *********************** 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 233 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 204 time to evaluate : 1.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 93 MET cc_start: 0.6755 (OUTLIER) cc_final: 0.6529 (pp-130) REVERT: G 216 ARG cc_start: 0.8002 (ttp80) cc_final: 0.7678 (tmm-80) REVERT: H 19 SER cc_start: 0.8700 (p) cc_final: 0.8455 (t) REVERT: H 134 TRP cc_start: 0.8124 (m100) cc_final: 0.7760 (m-10) REVERT: I 134 TRP cc_start: 0.8204 (m100) cc_final: 0.7998 (m-10) REVERT: I 216 ARG cc_start: 0.7583 (ttp80) cc_final: 0.7368 (tmm-80) REVERT: K 41 LYS cc_start: 0.8871 (tttt) cc_final: 0.8622 (tttp) REVERT: K 91 VAL cc_start: 0.8688 (t) cc_final: 0.8487 (m) REVERT: L 22 LYS cc_start: 0.7639 (mtmp) cc_final: 0.7293 (mttp) outliers start: 29 outliers final: 5 residues processed: 214 average time/residue: 1.0927 time to fit residues: 253.6789 Evaluate side-chains 200 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 194 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 93 MET Chi-restraints excluded: chain H residue 23 ILE 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 84 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 90 optimal weight: 10.0000 chunk 24 optimal weight: 0.6980 chunk 66 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 52 optimal weight: 0.5980 chunk 36 optimal weight: 0.7980 chunk 65 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3845 r_free = 0.3845 target = 0.124904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.081088 restraints weight = 14884.509| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 1.76 r_work: 0.2889 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2778 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9037 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 : 0.003 0.027 9726 Z= 0.155 Angle : 0.609 7.896 13134 Z= 0.319 Chirality : 0.043 0.139 1470 Planarity : 0.003 0.027 1542 Dihedral : 8.561 59.155 1398 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.47 % Allowed : 12.70 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.53 (0.25), residues: 1104 helix: 2.63 (0.18), residues: 738 sheet: 2.93 (0.56), residues: 66 loop : -1.20 (0.35), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 133 HIS 0.005 0.001 HIS J 73 PHE 0.018 0.002 PHE L 29 TYR 0.011 0.002 TYR H 136 ARG 0.008 0.001 ARG L 216 Details of bonding type rmsd hydrogen bonds : bond 0.06571 ( 600) hydrogen bonds : angle 4.13323 ( 1764) SS BOND : bond 0.00292 ( 18) SS BOND : angle 1.06111 ( 36) covalent geometry : bond 0.00334 ( 9708) covalent geometry : angle 0.60702 (13098) *********************** 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 235 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 200 time to evaluate : 1.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 216 ARG cc_start: 0.8046 (ttp80) cc_final: 0.7734 (tmm-80) REVERT: H 19 SER cc_start: 0.8611 (p) cc_final: 0.8394 (t) REVERT: H 134 TRP cc_start: 0.8095 (m100) cc_final: 0.7687 (m-10) REVERT: I 134 TRP cc_start: 0.8154 (m100) cc_final: 0.7886 (m-10) REVERT: I 216 ARG cc_start: 0.7640 (ttp80) cc_final: 0.7411 (tmm-80) REVERT: K 41 LYS cc_start: 0.8853 (tttt) cc_final: 0.8627 (tttp) REVERT: K 42 GLU cc_start: 0.8350 (pt0) cc_final: 0.8122 (pm20) REVERT: K 209 GLU cc_start: 0.8776 (tp30) cc_final: 0.8550 (tp30) REVERT: L 22 LYS cc_start: 0.7690 (mtmp) cc_final: 0.7427 (mttp) REVERT: L 216 ARG cc_start: 0.8156 (ttp80) cc_final: 0.7726 (tmm-80) outliers start: 35 outliers final: 13 residues processed: 216 average time/residue: 1.0179 time to fit residues: 238.3805 Evaluate side-chains 198 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 185 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 199 SER 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 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 25 LEU 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 51 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 92 optimal weight: 0.4980 chunk 68 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 45 optimal weight: 7.9990 chunk 63 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 78 optimal weight: 0.6980 chunk 58 optimal weight: 0.1980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3849 r_free = 0.3849 target = 0.125223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.081556 restraints weight = 14629.257| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 1.76 r_work: 0.2907 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9023 moved from start: 0.3141 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= 0.139 Angle : 0.609 8.579 13134 Z= 0.311 Chirality : 0.042 0.143 1470 Planarity : 0.003 0.031 1542 Dihedral : 8.048 59.133 1398 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.47 % Allowed : 13.39 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.75 (0.25), residues: 1104 helix: 2.85 (0.18), residues: 738 sheet: 2.78 (0.54), residues: 66 loop : -1.22 (0.35), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 24 HIS 0.004 0.001 HIS J 73 PHE 0.019 0.001 PHE G 29 TYR 0.010 0.002 TYR J 65 ARG 0.008 0.001 ARG J 216 Details of bonding type rmsd hydrogen bonds : bond 0.05797 ( 600) hydrogen bonds : angle 3.95759 ( 1764) SS BOND : bond 0.00232 ( 18) SS BOND : angle 0.97060 ( 36) covalent geometry : bond 0.00294 ( 9708) covalent geometry : angle 0.60744 (13098) *********************** 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 230 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 195 time to evaluate : 1.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 216 ARG cc_start: 0.8090 (ttp80) cc_final: 0.7869 (tmm-80) REVERT: H 23 ILE cc_start: 0.8423 (pt) cc_final: 0.8139 (mp) REVERT: H 134 TRP cc_start: 0.8060 (m100) cc_final: 0.7649 (m-10) REVERT: I 134 TRP cc_start: 0.8126 (m100) cc_final: 0.7860 (m-10) REVERT: I 216 ARG cc_start: 0.7680 (ttp80) cc_final: 0.7469 (tmm-80) REVERT: J 216 ARG cc_start: 0.7806 (ttp80) cc_final: 0.7430 (tmm-80) REVERT: K 41 LYS cc_start: 0.8849 (tttt) cc_final: 0.8628 (tttp) REVERT: K 42 GLU cc_start: 0.8345 (pt0) cc_final: 0.8104 (pm20) REVERT: K 216 ARG cc_start: 0.7926 (ttp80) cc_final: 0.7548 (tmm-80) REVERT: L 93 MET cc_start: 0.8067 (mmp) cc_final: 0.7425 (tmm) outliers start: 35 outliers final: 21 residues processed: 211 average time/residue: 0.9547 time to fit residues: 218.8152 Evaluate side-chains 211 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 190 time to evaluate : 1.083 ------------------------------------------------------------------------------- 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 38 VAL Chi-restraints excluded: chain H residue 42 GLU 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 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 J residue 213 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 14 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 60 optimal weight: 0.0980 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 95 optimal weight: 0.9980 chunk 54 optimal weight: 8.9990 chunk 102 optimal weight: 0.9990 chunk 103 optimal weight: 0.5980 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 = 0.3841 r_free = 0.3841 target = 0.124626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.080771 restraints weight = 14753.367| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 1.77 r_work: 0.2894 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9034 moved from start: 0.3232 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= 0.149 Angle : 0.593 8.440 13134 Z= 0.310 Chirality : 0.042 0.151 1470 Planarity : 0.003 0.034 1542 Dihedral : 7.906 59.944 1398 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.98 % Allowed : 15.08 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.88 (0.25), residues: 1104 helix: 2.97 (0.18), residues: 738 sheet: 2.73 (0.55), residues: 66 loop : -1.22 (0.36), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 133 HIS 0.004 0.001 HIS J 73 PHE 0.020 0.001 PHE J 29 TYR 0.011 0.002 TYR J 65 ARG 0.009 0.001 ARG L 216 Details of bonding type rmsd hydrogen bonds : bond 0.05783 ( 600) hydrogen bonds : angle 3.91889 ( 1764) SS BOND : bond 0.00278 ( 18) SS BOND : angle 1.01699 ( 36) covalent geometry : bond 0.00327 ( 9708) covalent geometry : angle 0.59166 (13098) *********************** 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 221 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 191 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 23 ILE cc_start: 0.8436 (pt) cc_final: 0.8169 (mp) REVERT: H 134 TRP cc_start: 0.8056 (m100) cc_final: 0.7655 (m-10) REVERT: I 134 TRP cc_start: 0.8109 (m100) cc_final: 0.7821 (m-10) REVERT: J 216 ARG cc_start: 0.7833 (ttp80) cc_final: 0.7489 (tmm-80) REVERT: K 41 LYS cc_start: 0.8851 (tttt) cc_final: 0.8633 (tttp) REVERT: K 42 GLU cc_start: 0.8338 (pt0) cc_final: 0.8095 (pm20) REVERT: K 216 ARG cc_start: 0.7971 (ttp80) cc_final: 0.7589 (tmm-80) REVERT: L 22 LYS cc_start: 0.7710 (mtmp) cc_final: 0.7454 (mttp) REVERT: L 93 MET cc_start: 0.8032 (mmp) cc_final: 0.7405 (tmm) REVERT: L 216 ARG cc_start: 0.8097 (ttp80) cc_final: 0.7780 (tmm-80) outliers start: 30 outliers final: 20 residues processed: 207 average time/residue: 1.0095 time to fit residues: 226.5468 Evaluate side-chains 204 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 184 time to evaluate : 1.142 ------------------------------------------------------------------------------- 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 85 SER Chi-restraints excluded: chain I residue 16 HIS 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 79 optimal weight: 0.9980 chunk 22 optimal weight: 0.4980 chunk 63 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 97 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 20 optimal weight: 0.0370 overall best weight: 0.6658 ------------------------------------------------------------------------------- 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 = 0.3845 r_free = 0.3845 target = 0.124826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.080634 restraints weight = 14719.141| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 1.81 r_work: 0.2897 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9032 moved from start: 0.3383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9726 Z= 0.145 Angle : 0.624 8.918 13134 Z= 0.321 Chirality : 0.042 0.151 1470 Planarity : 0.003 0.027 1542 Dihedral : 7.698 58.768 1398 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.37 % Allowed : 15.28 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.99 (0.25), residues: 1104 helix: 3.08 (0.18), residues: 738 sheet: 2.69 (0.55), residues: 66 loop : -1.23 (0.35), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 133 HIS 0.004 0.001 HIS J 73 PHE 0.012 0.001 PHE L 51 TYR 0.011 0.001 TYR H 68 ARG 0.007 0.001 ARG L 216 Details of bonding type rmsd hydrogen bonds : bond 0.05616 ( 600) hydrogen bonds : angle 3.84378 ( 1764) SS BOND : bond 0.00256 ( 18) SS BOND : angle 0.98314 ( 36) covalent geometry : bond 0.00318 ( 9708) covalent geometry : angle 0.62323 (13098) *********************** 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 224 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 190 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 22 LYS cc_start: 0.8081 (mmtp) cc_final: 0.7725 (mttp) REVERT: H 23 ILE cc_start: 0.8511 (pt) cc_final: 0.8276 (mp) REVERT: H 134 TRP cc_start: 0.8048 (m100) cc_final: 0.7670 (m-10) REVERT: I 134 TRP cc_start: 0.8054 (m100) cc_final: 0.7763 (m-10) REVERT: J 216 ARG cc_start: 0.7863 (ttp80) cc_final: 0.7544 (tmm-80) REVERT: K 41 LYS cc_start: 0.8842 (tttt) cc_final: 0.8611 (tttp) REVERT: K 216 ARG cc_start: 0.7998 (ttp80) cc_final: 0.7659 (tmm-80) REVERT: L 22 LYS cc_start: 0.7750 (mtmp) cc_final: 0.7461 (mttp) REVERT: L 93 MET cc_start: 0.8102 (OUTLIER) cc_final: 0.7366 (tmm) REVERT: L 216 ARG cc_start: 0.8041 (ttp80) cc_final: 0.7701 (tmm-80) outliers start: 34 outliers final: 25 residues processed: 207 average time/residue: 1.0567 time to fit residues: 236.1088 Evaluate side-chains 209 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 183 time to evaluate : 1.259 ------------------------------------------------------------------------------- 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 85 SER 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 H residue 213 LEU Chi-restraints excluded: chain I residue 16 HIS 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 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 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 94 optimal weight: 0.6980 chunk 96 optimal weight: 0.5980 chunk 84 optimal weight: 0.7980 chunk 69 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 70 optimal weight: 0.6980 chunk 86 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3845 r_free = 0.3845 target = 0.124860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.080740 restraints weight = 14728.316| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 1.80 r_work: 0.2896 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9028 moved from start: 0.3460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9726 Z= 0.143 Angle : 0.603 9.498 13134 Z= 0.315 Chirality : 0.042 0.143 1470 Planarity : 0.003 0.032 1542 Dihedral : 7.510 58.887 1398 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.47 % Allowed : 15.38 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 3.04 (0.25), residues: 1104 helix: 3.13 (0.18), residues: 738 sheet: 2.68 (0.55), residues: 66 loop : -1.25 (0.35), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 133 HIS 0.004 0.001 HIS G 73 PHE 0.012 0.001 PHE L 51 TYR 0.011 0.001 TYR H 68 ARG 0.014 0.001 ARG I 216 Details of bonding type rmsd hydrogen bonds : bond 0.05494 ( 600) hydrogen bonds : angle 3.82061 ( 1764) SS BOND : bond 0.00259 ( 18) SS BOND : angle 0.98012 ( 36) covalent geometry : bond 0.00313 ( 9708) covalent geometry : angle 0.60183 (13098) *********************** 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 219 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 184 time to evaluate : 1.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 22 LYS cc_start: 0.8097 (mmtp) cc_final: 0.7745 (mttp) REVERT: H 134 TRP cc_start: 0.8056 (m100) cc_final: 0.7669 (m-10) REVERT: H 216 ARG cc_start: 0.7783 (tmm-80) cc_final: 0.7513 (tmm-80) REVERT: I 216 ARG cc_start: 0.7787 (ttp80) cc_final: 0.7478 (tmm-80) REVERT: J 93 MET cc_start: 0.7751 (ptp) cc_final: 0.7427 (pp-130) REVERT: J 216 ARG cc_start: 0.7869 (ttp80) cc_final: 0.7554 (tmm-80) REVERT: K 41 LYS cc_start: 0.8808 (tttt) cc_final: 0.8580 (tttp) REVERT: K 216 ARG cc_start: 0.7960 (ttp80) cc_final: 0.7633 (tmm-80) REVERT: L 22 LYS cc_start: 0.7757 (mtmp) cc_final: 0.7476 (mttp) REVERT: L 93 MET cc_start: 0.8019 (OUTLIER) cc_final: 0.7358 (tmm) REVERT: L 216 ARG cc_start: 0.7995 (ttp80) cc_final: 0.7667 (tmm-80) outliers start: 35 outliers final: 18 residues processed: 203 average time/residue: 1.3001 time to fit residues: 287.5666 Evaluate side-chains 199 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 180 time to evaluate : 1.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 85 SER 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 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 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 105 optimal weight: 0.9990 chunk 106 optimal weight: 0.7980 chunk 96 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.124204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.079654 restraints weight = 14815.927| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 1.82 r_work: 0.2876 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9047 moved from start: 0.3504 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= 0.164 Angle : 0.655 10.427 13134 Z= 0.339 Chirality : 0.043 0.158 1470 Planarity : 0.003 0.029 1542 Dihedral : 7.475 58.084 1398 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.28 % Allowed : 16.57 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 3.05 (0.25), residues: 1104 helix: 3.13 (0.18), residues: 738 sheet: 2.67 (0.55), residues: 66 loop : -1.21 (0.35), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 133 HIS 0.004 0.001 HIS J 73 PHE 0.019 0.002 PHE L 29 TYR 0.013 0.002 TYR H 68 ARG 0.009 0.001 ARG I 216 Details of bonding type rmsd hydrogen bonds : bond 0.05747 ( 600) hydrogen bonds : angle 3.87365 ( 1764) SS BOND : bond 0.00303 ( 18) SS BOND : angle 1.08942 ( 36) covalent geometry : bond 0.00371 ( 9708) covalent geometry : angle 0.65343 (13098) *********************** 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 : 2.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 134 TRP cc_start: 0.8073 (m100) cc_final: 0.7690 (m-10) REVERT: H 216 ARG cc_start: 0.7838 (tmm-80) cc_final: 0.7599 (tmm-80) REVERT: I 216 ARG cc_start: 0.7816 (ttp80) cc_final: 0.7533 (tmm-80) REVERT: J 93 MET cc_start: 0.7793 (ptp) cc_final: 0.7454 (pp-130) REVERT: J 216 ARG cc_start: 0.7898 (ttp80) cc_final: 0.7593 (tmm-80) REVERT: K 41 LYS cc_start: 0.8801 (tttt) cc_final: 0.8573 (tttp) REVERT: K 216 ARG cc_start: 0.7980 (ttp80) cc_final: 0.7530 (tmm-80) REVERT: L 22 LYS cc_start: 0.7701 (OUTLIER) cc_final: 0.7404 (mttp) REVERT: L 93 MET cc_start: 0.8104 (OUTLIER) cc_final: 0.7341 (tmm) outliers start: 23 outliers final: 19 residues processed: 201 average time/residue: 1.0675 time to fit residues: 232.7023 Evaluate side-chains 207 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 186 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain H residue 16 HIS 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 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 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 213 LEU Chi-restraints excluded: chain K residue 25 LEU Chi-restraints excluded: chain K residue 85 SER Chi-restraints excluded: chain L residue 22 LYS 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 31 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 66 optimal weight: 0.9990 chunk 72 optimal weight: 0.9990 chunk 79 optimal weight: 0.7980 chunk 58 optimal weight: 0.0010 chunk 81 optimal weight: 0.9990 chunk 75 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 92 optimal weight: 0.0050 chunk 69 optimal weight: 0.4980 overall best weight: 0.4200 ------------------------------------------------------------------------------- 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 = 0.3856 r_free = 0.3856 target = 0.125547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.081751 restraints weight = 14664.301| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 1.81 r_work: 0.2917 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9016 moved from start: 0.3596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9726 Z= 0.129 Angle : 0.613 11.215 13134 Z= 0.318 Chirality : 0.041 0.153 1470 Planarity : 0.003 0.034 1542 Dihedral : 7.122 58.032 1398 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.88 % Allowed : 17.46 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 3.05 (0.25), residues: 1104 helix: 3.17 (0.17), residues: 738 sheet: 2.60 (0.55), residues: 66 loop : -1.31 (0.34), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 133 HIS 0.003 0.000 HIS J 73 PHE 0.029 0.001 PHE G 29 TYR 0.009 0.001 TYR H 68 ARG 0.009 0.000 ARG I 216 Details of bonding type rmsd hydrogen bonds : bond 0.05051 ( 600) hydrogen bonds : angle 3.73512 ( 1764) SS BOND : bond 0.00210 ( 18) SS BOND : angle 0.88463 ( 36) covalent geometry : bond 0.00266 ( 9708) covalent geometry : angle 0.61185 (13098) *********************** 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 211 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 192 time to evaluate : 1.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 134 TRP cc_start: 0.8026 (m100) cc_final: 0.7637 (m-10) REVERT: I 216 ARG cc_start: 0.7846 (ttp80) cc_final: 0.7541 (tmm-80) REVERT: J 93 MET cc_start: 0.7818 (ptp) cc_final: 0.7451 (pp-130) REVERT: J 216 ARG cc_start: 0.7899 (ttp80) cc_final: 0.7465 (tmm-80) REVERT: K 41 LYS cc_start: 0.8780 (tttt) cc_final: 0.8551 (tttp) REVERT: K 216 ARG cc_start: 0.8007 (ttp80) cc_final: 0.7575 (tmm-80) REVERT: L 22 LYS cc_start: 0.7650 (mtmp) cc_final: 0.7359 (mttp) REVERT: L 93 MET cc_start: 0.7948 (mmp) cc_final: 0.7308 (tmm) outliers start: 19 outliers final: 11 residues processed: 205 average time/residue: 1.2061 time to fit residues: 267.3753 Evaluate side-chains 194 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 183 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain H residue 25 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 J residue 23 ILE Chi-restraints excluded: chain J residue 25 LEU 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 37 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 31 optimal weight: 0.6980 chunk 43 optimal weight: 0.8980 chunk 67 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3835 r_free = 0.3835 target = 0.124104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.079937 restraints weight = 14763.231| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 1.79 r_work: 0.2883 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9037 moved from start: 0.3641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9726 Z= 0.158 Angle : 0.664 11.692 13134 Z= 0.343 Chirality : 0.043 0.164 1470 Planarity : 0.003 0.027 1542 Dihedral : 7.127 59.567 1398 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.59 % Allowed : 18.06 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 3.02 (0.25), residues: 1104 helix: 3.13 (0.18), residues: 738 sheet: 2.64 (0.56), residues: 66 loop : -1.27 (0.34), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP I 133 HIS 0.003 0.001 HIS J 73 PHE 0.026 0.002 PHE L 29 TYR 0.013 0.002 TYR H 68 ARG 0.008 0.001 ARG I 216 Details of bonding type rmsd hydrogen bonds : bond 0.05554 ( 600) hydrogen bonds : angle 3.83921 ( 1764) SS BOND : bond 0.00287 ( 18) SS BOND : angle 1.06334 ( 36) covalent geometry : bond 0.00354 ( 9708) covalent geometry : angle 0.66280 (13098) ********************** 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 205 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 189 time to evaluate : 2.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 93 MET cc_start: 0.7884 (ptp) cc_final: 0.7535 (pp-130) REVERT: H 134 TRP cc_start: 0.8064 (m100) cc_final: 0.7703 (m-10) REVERT: I 216 ARG cc_start: 0.7879 (ttp80) cc_final: 0.7568 (tmm-80) REVERT: J 93 MET cc_start: 0.7796 (ptp) cc_final: 0.7457 (pp-130) REVERT: J 216 ARG cc_start: 0.7962 (ttp80) cc_final: 0.7536 (tmm-80) REVERT: K 41 LYS cc_start: 0.8765 (tttt) cc_final: 0.8544 (tttp) REVERT: K 216 ARG cc_start: 0.8029 (ttp80) cc_final: 0.7615 (tmm-80) REVERT: L 22 LYS cc_start: 0.7673 (mtmp) cc_final: 0.7356 (mttp) REVERT: L 41 LYS cc_start: 0.8829 (tttt) cc_final: 0.8619 (tttp) REVERT: L 93 MET cc_start: 0.8059 (OUTLIER) cc_final: 0.7295 (tmm) outliers start: 16 outliers final: 11 residues processed: 201 average time/residue: 1.3813 time to fit residues: 301.8468 Evaluate side-chains 194 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 182 time to evaluate : 1.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain H residue 25 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 J residue 23 ILE Chi-restraints excluded: chain J residue 25 LEU 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 62 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 101 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 98 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 68 optimal weight: 0.5980 chunk 47 optimal weight: 0.8980 chunk 79 optimal weight: 0.8980 chunk 99 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3834 r_free = 0.3834 target = 0.124012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.080281 restraints weight = 14728.867| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 1.78 r_work: 0.2884 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9037 moved from start: 0.3658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9726 Z= 0.158 Angle : 0.650 12.172 13134 Z= 0.341 Chirality : 0.043 0.164 1470 Planarity : 0.003 0.044 1542 Dihedral : 7.047 59.065 1398 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.59 % Allowed : 18.15 % 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 (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: 2.96 (0.25), residues: 1104 helix: 3.08 (0.17), residues: 738 sheet: 2.65 (0.56), residues: 66 loop : -1.32 (0.34), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP I 133 HIS 0.004 0.001 HIS G 73 PHE 0.013 0.002 PHE L 51 TYR 0.012 0.002 TYR H 68 ARG 0.017 0.001 ARG L 216 Details of bonding type rmsd hydrogen bonds : bond 0.05534 ( 600) hydrogen bonds : angle 3.84640 ( 1764) SS BOND : bond 0.00299 ( 18) SS BOND : angle 1.05446 ( 36) covalent geometry : bond 0.00354 ( 9708) covalent geometry : angle 0.64888 (13098) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11673.24 seconds wall clock time: 204 minutes 3.69 seconds (12243.69 seconds total)