Starting phenix.real_space_refine on Sat Oct 11 22:46:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qjf_18446/10_2025/8qjf_18446_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qjf_18446/10_2025/8qjf_18446.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8qjf_18446/10_2025/8qjf_18446_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qjf_18446/10_2025/8qjf_18446_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8qjf_18446/10_2025/8qjf_18446.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qjf_18446/10_2025/8qjf_18446.map" } resolution = 2.86 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 180 5.16 5 C 12816 2.51 5 N 3024 2.21 5 O 3144 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19164 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 1569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1569 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 188} Chain breaks: 1 Chain: "C" Number of atoms: 1569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1569 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 188} Chain breaks: 1 Chain: "D" Number of atoms: 1569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1569 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 188} Chain breaks: 1 Chain: "E" Number of atoms: 1569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1569 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 188} Chain breaks: 1 Chain: "F" Number of atoms: 1569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1569 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 188} Chain breaks: 1 Chain: "G" Number of atoms: 1569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1569 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 188} Chain breaks: 1 Chain: "H" Number of atoms: 1569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1569 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 188} Chain breaks: 1 Chain: "I" Number of atoms: 1569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1569 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 188} Chain breaks: 1 Chain: "J" Number of atoms: 1569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1569 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 188} Chain breaks: 1 Chain: "K" Number of atoms: 1569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1569 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 188} Chain breaks: 1 Chain: "L" Number of atoms: 1569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1569 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 188} Chain breaks: 1 Chain: "M" Number of atoms: 1569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1569 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 188} Chain breaks: 1 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.67, per 1000 atoms: 0.24 Number of scatterers: 19164 At special positions: 0 Unit cell: (102.05, 93.6, 159.9, 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 180 16.00 O 3144 8.00 N 3024 7.00 C 12816 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 53 " - pdb=" SG CYS A 180 " distance=2.03 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 174 " distance=2.03 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 169 " distance=2.03 Simple disulfide: pdb=" SG CYS C 53 " - pdb=" SG CYS C 180 " distance=2.03 Simple disulfide: pdb=" SG CYS C 60 " - pdb=" SG CYS C 174 " distance=2.03 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 169 " distance=2.03 Simple disulfide: pdb=" SG CYS D 53 " - pdb=" SG CYS D 180 " distance=2.03 Simple disulfide: pdb=" SG CYS D 60 " - pdb=" SG CYS D 174 " distance=2.03 Simple disulfide: pdb=" SG CYS D 64 " - pdb=" SG CYS D 169 " distance=2.03 Simple disulfide: pdb=" SG CYS E 53 " - pdb=" SG CYS E 180 " distance=2.03 Simple disulfide: pdb=" SG CYS E 60 " - pdb=" SG CYS E 174 " distance=2.03 Simple disulfide: pdb=" SG CYS E 64 " - pdb=" SG CYS E 169 " distance=2.03 Simple disulfide: pdb=" SG CYS F 53 " - pdb=" SG CYS F 180 " distance=2.03 Simple disulfide: pdb=" SG CYS F 60 " - pdb=" SG CYS F 174 " distance=2.03 Simple disulfide: pdb=" SG CYS F 64 " - pdb=" SG CYS F 169 " distance=2.03 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 Simple disulfide: pdb=" SG CYS M 53 " - pdb=" SG CYS M 180 " distance=2.03 Simple disulfide: pdb=" SG CYS M 60 " - pdb=" SG CYS M 174 " distance=2.03 Simple disulfide: pdb=" SG CYS M 64 " - pdb=" SG CYS M 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: 2.06 Conformation dependent library (CDL) restraints added in 895.7 milliseconds Enol-peptide restraints added in 1.4 microseconds 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4512 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 12 sheets defined 74.0% alpha, 3.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 2 through 12 Processing helix chain 'A' and resid 18 through 41 removed outlier: 4.351A pdb=" N LEU A 25 " --> pdb=" O GLY A 21 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N SER A 26 " --> pdb=" O ARG A 22 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N GLU A 41 " --> pdb=" O VAL A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 69 Processing helix chain 'A' and resid 72 through 105 Proline residue: A 87 - end of helix Processing helix chain 'A' and resid 129 through 158 Processing helix chain 'A' and resid 184 through 218 Processing helix chain 'C' and resid 2 through 12 Processing helix chain 'C' and resid 18 through 41 removed outlier: 4.352A pdb=" N LEU C 25 " --> pdb=" O GLY C 21 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N SER C 26 " --> pdb=" O ARG C 22 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N GLU C 41 " --> pdb=" O VAL C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 69 Processing helix chain 'C' and resid 72 through 105 Proline residue: C 87 - end of helix Processing helix chain 'C' and resid 129 through 158 Processing helix chain 'C' and resid 184 through 218 Processing helix chain 'D' and resid 2 through 12 Processing helix chain 'D' and resid 18 through 41 removed outlier: 4.352A pdb=" N LEU D 25 " --> pdb=" O GLY D 21 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N SER D 26 " --> pdb=" O ARG D 22 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N GLU D 41 " --> pdb=" O VAL D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 59 through 69 Processing helix chain 'D' and resid 72 through 105 Proline residue: D 87 - end of helix Processing helix chain 'D' and resid 129 through 158 Processing helix chain 'D' and resid 184 through 218 Processing helix chain 'E' and resid 2 through 12 Processing helix chain 'E' and resid 18 through 41 removed outlier: 4.352A pdb=" N LEU E 25 " --> pdb=" O GLY E 21 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N SER E 26 " --> pdb=" O ARG E 22 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N GLU E 41 " --> pdb=" O VAL E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 59 through 69 Processing helix chain 'E' and resid 72 through 105 Proline residue: E 87 - end of helix Processing helix chain 'E' and resid 129 through 158 Processing helix chain 'E' and resid 184 through 218 Processing helix chain 'F' and resid 2 through 12 Processing helix chain 'F' and resid 18 through 41 removed outlier: 4.352A pdb=" N LEU F 25 " --> pdb=" O GLY F 21 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N SER F 26 " --> pdb=" O ARG F 22 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N GLU F 41 " --> pdb=" O VAL F 37 " (cutoff:3.500A) Processing helix chain 'F' and resid 59 through 69 Processing helix chain 'F' and resid 72 through 105 Proline residue: F 87 - end of helix Processing helix chain 'F' and resid 129 through 158 Processing helix chain 'F' and resid 184 through 218 Processing helix chain 'G' and resid 2 through 12 Processing helix chain 'G' and resid 18 through 41 removed outlier: 4.352A pdb=" N LEU G 25 " --> pdb=" O GLY G 21 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N SER G 26 " --> pdb=" O ARG G 22 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N GLU G 41 " --> pdb=" O VAL G 37 " (cutoff:3.500A) Processing helix chain 'G' and resid 59 through 69 Processing helix chain 'G' and resid 72 through 105 Proline residue: G 87 - end of helix Processing helix chain 'G' and resid 129 through 158 Processing helix chain 'G' and resid 184 through 218 Processing helix chain 'H' and resid 2 through 12 Processing helix chain 'H' and resid 18 through 41 removed outlier: 4.353A pdb=" N LEU H 25 " --> pdb=" O GLY H 21 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N SER H 26 " --> pdb=" O ARG H 22 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N GLU H 41 " --> pdb=" O VAL H 37 " (cutoff:3.500A) Processing helix chain 'H' and resid 59 through 69 Processing helix chain 'H' and resid 72 through 105 Proline residue: H 87 - end of helix Processing helix chain 'H' and resid 129 through 158 Processing helix chain 'H' and resid 184 through 218 Processing helix chain 'I' and resid 2 through 12 Processing helix chain 'I' and resid 18 through 41 removed outlier: 4.353A pdb=" N LEU I 25 " --> pdb=" O GLY I 21 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N SER I 26 " --> pdb=" O ARG I 22 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N GLU I 41 " --> pdb=" O VAL I 37 " (cutoff:3.500A) Processing helix chain 'I' and resid 59 through 69 Processing helix chain 'I' and resid 72 through 105 Proline residue: I 87 - end of helix Processing helix chain 'I' and resid 129 through 158 Processing helix chain 'I' and resid 184 through 218 Processing helix chain 'J' and resid 2 through 12 Processing helix chain 'J' and resid 18 through 41 removed outlier: 4.352A pdb=" N LEU J 25 " --> pdb=" O GLY J 21 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N SER J 26 " --> pdb=" O ARG J 22 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N GLU J 41 " --> pdb=" O VAL J 37 " (cutoff:3.500A) Processing helix chain 'J' and resid 59 through 69 Processing helix chain 'J' and resid 72 through 105 Proline residue: J 87 - end of helix Processing helix chain 'J' and resid 129 through 158 Processing helix chain 'J' and resid 184 through 218 Processing helix chain 'K' and resid 2 through 12 Processing helix chain 'K' and resid 18 through 41 removed outlier: 4.353A pdb=" N LEU K 25 " --> pdb=" O GLY K 21 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N SER K 26 " --> pdb=" O ARG K 22 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N GLU K 41 " --> pdb=" O VAL K 37 " (cutoff:3.500A) Processing helix chain 'K' and resid 59 through 69 Processing helix chain 'K' and resid 72 through 105 Proline residue: K 87 - end of helix Processing helix chain 'K' and resid 129 through 158 Processing helix chain 'K' and resid 184 through 218 Processing helix chain 'L' and resid 2 through 12 Processing helix chain 'L' and resid 18 through 41 removed outlier: 4.352A pdb=" N LEU L 25 " --> pdb=" O GLY L 21 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N SER L 26 " --> pdb=" O ARG L 22 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N GLU L 41 " --> pdb=" O VAL L 37 " (cutoff:3.500A) Processing helix chain 'L' and resid 59 through 69 Processing helix chain 'L' and resid 72 through 105 Proline residue: L 87 - end of helix Processing helix chain 'L' and resid 129 through 158 Processing helix chain 'L' and resid 184 through 218 Processing helix chain 'M' and resid 2 through 12 Processing helix chain 'M' and resid 18 through 41 removed outlier: 4.352A pdb=" N LEU M 25 " --> pdb=" O GLY M 21 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N SER M 26 " --> pdb=" O ARG M 22 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N GLU M 41 " --> pdb=" O VAL M 37 " (cutoff:3.500A) Processing helix chain 'M' and resid 59 through 69 Processing helix chain 'M' and resid 72 through 105 Proline residue: M 87 - end of helix Processing helix chain 'M' and resid 129 through 158 Processing helix chain 'M' and resid 184 through 218 Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 53 removed outlier: 3.665A pdb=" N ILE A 52 " --> pdb=" O PHE A 181 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 52 through 53 removed outlier: 3.666A pdb=" N ILE C 52 " --> pdb=" O PHE C 181 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 52 through 53 removed outlier: 3.666A pdb=" N ILE D 52 " --> pdb=" O PHE D 181 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 52 through 53 removed outlier: 3.666A pdb=" N ILE E 52 " --> pdb=" O PHE E 181 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 52 through 53 removed outlier: 3.665A pdb=" N ILE F 52 " --> pdb=" O PHE F 181 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 52 through 53 removed outlier: 3.665A pdb=" N ILE G 52 " --> pdb=" O PHE G 181 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 52 through 53 removed outlier: 3.665A pdb=" N ILE H 52 " --> pdb=" O PHE H 181 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 52 through 53 removed outlier: 3.665A pdb=" N ILE I 52 " --> pdb=" O PHE I 181 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'J' and resid 52 through 53 removed outlier: 3.666A pdb=" N ILE J 52 " --> pdb=" O PHE J 181 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'K' and resid 52 through 53 removed outlier: 3.665A pdb=" N ILE K 52 " --> pdb=" O PHE K 181 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 52 through 53 removed outlier: 3.665A pdb=" N ILE L 52 " --> pdb=" O PHE L 181 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'M' and resid 52 through 53 removed outlier: 3.665A pdb=" N ILE M 52 " --> pdb=" O PHE M 181 " (cutoff:3.500A) 1440 hydrogen bonds defined for protein. 4284 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: 3.42 Time building geometry restraints manager: 2.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5604 1.34 - 1.46: 4833 1.46 - 1.58: 8977 1.58 - 1.69: 38 1.69 - 1.81: 264 Bond restraints: 19716 Sorted by residual: bond pdb=" C6 CLR A 500 " pdb=" C7 CLR A 500 " ideal model delta sigma weight residual 1.492 1.543 -0.051 2.00e-02 2.50e+03 6.40e+00 bond pdb=" C6 CLR E 500 " pdb=" C7 CLR E 500 " ideal model delta sigma weight residual 1.492 1.542 -0.050 2.00e-02 2.50e+03 6.31e+00 bond pdb=" C6 CLR D 500 " pdb=" C7 CLR D 500 " ideal model delta sigma weight residual 1.492 1.542 -0.050 2.00e-02 2.50e+03 6.29e+00 bond pdb=" C6 CLR K 500 " pdb=" C7 CLR K 500 " ideal model delta sigma weight residual 1.492 1.542 -0.050 2.00e-02 2.50e+03 6.28e+00 bond pdb=" C6 CLR L 500 " pdb=" C7 CLR L 500 " ideal model delta sigma weight residual 1.492 1.542 -0.050 2.00e-02 2.50e+03 6.25e+00 ... (remaining 19711 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.40: 26286 1.40 - 2.80: 449 2.80 - 4.21: 157 4.21 - 5.61: 48 5.61 - 7.01: 36 Bond angle restraints: 26976 Sorted by residual: angle pdb=" C ASN M 176 " pdb=" CA ASN M 176 " pdb=" CB ASN M 176 " ideal model delta sigma weight residual 116.54 110.03 6.51 1.15e+00 7.56e-01 3.21e+01 angle pdb=" C ASN G 176 " pdb=" CA ASN G 176 " pdb=" CB ASN G 176 " ideal model delta sigma weight residual 116.54 110.03 6.51 1.15e+00 7.56e-01 3.20e+01 angle pdb=" C ASN K 176 " pdb=" CA ASN K 176 " pdb=" CB ASN K 176 " ideal model delta sigma weight residual 116.54 110.04 6.50 1.15e+00 7.56e-01 3.19e+01 angle pdb=" C ASN H 176 " pdb=" CA ASN H 176 " pdb=" CB ASN H 176 " ideal model delta sigma weight residual 116.54 110.04 6.50 1.15e+00 7.56e-01 3.19e+01 angle pdb=" C ASN J 176 " pdb=" CA ASN J 176 " pdb=" CB ASN J 176 " ideal model delta sigma weight residual 116.54 110.06 6.48 1.15e+00 7.56e-01 3.18e+01 ... (remaining 26971 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.59: 10853 11.59 - 23.19: 799 23.19 - 34.78: 263 34.78 - 46.38: 109 46.38 - 57.97: 24 Dihedral angle restraints: 12048 sinusoidal: 5100 harmonic: 6948 Sorted by residual: dihedral pdb=" N LEU F 196 " pdb=" CA LEU F 196 " pdb=" CB LEU F 196 " pdb=" CG LEU F 196 " ideal model delta sinusoidal sigma weight residual -60.00 -99.64 39.64 3 1.50e+01 4.44e-03 7.03e+00 dihedral pdb=" N LEU A 196 " pdb=" CA LEU A 196 " pdb=" CB LEU A 196 " pdb=" CG LEU A 196 " ideal model delta sinusoidal sigma weight residual -60.00 -99.62 39.62 3 1.50e+01 4.44e-03 7.03e+00 dihedral pdb=" N LEU I 196 " pdb=" CA LEU I 196 " pdb=" CB LEU I 196 " pdb=" CG LEU I 196 " ideal model delta sinusoidal sigma weight residual -60.00 -99.61 39.61 3 1.50e+01 4.44e-03 7.03e+00 ... (remaining 12045 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 2941 0.066 - 0.132: 251 0.132 - 0.198: 0 0.198 - 0.264: 12 0.264 - 0.330: 36 Chirality restraints: 3240 Sorted by residual: chirality pdb=" C17 CLR I 500 " pdb=" C13 CLR I 500 " pdb=" C16 CLR I 500 " pdb=" C20 CLR I 500 " both_signs ideal model delta sigma weight residual False 2.55 2.88 -0.33 2.00e-01 2.50e+01 2.72e+00 chirality pdb=" C17 CLR A 500 " pdb=" C13 CLR A 500 " pdb=" C16 CLR A 500 " pdb=" C20 CLR A 500 " both_signs ideal model delta sigma weight residual False 2.55 2.88 -0.33 2.00e-01 2.50e+01 2.71e+00 chirality pdb=" C17 CLR H 500 " pdb=" C13 CLR H 500 " pdb=" C16 CLR H 500 " pdb=" C20 CLR H 500 " both_signs ideal model delta sigma weight residual False 2.55 2.88 -0.33 2.00e-01 2.50e+01 2.71e+00 ... (remaining 3237 not shown) Planarity restraints: 3144 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE L 68 " 0.007 2.00e-02 2.50e+03 4.64e-03 3.77e-01 pdb=" CG PHE L 68 " -0.010 2.00e-02 2.50e+03 pdb=" CD1 PHE L 68 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE L 68 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE L 68 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE L 68 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE L 68 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE K 68 " -0.006 2.00e-02 2.50e+03 4.45e-03 3.47e-01 pdb=" CG PHE K 68 " 0.010 2.00e-02 2.50e+03 pdb=" CD1 PHE K 68 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE K 68 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE K 68 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE K 68 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE K 68 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 68 " 0.006 2.00e-02 2.50e+03 4.42e-03 3.43e-01 pdb=" CG PHE C 68 " -0.009 2.00e-02 2.50e+03 pdb=" CD1 PHE C 68 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE C 68 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE C 68 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE C 68 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE C 68 " 0.002 2.00e-02 2.50e+03 ... (remaining 3141 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 3579 2.77 - 3.30: 19414 3.30 - 3.84: 33720 3.84 - 4.37: 36423 4.37 - 4.90: 65923 Nonbonded interactions: 159059 Sorted by model distance: nonbonded pdb=" OH TYR A 7 " pdb=" ND1 HIS C 97 " model vdw 2.238 3.120 nonbonded pdb=" O ILE E 71 " pdb=" OH TYR E 158 " model vdw 2.247 3.040 nonbonded pdb=" O ILE G 71 " pdb=" OH TYR G 158 " model vdw 2.247 3.040 nonbonded pdb=" O ILE F 71 " pdb=" OH TYR F 158 " model vdw 2.247 3.040 nonbonded pdb=" O ILE D 71 " pdb=" OH TYR D 158 " model vdw 2.248 3.040 ... (remaining 159054 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' } 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: 5.500 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: 0.020 Extract box with map and model: 0.380 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 18.860 Find NCS groups from input model: 0.180 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:7.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 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 0.051 19752 Z= 0.219 Angle : 0.577 7.009 27048 Z= 0.284 Chirality : 0.052 0.330 3240 Planarity : 0.002 0.014 3144 Dihedral : 10.048 57.972 7428 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.57 % Allowed : 4.55 % Favored : 94.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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 aren not related in a simple way. whole: 3.35 (0.17), residues: 2304 helix: 3.17 (0.11), residues: 1704 sheet: 1.38 (0.50), residues: 132 loop : -1.48 (0.25), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 165 TYR 0.005 0.001 TYR M 65 PHE 0.010 0.001 PHE L 68 TRP 0.005 0.001 TRP F 77 HIS 0.001 0.000 HIS K 16 Details of bonding type rmsd covalent geometry : bond 0.00481 (19716) covalent geometry : angle 0.57644 (26976) SS BOND : bond 0.00127 ( 36) SS BOND : angle 0.70550 ( 72) hydrogen bonds : bond 0.10263 ( 1440) hydrogen bonds : angle 4.42006 ( 4284) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 362 time to evaluate : 0.786 Fit side-chains REVERT: D 14 ASN cc_start: 0.5285 (t0) cc_final: 0.4989 (t0) REVERT: J 143 ARG cc_start: 0.6772 (ttm170) cc_final: 0.6228 (ttp80) outliers start: 12 outliers final: 0 residues processed: 369 average time/residue: 0.8165 time to fit residues: 330.0194 Evaluate side-chains 268 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 268 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 0.4980 chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 7.9990 chunk 227 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 40.0000 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 0.0060 chunk 124 optimal weight: 30.0000 chunk 103 optimal weight: 5.9990 chunk 200 optimal weight: 30.0000 overall best weight: 1.9000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 98 GLN M 16 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.088653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.061004 restraints weight = 39665.611| |-----------------------------------------------------------------------------| r_work (start): 0.2809 rms_B_bonded: 2.07 r_work: 0.2666 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2543 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8887 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19752 Z= 0.137 Angle : 0.533 9.425 27048 Z= 0.269 Chirality : 0.039 0.175 3240 Planarity : 0.004 0.041 3144 Dihedral : 5.304 36.006 3312 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 2.18 % Allowed : 11.70 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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 aren not related in a simple way. whole: 3.44 (0.17), residues: 2304 helix: 3.29 (0.11), residues: 1704 sheet: 1.11 (0.48), residues: 132 loop : -1.56 (0.25), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG J 216 TYR 0.013 0.001 TYR F 155 PHE 0.021 0.001 PHE L 29 TRP 0.008 0.001 TRP D 3 HIS 0.003 0.001 HIS F 73 Details of bonding type rmsd covalent geometry : bond 0.00315 (19716) covalent geometry : angle 0.53173 (26976) SS BOND : bond 0.00204 ( 36) SS BOND : angle 0.79005 ( 72) hydrogen bonds : bond 0.03418 ( 1440) hydrogen bonds : angle 3.09321 ( 4284) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 289 time to evaluate : 0.781 Fit side-chains REVERT: A 1 MET cc_start: 0.4762 (mmt) cc_final: 0.4467 (mmt) REVERT: A 46 ASP cc_start: 0.9221 (p0) cc_final: 0.9017 (p0) REVERT: A 99 GLN cc_start: 0.8361 (OUTLIER) cc_final: 0.8094 (mp10) REVERT: A 216 ARG cc_start: 0.8870 (mmm-85) cc_final: 0.8654 (mmm-85) REVERT: C 14 ASN cc_start: 0.8940 (t0) cc_final: 0.8660 (t0) REVERT: C 46 ASP cc_start: 0.9045 (p0) cc_final: 0.8836 (p0) REVERT: C 99 GLN cc_start: 0.8424 (OUTLIER) cc_final: 0.8128 (mp10) REVERT: D 14 ASN cc_start: 0.8731 (t0) cc_final: 0.8518 (t0) REVERT: D 212 TYR cc_start: 0.8494 (t80) cc_final: 0.8248 (t80) REVERT: E 46 ASP cc_start: 0.9183 (p0) cc_final: 0.8969 (p0) REVERT: E 102 GLU cc_start: 0.8600 (pp20) cc_final: 0.8394 (pp20) REVERT: F 14 ASN cc_start: 0.9022 (t0) cc_final: 0.8789 (t0) REVERT: F 99 GLN cc_start: 0.8325 (tm-30) cc_final: 0.7817 (tm-30) REVERT: F 102 GLU cc_start: 0.8768 (pp20) cc_final: 0.8518 (pp20) REVERT: F 103 LYS cc_start: 0.8196 (pttt) cc_final: 0.7959 (pttt) REVERT: G 14 ASN cc_start: 0.8813 (t0) cc_final: 0.8607 (t0) REVERT: I 14 ASN cc_start: 0.8699 (m-40) cc_final: 0.8339 (m-40) REVERT: I 212 TYR cc_start: 0.7852 (t80) cc_final: 0.7633 (t80) REVERT: I 216 ARG cc_start: 0.8838 (mmm-85) cc_final: 0.8609 (mmm-85) REVERT: J 170 ASP cc_start: 0.9443 (p0) cc_final: 0.9232 (p0) REVERT: L 1 MET cc_start: 0.5924 (mmt) cc_final: 0.4398 (pmt) REVERT: L 89 LEU cc_start: 0.9227 (OUTLIER) cc_final: 0.8964 (tt) REVERT: M 46 ASP cc_start: 0.9122 (p0) cc_final: 0.8912 (p0) REVERT: M 212 TYR cc_start: 0.8365 (t80) cc_final: 0.8001 (t80) outliers start: 46 outliers final: 6 residues processed: 311 average time/residue: 0.8876 time to fit residues: 300.7273 Evaluate side-chains 271 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 262 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 GLN Chi-restraints excluded: chain C residue 99 GLN Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain I residue 2 ASN Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain L residue 20 ILE Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain M residue 42 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 51 optimal weight: 0.4980 chunk 207 optimal weight: 8.9990 chunk 91 optimal weight: 3.9990 chunk 162 optimal weight: 10.0000 chunk 95 optimal weight: 40.0000 chunk 10 optimal weight: 7.9990 chunk 120 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 132 optimal weight: 4.9990 chunk 68 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 GLN C 98 GLN C 99 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.087397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.059409 restraints weight = 39858.312| |-----------------------------------------------------------------------------| r_work (start): 0.2774 rms_B_bonded: 2.09 r_work: 0.2630 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2506 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8956 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 19752 Z= 0.139 Angle : 0.496 8.690 27048 Z= 0.253 Chirality : 0.038 0.162 3240 Planarity : 0.003 0.038 3144 Dihedral : 5.400 38.372 3312 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 1.37 % Allowed : 14.02 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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 aren not related in a simple way. whole: 3.69 (0.17), residues: 2304 helix: 3.47 (0.11), residues: 1704 sheet: 1.23 (0.48), residues: 132 loop : -1.50 (0.25), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 216 TYR 0.011 0.001 TYR C 212 PHE 0.017 0.001 PHE L 29 TRP 0.016 0.001 TRP I 3 HIS 0.005 0.001 HIS C 100 Details of bonding type rmsd covalent geometry : bond 0.00325 (19716) covalent geometry : angle 0.49587 (26976) SS BOND : bond 0.00144 ( 36) SS BOND : angle 0.55489 ( 72) hydrogen bonds : bond 0.03500 ( 1440) hydrogen bonds : angle 2.94890 ( 4284) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 283 time to evaluate : 0.811 Fit side-chains REVERT: A 1 MET cc_start: 0.5032 (mmt) cc_final: 0.4729 (mmt) REVERT: A 46 ASP cc_start: 0.9263 (p0) cc_final: 0.9035 (p0) REVERT: A 99 GLN cc_start: 0.8274 (OUTLIER) cc_final: 0.8012 (mp10) REVERT: C 14 ASN cc_start: 0.8996 (t0) cc_final: 0.8770 (t0) REVERT: C 46 ASP cc_start: 0.9174 (p0) cc_final: 0.8938 (p0) REVERT: C 99 GLN cc_start: 0.8278 (OUTLIER) cc_final: 0.8036 (mp10) REVERT: C 212 TYR cc_start: 0.8666 (t80) cc_final: 0.8459 (t80) REVERT: C 216 ARG cc_start: 0.8999 (tpp80) cc_final: 0.8721 (mmm-85) REVERT: D 14 ASN cc_start: 0.8766 (t0) cc_final: 0.8546 (t0) REVERT: D 46 ASP cc_start: 0.9094 (p0) cc_final: 0.8797 (p0) REVERT: D 212 TYR cc_start: 0.8442 (t80) cc_final: 0.8189 (t80) REVERT: E 41 GLU cc_start: 0.8969 (tt0) cc_final: 0.8698 (pm20) REVERT: E 46 ASP cc_start: 0.9240 (p0) cc_final: 0.9023 (p0) REVERT: E 103 LYS cc_start: 0.8329 (pttt) cc_final: 0.8048 (ptpp) REVERT: F 14 ASN cc_start: 0.9044 (t0) cc_final: 0.8797 (t0) REVERT: F 46 ASP cc_start: 0.9197 (p0) cc_final: 0.8996 (p0) REVERT: F 99 GLN cc_start: 0.8275 (tm-30) cc_final: 0.7781 (tm-30) REVERT: F 102 GLU cc_start: 0.8806 (pp20) cc_final: 0.8562 (pp20) REVERT: F 103 LYS cc_start: 0.8169 (pttt) cc_final: 0.7901 (pttt) REVERT: G 14 ASN cc_start: 0.8874 (t0) cc_final: 0.8650 (t0) REVERT: G 99 GLN cc_start: 0.8260 (OUTLIER) cc_final: 0.8041 (mp10) REVERT: H 46 ASP cc_start: 0.9100 (p0) cc_final: 0.8805 (p0) REVERT: H 216 ARG cc_start: 0.8955 (mmm-85) cc_final: 0.8634 (mmt-90) REVERT: I 14 ASN cc_start: 0.8770 (m-40) cc_final: 0.8379 (m-40) REVERT: J 170 ASP cc_start: 0.9498 (p0) cc_final: 0.9264 (p0) REVERT: K 46 ASP cc_start: 0.9390 (p0) cc_final: 0.9177 (p0) REVERT: L 1 MET cc_start: 0.5868 (mmt) cc_final: 0.4259 (pmt) REVERT: M 46 ASP cc_start: 0.9170 (p0) cc_final: 0.8933 (p0) REVERT: M 212 TYR cc_start: 0.8336 (t80) cc_final: 0.8135 (t80) REVERT: M 216 ARG cc_start: 0.8891 (mmm-85) cc_final: 0.8661 (mmm-85) outliers start: 29 outliers final: 10 residues processed: 301 average time/residue: 0.8839 time to fit residues: 289.2201 Evaluate side-chains 280 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 267 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 GLN Chi-restraints excluded: chain C residue 4 THR Chi-restraints excluded: chain C residue 99 GLN Chi-restraints excluded: chain D residue 151 MET Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain G residue 99 GLN Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain K residue 151 MET Chi-restraints excluded: chain L residue 20 ILE Chi-restraints excluded: chain L residue 25 LEU Chi-restraints excluded: chain M residue 4 THR Chi-restraints excluded: chain M residue 42 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 134 optimal weight: 30.0000 chunk 21 optimal weight: 9.9990 chunk 63 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 141 optimal weight: 7.9990 chunk 57 optimal weight: 40.0000 chunk 82 optimal weight: 5.9990 chunk 67 optimal weight: 30.0000 chunk 16 optimal weight: 0.0010 chunk 30 optimal weight: 4.9990 chunk 206 optimal weight: 2.9990 overall best weight: 3.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN C 98 GLN G 99 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.086065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.057695 restraints weight = 39960.003| |-----------------------------------------------------------------------------| r_work (start): 0.2727 rms_B_bonded: 2.14 r_work: 0.2579 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2453 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8999 moved from start: 0.3180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 19752 Z= 0.195 Angle : 0.519 7.847 27048 Z= 0.266 Chirality : 0.039 0.152 3240 Planarity : 0.003 0.039 3144 Dihedral : 5.500 39.686 3312 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.75 % Allowed : 15.01 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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 aren not related in a simple way. whole: 3.66 (0.17), residues: 2304 helix: 3.43 (0.11), residues: 1704 sheet: 1.35 (0.49), residues: 132 loop : -1.46 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 216 TYR 0.023 0.001 TYR H 212 PHE 0.013 0.002 PHE L 29 TRP 0.005 0.001 TRP L 44 HIS 0.002 0.001 HIS J 100 Details of bonding type rmsd covalent geometry : bond 0.00469 (19716) covalent geometry : angle 0.51867 (26976) SS BOND : bond 0.00194 ( 36) SS BOND : angle 0.64593 ( 72) hydrogen bonds : bond 0.03456 ( 1440) hydrogen bonds : angle 2.92931 ( 4284) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 269 time to evaluate : 0.745 Fit side-chains REVERT: A 46 ASP cc_start: 0.9323 (p0) cc_final: 0.9078 (p0) REVERT: C 14 ASN cc_start: 0.9012 (t0) cc_final: 0.8772 (t0) REVERT: C 46 ASP cc_start: 0.9219 (p0) cc_final: 0.8964 (p0) REVERT: C 216 ARG cc_start: 0.9018 (tpp80) cc_final: 0.8767 (mmm-85) REVERT: D 14 ASN cc_start: 0.8858 (t0) cc_final: 0.8626 (t0) REVERT: D 46 ASP cc_start: 0.9176 (p0) cc_final: 0.8865 (p0) REVERT: D 103 LYS cc_start: 0.8275 (pttt) cc_final: 0.7940 (ptpp) REVERT: D 212 TYR cc_start: 0.8445 (t80) cc_final: 0.8231 (t80) REVERT: E 46 ASP cc_start: 0.9307 (p0) cc_final: 0.9092 (p0) REVERT: E 103 LYS cc_start: 0.8304 (pttt) cc_final: 0.8067 (ptpp) REVERT: F 14 ASN cc_start: 0.9114 (t0) cc_final: 0.8835 (t0) REVERT: F 46 ASP cc_start: 0.9217 (p0) cc_final: 0.9010 (p0) REVERT: F 102 GLU cc_start: 0.8848 (pp20) cc_final: 0.8540 (pp20) REVERT: G 14 ASN cc_start: 0.8961 (t0) cc_final: 0.8736 (t0) REVERT: H 46 ASP cc_start: 0.9189 (p0) cc_final: 0.8883 (p0) REVERT: H 212 TYR cc_start: 0.8279 (t80) cc_final: 0.8064 (t80) REVERT: I 14 ASN cc_start: 0.8905 (m-40) cc_final: 0.8503 (m-40) REVERT: J 170 ASP cc_start: 0.9495 (p0) cc_final: 0.9285 (p0) REVERT: K 46 ASP cc_start: 0.9374 (p0) cc_final: 0.9172 (p0) REVERT: L 1 MET cc_start: 0.5865 (mmt) cc_final: 0.4172 (pmt) REVERT: M 46 ASP cc_start: 0.9220 (p0) cc_final: 0.9006 (p0) outliers start: 37 outliers final: 11 residues processed: 292 average time/residue: 0.8785 time to fit residues: 278.8361 Evaluate side-chains 269 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 258 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain C residue 151 MET Chi-restraints excluded: chain F residue 151 MET Chi-restraints excluded: chain G residue 151 MET Chi-restraints excluded: chain H residue 4 THR Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain L residue 20 ILE Chi-restraints excluded: chain L residue 25 LEU Chi-restraints excluded: chain M residue 25 LEU Chi-restraints excluded: chain M residue 42 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 1 optimal weight: 30.0000 chunk 187 optimal weight: 0.8980 chunk 169 optimal weight: 7.9990 chunk 46 optimal weight: 2.9990 chunk 199 optimal weight: 7.9990 chunk 123 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 90 optimal weight: 6.9990 chunk 98 optimal weight: 0.9980 chunk 119 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 GLN C 99 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.086994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.058873 restraints weight = 39712.580| |-----------------------------------------------------------------------------| r_work (start): 0.2763 rms_B_bonded: 2.10 r_work: 0.2617 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2491 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8990 moved from start: 0.3308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 19752 Z= 0.115 Angle : 0.484 8.048 27048 Z= 0.247 Chirality : 0.037 0.121 3240 Planarity : 0.003 0.037 3144 Dihedral : 5.544 40.333 3312 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.89 % Allowed : 15.34 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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 aren not related in a simple way. whole: 3.75 (0.17), residues: 2304 helix: 3.53 (0.11), residues: 1704 sheet: 1.27 (0.49), residues: 132 loop : -1.51 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG M 216 TYR 0.016 0.001 TYR H 212 PHE 0.014 0.001 PHE L 29 TRP 0.004 0.001 TRP L 44 HIS 0.002 0.000 HIS A 73 Details of bonding type rmsd covalent geometry : bond 0.00269 (19716) covalent geometry : angle 0.48373 (26976) SS BOND : bond 0.00133 ( 36) SS BOND : angle 0.53411 ( 72) hydrogen bonds : bond 0.03140 ( 1440) hydrogen bonds : angle 2.81972 ( 4284) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 281 time to evaluate : 0.797 Fit side-chains REVERT: A 46 ASP cc_start: 0.9292 (p0) cc_final: 0.9056 (p0) REVERT: A 99 GLN cc_start: 0.8258 (OUTLIER) cc_final: 0.8055 (mp10) REVERT: C 14 ASN cc_start: 0.9001 (t0) cc_final: 0.8764 (t0) REVERT: C 46 ASP cc_start: 0.9199 (p0) cc_final: 0.8937 (p0) REVERT: C 216 ARG cc_start: 0.8994 (tpp80) cc_final: 0.8773 (mmm-85) REVERT: D 14 ASN cc_start: 0.8819 (t0) cc_final: 0.8587 (t0) REVERT: D 46 ASP cc_start: 0.9176 (p0) cc_final: 0.8847 (p0) REVERT: D 212 TYR cc_start: 0.8444 (t80) cc_final: 0.8197 (t80) REVERT: E 46 ASP cc_start: 0.9286 (p0) cc_final: 0.9081 (p0) REVERT: E 103 LYS cc_start: 0.8330 (pttt) cc_final: 0.8108 (ptpp) REVERT: E 216 ARG cc_start: 0.9027 (tpp80) cc_final: 0.8705 (mmm-85) REVERT: F 14 ASN cc_start: 0.9077 (t0) cc_final: 0.8839 (t0) REVERT: F 46 ASP cc_start: 0.9215 (p0) cc_final: 0.9011 (p0) REVERT: F 102 GLU cc_start: 0.8805 (pp20) cc_final: 0.8587 (pp20) REVERT: F 103 LYS cc_start: 0.8310 (pttt) cc_final: 0.8018 (ptpp) REVERT: H 46 ASP cc_start: 0.9161 (p0) cc_final: 0.8848 (p0) REVERT: I 14 ASN cc_start: 0.8901 (m-40) cc_final: 0.8518 (m-40) REVERT: J 1 MET cc_start: 0.5848 (mmt) cc_final: 0.5514 (mmt) REVERT: J 103 LYS cc_start: 0.7838 (pttt) cc_final: 0.7427 (ptpp) REVERT: K 1 MET cc_start: 0.5844 (mmt) cc_final: 0.4454 (pmt) REVERT: K 46 ASP cc_start: 0.9356 (p0) cc_final: 0.9151 (p0) REVERT: L 1 MET cc_start: 0.5872 (mmt) cc_final: 0.4259 (pmt) REVERT: L 99 GLN cc_start: 0.8274 (mm110) cc_final: 0.8068 (mp10) REVERT: M 15 ARG cc_start: 0.8384 (OUTLIER) cc_final: 0.8178 (ppp80) REVERT: M 46 ASP cc_start: 0.9203 (p0) cc_final: 0.8985 (p0) outliers start: 40 outliers final: 13 residues processed: 308 average time/residue: 0.8537 time to fit residues: 286.5784 Evaluate side-chains 281 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 266 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 99 GLN Chi-restraints excluded: chain C residue 4 THR Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain F residue 151 MET Chi-restraints excluded: chain H residue 4 THR Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 151 MET Chi-restraints excluded: chain L residue 20 ILE Chi-restraints excluded: chain L residue 25 LEU Chi-restraints excluded: chain M residue 4 THR Chi-restraints excluded: chain M residue 15 ARG Chi-restraints excluded: chain M residue 25 LEU Chi-restraints excluded: chain M residue 42 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 120 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 164 optimal weight: 1.9990 chunk 141 optimal weight: 7.9990 chunk 140 optimal weight: 0.7980 chunk 55 optimal weight: 6.9990 chunk 218 optimal weight: 6.9990 chunk 1 optimal weight: 10.0000 chunk 34 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 189 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN A 99 GLN C 99 GLN F 99 GLN G 99 GLN K 16 HIS K 99 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.087230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.059216 restraints weight = 39512.813| |-----------------------------------------------------------------------------| r_work (start): 0.2771 rms_B_bonded: 2.10 r_work: 0.2626 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2501 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8984 moved from start: 0.3466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19752 Z= 0.110 Angle : 0.484 8.346 27048 Z= 0.248 Chirality : 0.037 0.135 3240 Planarity : 0.003 0.038 3144 Dihedral : 5.520 40.370 3312 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 1.66 % Allowed : 15.96 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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 aren not related in a simple way. whole: 3.77 (0.17), residues: 2304 helix: 3.54 (0.11), residues: 1704 sheet: 1.27 (0.49), residues: 132 loop : -1.52 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 216 TYR 0.010 0.001 TYR G 65 PHE 0.013 0.001 PHE L 29 TRP 0.004 0.000 TRP L 24 HIS 0.004 0.000 HIS A 100 Details of bonding type rmsd covalent geometry : bond 0.00253 (19716) covalent geometry : angle 0.48359 (26976) SS BOND : bond 0.00125 ( 36) SS BOND : angle 0.49006 ( 72) hydrogen bonds : bond 0.03030 ( 1440) hydrogen bonds : angle 2.78664 ( 4284) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 278 time to evaluate : 0.786 Fit side-chains REVERT: A 46 ASP cc_start: 0.9284 (p0) cc_final: 0.9054 (p0) REVERT: C 14 ASN cc_start: 0.9003 (t0) cc_final: 0.8733 (t0) REVERT: C 46 ASP cc_start: 0.9188 (p0) cc_final: 0.8938 (p0) REVERT: C 103 LYS cc_start: 0.8221 (pttt) cc_final: 0.7974 (ptpp) REVERT: C 216 ARG cc_start: 0.8993 (tpp80) cc_final: 0.8783 (mmm-85) REVERT: D 14 ASN cc_start: 0.8825 (t0) cc_final: 0.8584 (t0) REVERT: D 46 ASP cc_start: 0.9155 (p0) cc_final: 0.8831 (p0) REVERT: D 103 LYS cc_start: 0.8269 (pttt) cc_final: 0.7980 (ptpp) REVERT: D 212 TYR cc_start: 0.8432 (t80) cc_final: 0.8187 (t80) REVERT: E 46 ASP cc_start: 0.9276 (p0) cc_final: 0.9046 (p0) REVERT: E 216 ARG cc_start: 0.9000 (tpp80) cc_final: 0.8732 (mmm-85) REVERT: F 14 ASN cc_start: 0.9069 (t0) cc_final: 0.8858 (t0) REVERT: F 46 ASP cc_start: 0.9233 (p0) cc_final: 0.9015 (p0) REVERT: F 102 GLU cc_start: 0.8812 (pp20) cc_final: 0.8575 (pp20) REVERT: H 46 ASP cc_start: 0.9155 (p0) cc_final: 0.8838 (p0) REVERT: I 14 ASN cc_start: 0.8926 (m-40) cc_final: 0.8538 (m-40) REVERT: J 1 MET cc_start: 0.5852 (mmt) cc_final: 0.5482 (mmt) REVERT: K 1 MET cc_start: 0.5889 (mmt) cc_final: 0.4492 (pmt) REVERT: K 46 ASP cc_start: 0.9350 (p0) cc_final: 0.9146 (p0) REVERT: L 1 MET cc_start: 0.5860 (mmt) cc_final: 0.4241 (pmt) REVERT: M 46 ASP cc_start: 0.9206 (p0) cc_final: 0.8985 (p0) outliers start: 35 outliers final: 14 residues processed: 300 average time/residue: 0.8999 time to fit residues: 293.8899 Evaluate side-chains 277 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 263 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain C residue 4 THR Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain F residue 99 GLN Chi-restraints excluded: chain F residue 151 MET Chi-restraints excluded: chain H residue 4 THR Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain L residue 20 ILE Chi-restraints excluded: chain L residue 25 LEU Chi-restraints excluded: chain M residue 4 THR Chi-restraints excluded: chain M residue 25 LEU Chi-restraints excluded: chain M residue 42 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 177 optimal weight: 4.9990 chunk 226 optimal weight: 3.9990 chunk 201 optimal weight: 7.9990 chunk 62 optimal weight: 6.9990 chunk 70 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 172 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 chunk 118 optimal weight: 7.9990 chunk 161 optimal weight: 4.9990 chunk 68 optimal weight: 6.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 GLN C 57 GLN C 99 GLN G 99 GLN K 16 HIS L 57 GLN L 99 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.085784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.057528 restraints weight = 40010.854| |-----------------------------------------------------------------------------| r_work (start): 0.2729 rms_B_bonded: 2.11 r_work: 0.2584 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2458 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9014 moved from start: 0.3615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 19752 Z= 0.190 Angle : 0.530 9.392 27048 Z= 0.274 Chirality : 0.039 0.135 3240 Planarity : 0.003 0.041 3144 Dihedral : 5.584 41.466 3312 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.52 % Allowed : 16.29 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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 aren not related in a simple way. whole: 3.66 (0.17), residues: 2304 helix: 3.42 (0.11), residues: 1704 sheet: 1.41 (0.49), residues: 132 loop : -1.44 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG M 216 TYR 0.020 0.001 TYR H 212 PHE 0.012 0.002 PHE I 191 TRP 0.004 0.001 TRP M 134 HIS 0.017 0.001 HIS F 100 Details of bonding type rmsd covalent geometry : bond 0.00455 (19716) covalent geometry : angle 0.52978 (26976) SS BOND : bond 0.00187 ( 36) SS BOND : angle 0.60291 ( 72) hydrogen bonds : bond 0.03321 ( 1440) hydrogen bonds : angle 2.87989 ( 4284) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 263 time to evaluate : 0.528 Fit side-chains REVERT: A 46 ASP cc_start: 0.9317 (p0) cc_final: 0.9083 (p0) REVERT: C 14 ASN cc_start: 0.9012 (t0) cc_final: 0.8745 (t0) REVERT: C 46 ASP cc_start: 0.9238 (p0) cc_final: 0.8987 (p0) REVERT: C 103 LYS cc_start: 0.8192 (pttt) cc_final: 0.7949 (ptpp) REVERT: D 14 ASN cc_start: 0.8868 (t0) cc_final: 0.8629 (t0) REVERT: D 46 ASP cc_start: 0.9221 (p0) cc_final: 0.8919 (p0) REVERT: D 103 LYS cc_start: 0.8289 (pttt) cc_final: 0.8018 (ptpp) REVERT: D 212 TYR cc_start: 0.8470 (t80) cc_final: 0.8194 (t80) REVERT: E 212 TYR cc_start: 0.8591 (t80) cc_final: 0.8372 (t80) REVERT: E 216 ARG cc_start: 0.8953 (tpp80) cc_final: 0.8681 (mmm-85) REVERT: F 14 ASN cc_start: 0.9108 (t0) cc_final: 0.8885 (t0) REVERT: F 46 ASP cc_start: 0.9256 (p0) cc_final: 0.9045 (p0) REVERT: F 102 GLU cc_start: 0.8831 (pp20) cc_final: 0.8530 (pp20) REVERT: F 103 LYS cc_start: 0.8383 (pttt) cc_final: 0.8097 (ptpp) REVERT: H 46 ASP cc_start: 0.9200 (p0) cc_final: 0.8899 (p0) REVERT: H 212 TYR cc_start: 0.8365 (t80) cc_final: 0.8127 (t80) REVERT: I 14 ASN cc_start: 0.8986 (m-40) cc_final: 0.8594 (m-40) REVERT: I 145 LEU cc_start: 0.9288 (OUTLIER) cc_final: 0.9083 (mp) REVERT: J 1 MET cc_start: 0.5962 (mmt) cc_final: 0.5574 (mmt) REVERT: J 103 LYS cc_start: 0.7896 (pttt) cc_final: 0.7569 (ptpp) REVERT: K 46 ASP cc_start: 0.9357 (p0) cc_final: 0.9142 (p0) REVERT: K 102 GLU cc_start: 0.8999 (pp20) cc_final: 0.8759 (pp20) REVERT: L 1 MET cc_start: 0.5858 (mmt) cc_final: 0.4146 (pmt) REVERT: L 15 ARG cc_start: 0.8501 (OUTLIER) cc_final: 0.8196 (ppp-140) REVERT: M 46 ASP cc_start: 0.9212 (p0) cc_final: 0.9007 (p0) REVERT: M 102 GLU cc_start: 0.8521 (pp20) cc_final: 0.8313 (pp20) outliers start: 32 outliers final: 12 residues processed: 283 average time/residue: 0.9309 time to fit residues: 286.0091 Evaluate side-chains 271 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 257 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain C residue 4 THR Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain F residue 151 MET Chi-restraints excluded: chain H residue 4 THR Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 145 LEU Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain L residue 15 ARG Chi-restraints excluded: chain L residue 20 ILE Chi-restraints excluded: chain L residue 25 LEU Chi-restraints excluded: chain M residue 4 THR Chi-restraints excluded: chain M residue 25 LEU Chi-restraints excluded: chain M residue 42 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 172 optimal weight: 20.0000 chunk 68 optimal weight: 4.9990 chunk 64 optimal weight: 0.9990 chunk 104 optimal weight: 20.0000 chunk 214 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 chunk 87 optimal weight: 6.9990 chunk 93 optimal weight: 5.9990 chunk 122 optimal weight: 3.9990 chunk 126 optimal weight: 3.9990 chunk 21 optimal weight: 10.0000 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 GLN E 16 HIS K 16 HIS L 99 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.085898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.057841 restraints weight = 40145.904| |-----------------------------------------------------------------------------| r_work (start): 0.2737 rms_B_bonded: 2.14 r_work: 0.2589 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2461 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9003 moved from start: 0.3815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 19752 Z= 0.169 Angle : 0.529 10.150 27048 Z= 0.274 Chirality : 0.039 0.145 3240 Planarity : 0.003 0.053 3144 Dihedral : 5.703 42.432 3312 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.61 % Allowed : 16.52 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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 aren not related in a simple way. whole: 3.59 (0.17), residues: 2304 helix: 3.37 (0.11), residues: 1704 sheet: 1.31 (0.49), residues: 132 loop : -1.43 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 216 TYR 0.017 0.001 TYR H 212 PHE 0.014 0.002 PHE G 29 TRP 0.005 0.001 TRP I 134 HIS 0.002 0.001 HIS E 100 Details of bonding type rmsd covalent geometry : bond 0.00404 (19716) covalent geometry : angle 0.52912 (26976) SS BOND : bond 0.00158 ( 36) SS BOND : angle 0.55198 ( 72) hydrogen bonds : bond 0.03273 ( 1440) hydrogen bonds : angle 2.88744 ( 4284) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 274 time to evaluate : 0.774 Fit side-chains REVERT: A 46 ASP cc_start: 0.9302 (p0) cc_final: 0.9074 (p0) REVERT: C 46 ASP cc_start: 0.9244 (p0) cc_final: 0.8995 (p0) REVERT: C 212 TYR cc_start: 0.8594 (t80) cc_final: 0.8390 (t80) REVERT: D 14 ASN cc_start: 0.8861 (t0) cc_final: 0.8625 (t0) REVERT: D 46 ASP cc_start: 0.9235 (p0) cc_final: 0.8915 (p0) REVERT: D 212 TYR cc_start: 0.8487 (t80) cc_final: 0.8199 (t80) REVERT: E 216 ARG cc_start: 0.8927 (tpp80) cc_final: 0.8693 (mmm-85) REVERT: F 14 ASN cc_start: 0.9099 (t0) cc_final: 0.8886 (t0) REVERT: F 46 ASP cc_start: 0.9260 (p0) cc_final: 0.9051 (p0) REVERT: F 102 GLU cc_start: 0.8846 (pp20) cc_final: 0.8566 (pp20) REVERT: F 216 ARG cc_start: 0.8947 (tpp80) cc_final: 0.8698 (mmm-85) REVERT: G 216 ARG cc_start: 0.8926 (tpp80) cc_final: 0.8517 (mmm-85) REVERT: H 46 ASP cc_start: 0.9221 (p0) cc_final: 0.8924 (p0) REVERT: I 14 ASN cc_start: 0.8977 (m-40) cc_final: 0.8607 (m-40) REVERT: J 1 MET cc_start: 0.5716 (mmt) cc_final: 0.5399 (mmt) REVERT: K 1 MET cc_start: 0.5847 (mmt) cc_final: 0.4402 (pmt) REVERT: K 99 GLN cc_start: 0.8178 (OUTLIER) cc_final: 0.7821 (mm110) REVERT: K 102 GLU cc_start: 0.9000 (pp20) cc_final: 0.8729 (pp20) REVERT: L 1 MET cc_start: 0.5961 (mmt) cc_final: 0.4245 (pmt) REVERT: L 15 ARG cc_start: 0.8512 (OUTLIER) cc_final: 0.8188 (ppp-140) REVERT: L 99 GLN cc_start: 0.8084 (OUTLIER) cc_final: 0.7834 (mp10) REVERT: M 14 ASN cc_start: 0.8757 (t0) cc_final: 0.8537 (t0) REVERT: M 46 ASP cc_start: 0.9247 (p0) cc_final: 0.9045 (p0) REVERT: M 102 GLU cc_start: 0.8568 (pp20) cc_final: 0.8325 (pp20) outliers start: 34 outliers final: 11 residues processed: 296 average time/residue: 0.9111 time to fit residues: 293.1793 Evaluate side-chains 277 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 263 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 4 THR Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain F residue 151 MET Chi-restraints excluded: chain H residue 4 THR Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain K residue 99 GLN Chi-restraints excluded: chain L residue 15 ARG Chi-restraints excluded: chain L residue 20 ILE Chi-restraints excluded: chain L residue 25 LEU Chi-restraints excluded: chain L residue 99 GLN Chi-restraints excluded: chain M residue 4 THR Chi-restraints excluded: chain M residue 25 LEU Chi-restraints excluded: chain M residue 42 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 103 optimal weight: 4.9990 chunk 225 optimal weight: 0.1980 chunk 73 optimal weight: 0.7980 chunk 72 optimal weight: 9.9990 chunk 23 optimal weight: 8.9990 chunk 136 optimal weight: 0.9980 chunk 154 optimal weight: 5.9990 chunk 158 optimal weight: 1.9990 chunk 207 optimal weight: 0.9990 chunk 216 optimal weight: 4.9990 chunk 193 optimal weight: 2.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 GLN C 99 GLN G 99 GLN I 14 ASN ** J 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 16 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.087320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.059392 restraints weight = 39565.474| |-----------------------------------------------------------------------------| r_work (start): 0.2774 rms_B_bonded: 2.14 r_work: 0.2629 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2502 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8974 moved from start: 0.3884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 19752 Z= 0.108 Angle : 0.515 9.705 27048 Z= 0.268 Chirality : 0.038 0.140 3240 Planarity : 0.003 0.039 3144 Dihedral : 5.674 42.019 3312 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.04 % Allowed : 17.47 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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 aren not related in a simple way. whole: 3.65 (0.17), residues: 2304 helix: 3.44 (0.11), residues: 1704 sheet: 1.14 (0.48), residues: 132 loop : -1.47 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 216 TYR 0.018 0.001 TYR H 136 PHE 0.019 0.001 PHE G 29 TRP 0.005 0.000 TRP L 24 HIS 0.005 0.001 HIS L 94 Details of bonding type rmsd covalent geometry : bond 0.00241 (19716) covalent geometry : angle 0.51481 (26976) SS BOND : bond 0.00121 ( 36) SS BOND : angle 0.47940 ( 72) hydrogen bonds : bond 0.03010 ( 1440) hydrogen bonds : angle 2.82110 ( 4284) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 283 time to evaluate : 0.769 Fit side-chains REVERT: A 46 ASP cc_start: 0.9261 (p0) cc_final: 0.9015 (p0) REVERT: C 14 ASN cc_start: 0.8853 (t0) cc_final: 0.8647 (t0) REVERT: C 46 ASP cc_start: 0.9224 (p0) cc_final: 0.8984 (p0) REVERT: C 103 LYS cc_start: 0.8255 (pttt) cc_final: 0.8012 (ptpp) REVERT: D 14 ASN cc_start: 0.8827 (t0) cc_final: 0.8594 (t0) REVERT: D 46 ASP cc_start: 0.9177 (p0) cc_final: 0.8845 (p0) REVERT: D 212 TYR cc_start: 0.8481 (t80) cc_final: 0.8190 (t80) REVERT: E 1 MET cc_start: 0.5229 (mmt) cc_final: 0.4853 (mmt) REVERT: E 14 ASN cc_start: 0.9120 (t0) cc_final: 0.8862 (t0) REVERT: E 216 ARG cc_start: 0.8898 (tpp80) cc_final: 0.8677 (mmm-85) REVERT: F 14 ASN cc_start: 0.9069 (t0) cc_final: 0.8835 (t0) REVERT: F 46 ASP cc_start: 0.9243 (p0) cc_final: 0.9026 (p0) REVERT: F 102 GLU cc_start: 0.8855 (pp20) cc_final: 0.8553 (pp20) REVERT: F 103 LYS cc_start: 0.8368 (pttt) cc_final: 0.8085 (ptpp) REVERT: F 216 ARG cc_start: 0.8909 (tpp80) cc_final: 0.8641 (mmm-85) REVERT: H 46 ASP cc_start: 0.9186 (p0) cc_final: 0.8908 (p0) REVERT: I 14 ASN cc_start: 0.8946 (OUTLIER) cc_final: 0.8592 (m-40) REVERT: I 136 TYR cc_start: 0.8982 (t80) cc_final: 0.8684 (t80) REVERT: J 1 MET cc_start: 0.5759 (mmt) cc_final: 0.5459 (mmt) REVERT: J 103 LYS cc_start: 0.7952 (pttt) cc_final: 0.7611 (ptpp) REVERT: K 1 MET cc_start: 0.5864 (mmt) cc_final: 0.4296 (pmt) REVERT: K 99 GLN cc_start: 0.8151 (OUTLIER) cc_final: 0.7798 (mm110) REVERT: K 102 GLU cc_start: 0.9018 (pp20) cc_final: 0.8744 (pp20) REVERT: L 1 MET cc_start: 0.5862 (mmt) cc_final: 0.4213 (pmt) REVERT: L 15 ARG cc_start: 0.8492 (OUTLIER) cc_final: 0.8144 (ppp-140) REVERT: L 103 LYS cc_start: 0.8206 (pttt) cc_final: 0.7874 (pmtt) REVERT: M 46 ASP cc_start: 0.9227 (p0) cc_final: 0.9003 (p0) REVERT: M 102 GLU cc_start: 0.8583 (pp20) cc_final: 0.8328 (pp20) outliers start: 22 outliers final: 10 residues processed: 295 average time/residue: 0.9504 time to fit residues: 304.1138 Evaluate side-chains 280 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 267 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 4 THR Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain F residue 151 MET Chi-restraints excluded: chain H residue 4 THR Chi-restraints excluded: chain I residue 14 ASN Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain K residue 99 GLN Chi-restraints excluded: chain L residue 15 ARG Chi-restraints excluded: chain L residue 20 ILE Chi-restraints excluded: chain L residue 25 LEU Chi-restraints excluded: chain M residue 4 THR Chi-restraints excluded: chain M residue 25 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 224 optimal weight: 3.9990 chunk 61 optimal weight: 8.9990 chunk 216 optimal weight: 0.9980 chunk 149 optimal weight: 0.8980 chunk 148 optimal weight: 10.0000 chunk 8 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 207 optimal weight: 8.9990 chunk 87 optimal weight: 4.9990 chunk 155 optimal weight: 2.9990 chunk 196 optimal weight: 2.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 GLN C 99 GLN I 14 ASN ** J 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 16 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.086664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.058626 restraints weight = 39772.044| |-----------------------------------------------------------------------------| r_work (start): 0.2756 rms_B_bonded: 2.14 r_work: 0.2609 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2481 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8990 moved from start: 0.3956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19752 Z= 0.143 Angle : 0.545 9.491 27048 Z= 0.283 Chirality : 0.039 0.147 3240 Planarity : 0.003 0.041 3144 Dihedral : 5.646 41.920 3312 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.42 % Allowed : 17.42 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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 aren not related in a simple way. whole: 3.62 (0.17), residues: 2304 helix: 3.40 (0.11), residues: 1704 sheet: 1.19 (0.48), residues: 132 loop : -1.40 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 216 TYR 0.019 0.001 TYR H 212 PHE 0.017 0.001 PHE G 29 TRP 0.004 0.001 TRP H 3 HIS 0.002 0.000 HIS A 73 Details of bonding type rmsd covalent geometry : bond 0.00338 (19716) covalent geometry : angle 0.54465 (26976) SS BOND : bond 0.00139 ( 36) SS BOND : angle 0.52368 ( 72) hydrogen bonds : bond 0.03073 ( 1440) hydrogen bonds : angle 2.84627 ( 4284) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 260 time to evaluate : 0.839 Fit side-chains REVERT: A 46 ASP cc_start: 0.9276 (p0) cc_final: 0.9031 (p0) REVERT: C 46 ASP cc_start: 0.9229 (p0) cc_final: 0.8985 (p0) REVERT: D 14 ASN cc_start: 0.8861 (t0) cc_final: 0.8568 (t0) REVERT: D 46 ASP cc_start: 0.9201 (p0) cc_final: 0.8895 (p0) REVERT: D 212 TYR cc_start: 0.8473 (t80) cc_final: 0.8203 (t80) REVERT: E 1 MET cc_start: 0.5248 (mmt) cc_final: 0.4826 (mmt) REVERT: E 14 ASN cc_start: 0.9130 (t0) cc_final: 0.8872 (t0) REVERT: E 216 ARG cc_start: 0.8903 (tpp80) cc_final: 0.8683 (mmm-85) REVERT: F 14 ASN cc_start: 0.9081 (t0) cc_final: 0.8851 (t0) REVERT: F 46 ASP cc_start: 0.9268 (p0) cc_final: 0.9061 (p0) REVERT: F 102 GLU cc_start: 0.8870 (pp20) cc_final: 0.8580 (pp20) REVERT: F 103 LYS cc_start: 0.8339 (pttt) cc_final: 0.8016 (ptpp) REVERT: F 216 ARG cc_start: 0.8916 (tpp80) cc_final: 0.8647 (mmm-85) REVERT: G 216 ARG cc_start: 0.8943 (tpp80) cc_final: 0.8524 (mmm-85) REVERT: H 46 ASP cc_start: 0.9207 (p0) cc_final: 0.8924 (p0) REVERT: J 1 MET cc_start: 0.5873 (mmt) cc_final: 0.5577 (mmt) REVERT: K 1 MET cc_start: 0.5891 (mmt) cc_final: 0.4307 (pmt) REVERT: K 99 GLN cc_start: 0.8182 (OUTLIER) cc_final: 0.7824 (mm110) REVERT: K 102 GLU cc_start: 0.9020 (pp20) cc_final: 0.8745 (pp20) REVERT: L 1 MET cc_start: 0.5898 (mmt) cc_final: 0.4203 (pmt) REVERT: L 15 ARG cc_start: 0.8509 (OUTLIER) cc_final: 0.8155 (ppp-140) REVERT: M 46 ASP cc_start: 0.9242 (p0) cc_final: 0.9020 (p0) REVERT: M 102 GLU cc_start: 0.8590 (pp20) cc_final: 0.8311 (pp20) outliers start: 30 outliers final: 15 residues processed: 277 average time/residue: 0.9530 time to fit residues: 285.7499 Evaluate side-chains 276 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 259 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 GLN Chi-restraints excluded: chain C residue 4 THR Chi-restraints excluded: chain C residue 99 GLN Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain F residue 151 MET Chi-restraints excluded: chain H residue 93 MET Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 151 MET Chi-restraints excluded: chain K residue 99 GLN Chi-restraints excluded: chain L residue 15 ARG Chi-restraints excluded: chain L residue 20 ILE Chi-restraints excluded: chain L residue 25 LEU Chi-restraints excluded: chain L residue 132 LEU Chi-restraints excluded: chain M residue 4 THR Chi-restraints excluded: chain M residue 25 LEU Chi-restraints excluded: chain M residue 42 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 66 optimal weight: 10.0000 chunk 24 optimal weight: 8.9990 chunk 124 optimal weight: 8.9990 chunk 6 optimal weight: 0.6980 chunk 112 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 216 optimal weight: 0.7980 chunk 71 optimal weight: 0.8980 chunk 189 optimal weight: 7.9990 chunk 82 optimal weight: 2.9990 chunk 30 optimal weight: 6.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 GLN C 99 GLN G 99 GLN I 14 ASN ** J 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 16 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.086682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.058648 restraints weight = 39750.113| |-----------------------------------------------------------------------------| r_work (start): 0.2756 rms_B_bonded: 2.14 r_work: 0.2610 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2483 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8985 moved from start: 0.3928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.187 19752 Z= 0.194 Angle : 0.842 59.200 27048 Z= 0.491 Chirality : 0.038 0.147 3240 Planarity : 0.003 0.040 3144 Dihedral : 5.649 41.912 3312 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.14 % Allowed : 17.66 % Favored : 81.20 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 14.29 % 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 aren not related in a simple way. whole: 3.60 (0.17), residues: 2304 helix: 3.38 (0.11), residues: 1704 sheet: 1.19 (0.48), residues: 132 loop : -1.39 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 216 TYR 0.015 0.001 TYR H 136 PHE 0.016 0.001 PHE G 29 TRP 0.004 0.000 TRP L 24 HIS 0.003 0.001 HIS E 73 Details of bonding type rmsd covalent geometry : bond 0.00427 (19716) covalent geometry : angle 0.84247 (26976) SS BOND : bond 0.00129 ( 36) SS BOND : angle 0.52118 ( 72) hydrogen bonds : bond 0.03124 ( 1440) hydrogen bonds : angle 2.86481 ( 4284) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7781.71 seconds wall clock time: 133 minutes 8.94 seconds (7988.94 seconds total)