Starting phenix.real_space_refine on Mon May 19 13:46:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qjf_18446/05_2025/8qjf_18446_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qjf_18446/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8qjf_18446/05_2025/8qjf_18446.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qjf_18446/05_2025/8qjf_18446.map" model { file = "/net/cci-nas-00/data/ceres_data/8qjf_18446/05_2025/8qjf_18446_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qjf_18446/05_2025/8qjf_18446_neut.cif" } resolution = 2.86 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 10.58, per 1000 atoms: 0.55 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: 4.51 Conformation dependent library (CDL) restraints added in 2.2 seconds 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: 1.59 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: 5.62 Time building geometry restraints manager: 5.34 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: 0.16 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'K' selection = chain 'J' selection = chain 'M' selection = chain 'L' } 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: 4.730 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: 0.890 Check model and map are aligned: 0.140 Set scattering table: 0.190 Process input model: 39.820 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.460 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.35 (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 TRP 0.005 0.001 TRP F 77 HIS 0.001 0.000 HIS K 16 PHE 0.010 0.001 PHE L 68 TYR 0.005 0.001 TYR M 65 ARG 0.002 0.000 ARG J 165 Details of bonding type rmsd hydrogen bonds : bond 0.10263 ( 1440) hydrogen bonds : angle 4.42006 ( 4284) SS BOND : bond 0.00127 ( 36) SS BOND : angle 0.70550 ( 72) covalent geometry : bond 0.00481 (19716) covalent geometry : angle 0.57644 (26976) *********************** 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 : 2.226 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: 1.5730 time to fit residues: 638.6000 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 : 2.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 9.9990 chunk 172 optimal weight: 10.0000 chunk 95 optimal weight: 5.9990 chunk 59 optimal weight: 9.9990 chunk 116 optimal weight: 1.9990 chunk 92 optimal weight: 0.5980 chunk 178 optimal weight: 2.9990 chunk 69 optimal weight: 8.9990 chunk 108 optimal weight: 0.8980 chunk 133 optimal weight: 7.9990 chunk 207 optimal weight: 1.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 99 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 = 0.3429 r_free = 0.3429 target = 0.088834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.061152 restraints weight = 39737.978| |-----------------------------------------------------------------------------| r_work (start): 0.2812 rms_B_bonded: 2.06 r_work: 0.2671 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2548 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8866 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19752 Z= 0.132 Angle : 0.515 9.079 27048 Z= 0.263 Chirality : 0.039 0.160 3240 Planarity : 0.004 0.040 3144 Dihedral : 5.288 35.949 3312 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.99 % Allowed : 11.74 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.57 (0.17), residues: 2304 helix: 3.39 (0.11), residues: 1704 sheet: 1.14 (0.48), residues: 132 loop : -1.55 (0.25), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 3 HIS 0.003 0.001 HIS E 100 PHE 0.023 0.001 PHE L 29 TYR 0.011 0.001 TYR F 155 ARG 0.008 0.001 ARG A 216 Details of bonding type rmsd hydrogen bonds : bond 0.03439 ( 1440) hydrogen bonds : angle 3.08949 ( 4284) SS BOND : bond 0.00200 ( 36) SS BOND : angle 0.77540 ( 72) covalent geometry : bond 0.00298 (19716) covalent geometry : angle 0.51450 (26976) *********************** 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 331 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 289 time to evaluate : 2.111 Fit side-chains REVERT: A 1 MET cc_start: 0.4768 (mmt) cc_final: 0.4484 (mmt) REVERT: A 99 GLN cc_start: 0.8319 (OUTLIER) cc_final: 0.8082 (mp10) REVERT: A 216 ARG cc_start: 0.8861 (mmm-85) cc_final: 0.8632 (mmm-85) REVERT: C 14 ASN cc_start: 0.8902 (t0) cc_final: 0.8630 (t0) REVERT: D 14 ASN cc_start: 0.8695 (t0) cc_final: 0.8471 (t0) REVERT: E 46 ASP cc_start: 0.9146 (p0) cc_final: 0.8925 (p0) REVERT: F 14 ASN cc_start: 0.9011 (t0) cc_final: 0.8771 (t0) REVERT: F 99 GLN cc_start: 0.8274 (tm-30) cc_final: 0.7811 (tm-30) REVERT: F 102 GLU cc_start: 0.8752 (pp20) cc_final: 0.8524 (pp20) REVERT: F 103 LYS cc_start: 0.8112 (pttt) cc_final: 0.7873 (pttt) REVERT: G 99 GLN cc_start: 0.8223 (OUTLIER) cc_final: 0.7999 (mp10) REVERT: I 14 ASN cc_start: 0.8678 (m-40) cc_final: 0.8293 (m-40) REVERT: I 216 ARG cc_start: 0.8814 (mmm-85) cc_final: 0.8595 (mmm-85) REVERT: J 170 ASP cc_start: 0.9447 (p0) cc_final: 0.9246 (p0) REVERT: J 216 ARG cc_start: 0.8830 (mmm-85) cc_final: 0.8616 (mmm-85) REVERT: L 1 MET cc_start: 0.5939 (mmt) cc_final: 0.4408 (pmt) REVERT: L 89 LEU cc_start: 0.9204 (OUTLIER) cc_final: 0.8939 (tt) REVERT: M 46 ASP cc_start: 0.9096 (p0) cc_final: 0.8877 (p0) outliers start: 42 outliers final: 7 residues processed: 311 average time/residue: 1.6859 time to fit residues: 574.7684 Evaluate side-chains 275 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 265 time to evaluate : 1.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 GLN Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain G 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 211 optimal weight: 9.9990 chunk 38 optimal weight: 40.0000 chunk 215 optimal weight: 4.9990 chunk 222 optimal weight: 5.9990 chunk 12 optimal weight: 6.9990 chunk 176 optimal weight: 0.9980 chunk 123 optimal weight: 5.9990 chunk 49 optimal weight: 0.9980 chunk 165 optimal weight: 5.9990 chunk 134 optimal weight: 20.0000 chunk 84 optimal weight: 7.9990 overall best weight: 3.7986 ------------------------------------------------------------------------------- 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 G 57 GLN G 98 GLN H 57 GLN L 57 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.085914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.057816 restraints weight = 39580.174| |-----------------------------------------------------------------------------| r_work (start): 0.2740 rms_B_bonded: 2.07 r_work: 0.2594 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2470 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8990 moved from start: 0.2945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 19752 Z= 0.216 Angle : 0.544 8.255 27048 Z= 0.280 Chirality : 0.041 0.187 3240 Planarity : 0.004 0.041 3144 Dihedral : 5.542 38.894 3312 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.61 % Allowed : 13.87 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.59 (0.17), residues: 2304 helix: 3.37 (0.11), residues: 1704 sheet: 1.34 (0.49), residues: 132 loop : -1.45 (0.25), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 3 HIS 0.008 0.001 HIS G 97 PHE 0.015 0.002 PHE L 29 TYR 0.015 0.001 TYR M 65 ARG 0.008 0.001 ARG K 15 Details of bonding type rmsd hydrogen bonds : bond 0.03833 ( 1440) hydrogen bonds : angle 3.09165 ( 4284) SS BOND : bond 0.00196 ( 36) SS BOND : angle 0.63332 ( 72) covalent geometry : bond 0.00514 (19716) covalent geometry : angle 0.54327 (26976) *********************** 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 310 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 276 time to evaluate : 1.990 Fit side-chains REVERT: A 1 MET cc_start: 0.5010 (mmt) cc_final: 0.4713 (mmt) REVERT: A 99 GLN cc_start: 0.8254 (OUTLIER) cc_final: 0.7986 (mp10) REVERT: C 14 ASN cc_start: 0.9002 (t0) cc_final: 0.8752 (t0) REVERT: C 99 GLN cc_start: 0.8312 (OUTLIER) cc_final: 0.8103 (mp10) REVERT: C 216 ARG cc_start: 0.9013 (tpp80) cc_final: 0.8711 (mmm-85) REVERT: D 14 ASN cc_start: 0.8824 (t0) cc_final: 0.8598 (t0) REVERT: D 46 ASP cc_start: 0.9159 (p0) cc_final: 0.8866 (p0) REVERT: D 102 GLU cc_start: 0.8479 (pp20) cc_final: 0.8277 (pp20) REVERT: D 103 LYS cc_start: 0.8324 (pttt) cc_final: 0.8110 (ptpp) REVERT: E 102 GLU cc_start: 0.8631 (pp20) cc_final: 0.8387 (pp20) REVERT: F 14 ASN cc_start: 0.9096 (t0) cc_final: 0.8797 (t0) REVERT: F 99 GLN cc_start: 0.8277 (tm-30) cc_final: 0.7832 (tm-30) REVERT: F 102 GLU cc_start: 0.8794 (pp20) cc_final: 0.8559 (pp20) REVERT: F 103 LYS cc_start: 0.8139 (pttt) cc_final: 0.7865 (pttt) REVERT: G 14 ASN cc_start: 0.8870 (t0) cc_final: 0.8582 (t0) REVERT: G 102 GLU cc_start: 0.8665 (pp20) cc_final: 0.8436 (pp20) REVERT: H 46 ASP cc_start: 0.9200 (p0) cc_final: 0.8914 (p0) REVERT: H 212 TYR cc_start: 0.8309 (t80) cc_final: 0.8089 (t80) REVERT: H 216 ARG cc_start: 0.9040 (mmm-85) cc_final: 0.8717 (mmt-90) REVERT: I 14 ASN cc_start: 0.8863 (m-40) cc_final: 0.8455 (m-40) REVERT: I 216 ARG cc_start: 0.8911 (mmm-85) cc_final: 0.8680 (mmm-85) REVERT: J 145 LEU cc_start: 0.9244 (OUTLIER) cc_final: 0.8933 (mp) REVERT: J 170 ASP cc_start: 0.9508 (p0) cc_final: 0.9296 (p0) REVERT: L 1 MET cc_start: 0.5990 (mmt) cc_final: 0.4264 (pmt) REVERT: L 212 TYR cc_start: 0.8410 (t80) cc_final: 0.8205 (t80) REVERT: M 46 ASP cc_start: 0.9195 (p0) cc_final: 0.8991 (p0) REVERT: M 151 MET cc_start: 0.9593 (tpp) cc_final: 0.9376 (ttt) REVERT: M 212 TYR cc_start: 0.8430 (t80) cc_final: 0.8145 (t80) outliers start: 34 outliers final: 8 residues processed: 297 average time/residue: 1.7306 time to fit residues: 561.5502 Evaluate side-chains 268 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 257 time to evaluate : 2.029 ------------------------------------------------------------------------------- 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 I residue 25 LEU Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 145 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 147 optimal weight: 0.9980 chunk 216 optimal weight: 0.7980 chunk 0 optimal weight: 30.0000 chunk 133 optimal weight: 40.0000 chunk 192 optimal weight: 5.9990 chunk 98 optimal weight: 0.8980 chunk 137 optimal weight: 0.6980 chunk 199 optimal weight: 10.0000 chunk 179 optimal weight: 0.9980 chunk 18 optimal weight: 6.9990 chunk 144 optimal weight: 10.0000 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 98 GLN C 99 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.087799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.059814 restraints weight = 39512.114| |-----------------------------------------------------------------------------| r_work (start): 0.2784 rms_B_bonded: 2.10 r_work: 0.2638 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2513 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8967 moved from start: 0.3133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 19752 Z= 0.098 Angle : 0.474 7.958 27048 Z= 0.242 Chirality : 0.037 0.159 3240 Planarity : 0.003 0.036 3144 Dihedral : 5.530 39.754 3312 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 1.66 % Allowed : 14.54 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.76 (0.17), residues: 2304 helix: 3.54 (0.11), residues: 1704 sheet: 1.21 (0.48), residues: 132 loop : -1.50 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP L 44 HIS 0.001 0.000 HIS J 73 PHE 0.017 0.001 PHE L 29 TYR 0.012 0.001 TYR D 212 ARG 0.009 0.001 ARG M 216 Details of bonding type rmsd hydrogen bonds : bond 0.03139 ( 1440) hydrogen bonds : angle 2.85812 ( 4284) SS BOND : bond 0.00121 ( 36) SS BOND : angle 0.51651 ( 72) covalent geometry : bond 0.00216 (19716) covalent geometry : angle 0.47382 (26976) *********************** 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 316 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 281 time to evaluate : 1.966 Fit side-chains REVERT: C 14 ASN cc_start: 0.8968 (t0) cc_final: 0.8755 (t0) REVERT: C 99 GLN cc_start: 0.8264 (OUTLIER) cc_final: 0.8053 (mp10) REVERT: C 216 ARG cc_start: 0.9000 (tpp80) cc_final: 0.8761 (mmm-85) REVERT: D 14 ASN cc_start: 0.8802 (t0) cc_final: 0.8564 (t0) REVERT: D 46 ASP cc_start: 0.9154 (p0) cc_final: 0.8826 (p0) REVERT: F 14 ASN cc_start: 0.9059 (t0) cc_final: 0.8817 (t0) REVERT: F 41 GLU cc_start: 0.8952 (tt0) cc_final: 0.8660 (pm20) REVERT: F 102 GLU cc_start: 0.8829 (pp20) cc_final: 0.8528 (pp20) REVERT: G 14 ASN cc_start: 0.8837 (t0) cc_final: 0.8618 (t0) REVERT: G 102 GLU cc_start: 0.8726 (pp20) cc_final: 0.8497 (pp20) REVERT: H 46 ASP cc_start: 0.9139 (p0) cc_final: 0.8828 (p0) REVERT: H 212 TYR cc_start: 0.8341 (t80) cc_final: 0.8133 (t80) REVERT: H 216 ARG cc_start: 0.9020 (mmm-85) cc_final: 0.8730 (mmt-90) REVERT: I 14 ASN cc_start: 0.8839 (m-40) cc_final: 0.8436 (m-40) REVERT: L 1 MET cc_start: 0.5924 (mmt) cc_final: 0.4260 (pmt) REVERT: M 15 ARG cc_start: 0.8366 (OUTLIER) cc_final: 0.8147 (ppp80) REVERT: M 46 ASP cc_start: 0.9190 (p0) cc_final: 0.8966 (p0) REVERT: M 151 MET cc_start: 0.9567 (tpp) cc_final: 0.9356 (ttt) REVERT: M 212 TYR cc_start: 0.8349 (t80) cc_final: 0.8134 (t80) REVERT: M 216 ARG cc_start: 0.8878 (mmm-85) cc_final: 0.8542 (mmm-85) outliers start: 35 outliers final: 10 residues processed: 304 average time/residue: 1.6713 time to fit residues: 554.5641 Evaluate side-chains 280 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 268 time to evaluate : 2.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain C residue 99 GLN Chi-restraints excluded: chain D 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 J residue 151 MET Chi-restraints excluded: chain L residue 20 ILE Chi-restraints excluded: chain M residue 15 ARG Chi-restraints excluded: chain M residue 25 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 71 optimal weight: 3.9990 chunk 211 optimal weight: 10.0000 chunk 29 optimal weight: 7.9990 chunk 108 optimal weight: 3.9990 chunk 205 optimal weight: 3.9990 chunk 143 optimal weight: 8.9990 chunk 114 optimal weight: 40.0000 chunk 183 optimal weight: 0.9980 chunk 118 optimal weight: 8.9990 chunk 57 optimal weight: 40.0000 chunk 77 optimal weight: 2.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- 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 G 99 GLN K 99 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.086216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.057888 restraints weight = 39840.690| |-----------------------------------------------------------------------------| r_work (start): 0.2734 rms_B_bonded: 2.14 r_work: 0.2585 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2460 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8990 moved from start: 0.3347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 19752 Z= 0.178 Angle : 0.508 8.182 27048 Z= 0.260 Chirality : 0.039 0.151 3240 Planarity : 0.003 0.036 3144 Dihedral : 5.569 40.683 3312 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.75 % Allowed : 15.44 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.72 (0.17), residues: 2304 helix: 3.48 (0.11), residues: 1704 sheet: 1.32 (0.49), residues: 132 loop : -1.45 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP L 44 HIS 0.003 0.001 HIS C 100 PHE 0.011 0.002 PHE K 29 TYR 0.014 0.001 TYR M 65 ARG 0.011 0.001 ARG D 216 Details of bonding type rmsd hydrogen bonds : bond 0.03341 ( 1440) hydrogen bonds : angle 2.88806 ( 4284) SS BOND : bond 0.00182 ( 36) SS BOND : angle 0.58982 ( 72) covalent geometry : bond 0.00427 (19716) covalent geometry : angle 0.50735 (26976) *********************** 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 303 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 266 time to evaluate : 1.982 Fit side-chains REVERT: A 99 GLN cc_start: 0.8270 (OUTLIER) cc_final: 0.8068 (mp10) REVERT: C 14 ASN cc_start: 0.9035 (t0) cc_final: 0.8794 (t0) REVERT: C 216 ARG cc_start: 0.9008 (tpp80) cc_final: 0.8769 (mmm-85) REVERT: D 14 ASN cc_start: 0.8867 (t0) cc_final: 0.8622 (t0) REVERT: D 46 ASP cc_start: 0.9183 (p0) cc_final: 0.8880 (p0) REVERT: D 103 LYS cc_start: 0.8304 (pttt) cc_final: 0.8024 (ptpp) REVERT: E 102 GLU cc_start: 0.8589 (pp20) cc_final: 0.8379 (pp20) REVERT: F 14 ASN cc_start: 0.9117 (t0) cc_final: 0.8860 (t0) REVERT: F 102 GLU cc_start: 0.8772 (pp20) cc_final: 0.8505 (pp20) REVERT: F 103 LYS cc_start: 0.8282 (pttt) cc_final: 0.7975 (ptpp) REVERT: G 14 ASN cc_start: 0.8926 (t0) cc_final: 0.8676 (t0) REVERT: G 99 GLN cc_start: 0.8121 (OUTLIER) cc_final: 0.7919 (mp10) REVERT: G 102 GLU cc_start: 0.8754 (pp20) cc_final: 0.8539 (pp20) REVERT: G 103 LYS cc_start: 0.8160 (pttt) cc_final: 0.7939 (ptpp) REVERT: H 46 ASP cc_start: 0.9182 (p0) cc_final: 0.8880 (p0) REVERT: H 216 ARG cc_start: 0.9039 (mmm-85) cc_final: 0.8759 (mmt-90) REVERT: I 14 ASN cc_start: 0.8939 (m-40) cc_final: 0.8533 (m-40) REVERT: I 151 MET cc_start: 0.9498 (OUTLIER) cc_final: 0.9284 (mmm) REVERT: J 103 LYS cc_start: 0.7836 (OUTLIER) cc_final: 0.7410 (ptpp) REVERT: L 1 MET cc_start: 0.5913 (mmt) cc_final: 0.4177 (pmt) REVERT: M 46 ASP cc_start: 0.9214 (p0) cc_final: 0.9005 (p0) outliers start: 37 outliers final: 12 residues processed: 290 average time/residue: 1.6580 time to fit residues: 525.9821 Evaluate side-chains 276 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 260 time to evaluate : 1.978 ------------------------------------------------------------------------------- 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 F residue 151 MET Chi-restraints excluded: chain G residue 99 GLN Chi-restraints excluded: chain H residue 4 THR Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 151 MET Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 103 LYS Chi-restraints excluded: chain J residue 151 MET Chi-restraints excluded: chain K 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 217 optimal weight: 0.9990 chunk 185 optimal weight: 4.9990 chunk 196 optimal weight: 4.9990 chunk 153 optimal weight: 20.0000 chunk 205 optimal weight: 6.9990 chunk 66 optimal weight: 9.9990 chunk 190 optimal weight: 20.0000 chunk 199 optimal weight: 10.0000 chunk 181 optimal weight: 40.0000 chunk 177 optimal weight: 0.7980 chunk 40 optimal weight: 9.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN C 99 GLN F 99 GLN K 16 HIS L 99 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.085731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.057334 restraints weight = 39899.241| |-----------------------------------------------------------------------------| r_work (start): 0.2716 rms_B_bonded: 2.15 r_work: 0.2568 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2441 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9002 moved from start: 0.3587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 19752 Z= 0.202 Angle : 0.524 8.317 27048 Z= 0.269 Chirality : 0.039 0.135 3240 Planarity : 0.003 0.036 3144 Dihedral : 5.687 41.800 3312 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 1.85 % Allowed : 15.77 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.68 (0.17), residues: 2304 helix: 3.42 (0.11), residues: 1704 sheet: 1.41 (0.50), residues: 132 loop : -1.40 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP L 24 HIS 0.010 0.001 HIS G 100 PHE 0.012 0.002 PHE I 191 TYR 0.017 0.001 TYR H 212 ARG 0.010 0.001 ARG M 216 Details of bonding type rmsd hydrogen bonds : bond 0.03416 ( 1440) hydrogen bonds : angle 2.92107 ( 4284) SS BOND : bond 0.00192 ( 36) SS BOND : angle 0.61648 ( 72) covalent geometry : bond 0.00483 (19716) covalent geometry : angle 0.52416 (26976) *********************** 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 303 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 264 time to evaluate : 2.141 Fit side-chains REVERT: C 14 ASN cc_start: 0.9035 (t0) cc_final: 0.8759 (t0) REVERT: C 216 ARG cc_start: 0.8987 (tpp80) cc_final: 0.8751 (mmm-85) REVERT: D 14 ASN cc_start: 0.8881 (t0) cc_final: 0.8638 (t0) REVERT: D 46 ASP cc_start: 0.9203 (p0) cc_final: 0.8906 (p0) REVERT: D 103 LYS cc_start: 0.8265 (OUTLIER) cc_final: 0.7953 (ptpp) REVERT: D 212 TYR cc_start: 0.8470 (t80) cc_final: 0.8220 (t80) REVERT: F 14 ASN cc_start: 0.9125 (t0) cc_final: 0.8877 (t0) REVERT: F 99 GLN cc_start: 0.8098 (OUTLIER) cc_final: 0.7854 (mp10) REVERT: F 102 GLU cc_start: 0.8801 (pp20) cc_final: 0.8594 (pp20) REVERT: G 14 ASN cc_start: 0.8964 (t0) cc_final: 0.8718 (t0) REVERT: H 46 ASP cc_start: 0.9213 (p0) cc_final: 0.8908 (p0) REVERT: H 212 TYR cc_start: 0.8349 (t80) cc_final: 0.8138 (t80) REVERT: I 14 ASN cc_start: 0.8993 (m-40) cc_final: 0.8570 (m-40) REVERT: I 145 LEU cc_start: 0.9277 (OUTLIER) cc_final: 0.9061 (mp) REVERT: K 102 GLU cc_start: 0.8987 (pp20) cc_final: 0.8753 (pp20) REVERT: L 1 MET cc_start: 0.5898 (mmt) cc_final: 0.4175 (pmt) REVERT: L 99 GLN cc_start: 0.8117 (OUTLIER) cc_final: 0.7896 (mp10) REVERT: M 102 GLU cc_start: 0.8473 (pp20) cc_final: 0.8259 (pp20) outliers start: 39 outliers final: 11 residues processed: 288 average time/residue: 1.7284 time to fit residues: 544.4116 Evaluate side-chains 270 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 255 time to evaluate : 2.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain C residue 4 THR Chi-restraints excluded: chain D residue 103 LYS 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 I residue 145 LEU Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain K residue 25 LEU 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 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 148 optimal weight: 0.8980 chunk 161 optimal weight: 3.9990 chunk 169 optimal weight: 1.9990 chunk 225 optimal weight: 0.6980 chunk 113 optimal weight: 6.9990 chunk 95 optimal weight: 30.0000 chunk 143 optimal weight: 9.9990 chunk 216 optimal weight: 0.6980 chunk 69 optimal weight: 3.9990 chunk 114 optimal weight: 30.0000 chunk 48 optimal weight: 30.0000 overall best weight: 1.6584 ------------------------------------------------------------------------------- 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 F 99 GLN G 99 GLN I 98 GLN K 16 HIS L 99 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.086823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.058541 restraints weight = 39376.019| |-----------------------------------------------------------------------------| r_work (start): 0.2743 rms_B_bonded: 2.15 r_work: 0.2596 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2470 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8984 moved from start: 0.3663 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= 0.121 Angle : 0.503 8.803 27048 Z= 0.259 Chirality : 0.038 0.134 3240 Planarity : 0.003 0.042 3144 Dihedral : 5.719 42.039 3312 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.52 % Allowed : 16.38 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.70 (0.17), residues: 2304 helix: 3.46 (0.11), residues: 1704 sheet: 1.30 (0.49), residues: 132 loop : -1.43 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP L 24 HIS 0.006 0.001 HIS F 100 PHE 0.012 0.001 PHE L 29 TYR 0.015 0.001 TYR H 212 ARG 0.010 0.001 ARG E 216 Details of bonding type rmsd hydrogen bonds : bond 0.03181 ( 1440) hydrogen bonds : angle 2.86153 ( 4284) SS BOND : bond 0.00142 ( 36) SS BOND : angle 0.52441 ( 72) covalent geometry : bond 0.00282 (19716) covalent geometry : angle 0.50310 (26976) *********************** 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 309 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 277 time to evaluate : 2.199 Fit side-chains REVERT: C 14 ASN cc_start: 0.9008 (t0) cc_final: 0.8795 (t0) REVERT: C 103 LYS cc_start: 0.8277 (pttt) cc_final: 0.7991 (pttp) REVERT: D 14 ASN cc_start: 0.8856 (t0) cc_final: 0.8610 (t0) REVERT: D 46 ASP cc_start: 0.9204 (p0) cc_final: 0.8886 (p0) REVERT: D 103 LYS cc_start: 0.8271 (OUTLIER) cc_final: 0.7984 (ptpp) REVERT: D 212 TYR cc_start: 0.8440 (t80) cc_final: 0.8183 (t80) REVERT: F 14 ASN cc_start: 0.9112 (t0) cc_final: 0.8894 (t0) REVERT: F 102 GLU cc_start: 0.8829 (pp20) cc_final: 0.8608 (pp20) REVERT: G 14 ASN cc_start: 0.8949 (t0) cc_final: 0.8703 (t0) REVERT: G 103 LYS cc_start: 0.8191 (pttt) cc_final: 0.7949 (ptpp) REVERT: H 46 ASP cc_start: 0.9193 (p0) cc_final: 0.8889 (p0) REVERT: H 212 TYR cc_start: 0.8295 (t80) cc_final: 0.7944 (t80) REVERT: H 216 ARG cc_start: 0.9033 (mmm-85) cc_final: 0.8729 (mmm-85) REVERT: I 14 ASN cc_start: 0.8997 (m-40) cc_final: 0.8578 (m-40) REVERT: J 103 LYS cc_start: 0.7776 (pttt) cc_final: 0.7424 (ptpp) REVERT: K 1 MET cc_start: 0.5856 (mmt) cc_final: 0.4453 (pmt) REVERT: K 99 GLN cc_start: 0.8293 (mm110) cc_final: 0.7925 (mp10) REVERT: K 102 GLU cc_start: 0.8979 (pp20) cc_final: 0.8748 (pp20) REVERT: L 1 MET cc_start: 0.5864 (mmt) cc_final: 0.4249 (pmt) REVERT: M 102 GLU cc_start: 0.8518 (pp20) cc_final: 0.8311 (pp20) outliers start: 32 outliers final: 12 residues processed: 298 average time/residue: 1.7197 time to fit residues: 559.9546 Evaluate side-chains 277 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 264 time to evaluate : 2.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain F residue 151 MET Chi-restraints excluded: chain G residue 99 GLN Chi-restraints excluded: chain H residue 4 THR Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 151 MET 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 143 optimal weight: 9.9990 chunk 6 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 chunk 159 optimal weight: 0.7980 chunk 83 optimal weight: 0.9980 chunk 147 optimal weight: 5.9990 chunk 16 optimal weight: 0.3980 chunk 93 optimal weight: 4.9990 chunk 46 optimal weight: 5.9990 chunk 183 optimal weight: 9.9990 chunk 144 optimal weight: 5.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 16 HIS F 99 GLN 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 = 0.3398 r_free = 0.3398 target = 0.087845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.059714 restraints weight = 39459.206| |-----------------------------------------------------------------------------| r_work (start): 0.2771 rms_B_bonded: 2.15 r_work: 0.2626 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2501 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8966 moved from start: 0.3774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 19752 Z= 0.102 Angle : 0.510 9.142 27048 Z= 0.263 Chirality : 0.038 0.148 3240 Planarity : 0.003 0.047 3144 Dihedral : 5.663 41.612 3312 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 1.28 % Allowed : 16.95 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.73 (0.17), residues: 2304 helix: 3.50 (0.11), residues: 1704 sheet: 1.17 (0.48), residues: 132 loop : -1.48 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP H 133 HIS 0.008 0.000 HIS G 100 PHE 0.013 0.001 PHE L 29 TYR 0.014 0.001 TYR H 212 ARG 0.012 0.001 ARG C 216 Details of bonding type rmsd hydrogen bonds : bond 0.02976 ( 1440) hydrogen bonds : angle 2.79303 ( 4284) SS BOND : bond 0.00111 ( 36) SS BOND : angle 0.47640 ( 72) covalent geometry : bond 0.00227 (19716) covalent geometry : angle 0.50976 (26976) *********************** 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 309 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 282 time to evaluate : 2.349 Fit side-chains REVERT: C 14 ASN cc_start: 0.8973 (t0) cc_final: 0.8705 (t0) REVERT: C 103 LYS cc_start: 0.8294 (pttt) cc_final: 0.8063 (ptpp) REVERT: D 46 ASP cc_start: 0.9162 (p0) cc_final: 0.8854 (p0) REVERT: D 212 TYR cc_start: 0.8428 (t80) cc_final: 0.8124 (t80) REVERT: E 102 GLU cc_start: 0.8550 (pp20) cc_final: 0.8291 (pp20) REVERT: F 102 GLU cc_start: 0.8803 (pp20) cc_final: 0.8565 (pp20) REVERT: F 103 LYS cc_start: 0.8330 (pttt) cc_final: 0.8028 (ptpp) REVERT: F 216 ARG cc_start: 0.8961 (tpp80) cc_final: 0.8718 (mmm-85) REVERT: G 14 ASN cc_start: 0.8916 (t0) cc_final: 0.8705 (t0) REVERT: H 46 ASP cc_start: 0.9165 (p0) cc_final: 0.8854 (p0) REVERT: I 14 ASN cc_start: 0.8958 (m-40) cc_final: 0.8563 (m-40) REVERT: J 103 LYS cc_start: 0.7840 (pttt) cc_final: 0.7502 (ptpp) REVERT: K 1 MET cc_start: 0.5914 (mmt) cc_final: 0.4450 (pmt) REVERT: K 99 GLN cc_start: 0.8351 (mm110) cc_final: 0.7961 (mp10) REVERT: K 102 GLU cc_start: 0.8993 (pp20) cc_final: 0.8758 (pp20) REVERT: L 1 MET cc_start: 0.5839 (mmt) cc_final: 0.4237 (pmt) REVERT: L 99 GLN cc_start: 0.8074 (OUTLIER) cc_final: 0.7873 (mp10) REVERT: M 102 GLU cc_start: 0.8554 (pp20) cc_final: 0.8287 (pp20) outliers start: 27 outliers final: 11 residues processed: 298 average time/residue: 1.7163 time to fit residues: 558.5148 Evaluate side-chains 281 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 269 time to evaluate : 1.943 ------------------------------------------------------------------------------- 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 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 L residue 99 GLN 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 110 optimal weight: 6.9990 chunk 29 optimal weight: 40.0000 chunk 203 optimal weight: 0.7980 chunk 120 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 124 optimal weight: 7.9990 chunk 209 optimal weight: 10.0000 chunk 73 optimal weight: 2.9990 chunk 109 optimal weight: 0.9990 chunk 180 optimal weight: 9.9990 chunk 123 optimal weight: 5.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 GLN F 99 GLN 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 = 0.3392 r_free = 0.3392 target = 0.087437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.059214 restraints weight = 39424.272| |-----------------------------------------------------------------------------| r_work (start): 0.2760 rms_B_bonded: 2.14 r_work: 0.2617 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2493 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8965 moved from start: 0.3824 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= 0.119 Angle : 0.515 7.407 27048 Z= 0.269 Chirality : 0.038 0.137 3240 Planarity : 0.003 0.041 3144 Dihedral : 5.614 41.315 3312 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.09 % Allowed : 17.38 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.70 (0.17), residues: 2304 helix: 3.47 (0.11), residues: 1704 sheet: 1.22 (0.48), residues: 132 loop : -1.44 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP L 24 HIS 0.004 0.001 HIS F 100 PHE 0.010 0.001 PHE L 29 TYR 0.019 0.001 TYR M 136 ARG 0.011 0.001 ARG C 216 Details of bonding type rmsd hydrogen bonds : bond 0.02972 ( 1440) hydrogen bonds : angle 2.80662 ( 4284) SS BOND : bond 0.00127 ( 36) SS BOND : angle 0.49416 ( 72) covalent geometry : bond 0.00273 (19716) covalent geometry : angle 0.51500 (26976) *********************** 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 297 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 274 time to evaluate : 1.972 Fit side-chains REVERT: C 14 ASN cc_start: 0.8989 (t0) cc_final: 0.8731 (t0) REVERT: C 103 LYS cc_start: 0.8275 (pttt) cc_final: 0.8068 (ptpp) REVERT: D 46 ASP cc_start: 0.9174 (p0) cc_final: 0.8862 (p0) REVERT: D 103 LYS cc_start: 0.8378 (pttt) cc_final: 0.8141 (ptpp) REVERT: D 212 TYR cc_start: 0.8407 (t80) cc_final: 0.8118 (t80) REVERT: E 1 MET cc_start: 0.5263 (mmt) cc_final: 0.4869 (mmt) REVERT: E 14 ASN cc_start: 0.9131 (t0) cc_final: 0.8858 (t0) REVERT: E 102 GLU cc_start: 0.8558 (pp20) cc_final: 0.8355 (pp20) REVERT: F 14 ASN cc_start: 0.8654 (t0) cc_final: 0.8434 (t0) REVERT: F 99 GLN cc_start: 0.8065 (OUTLIER) cc_final: 0.7845 (mm110) REVERT: F 102 GLU cc_start: 0.8797 (pp20) cc_final: 0.8516 (pp20) REVERT: G 14 ASN cc_start: 0.8931 (t0) cc_final: 0.8710 (t0) REVERT: H 46 ASP cc_start: 0.9163 (p0) cc_final: 0.8854 (p0) REVERT: I 14 ASN cc_start: 0.8969 (m-40) cc_final: 0.8568 (m-40) REVERT: J 103 LYS cc_start: 0.7847 (pttt) cc_final: 0.7565 (ptpp) REVERT: K 1 MET cc_start: 0.5870 (mmt) cc_final: 0.4376 (pmt) REVERT: L 1 MET cc_start: 0.5825 (mmt) cc_final: 0.4215 (pmt) REVERT: L 99 GLN cc_start: 0.8101 (OUTLIER) cc_final: 0.7876 (mp10) REVERT: L 103 LYS cc_start: 0.8210 (pttt) cc_final: 0.7897 (pmtt) REVERT: M 102 GLU cc_start: 0.8585 (pp20) cc_final: 0.8333 (pp20) outliers start: 23 outliers final: 11 residues processed: 290 average time/residue: 1.7115 time to fit residues: 544.6308 Evaluate side-chains 275 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 262 time to evaluate : 2.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 L residue 99 GLN 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 227 optimal weight: 4.9990 chunk 125 optimal weight: 6.9990 chunk 77 optimal weight: 4.9990 chunk 155 optimal weight: 3.9990 chunk 195 optimal weight: 1.9990 chunk 208 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 147 optimal weight: 8.9990 chunk 20 optimal weight: 5.9990 chunk 121 optimal weight: 0.8980 chunk 30 optimal weight: 10.0000 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 F 99 GLN G 99 GLN ** J 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 16 HIS K 99 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 = 0.3383 r_free = 0.3383 target = 0.086995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.058732 restraints weight = 39502.489| |-----------------------------------------------------------------------------| r_work (start): 0.2750 rms_B_bonded: 2.14 r_work: 0.2605 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2480 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8980 moved from start: 0.3896 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= 0.142 Angle : 0.544 9.403 27048 Z= 0.282 Chirality : 0.039 0.143 3240 Planarity : 0.003 0.041 3144 Dihedral : 5.617 41.420 3312 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.14 % Allowed : 17.80 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.67 (0.17), residues: 2304 helix: 3.44 (0.11), residues: 1704 sheet: 1.20 (0.48), residues: 132 loop : -1.42 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP G 44 HIS 0.003 0.001 HIS A 100 PHE 0.009 0.001 PHE L 29 TYR 0.022 0.001 TYR D 136 ARG 0.010 0.001 ARG H 216 Details of bonding type rmsd hydrogen bonds : bond 0.03049 ( 1440) hydrogen bonds : angle 2.83736 ( 4284) SS BOND : bond 0.00147 ( 36) SS BOND : angle 0.52140 ( 72) covalent geometry : bond 0.00336 (19716) covalent geometry : angle 0.54358 (26976) ********************** 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 285 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 261 time to evaluate : 2.189 Fit side-chains REVERT: C 14 ASN cc_start: 0.8973 (t0) cc_final: 0.8723 (t0) REVERT: D 46 ASP cc_start: 0.9183 (p0) cc_final: 0.8879 (p0) REVERT: D 103 LYS cc_start: 0.8361 (pttt) cc_final: 0.8138 (ptpp) REVERT: D 212 TYR cc_start: 0.8412 (t80) cc_final: 0.8106 (t80) REVERT: E 1 MET cc_start: 0.5291 (mmt) cc_final: 0.4908 (mmt) REVERT: E 14 ASN cc_start: 0.9135 (t0) cc_final: 0.8846 (t0) REVERT: E 102 GLU cc_start: 0.8576 (pp20) cc_final: 0.8376 (pp20) REVERT: E 103 LYS cc_start: 0.8362 (pttm) cc_final: 0.8141 (ptpp) REVERT: F 14 ASN cc_start: 0.8699 (t0) cc_final: 0.8483 (t0) REVERT: F 102 GLU cc_start: 0.8828 (pp20) cc_final: 0.8524 (pp20) REVERT: F 103 LYS cc_start: 0.8318 (pttt) cc_final: 0.8021 (ptpp) REVERT: G 14 ASN cc_start: 0.8921 (t0) cc_final: 0.8697 (t0) REVERT: H 46 ASP cc_start: 0.9169 (p0) cc_final: 0.8878 (p0) REVERT: J 103 LYS cc_start: 0.7917 (pttt) cc_final: 0.7623 (ptpp) REVERT: K 1 MET cc_start: 0.5879 (mmt) cc_final: 0.4357 (pmt) REVERT: K 102 GLU cc_start: 0.8988 (pp20) cc_final: 0.8727 (pp20) REVERT: L 1 MET cc_start: 0.5820 (mmt) cc_final: 0.4204 (pmt) REVERT: M 102 GLU cc_start: 0.8586 (pp20) cc_final: 0.8311 (pp20) outliers start: 24 outliers final: 13 residues processed: 275 average time/residue: 1.8042 time to fit residues: 540.0274 Evaluate side-chains 268 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 255 time to evaluate : 2.246 ------------------------------------------------------------------------------- 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 G residue 99 GLN 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 L residue 132 LEU 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 67 optimal weight: 20.0000 chunk 192 optimal weight: 7.9990 chunk 74 optimal weight: 6.9990 chunk 17 optimal weight: 5.9990 chunk 215 optimal weight: 1.9990 chunk 14 optimal weight: 10.0000 chunk 61 optimal weight: 7.9990 chunk 160 optimal weight: 3.9990 chunk 71 optimal weight: 9.9990 chunk 76 optimal weight: 30.0000 chunk 151 optimal weight: 8.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.086860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.058636 restraints weight = 39607.935| |-----------------------------------------------------------------------------| r_work (start): 0.2748 rms_B_bonded: 2.15 r_work: 0.2602 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2479 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8975 moved from start: 0.3885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.248 19752 Z= 0.296 Angle : 0.882 59.199 27048 Z= 0.519 Chirality : 0.041 0.417 3240 Planarity : 0.004 0.162 3144 Dihedral : 5.626 41.448 3312 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.04 % Allowed : 17.61 % Favored : 81.34 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.59 (0.17), residues: 2304 helix: 3.37 (0.11), residues: 1704 sheet: 1.20 (0.48), residues: 132 loop : -1.42 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP G 44 HIS 0.002 0.001 HIS A 73 PHE 0.009 0.001 PHE K 181 TYR 0.023 0.001 TYR D 136 ARG 0.009 0.001 ARG H 216 Details of bonding type rmsd hydrogen bonds : bond 0.03207 ( 1440) hydrogen bonds : angle 2.85689 ( 4284) SS BOND : bond 0.00205 ( 36) SS BOND : angle 0.53390 ( 72) covalent geometry : bond 0.00626 (19716) covalent geometry : angle 0.88289 (26976) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14333.64 seconds wall clock time: 247 minutes 28.55 seconds (14848.55 seconds total)