Starting phenix.real_space_refine on Mon Jun 16 11:25:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qjf_18446/06_2025/8qjf_18446_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qjf_18446/06_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_18446/06_2025/8qjf_18446.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qjf_18446/06_2025/8qjf_18446.map" model { file = "/net/cci-nas-00/data/ceres_data/8qjf_18446/06_2025/8qjf_18446_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qjf_18446/06_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 11.38, per 1000 atoms: 0.59 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: 4.62 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: 1.67 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: 5.77 Time building geometry restraints manager: 5.52 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: 0.17 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: 3.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.810 Check model and map are aligned: 0.130 Set scattering table: 0.150 Process input model: 41.740 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.100 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:14.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.280 ------------------------------------------------------------------------------- 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 : 2.128 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: 1.5786 time to fit residues: 641.6864 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 : 1.999 ------------------------------------------------------------------------------- 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 = 0.061151 restraints weight = 39738.042| |-----------------------------------------------------------------------------| 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: 4.25 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 3.08952 ( 4284) SS BOND : bond 0.00200 ( 36) SS BOND : angle 0.77539 ( 72) covalent geometry : bond 0.00298 (19716) covalent geometry : angle 0.51448 (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 : 2.014 Fit side-chains REVERT: A 1 MET cc_start: 0.4761 (mmt) cc_final: 0.4478 (mmt) REVERT: A 99 GLN cc_start: 0.8317 (OUTLIER) cc_final: 0.8080 (mp10) REVERT: A 216 ARG cc_start: 0.8858 (mmm-85) cc_final: 0.8629 (mmm-85) REVERT: C 14 ASN cc_start: 0.8904 (t0) cc_final: 0.8632 (t0) REVERT: D 14 ASN cc_start: 0.8697 (t0) cc_final: 0.8473 (t0) REVERT: E 46 ASP cc_start: 0.9148 (p0) cc_final: 0.8927 (p0) REVERT: F 14 ASN cc_start: 0.9011 (t0) cc_final: 0.8772 (t0) REVERT: F 99 GLN cc_start: 0.8273 (tm-30) cc_final: 0.7809 (tm-30) REVERT: F 102 GLU cc_start: 0.8752 (pp20) cc_final: 0.8524 (pp20) REVERT: F 103 LYS cc_start: 0.8111 (pttt) cc_final: 0.7872 (pttt) REVERT: G 99 GLN cc_start: 0.8222 (OUTLIER) cc_final: 0.7998 (mp10) REVERT: I 14 ASN cc_start: 0.8678 (m-40) cc_final: 0.8294 (m-40) REVERT: I 216 ARG cc_start: 0.8813 (mmm-85) cc_final: 0.8594 (mmm-85) REVERT: J 170 ASP cc_start: 0.9447 (p0) cc_final: 0.9246 (p0) REVERT: J 216 ARG cc_start: 0.8829 (mmm-85) cc_final: 0.8616 (mmm-85) REVERT: L 1 MET cc_start: 0.5932 (mmt) cc_final: 0.4404 (pmt) REVERT: L 89 LEU cc_start: 0.9200 (OUTLIER) cc_final: 0.8936 (tt) REVERT: M 46 ASP cc_start: 0.9098 (p0) cc_final: 0.8879 (p0) outliers start: 42 outliers final: 7 residues processed: 311 average time/residue: 1.6908 time to fit residues: 577.1284 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 : 2.284 ------------------------------------------------------------------------------- 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: 1.9990 chunk 123 optimal weight: 5.9990 chunk 49 optimal weight: 0.9980 chunk 165 optimal weight: 6.9990 chunk 134 optimal weight: 20.0000 chunk 84 optimal weight: 7.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- 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 = 0.3371 r_free = 0.3371 target = 0.085718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.057633 restraints weight = 39608.818| |-----------------------------------------------------------------------------| r_work (start): 0.2732 rms_B_bonded: 2.07 r_work: 0.2584 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2459 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9008 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 19752 Z= 0.224 Angle : 0.545 8.478 27048 Z= 0.280 Chirality : 0.041 0.159 3240 Planarity : 0.003 0.037 3144 Dihedral : 5.559 39.127 3312 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.61 % Allowed : 13.92 % Favored : 84.47 % 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: 1.36 (0.49), residues: 132 loop : -1.44 (0.25), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 3 HIS 0.006 0.001 HIS A 100 PHE 0.016 0.002 PHE L 29 TYR 0.017 0.001 TYR M 65 ARG 0.008 0.001 ARG E 216 Details of bonding type rmsd hydrogen bonds : bond 0.03879 ( 1440) hydrogen bonds : angle 3.09844 ( 4284) SS BOND : bond 0.00226 ( 36) SS BOND : angle 0.67182 ( 72) covalent geometry : bond 0.00537 (19716) covalent geometry : angle 0.54510 (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 307 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 273 time to evaluate : 2.031 Fit side-chains REVERT: A 1 MET cc_start: 0.5042 (mmt) cc_final: 0.4743 (mmt) REVERT: A 99 GLN cc_start: 0.8255 (OUTLIER) cc_final: 0.7997 (mp10) REVERT: C 14 ASN cc_start: 0.9005 (t0) cc_final: 0.8760 (t0) REVERT: C 99 GLN cc_start: 0.8308 (OUTLIER) cc_final: 0.8093 (mp10) REVERT: C 216 ARG cc_start: 0.9019 (tpp80) cc_final: 0.8715 (mmm-85) REVERT: D 14 ASN cc_start: 0.8825 (t0) cc_final: 0.8605 (t0) REVERT: D 46 ASP cc_start: 0.9168 (p0) cc_final: 0.8887 (p0) REVERT: D 102 GLU cc_start: 0.8478 (pp20) cc_final: 0.8276 (pp20) REVERT: F 14 ASN cc_start: 0.9095 (t0) cc_final: 0.8797 (t0) REVERT: F 99 GLN cc_start: 0.8267 (tm-30) cc_final: 0.7793 (tm-30) REVERT: F 102 GLU cc_start: 0.8799 (pp20) cc_final: 0.8566 (pp20) REVERT: F 103 LYS cc_start: 0.8141 (pttt) cc_final: 0.7864 (pttt) REVERT: G 14 ASN cc_start: 0.8879 (t0) cc_final: 0.8597 (t0) REVERT: H 46 ASP cc_start: 0.9205 (p0) cc_final: 0.8946 (p0) REVERT: H 136 TYR cc_start: 0.8991 (t80) cc_final: 0.8771 (t80) REVERT: H 212 TYR cc_start: 0.8327 (t80) cc_final: 0.8106 (t80) REVERT: H 216 ARG cc_start: 0.9041 (mmm-85) cc_final: 0.8717 (mmt-90) REVERT: I 14 ASN cc_start: 0.8869 (m-40) cc_final: 0.8464 (m-40) REVERT: I 216 ARG cc_start: 0.8908 (mmm-85) cc_final: 0.8677 (mmm-85) REVERT: J 145 LEU cc_start: 0.9260 (OUTLIER) cc_final: 0.8950 (mp) REVERT: J 209 GLU cc_start: 0.9318 (tp30) cc_final: 0.9104 (tp30) REVERT: L 1 MET cc_start: 0.5992 (mmt) cc_final: 0.4269 (pmt) REVERT: L 212 TYR cc_start: 0.8423 (t80) cc_final: 0.8219 (t80) REVERT: M 46 ASP cc_start: 0.9201 (p0) cc_final: 0.8996 (p0) REVERT: M 151 MET cc_start: 0.9594 (tpp) cc_final: 0.9378 (ttt) REVERT: M 212 TYR cc_start: 0.8446 (t80) cc_final: 0.8162 (t80) outliers start: 34 outliers final: 8 residues processed: 294 average time/residue: 1.7347 time to fit residues: 557.1120 Evaluate side-chains 266 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 255 time to evaluate : 2.048 ------------------------------------------------------------------------------- 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: 2.9990 chunk 216 optimal weight: 0.6980 chunk 0 optimal weight: 30.0000 chunk 133 optimal weight: 40.0000 chunk 192 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 chunk 137 optimal weight: 0.2980 chunk 199 optimal weight: 10.0000 chunk 179 optimal weight: 0.9980 chunk 18 optimal weight: 7.9990 chunk 144 optimal weight: 8.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- 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 = 0.3399 r_free = 0.3399 target = 0.087291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.059228 restraints weight = 39542.438| |-----------------------------------------------------------------------------| r_work (start): 0.2775 rms_B_bonded: 2.09 r_work: 0.2630 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2506 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8987 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 19752 Z= 0.111 Angle : 0.481 7.711 27048 Z= 0.245 Chirality : 0.038 0.145 3240 Planarity : 0.003 0.035 3144 Dihedral : 5.561 40.130 3312 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.66 % Allowed : 14.58 % Favored : 83.76 % 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: 3.50 (0.11), residues: 1704 sheet: 1.22 (0.48), residues: 132 loop : -1.49 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP L 44 HIS 0.004 0.001 HIS A 100 PHE 0.016 0.001 PHE L 29 TYR 0.010 0.001 TYR M 65 ARG 0.009 0.001 ARG D 216 Details of bonding type rmsd hydrogen bonds : bond 0.03228 ( 1440) hydrogen bonds : angle 2.87463 ( 4284) SS BOND : bond 0.00140 ( 36) SS BOND : angle 0.54036 ( 72) covalent geometry : bond 0.00255 (19716) covalent geometry : angle 0.48116 (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 317 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 282 time to evaluate : 2.032 Fit side-chains REVERT: C 14 ASN cc_start: 0.8985 (t0) cc_final: 0.8764 (t0) REVERT: C 99 GLN cc_start: 0.8250 (OUTLIER) cc_final: 0.8049 (mp10) REVERT: C 216 ARG cc_start: 0.9005 (tpp80) cc_final: 0.8767 (mmm-85) REVERT: D 14 ASN cc_start: 0.8819 (t0) cc_final: 0.8583 (t0) REVERT: D 46 ASP cc_start: 0.9188 (p0) cc_final: 0.8877 (p0) REVERT: E 102 GLU cc_start: 0.8489 (pp20) cc_final: 0.8264 (pp20) REVERT: F 14 ASN cc_start: 0.9071 (t0) cc_final: 0.8818 (t0) REVERT: F 102 GLU cc_start: 0.8837 (pp20) cc_final: 0.8536 (pp20) REVERT: G 14 ASN cc_start: 0.8848 (t0) cc_final: 0.8616 (t0) REVERT: H 46 ASP cc_start: 0.9167 (p0) cc_final: 0.8854 (p0) REVERT: H 212 TYR cc_start: 0.8372 (t80) cc_final: 0.8156 (t80) REVERT: H 216 ARG cc_start: 0.9030 (mmm-85) cc_final: 0.8747 (mmt-90) REVERT: I 14 ASN cc_start: 0.8867 (m-40) cc_final: 0.8468 (m-40) REVERT: J 46 ASP cc_start: 0.9240 (p0) cc_final: 0.9022 (p0) REVERT: J 209 GLU cc_start: 0.9343 (tp30) cc_final: 0.9104 (tp30) REVERT: L 1 MET cc_start: 0.5972 (mmt) cc_final: 0.4264 (pmt) REVERT: M 15 ARG cc_start: 0.8384 (OUTLIER) cc_final: 0.8170 (ppp80) REVERT: M 46 ASP cc_start: 0.9205 (p0) cc_final: 0.9000 (p0) REVERT: M 216 ARG cc_start: 0.8888 (mmm-85) cc_final: 0.8654 (mmm-85) outliers start: 35 outliers final: 14 residues processed: 307 average time/residue: 1.8225 time to fit residues: 610.8040 Evaluate side-chains 282 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 266 time to evaluate : 3.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain C residue 99 GLN Chi-restraints excluded: chain C residue 151 MET Chi-restraints excluded: chain D residue 151 MET Chi-restraints excluded: chain E 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 L residue 25 LEU Chi-restraints excluded: chain M residue 15 ARG Chi-restraints excluded: chain M residue 25 LEU Chi-restraints excluded: chain M residue 42 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 71 optimal weight: 6.9990 chunk 211 optimal weight: 7.9990 chunk 29 optimal weight: 20.0000 chunk 108 optimal weight: 3.9990 chunk 205 optimal weight: 5.9990 chunk 143 optimal weight: 20.0000 chunk 114 optimal weight: 40.0000 chunk 183 optimal weight: 4.9990 chunk 118 optimal weight: 8.9990 chunk 57 optimal weight: 40.0000 chunk 77 optimal weight: 0.0010 overall best weight: 4.3994 ------------------------------------------------------------------------------- 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 G 99 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.085339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.057094 restraints weight = 39883.846| |-----------------------------------------------------------------------------| r_work (start): 0.2709 rms_B_bonded: 2.13 r_work: 0.2558 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2433 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9011 moved from start: 0.3500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 19752 Z= 0.237 Angle : 0.539 8.482 27048 Z= 0.277 Chirality : 0.040 0.158 3240 Planarity : 0.003 0.037 3144 Dihedral : 5.688 41.578 3312 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.13 % Allowed : 15.34 % Favored : 82.53 % 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: 3.66 (0.17), residues: 2304 helix: 3.41 (0.11), residues: 1704 sheet: 1.41 (0.50), residues: 132 loop : -1.38 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP L 44 HIS 0.004 0.001 HIS C 100 PHE 0.013 0.002 PHE L 68 TYR 0.016 0.001 TYR M 65 ARG 0.010 0.001 ARG D 216 Details of bonding type rmsd hydrogen bonds : bond 0.03586 ( 1440) hydrogen bonds : angle 2.97147 ( 4284) SS BOND : bond 0.00217 ( 36) SS BOND : angle 0.64388 ( 72) covalent geometry : bond 0.00566 (19716) covalent geometry : angle 0.53914 (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 306 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 261 time to evaluate : 2.308 Fit side-chains REVERT: A 99 GLN cc_start: 0.8250 (OUTLIER) cc_final: 0.8008 (mp10) REVERT: C 14 ASN cc_start: 0.9039 (t0) cc_final: 0.8797 (t0) REVERT: C 216 ARG cc_start: 0.9007 (tpp80) cc_final: 0.8751 (mmm-85) REVERT: D 14 ASN cc_start: 0.8898 (t0) cc_final: 0.8664 (t0) REVERT: D 46 ASP cc_start: 0.9202 (p0) cc_final: 0.8907 (p0) REVERT: D 212 TYR cc_start: 0.8501 (t80) cc_final: 0.8284 (t80) REVERT: F 14 ASN cc_start: 0.9144 (t0) cc_final: 0.8880 (t0) REVERT: F 102 GLU cc_start: 0.8787 (pp20) cc_final: 0.8512 (pp20) REVERT: F 103 LYS cc_start: 0.8297 (pttt) cc_final: 0.8007 (ptpp) REVERT: G 14 ASN cc_start: 0.8967 (t0) cc_final: 0.8700 (t0) REVERT: H 46 ASP cc_start: 0.9240 (p0) cc_final: 0.8945 (p0) REVERT: H 216 ARG cc_start: 0.9052 (mmm-85) cc_final: 0.8782 (mmt-90) REVERT: I 14 ASN cc_start: 0.8979 (m-40) cc_final: 0.8560 (m-40) REVERT: J 46 ASP cc_start: 0.9257 (p0) cc_final: 0.8992 (p0) REVERT: J 103 LYS cc_start: 0.7948 (OUTLIER) cc_final: 0.7550 (ptpp) REVERT: K 99 GLN cc_start: 0.8086 (OUTLIER) cc_final: 0.7761 (mm110) REVERT: K 102 GLU cc_start: 0.8973 (pp20) cc_final: 0.8759 (pp20) REVERT: K 103 LYS cc_start: 0.8267 (pttt) cc_final: 0.8049 (ptpp) REVERT: L 1 MET cc_start: 0.5912 (mmt) cc_final: 0.4162 (pmt) outliers start: 45 outliers final: 13 residues processed: 290 average time/residue: 1.8175 time to fit residues: 575.6756 Evaluate side-chains 272 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 256 time to evaluate : 2.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 99 GLN Chi-restraints excluded: chain C residue 4 THR Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain F residue 151 MET Chi-restraints excluded: chain 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 103 LYS Chi-restraints excluded: chain K residue 25 LEU Chi-restraints excluded: chain K residue 99 GLN 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: 0.4980 chunk 196 optimal weight: 0.7980 chunk 153 optimal weight: 0.0040 chunk 205 optimal weight: 4.9990 chunk 66 optimal weight: 10.0000 chunk 190 optimal weight: 20.0000 chunk 199 optimal weight: 10.0000 chunk 181 optimal weight: 9.9990 chunk 177 optimal weight: 1.9990 chunk 40 optimal weight: 9.9990 overall best weight: 0.8596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN C 98 GLN C 99 GLN F 99 GLN G 99 GLN K 16 HIS K 99 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.087372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.059205 restraints weight = 39540.209| |-----------------------------------------------------------------------------| r_work (start): 0.2758 rms_B_bonded: 2.15 r_work: 0.2612 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2486 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8972 moved from start: 0.3623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 19752 Z= 0.100 Angle : 0.489 8.221 27048 Z= 0.250 Chirality : 0.037 0.135 3240 Planarity : 0.003 0.036 3144 Dihedral : 5.709 41.619 3312 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.61 % Allowed : 15.96 % Favored : 82.43 % 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: 3.50 (0.11), residues: 1704 sheet: 1.18 (0.48), residues: 132 loop : -1.49 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP C 134 HIS 0.009 0.000 HIS A 100 PHE 0.014 0.001 PHE L 29 TYR 0.016 0.001 TYR H 212 ARG 0.010 0.001 ARG M 216 Details of bonding type rmsd hydrogen bonds : bond 0.03092 ( 1440) hydrogen bonds : angle 2.82166 ( 4284) SS BOND : bond 0.00126 ( 36) SS BOND : angle 0.50147 ( 72) covalent geometry : bond 0.00219 (19716) covalent geometry : angle 0.48871 (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 315 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 281 time to evaluate : 2.293 Fit side-chains REVERT: C 14 ASN cc_start: 0.9003 (t0) cc_final: 0.8774 (t0) REVERT: C 103 LYS cc_start: 0.8285 (pttt) cc_final: 0.8023 (ptpp) REVERT: C 216 ARG cc_start: 0.8984 (tpp80) cc_final: 0.8782 (mmm-85) REVERT: D 14 ASN cc_start: 0.8830 (t0) cc_final: 0.8588 (t0) REVERT: D 46 ASP cc_start: 0.9176 (p0) cc_final: 0.8867 (p0) REVERT: D 103 LYS cc_start: 0.8358 (pttt) cc_final: 0.8043 (ptpp) REVERT: D 212 TYR cc_start: 0.8442 (t80) cc_final: 0.8218 (t80) REVERT: E 102 GLU cc_start: 0.8499 (pp20) cc_final: 0.8297 (pp20) REVERT: F 99 GLN cc_start: 0.8088 (OUTLIER) cc_final: 0.7849 (mp10) REVERT: F 102 GLU cc_start: 0.8798 (pp20) cc_final: 0.8589 (pp20) REVERT: F 216 ARG cc_start: 0.8955 (tpp80) cc_final: 0.8693 (mmm-85) REVERT: H 46 ASP cc_start: 0.9188 (p0) cc_final: 0.8873 (p0) REVERT: I 14 ASN cc_start: 0.8959 (m-40) cc_final: 0.8552 (m-40) REVERT: J 46 ASP cc_start: 0.9218 (p0) cc_final: 0.8929 (p0) REVERT: K 1 MET cc_start: 0.5798 (mmt) cc_final: 0.4459 (pmt) REVERT: L 1 MET cc_start: 0.5844 (mmt) cc_final: 0.4241 (pmt) outliers start: 34 outliers final: 10 residues processed: 300 average time/residue: 2.0939 time to fit residues: 686.7512 Evaluate side-chains 278 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 267 time to evaluate : 2.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain F residue 99 GLN Chi-restraints excluded: chain F residue 151 MET Chi-restraints excluded: chain H residue 4 THR Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain L residue 20 ILE Chi-restraints excluded: chain L residue 25 LEU Chi-restraints excluded: chain M residue 25 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 148 optimal weight: 0.9980 chunk 161 optimal weight: 5.9990 chunk 169 optimal weight: 8.9990 chunk 225 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 95 optimal weight: 30.0000 chunk 143 optimal weight: 9.9990 chunk 216 optimal weight: 4.9990 chunk 69 optimal weight: 5.9990 chunk 114 optimal weight: 30.0000 chunk 48 optimal weight: 40.0000 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 GLN C 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 = 0.3363 r_free = 0.3363 target = 0.085862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.057552 restraints weight = 39581.658| |-----------------------------------------------------------------------------| r_work (start): 0.2724 rms_B_bonded: 2.14 r_work: 0.2576 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2451 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8995 moved from start: 0.3730 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= 0.188 Angle : 0.528 8.833 27048 Z= 0.273 Chirality : 0.039 0.133 3240 Planarity : 0.003 0.043 3144 Dihedral : 5.718 42.246 3312 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.61 % Allowed : 16.34 % Favored : 82.05 % 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: 3.44 (0.11), residues: 1704 sheet: 1.30 (0.49), residues: 132 loop : -1.38 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP M 134 HIS 0.008 0.001 HIS F 100 PHE 0.011 0.002 PHE K 68 TYR 0.014 0.001 TYR A 65 ARG 0.011 0.001 ARG H 216 Details of bonding type rmsd hydrogen bonds : bond 0.03305 ( 1440) hydrogen bonds : angle 2.88826 ( 4284) SS BOND : bond 0.00179 ( 36) SS BOND : angle 0.59546 ( 72) covalent geometry : bond 0.00449 (19716) covalent geometry : angle 0.52826 (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 300 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 266 time to evaluate : 3.362 Fit side-chains REVERT: C 14 ASN cc_start: 0.9027 (t0) cc_final: 0.8745 (t0) REVERT: C 103 LYS cc_start: 0.8289 (pttt) cc_final: 0.8077 (ptpp) REVERT: C 216 ARG cc_start: 0.8963 (tpp80) cc_final: 0.8759 (mmm-85) REVERT: D 14 ASN cc_start: 0.8892 (t0) cc_final: 0.8679 (t0) REVERT: D 46 ASP cc_start: 0.9221 (p0) cc_final: 0.8935 (p0) REVERT: D 212 TYR cc_start: 0.8446 (t80) cc_final: 0.8171 (t80) REVERT: F 14 ASN cc_start: 0.8693 (t0) cc_final: 0.8470 (t0) REVERT: F 102 GLU cc_start: 0.8848 (pp20) cc_final: 0.8623 (pp20) REVERT: F 103 LYS cc_start: 0.8346 (pttt) cc_final: 0.8055 (ptpp) REVERT: F 216 ARG cc_start: 0.8944 (tpp80) cc_final: 0.8683 (mmm-85) REVERT: G 14 ASN cc_start: 0.8784 (t0) cc_final: 0.8564 (t0) REVERT: H 46 ASP cc_start: 0.9209 (p0) cc_final: 0.8905 (p0) REVERT: I 14 ASN cc_start: 0.9010 (m-40) cc_final: 0.8596 (m-40) REVERT: I 145 LEU cc_start: 0.9265 (OUTLIER) cc_final: 0.9062 (mp) REVERT: J 46 ASP cc_start: 0.9226 (p0) cc_final: 0.8956 (p0) REVERT: K 1 MET cc_start: 0.5831 (mmt) cc_final: 0.4418 (pmt) REVERT: K 99 GLN cc_start: 0.8088 (OUTLIER) cc_final: 0.7633 (mp10) REVERT: K 102 GLU cc_start: 0.8979 (pp20) cc_final: 0.8739 (pp20) REVERT: K 103 LYS cc_start: 0.8254 (pttt) cc_final: 0.8046 (ptpp) REVERT: L 1 MET cc_start: 0.5874 (mmt) cc_final: 0.4223 (pmt) REVERT: M 14 ASN cc_start: 0.8718 (t0) cc_final: 0.8471 (t0) outliers start: 34 outliers final: 11 residues processed: 286 average time/residue: 1.8045 time to fit residues: 564.8671 Evaluate side-chains 271 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 258 time to evaluate : 2.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain C residue 4 THR Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain F residue 151 MET Chi-restraints excluded: chain H residue 4 THR Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 145 LEU Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain K residue 99 GLN 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: 0.7980 chunk 51 optimal weight: 3.9990 chunk 159 optimal weight: 0.8980 chunk 83 optimal weight: 0.7980 chunk 147 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 93 optimal weight: 6.9990 chunk 46 optimal weight: 3.9990 chunk 183 optimal weight: 9.9990 chunk 144 optimal weight: 5.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 GLN E 16 HIS 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 = 0.3382 r_free = 0.3382 target = 0.086933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.058743 restraints weight = 39539.410| |-----------------------------------------------------------------------------| r_work (start): 0.2752 rms_B_bonded: 2.16 r_work: 0.2605 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2480 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8975 moved from start: 0.3827 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= 0.122 Angle : 0.516 9.194 27048 Z= 0.266 Chirality : 0.038 0.143 3240 Planarity : 0.003 0.041 3144 Dihedral : 5.743 42.335 3312 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.70 % Allowed : 16.48 % Favored : 81.82 % 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: 3.66 (0.17), residues: 2304 helix: 3.44 (0.11), residues: 1704 sheet: 1.17 (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 K 24 HIS 0.002 0.000 HIS A 100 PHE 0.011 0.001 PHE L 29 TYR 0.020 0.001 TYR H 212 ARG 0.011 0.001 ARG H 216 Details of bonding type rmsd hydrogen bonds : bond 0.03095 ( 1440) hydrogen bonds : angle 2.83098 ( 4284) SS BOND : bond 0.00136 ( 36) SS BOND : angle 0.50032 ( 72) covalent geometry : bond 0.00285 (19716) covalent geometry : angle 0.51615 (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 318 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 282 time to evaluate : 2.179 Fit side-chains REVERT: C 14 ASN cc_start: 0.8985 (t0) cc_final: 0.8715 (t0) REVERT: C 103 LYS cc_start: 0.8292 (pttt) cc_final: 0.8081 (ptpp) REVERT: D 46 ASP cc_start: 0.9189 (p0) cc_final: 0.8882 (p0) REVERT: D 103 LYS cc_start: 0.8373 (pttt) cc_final: 0.8133 (ptpp) REVERT: D 212 TYR cc_start: 0.8428 (t80) cc_final: 0.8123 (t80) REVERT: E 14 ASN cc_start: 0.9166 (t0) cc_final: 0.8893 (t0) REVERT: F 14 ASN cc_start: 0.8746 (t0) cc_final: 0.8544 (t0) REVERT: F 102 GLU cc_start: 0.8812 (pp20) cc_final: 0.8580 (pp20) REVERT: F 216 ARG cc_start: 0.8910 (tpp80) cc_final: 0.8652 (mmm-85) REVERT: H 46 ASP cc_start: 0.9187 (p0) cc_final: 0.8885 (p0) REVERT: H 145 LEU cc_start: 0.9264 (OUTLIER) cc_final: 0.9033 (mp) REVERT: J 46 ASP cc_start: 0.9229 (p0) cc_final: 0.8978 (p0) REVERT: J 103 LYS cc_start: 0.7969 (pttt) cc_final: 0.7692 (ptpp) REVERT: K 1 MET cc_start: 0.5830 (mmt) cc_final: 0.4342 (pmt) REVERT: K 99 GLN cc_start: 0.8107 (OUTLIER) cc_final: 0.7773 (mm110) REVERT: K 102 GLU cc_start: 0.8981 (pp20) cc_final: 0.8733 (pp20) REVERT: K 103 LYS cc_start: 0.8267 (pttt) cc_final: 0.8052 (ptpp) REVERT: L 1 MET cc_start: 0.5896 (mmt) cc_final: 0.4231 (pmt) REVERT: L 99 GLN cc_start: 0.8098 (OUTLIER) cc_final: 0.7897 (mp10) REVERT: M 14 ASN cc_start: 0.8726 (t0) cc_final: 0.8497 (t0) outliers start: 36 outliers final: 12 residues processed: 305 average time/residue: 1.7450 time to fit residues: 582.1864 Evaluate side-chains 278 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 263 time to evaluate : 2.306 ------------------------------------------------------------------------------- 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 H residue 145 LEU Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain K residue 99 GLN Chi-restraints excluded: chain L residue 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 Chi-restraints excluded: chain M residue 209 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 110 optimal weight: 1.9990 chunk 29 optimal weight: 30.0000 chunk 203 optimal weight: 0.8980 chunk 120 optimal weight: 0.6980 chunk 60 optimal weight: 0.9990 chunk 124 optimal weight: 7.9990 chunk 209 optimal weight: 20.0000 chunk 73 optimal weight: 0.9990 chunk 109 optimal weight: 0.9990 chunk 180 optimal weight: 9.9990 chunk 123 optimal weight: 6.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- 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 G 99 GLN I 14 ASN L 99 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.087453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.059548 restraints weight = 39520.802| |-----------------------------------------------------------------------------| r_work (start): 0.2776 rms_B_bonded: 2.15 r_work: 0.2627 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2499 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8978 moved from start: 0.3888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 19752 Z= 0.107 Angle : 0.515 7.569 27048 Z= 0.269 Chirality : 0.038 0.146 3240 Planarity : 0.003 0.043 3144 Dihedral : 5.698 41.864 3312 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.28 % Allowed : 17.33 % Favored : 81.39 % 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: 3.70 (0.17), residues: 2304 helix: 3.47 (0.11), residues: 1704 sheet: 1.11 (0.47), residues: 132 loop : -1.43 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP L 24 HIS 0.003 0.000 HIS F 94 PHE 0.012 0.001 PHE L 29 TYR 0.014 0.001 TYR H 136 ARG 0.011 0.001 ARG C 216 Details of bonding type rmsd hydrogen bonds : bond 0.02971 ( 1440) hydrogen bonds : angle 2.80723 ( 4284) SS BOND : bond 0.00119 ( 36) SS BOND : angle 0.49026 ( 72) covalent geometry : bond 0.00239 (19716) covalent geometry : angle 0.51457 (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 302 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 275 time to evaluate : 2.066 Fit side-chains REVERT: D 46 ASP cc_start: 0.9210 (p0) cc_final: 0.8908 (p0) REVERT: D 212 TYR cc_start: 0.8454 (t80) cc_final: 0.8165 (t80) REVERT: E 1 MET cc_start: 0.5274 (mmt) cc_final: 0.4878 (mmt) REVERT: E 14 ASN cc_start: 0.9134 (t0) cc_final: 0.8873 (t0) REVERT: F 14 ASN cc_start: 0.8761 (t0) cc_final: 0.8544 (t0) REVERT: F 102 GLU cc_start: 0.8813 (pp20) cc_final: 0.8519 (pp20) REVERT: F 103 LYS cc_start: 0.8351 (pttt) cc_final: 0.8051 (ptpp) REVERT: H 46 ASP cc_start: 0.9157 (p0) cc_final: 0.8851 (p0) REVERT: H 145 LEU cc_start: 0.9285 (OUTLIER) cc_final: 0.9072 (mp) REVERT: J 46 ASP cc_start: 0.9216 (p0) cc_final: 0.8942 (p0) REVERT: J 103 LYS cc_start: 0.7971 (pttt) cc_final: 0.7736 (ptpp) REVERT: K 1 MET cc_start: 0.5869 (mmt) cc_final: 0.4306 (pmt) REVERT: K 99 GLN cc_start: 0.8155 (OUTLIER) cc_final: 0.7819 (mm110) REVERT: K 102 GLU cc_start: 0.8997 (pp20) cc_final: 0.8758 (pp20) REVERT: K 103 LYS cc_start: 0.8285 (pttt) cc_final: 0.8060 (ptpp) REVERT: L 1 MET cc_start: 0.5918 (mmt) cc_final: 0.4260 (pmt) REVERT: L 99 GLN cc_start: 0.8143 (OUTLIER) cc_final: 0.7895 (mp10) outliers start: 27 outliers final: 11 residues processed: 291 average time/residue: 1.8261 time to fit residues: 583.8059 Evaluate side-chains 281 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 267 time to evaluate : 2.005 ------------------------------------------------------------------------------- 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 G residue 99 GLN Chi-restraints excluded: chain H residue 4 THR Chi-restraints excluded: chain H residue 145 LEU Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain K residue 99 GLN Chi-restraints excluded: chain L residue 20 ILE Chi-restraints excluded: chain L residue 99 GLN Chi-restraints excluded: chain L residue 132 LEU Chi-restraints excluded: chain M residue 25 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 227 optimal weight: 3.9990 chunk 125 optimal weight: 7.9990 chunk 77 optimal weight: 20.0000 chunk 155 optimal weight: 4.9990 chunk 195 optimal weight: 3.9990 chunk 208 optimal weight: 3.9990 chunk 122 optimal weight: 0.9990 chunk 147 optimal weight: 7.9990 chunk 20 optimal weight: 6.9990 chunk 121 optimal weight: 0.9980 chunk 30 optimal weight: 7.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 99 GLN G 99 GLN I 14 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.086368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.058357 restraints weight = 39801.894| |-----------------------------------------------------------------------------| r_work (start): 0.2750 rms_B_bonded: 2.14 r_work: 0.2601 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2473 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8996 moved from start: 0.3938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 19752 Z= 0.166 Angle : 0.557 9.904 27048 Z= 0.290 Chirality : 0.039 0.144 3240 Planarity : 0.004 0.041 3144 Dihedral : 5.688 41.934 3312 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.04 % Allowed : 17.90 % 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: 3.65 (0.17), residues: 2304 helix: 3.42 (0.11), residues: 1704 sheet: 1.18 (0.48), residues: 132 loop : -1.39 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 3 HIS 0.003 0.001 HIS L 100 PHE 0.010 0.001 PHE K 181 TYR 0.022 0.001 TYR D 136 ARG 0.011 0.001 ARG C 216 Details of bonding type rmsd hydrogen bonds : bond 0.03120 ( 1440) hydrogen bonds : angle 2.85089 ( 4284) SS BOND : bond 0.00154 ( 36) SS BOND : angle 0.55017 ( 72) covalent geometry : bond 0.00396 (19716) covalent geometry : angle 0.55682 (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 282 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 260 time to evaluate : 2.034 Fit side-chains REVERT: C 14 ASN cc_start: 0.8749 (t0) cc_final: 0.8537 (t0) REVERT: C 103 LYS cc_start: 0.8246 (pttt) cc_final: 0.8032 (ptpp) REVERT: D 46 ASP cc_start: 0.9242 (p0) cc_final: 0.8941 (p0) REVERT: D 103 LYS cc_start: 0.8384 (pttt) cc_final: 0.8170 (ptpp) REVERT: D 212 TYR cc_start: 0.8455 (t80) cc_final: 0.8148 (t80) REVERT: E 1 MET cc_start: 0.5309 (mmt) cc_final: 0.4926 (mmt) REVERT: E 14 ASN cc_start: 0.9147 (t0) cc_final: 0.8872 (t0) REVERT: F 14 ASN cc_start: 0.8780 (t0) cc_final: 0.8580 (t0) REVERT: F 99 GLN cc_start: 0.8129 (OUTLIER) cc_final: 0.7884 (mm110) REVERT: F 102 GLU cc_start: 0.8825 (pp20) cc_final: 0.8556 (pp20) REVERT: H 46 ASP cc_start: 0.9184 (p0) cc_final: 0.8890 (p0) REVERT: H 145 LEU cc_start: 0.9294 (OUTLIER) cc_final: 0.9076 (mp) REVERT: J 46 ASP cc_start: 0.9227 (p0) cc_final: 0.8974 (p0) REVERT: J 103 LYS cc_start: 0.8006 (pttt) cc_final: 0.7758 (ptpp) REVERT: K 1 MET cc_start: 0.5879 (mmt) cc_final: 0.4320 (pmt) REVERT: K 99 GLN cc_start: 0.8163 (OUTLIER) cc_final: 0.7829 (mm110) REVERT: K 102 GLU cc_start: 0.8997 (pp20) cc_final: 0.8737 (pp20) REVERT: K 103 LYS cc_start: 0.8285 (pttt) cc_final: 0.8076 (ptpp) REVERT: L 1 MET cc_start: 0.5907 (mmt) cc_final: 0.4191 (pmt) outliers start: 22 outliers final: 12 residues processed: 273 average time/residue: 1.8811 time to fit residues: 558.4115 Evaluate side-chains 273 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 258 time to evaluate : 2.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 4 THR Chi-restraints excluded: chain C residue 99 GLN Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain F residue 99 GLN Chi-restraints excluded: chain G residue 99 GLN Chi-restraints excluded: chain H residue 145 LEU Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 151 MET Chi-restraints excluded: chain K residue 99 GLN Chi-restraints excluded: chain L residue 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: 10.0000 chunk 192 optimal weight: 2.9990 chunk 74 optimal weight: 6.9990 chunk 17 optimal weight: 4.9990 chunk 215 optimal weight: 2.9990 chunk 14 optimal weight: 10.0000 chunk 61 optimal weight: 7.9990 chunk 160 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 chunk 76 optimal weight: 30.0000 chunk 151 optimal weight: 8.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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** ** G 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 14 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.086325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.058307 restraints weight = 39837.806| |-----------------------------------------------------------------------------| r_work (start): 0.2749 rms_B_bonded: 2.14 r_work: 0.2599 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2471 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8998 moved from start: 0.3925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.241 19752 Z= 0.271 Angle : 0.756 59.105 27048 Z= 0.437 Chirality : 0.040 0.350 3240 Planarity : 0.004 0.158 3144 Dihedral : 5.691 41.948 3312 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 0.90 % Allowed : 18.04 % Favored : 81.06 % Cbeta Deviations : 0.09 % 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: 3.60 (0.17), residues: 2304 helix: 3.38 (0.11), residues: 1704 sheet: 1.19 (0.48), residues: 132 loop : -1.38 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP M 44 HIS 0.008 0.001 HIS G 100 PHE 0.010 0.002 PHE K 68 TYR 0.022 0.001 TYR D 136 ARG 0.008 0.001 ARG J 216 Details of bonding type rmsd hydrogen bonds : bond 0.03201 ( 1440) hydrogen bonds : angle 2.86317 ( 4284) SS BOND : bond 0.00183 ( 36) SS BOND : angle 0.55431 ( 72) covalent geometry : bond 0.00592 (19716) covalent geometry : angle 0.75691 (26976) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15344.86 seconds wall clock time: 265 minutes 36.68 seconds (15936.68 seconds total)