Starting phenix.real_space_refine on Tue Nov 19 05:20:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qjf_18446/11_2024/8qjf_18446_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qjf_18446/11_2024/8qjf_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qjf_18446/11_2024/8qjf_18446.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qjf_18446/11_2024/8qjf_18446.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qjf_18446/11_2024/8qjf_18446_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qjf_18446/11_2024/8qjf_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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 12.43, per 1000 atoms: 0.65 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: 5.10 Conformation dependent library (CDL) restraints added in 2.5 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: 1.65 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: 6.02 Time building geometry restraints manager: 5.86 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.740 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: 0.030 Extract box with map and model: 0.800 Check model and map are aligned: 0.150 Set scattering table: 0.190 Process input model: 43.540 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.820 ------------------------------------------------------------------------------- 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 19716 Z= 0.315 Angle : 0.576 7.009 26976 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 *********************** 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 : 1.841 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: 1.6668 time to fit residues: 676.0253 Evaluate side-chains 268 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 268 time to evaluate : 2.171 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 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 19716 Z= 0.191 Angle : 0.514 9.079 26976 Z= 0.262 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 *********************** 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 : 2.164 Fit side-chains REVERT: A 1 MET cc_start: 0.5850 (mmt) cc_final: 0.5584 (mmt) outliers start: 42 outliers final: 7 residues processed: 311 average time/residue: 1.7447 time to fit residues: 594.9775 Evaluate side-chains 272 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 265 time to evaluate : 2.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 85 SER 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 M residue 42 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 115 optimal weight: 20.0000 chunk 64 optimal weight: 4.9990 chunk 172 optimal weight: 0.7980 chunk 140 optimal weight: 2.9990 chunk 57 optimal weight: 30.0000 chunk 207 optimal weight: 7.9990 chunk 224 optimal weight: 0.2980 chunk 184 optimal weight: 5.9990 chunk 205 optimal weight: 0.5980 chunk 70 optimal weight: 5.9990 chunk 166 optimal weight: 7.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 19716 Z= 0.206 Angle : 0.498 8.839 26976 Z= 0.255 Chirality : 0.038 0.172 3240 Planarity : 0.003 0.038 3144 Dihedral : 5.395 37.344 3312 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.33 % Allowed : 13.83 % Favored : 84.85 % 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: 3.71 (0.17), residues: 2304 helix: 3.49 (0.11), residues: 1704 sheet: 1.21 (0.48), residues: 132 loop : -1.50 (0.25), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP I 3 HIS 0.005 0.001 HIS F 100 PHE 0.017 0.001 PHE L 29 TYR 0.013 0.001 TYR M 65 ARG 0.008 0.001 ARG K 15 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 282 time to evaluate : 2.142 Fit side-chains REVERT: A 1 MET cc_start: 0.5902 (mmt) cc_final: 0.5679 (mmt) outliers start: 28 outliers final: 6 residues processed: 295 average time/residue: 1.8570 time to fit residues: 598.5292 Evaluate side-chains 272 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 266 time to evaluate : 2.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 151 MET Chi-restraints excluded: chain E residue 151 MET 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 M residue 42 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 204 optimal weight: 10.0000 chunk 155 optimal weight: 4.9990 chunk 107 optimal weight: 9.9990 chunk 22 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 139 optimal weight: 4.9990 chunk 208 optimal weight: 1.9990 chunk 220 optimal weight: 6.9990 chunk 108 optimal weight: 3.9990 chunk 197 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 98 GLN K 16 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.2950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 19716 Z= 0.182 Angle : 0.490 8.299 26976 Z= 0.249 Chirality : 0.038 0.153 3240 Planarity : 0.003 0.056 3144 Dihedral : 5.375 38.375 3312 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 1.75 % Allowed : 14.39 % Favored : 83.85 % 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: 3.79 (0.17), residues: 2304 helix: 3.56 (0.11), residues: 1704 sheet: 1.22 (0.48), residues: 132 loop : -1.52 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP M 44 HIS 0.004 0.001 HIS G 100 PHE 0.010 0.001 PHE K 29 TYR 0.023 0.001 TYR H 212 ARG 0.011 0.001 ARG C 216 *********************** 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 320 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 283 time to evaluate : 3.109 Fit side-chains REVERT: A 1 MET cc_start: 0.5967 (mmt) cc_final: 0.5766 (mmt) REVERT: M 15 ARG cc_start: 0.5766 (OUTLIER) cc_final: 0.5275 (ppp80) outliers start: 37 outliers final: 10 residues processed: 308 average time/residue: 1.9363 time to fit residues: 652.7312 Evaluate side-chains 279 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 268 time to evaluate : 2.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain C residue 4 THR Chi-restraints excluded: chain C residue 151 MET 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 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 183 optimal weight: 1.9990 chunk 125 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 164 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 188 optimal weight: 3.9990 chunk 152 optimal weight: 20.0000 chunk 0 optimal weight: 30.0000 chunk 112 optimal weight: 5.9990 chunk 197 optimal weight: 2.9990 chunk 55 optimal weight: 8.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.3300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 19716 Z= 0.224 Angle : 0.499 7.973 26976 Z= 0.257 Chirality : 0.038 0.130 3240 Planarity : 0.003 0.046 3144 Dihedral : 5.482 39.788 3312 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 1.89 % Allowed : 15.29 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.75 (0.17), residues: 2304 helix: 3.51 (0.11), residues: 1704 sheet: 1.33 (0.49), residues: 132 loop : -1.50 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 44 HIS 0.002 0.001 HIS E 100 PHE 0.014 0.002 PHE L 29 TYR 0.013 0.001 TYR M 65 ARG 0.010 0.001 ARG D 216 *********************** 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 315 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 275 time to evaluate : 2.246 Fit side-chains outliers start: 40 outliers final: 11 residues processed: 297 average time/residue: 1.8105 time to fit residues: 588.1113 Evaluate side-chains 273 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 262 time to evaluate : 2.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain C residue 4 THR Chi-restraints excluded: chain F residue 151 MET Chi-restraints excluded: chain H residue 4 THR Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 151 MET Chi-restraints excluded: chain L residue 20 ILE Chi-restraints excluded: chain L residue 25 LEU Chi-restraints excluded: chain M residue 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 74 optimal weight: 0.5980 chunk 198 optimal weight: 5.9990 chunk 43 optimal weight: 6.9990 chunk 129 optimal weight: 2.9990 chunk 54 optimal weight: 0.5980 chunk 220 optimal weight: 3.9990 chunk 183 optimal weight: 7.9990 chunk 102 optimal weight: 0.1980 chunk 18 optimal weight: 4.9990 chunk 72 optimal weight: 0.9990 chunk 115 optimal weight: 20.0000 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.3465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 19716 Z= 0.152 Angle : 0.494 8.310 26976 Z= 0.252 Chirality : 0.038 0.150 3240 Planarity : 0.003 0.043 3144 Dihedral : 5.489 39.651 3312 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.33 % Allowed : 16.34 % Favored : 82.34 % 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: 3.78 (0.17), residues: 2304 helix: 3.56 (0.11), residues: 1704 sheet: 1.19 (0.48), residues: 132 loop : -1.52 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP C 134 HIS 0.002 0.000 HIS L 100 PHE 0.014 0.001 PHE L 29 TYR 0.019 0.001 TYR H 212 ARG 0.011 0.001 ARG C 216 *********************** 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 308 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 280 time to evaluate : 2.418 Fit side-chains REVERT: M 15 ARG cc_start: 0.5777 (OUTLIER) cc_final: 0.5369 (ppp80) outliers start: 28 outliers final: 9 residues processed: 299 average time/residue: 1.5784 time to fit residues: 515.6819 Evaluate side-chains 275 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 265 time to evaluate : 1.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain C residue 4 THR Chi-restraints excluded: chain F residue 151 MET Chi-restraints excluded: chain H residue 4 THR Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 212 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 125 optimal weight: 5.9990 chunk 161 optimal weight: 5.9990 chunk 124 optimal weight: 6.9990 chunk 185 optimal weight: 7.9990 chunk 123 optimal weight: 5.9990 chunk 219 optimal weight: 6.9990 chunk 137 optimal weight: 10.0000 chunk 133 optimal weight: 30.0000 chunk 101 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 GLN C 57 GLN C 99 GLN G 57 GLN H 57 GLN L 57 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.3782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.040 19716 Z= 0.423 Angle : 0.589 8.719 26976 Z= 0.305 Chirality : 0.042 0.145 3240 Planarity : 0.004 0.046 3144 Dihedral : 5.754 41.939 3312 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.66 % Allowed : 16.24 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.52 (0.17), residues: 2304 helix: 3.28 (0.11), residues: 1704 sheet: 1.49 (0.50), residues: 132 loop : -1.32 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 3 HIS 0.004 0.001 HIS H 73 PHE 0.016 0.002 PHE F 68 TYR 0.020 0.002 TYR M 65 ARG 0.010 0.001 ARG M 216 *********************** 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 288 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 253 time to evaluate : 2.258 Fit side-chains outliers start: 35 outliers final: 14 residues processed: 273 average time/residue: 1.8972 time to fit residues: 565.4690 Evaluate side-chains 263 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 249 time to evaluate : 2.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain C residue 4 THR Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain F residue 151 MET Chi-restraints excluded: chain H residue 4 THR Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain K residue 25 LEU Chi-restraints excluded: chain L residue 20 ILE Chi-restraints excluded: chain L residue 25 LEU Chi-restraints excluded: chain L residue 151 MET 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 135 optimal weight: 0.9980 chunk 87 optimal weight: 5.9990 chunk 131 optimal weight: 0.9990 chunk 66 optimal weight: 9.9990 chunk 43 optimal weight: 5.9990 chunk 42 optimal weight: 0.7980 chunk 139 optimal weight: 0.9990 chunk 149 optimal weight: 0.9980 chunk 108 optimal weight: 5.9990 chunk 20 optimal weight: 20.0000 chunk 172 optimal weight: 20.0000 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 GLN C 99 GLN F 99 GLN G 99 GLN I 98 GLN ** J 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 99 GLN L 99 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.3880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 19716 Z= 0.162 Angle : 0.534 9.972 26976 Z= 0.275 Chirality : 0.038 0.142 3240 Planarity : 0.003 0.037 3144 Dihedral : 5.784 42.059 3312 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % 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: 3.65 (0.17), residues: 2304 helix: 3.42 (0.11), residues: 1704 sheet: 1.17 (0.48), residues: 132 loop : -1.41 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP L 24 HIS 0.003 0.001 HIS L 100 PHE 0.014 0.001 PHE L 29 TYR 0.017 0.001 TYR H 212 ARG 0.010 0.001 ARG C 216 *********************** 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 312 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 278 time to evaluate : 2.193 Fit side-chains revert: symmetry clash REVERT: M 15 ARG cc_start: 0.5985 (OUTLIER) cc_final: 0.5696 (ppp80) outliers start: 34 outliers final: 12 residues processed: 298 average time/residue: 1.8074 time to fit residues: 587.7988 Evaluate side-chains 277 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 264 time to evaluate : 2.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain C residue 4 THR Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain F residue 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 15 ARG Chi-restraints excluded: chain M residue 25 LEU Chi-restraints excluded: chain M residue 42 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 199 optimal weight: 6.9990 chunk 210 optimal weight: 6.9990 chunk 192 optimal weight: 10.0000 chunk 204 optimal weight: 7.9990 chunk 123 optimal weight: 7.9990 chunk 89 optimal weight: 2.9990 chunk 160 optimal weight: 6.9990 chunk 62 optimal weight: 5.9990 chunk 185 optimal weight: 5.9990 chunk 193 optimal weight: 2.9990 chunk 134 optimal weight: 0.5980 overall best weight: 3.7188 ------------------------------------------------------------------------------- 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 I 14 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.3975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 19716 Z= 0.324 Angle : 0.578 7.592 26976 Z= 0.302 Chirality : 0.041 0.162 3240 Planarity : 0.004 0.046 3144 Dihedral : 5.803 42.580 3312 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.61 % Allowed : 16.76 % Favored : 81.63 % 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: 3.32 (0.12), residues: 1704 sheet: 1.29 (0.48), residues: 132 loop : -1.29 (0.27), 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 F 68 TYR 0.016 0.001 TYR D 212 ARG 0.012 0.001 ARG H 216 *********************** 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 292 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 258 time to evaluate : 2.221 Fit side-chains revert: symmetry clash outliers start: 34 outliers final: 11 residues processed: 276 average time/residue: 1.9090 time to fit residues: 575.0936 Evaluate side-chains 264 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 253 time to evaluate : 2.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain C residue 4 THR Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain F residue 151 MET Chi-restraints excluded: chain H residue 4 THR Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 0.7980 chunk 132 optimal weight: 1.9990 chunk 102 optimal weight: 5.9990 chunk 150 optimal weight: 8.9990 chunk 227 optimal weight: 0.9990 chunk 209 optimal weight: 6.9990 chunk 180 optimal weight: 10.0000 chunk 18 optimal weight: 8.9990 chunk 139 optimal weight: 0.9980 chunk 110 optimal weight: 0.2980 chunk 143 optimal weight: 10.0000 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 GLN C 99 GLN F 99 GLN I 14 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.4070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19716 Z= 0.171 Angle : 0.558 9.855 26976 Z= 0.291 Chirality : 0.039 0.180 3240 Planarity : 0.003 0.041 3144 Dihedral : 5.797 42.161 3312 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 0.90 % Allowed : 17.52 % Favored : 81.58 % 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: 3.61 (0.17), residues: 2304 helix: 3.38 (0.11), residues: 1704 sheet: 1.09 (0.47), residues: 132 loop : -1.31 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP K 133 HIS 0.003 0.001 HIS F 100 PHE 0.013 0.001 PHE L 29 TYR 0.018 0.001 TYR H 212 ARG 0.010 0.001 ARG G 216 ********************** 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 286 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 267 time to evaluate : 2.114 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 12 residues processed: 278 average time/residue: 1.9285 time to fit residues: 582.9263 Evaluate side-chains 273 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 261 time to evaluate : 2.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 MET 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 F residue 151 MET Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain L residue 20 ILE Chi-restraints excluded: chain L residue 25 LEU Chi-restraints excluded: chain M residue 25 LEU Chi-restraints excluded: chain M residue 42 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 5.9990 chunk 55 optimal weight: 7.9990 chunk 166 optimal weight: 8.9990 chunk 26 optimal weight: 0.9990 chunk 50 optimal weight: 9.9990 chunk 181 optimal weight: 10.0000 chunk 75 optimal weight: 0.9990 chunk 186 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 159 optimal weight: 0.8980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 GLN C 99 GLN F 99 GLN G 99 GLN K 99 GLN ** L 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.087008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.058992 restraints weight = 39774.074| |-----------------------------------------------------------------------------| r_work (start): 0.2763 rms_B_bonded: 2.17 r_work: 0.2618 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2490 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8976 moved from start: 0.4051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.180 19716 Z= 0.270 Angle : 0.846 59.170 26976 Z= 0.491 Chirality : 0.039 0.237 3240 Planarity : 0.003 0.040 3144 Dihedral : 5.794 42.168 3312 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 0.95 % Allowed : 17.66 % Favored : 81.39 % 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: 3.59 (0.17), residues: 2304 helix: 3.35 (0.11), residues: 1704 sheet: 1.09 (0.47), residues: 132 loop : -1.29 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP K 133 HIS 0.003 0.000 HIS L 100 PHE 0.013 0.001 PHE L 29 TYR 0.017 0.001 TYR D 136 ARG 0.009 0.001 ARG D 216 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8445.64 seconds wall clock time: 161 minutes 14.66 seconds (9674.66 seconds total)