Starting phenix.real_space_refine on Mon Oct 14 16:52:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qko_18468/10_2024/8qko_18468_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qko_18468/10_2024/8qko_18468.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qko_18468/10_2024/8qko_18468.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qko_18468/10_2024/8qko_18468.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qko_18468/10_2024/8qko_18468_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qko_18468/10_2024/8qko_18468_neut.cif" } resolution = 3.73 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 96 5.16 5 C 12396 2.51 5 N 2892 2.21 5 O 3108 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 18492 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1541 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 6, 'TRANS': 182} Chain breaks: 1 Chain: "B" Number of atoms: 1541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1541 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 6, 'TRANS': 182} Chain breaks: 1 Chain: "C" Number of atoms: 1541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1541 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 6, 'TRANS': 182} Chain breaks: 1 Chain: "D" Number of atoms: 1541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1541 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 6, 'TRANS': 182} Chain breaks: 1 Chain: "E" Number of atoms: 1541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1541 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 6, 'TRANS': 182} Chain breaks: 1 Chain: "F" Number of atoms: 1541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1541 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 6, 'TRANS': 182} Chain breaks: 1 Chain: "G" Number of atoms: 1541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1541 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 6, 'TRANS': 182} Chain breaks: 1 Chain: "H" Number of atoms: 1541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1541 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 6, 'TRANS': 182} Chain breaks: 1 Chain: "I" Number of atoms: 1541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1541 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 6, 'TRANS': 182} Chain breaks: 1 Chain: "J" Number of atoms: 1541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1541 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 6, 'TRANS': 182} Chain breaks: 1 Chain: "K" Number of atoms: 1541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1541 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 6, 'TRANS': 182} Chain breaks: 1 Chain: "L" Number of atoms: 1541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1541 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 6, 'TRANS': 182} Chain breaks: 1 Time building chain proxies: 11.56, per 1000 atoms: 0.63 Number of scatterers: 18492 At special positions: 0 Unit cell: (100.876, 98.2724, 158.798, 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 96 16.00 O 3108 8.00 N 2892 7.00 C 12396 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 198 " distance=2.03 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 192 " distance=2.03 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 187 " distance=2.03 Simple disulfide: pdb=" SG CYS B 53 " - pdb=" SG CYS B 198 " distance=2.03 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 192 " distance=2.03 Simple disulfide: pdb=" SG CYS B 64 " - pdb=" SG CYS B 187 " distance=2.03 Simple disulfide: pdb=" SG CYS C 53 " - pdb=" SG CYS C 198 " distance=2.03 Simple disulfide: pdb=" SG CYS C 60 " - pdb=" SG CYS C 192 " distance=2.03 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 187 " distance=2.03 Simple disulfide: pdb=" SG CYS D 53 " - pdb=" SG CYS D 198 " distance=2.03 Simple disulfide: pdb=" SG CYS D 60 " - pdb=" SG CYS D 192 " distance=2.03 Simple disulfide: pdb=" SG CYS D 64 " - pdb=" SG CYS D 187 " distance=2.03 Simple disulfide: pdb=" SG CYS E 53 " - pdb=" SG CYS E 198 " distance=2.03 Simple disulfide: pdb=" SG CYS E 60 " - pdb=" SG CYS E 192 " distance=2.03 Simple disulfide: pdb=" SG CYS E 64 " - pdb=" SG CYS E 187 " distance=2.03 Simple disulfide: pdb=" SG CYS F 53 " - pdb=" SG CYS F 198 " distance=2.03 Simple disulfide: pdb=" SG CYS F 60 " - pdb=" SG CYS F 192 " distance=2.03 Simple disulfide: pdb=" SG CYS F 64 " - pdb=" SG CYS F 187 " distance=2.03 Simple disulfide: pdb=" SG CYS G 53 " - pdb=" SG CYS G 198 " distance=2.03 Simple disulfide: pdb=" SG CYS G 60 " - pdb=" SG CYS G 192 " distance=2.03 Simple disulfide: pdb=" SG CYS G 64 " - pdb=" SG CYS G 187 " distance=2.03 Simple disulfide: pdb=" SG CYS H 53 " - pdb=" SG CYS H 198 " distance=2.03 Simple disulfide: pdb=" SG CYS H 60 " - pdb=" SG CYS H 192 " distance=2.03 Simple disulfide: pdb=" SG CYS H 64 " - pdb=" SG CYS H 187 " distance=2.03 Simple disulfide: pdb=" SG CYS I 53 " - pdb=" SG CYS I 198 " distance=2.03 Simple disulfide: pdb=" SG CYS I 60 " - pdb=" SG CYS I 192 " distance=2.03 Simple disulfide: pdb=" SG CYS I 64 " - pdb=" SG CYS I 187 " distance=2.03 Simple disulfide: pdb=" SG CYS J 53 " - pdb=" SG CYS J 198 " distance=2.03 Simple disulfide: pdb=" SG CYS J 60 " - pdb=" SG CYS J 192 " distance=2.03 Simple disulfide: pdb=" SG CYS J 64 " - pdb=" SG CYS J 187 " distance=2.03 Simple disulfide: pdb=" SG CYS K 53 " - pdb=" SG CYS K 198 " distance=2.03 Simple disulfide: pdb=" SG CYS K 60 " - pdb=" SG CYS K 192 " distance=2.03 Simple disulfide: pdb=" SG CYS K 64 " - pdb=" SG CYS K 187 " distance=2.03 Simple disulfide: pdb=" SG CYS L 53 " - pdb=" SG CYS L 198 " distance=2.03 Simple disulfide: pdb=" SG CYS L 60 " - pdb=" SG CYS L 192 " distance=2.03 Simple disulfide: pdb=" SG CYS L 64 " - pdb=" SG CYS L 187 " 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: 4.98 Conformation dependent library (CDL) restraints added in 2.2 seconds 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4320 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 12 sheets defined 75.1% alpha, 4.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.59 Creating SS restraints... Processing helix chain 'A' and resid 2 through 15 Processing helix chain 'A' and resid 20 through 44 removed outlier: 3.993A pdb=" N VAL A 40 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N GLU A 41 " --> pdb=" O GLY A 37 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N SER A 42 " --> pdb=" O THR A 38 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA A 43 " --> pdb=" O ALA A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 69 Processing helix chain 'A' and resid 72 through 104 Proline residue: A 87 - end of helix Processing helix chain 'A' and resid 152 through 177 Processing helix chain 'A' and resid 202 through 235 Processing helix chain 'B' and resid 2 through 15 Processing helix chain 'B' and resid 20 through 44 removed outlier: 3.994A pdb=" N VAL B 40 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N GLU B 41 " --> pdb=" O GLY B 37 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N SER B 42 " --> pdb=" O THR B 38 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA B 43 " --> pdb=" O ALA B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 69 Processing helix chain 'B' and resid 72 through 104 Proline residue: B 87 - end of helix Processing helix chain 'B' and resid 152 through 177 Processing helix chain 'B' and resid 202 through 235 Processing helix chain 'C' and resid 2 through 15 Processing helix chain 'C' and resid 20 through 44 removed outlier: 3.994A pdb=" N VAL C 40 " --> pdb=" O LEU C 36 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N GLU C 41 " --> pdb=" O GLY C 37 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N SER C 42 " --> pdb=" O THR C 38 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA C 43 " --> pdb=" O ALA C 39 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 69 Processing helix chain 'C' and resid 72 through 104 Proline residue: C 87 - end of helix Processing helix chain 'C' and resid 152 through 177 Processing helix chain 'C' and resid 202 through 235 Processing helix chain 'D' and resid 2 through 15 Processing helix chain 'D' and resid 20 through 44 removed outlier: 3.994A pdb=" N VAL D 40 " --> pdb=" O LEU D 36 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N GLU D 41 " --> pdb=" O GLY D 37 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N SER D 42 " --> pdb=" O THR D 38 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA D 43 " --> pdb=" O ALA D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 60 through 69 Processing helix chain 'D' and resid 72 through 104 Proline residue: D 87 - end of helix Processing helix chain 'D' and resid 152 through 177 Processing helix chain 'D' and resid 202 through 235 Processing helix chain 'E' and resid 2 through 15 Processing helix chain 'E' and resid 20 through 44 removed outlier: 3.994A pdb=" N VAL E 40 " --> pdb=" O LEU E 36 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N GLU E 41 " --> pdb=" O GLY E 37 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N SER E 42 " --> pdb=" O THR E 38 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA E 43 " --> pdb=" O ALA E 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 69 Processing helix chain 'E' and resid 72 through 104 Proline residue: E 87 - end of helix Processing helix chain 'E' and resid 152 through 177 Processing helix chain 'E' and resid 202 through 235 Processing helix chain 'F' and resid 2 through 15 Processing helix chain 'F' and resid 20 through 44 removed outlier: 3.994A pdb=" N VAL F 40 " --> pdb=" O LEU F 36 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N GLU F 41 " --> pdb=" O GLY F 37 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N SER F 42 " --> pdb=" O THR F 38 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA F 43 " --> pdb=" O ALA F 39 " (cutoff:3.500A) Processing helix chain 'F' and resid 60 through 69 Processing helix chain 'F' and resid 72 through 104 Proline residue: F 87 - end of helix Processing helix chain 'F' and resid 152 through 177 Processing helix chain 'F' and resid 202 through 235 Processing helix chain 'G' and resid 2 through 15 Processing helix chain 'G' and resid 20 through 44 removed outlier: 3.994A pdb=" N VAL G 40 " --> pdb=" O LEU G 36 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N GLU G 41 " --> pdb=" O GLY G 37 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N SER G 42 " --> pdb=" O THR G 38 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA G 43 " --> pdb=" O ALA G 39 " (cutoff:3.500A) Processing helix chain 'G' and resid 60 through 69 Processing helix chain 'G' and resid 72 through 104 Proline residue: G 87 - end of helix Processing helix chain 'G' and resid 152 through 177 Processing helix chain 'G' and resid 202 through 235 Processing helix chain 'H' and resid 2 through 15 Processing helix chain 'H' and resid 20 through 44 removed outlier: 3.994A pdb=" N VAL H 40 " --> pdb=" O LEU H 36 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N GLU H 41 " --> pdb=" O GLY H 37 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N SER H 42 " --> pdb=" O THR H 38 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA H 43 " --> pdb=" O ALA H 39 " (cutoff:3.500A) Processing helix chain 'H' and resid 60 through 69 Processing helix chain 'H' and resid 72 through 104 Proline residue: H 87 - end of helix Processing helix chain 'H' and resid 152 through 177 Processing helix chain 'H' and resid 202 through 235 Processing helix chain 'I' and resid 2 through 15 Processing helix chain 'I' and resid 20 through 44 removed outlier: 3.995A pdb=" N VAL I 40 " --> pdb=" O LEU I 36 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N GLU I 41 " --> pdb=" O GLY I 37 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N SER I 42 " --> pdb=" O THR I 38 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA I 43 " --> pdb=" O ALA I 39 " (cutoff:3.500A) Processing helix chain 'I' and resid 60 through 69 Processing helix chain 'I' and resid 72 through 104 Proline residue: I 87 - end of helix Processing helix chain 'I' and resid 152 through 177 Processing helix chain 'I' and resid 202 through 235 Processing helix chain 'J' and resid 2 through 15 Processing helix chain 'J' and resid 20 through 44 removed outlier: 3.994A pdb=" N VAL J 40 " --> pdb=" O LEU J 36 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N GLU J 41 " --> pdb=" O GLY J 37 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N SER J 42 " --> pdb=" O THR J 38 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA J 43 " --> pdb=" O ALA J 39 " (cutoff:3.500A) Processing helix chain 'J' and resid 60 through 69 Processing helix chain 'J' and resid 72 through 104 Proline residue: J 87 - end of helix Processing helix chain 'J' and resid 152 through 177 Processing helix chain 'J' and resid 202 through 235 Processing helix chain 'K' and resid 2 through 15 Processing helix chain 'K' and resid 20 through 44 removed outlier: 3.994A pdb=" N VAL K 40 " --> pdb=" O LEU K 36 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N GLU K 41 " --> pdb=" O GLY K 37 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N SER K 42 " --> pdb=" O THR K 38 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA K 43 " --> pdb=" O ALA K 39 " (cutoff:3.500A) Processing helix chain 'K' and resid 60 through 69 Processing helix chain 'K' and resid 72 through 104 Proline residue: K 87 - end of helix Processing helix chain 'K' and resid 152 through 177 Processing helix chain 'K' and resid 202 through 235 Processing helix chain 'L' and resid 2 through 15 Processing helix chain 'L' and resid 20 through 44 removed outlier: 3.994A pdb=" N VAL L 40 " --> pdb=" O LEU L 36 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N GLU L 41 " --> pdb=" O GLY L 37 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N SER L 42 " --> pdb=" O THR L 38 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA L 43 " --> pdb=" O ALA L 39 " (cutoff:3.500A) Processing helix chain 'L' and resid 60 through 69 Processing helix chain 'L' and resid 72 through 104 Proline residue: L 87 - end of helix Processing helix chain 'L' and resid 152 through 177 Processing helix chain 'L' and resid 202 through 235 Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 53 removed outlier: 3.820A pdb=" N ARG A 52 " --> pdb=" O PHE A 199 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 52 through 53 removed outlier: 3.820A pdb=" N ARG B 52 " --> pdb=" O PHE B 199 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 52 through 53 removed outlier: 3.818A pdb=" N ARG C 52 " --> pdb=" O PHE C 199 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 52 through 53 removed outlier: 3.818A pdb=" N ARG D 52 " --> pdb=" O PHE D 199 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 52 through 53 removed outlier: 3.818A pdb=" N ARG E 52 " --> pdb=" O PHE E 199 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 52 through 53 removed outlier: 3.819A pdb=" N ARG F 52 " --> pdb=" O PHE F 199 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 52 through 53 removed outlier: 3.819A pdb=" N ARG G 52 " --> pdb=" O PHE G 199 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 52 through 53 removed outlier: 3.818A pdb=" N ARG H 52 " --> pdb=" O PHE H 199 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 52 through 53 removed outlier: 3.819A pdb=" N ARG I 52 " --> pdb=" O PHE I 199 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 52 through 53 removed outlier: 3.818A pdb=" N ARG J 52 " --> pdb=" O PHE J 199 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 52 through 53 removed outlier: 3.818A pdb=" N ARG K 52 " --> pdb=" O PHE K 199 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 52 through 53 removed outlier: 3.818A pdb=" N ARG L 52 " --> pdb=" O PHE L 199 " (cutoff:3.500A) 1392 hydrogen bonds defined for protein. 4176 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: 6.55 Time building geometry restraints manager: 5.45 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: 5412 1.34 - 1.46: 5116 1.46 - 1.58: 8360 1.58 - 1.69: 0 1.69 - 1.81: 120 Bond restraints: 19008 Sorted by residual: bond pdb=" CA VAL B 86 " pdb=" C VAL B 86 " ideal model delta sigma weight residual 1.523 1.533 -0.010 9.20e-03 1.18e+04 1.18e+00 bond pdb=" CA VAL D 86 " pdb=" C VAL D 86 " ideal model delta sigma weight residual 1.523 1.533 -0.010 9.20e-03 1.18e+04 1.16e+00 bond pdb=" CA VAL H 86 " pdb=" C VAL H 86 " ideal model delta sigma weight residual 1.523 1.533 -0.010 9.20e-03 1.18e+04 1.16e+00 bond pdb=" CA VAL L 86 " pdb=" C VAL L 86 " ideal model delta sigma weight residual 1.523 1.533 -0.010 9.20e-03 1.18e+04 1.16e+00 bond pdb=" CA VAL J 86 " pdb=" C VAL J 86 " ideal model delta sigma weight residual 1.523 1.533 -0.010 9.20e-03 1.18e+04 1.16e+00 ... (remaining 19003 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.10: 24937 1.10 - 2.21: 612 2.21 - 3.31: 131 3.31 - 4.42: 72 4.42 - 5.52: 48 Bond angle restraints: 25800 Sorted by residual: angle pdb=" C HIS G 194 " pdb=" CA HIS G 194 " pdb=" CB HIS G 194 " ideal model delta sigma weight residual 116.34 110.82 5.52 1.40e+00 5.10e-01 1.56e+01 angle pdb=" C HIS A 194 " pdb=" CA HIS A 194 " pdb=" CB HIS A 194 " ideal model delta sigma weight residual 116.34 110.82 5.52 1.40e+00 5.10e-01 1.56e+01 angle pdb=" C HIS I 194 " pdb=" CA HIS I 194 " pdb=" CB HIS I 194 " ideal model delta sigma weight residual 116.34 110.82 5.52 1.40e+00 5.10e-01 1.56e+01 angle pdb=" C HIS C 194 " pdb=" CA HIS C 194 " pdb=" CB HIS C 194 " ideal model delta sigma weight residual 116.34 110.82 5.52 1.40e+00 5.10e-01 1.56e+01 angle pdb=" C HIS F 194 " pdb=" CA HIS F 194 " pdb=" CB HIS F 194 " ideal model delta sigma weight residual 116.34 110.82 5.52 1.40e+00 5.10e-01 1.56e+01 ... (remaining 25795 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.14: 9588 12.14 - 24.28: 876 24.28 - 36.43: 384 36.43 - 48.57: 168 48.57 - 60.71: 48 Dihedral angle restraints: 11064 sinusoidal: 4392 harmonic: 6672 Sorted by residual: dihedral pdb=" N ARG L 52 " pdb=" CA ARG L 52 " pdb=" CB ARG L 52 " pdb=" CG ARG L 52 " ideal model delta sinusoidal sigma weight residual 60.00 4.37 55.63 3 1.50e+01 4.44e-03 9.36e+00 dihedral pdb=" N ARG J 52 " pdb=" CA ARG J 52 " pdb=" CB ARG J 52 " pdb=" CG ARG J 52 " ideal model delta sinusoidal sigma weight residual 60.00 4.37 55.63 3 1.50e+01 4.44e-03 9.36e+00 dihedral pdb=" N ARG D 52 " pdb=" CA ARG D 52 " pdb=" CB ARG D 52 " pdb=" CG ARG D 52 " ideal model delta sinusoidal sigma weight residual 60.00 4.37 55.63 3 1.50e+01 4.44e-03 9.36e+00 ... (remaining 11061 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1961 0.026 - 0.052: 588 0.052 - 0.079: 319 0.079 - 0.105: 72 0.105 - 0.131: 12 Chirality restraints: 2952 Sorted by residual: chirality pdb=" CA PRO F 203 " pdb=" N PRO F 203 " pdb=" C PRO F 203 " pdb=" CB PRO F 203 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.30e-01 chirality pdb=" CA PRO A 203 " pdb=" N PRO A 203 " pdb=" C PRO A 203 " pdb=" CB PRO A 203 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.23e-01 chirality pdb=" CA PRO E 203 " pdb=" N PRO E 203 " pdb=" C PRO E 203 " pdb=" CB PRO E 203 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.19e-01 ... (remaining 2949 not shown) Planarity restraints: 3096 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG E 52 " -0.159 9.50e-02 1.11e+02 7.14e-02 3.15e+00 pdb=" NE ARG E 52 " 0.008 2.00e-02 2.50e+03 pdb=" CZ ARG E 52 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG E 52 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG E 52 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG F 52 " -0.159 9.50e-02 1.11e+02 7.11e-02 3.14e+00 pdb=" NE ARG F 52 " 0.008 2.00e-02 2.50e+03 pdb=" CZ ARG F 52 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG F 52 " 0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG F 52 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG I 52 " 0.158 9.50e-02 1.11e+02 7.10e-02 3.13e+00 pdb=" NE ARG I 52 " -0.008 2.00e-02 2.50e+03 pdb=" CZ ARG I 52 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG I 52 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG I 52 " 0.007 2.00e-02 2.50e+03 ... (remaining 3093 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.37: 89 2.37 - 3.00: 10689 3.00 - 3.63: 30943 3.63 - 4.27: 40588 4.27 - 4.90: 68823 Nonbonded interactions: 151132 Sorted by model distance: nonbonded pdb=" OG1 THR B 204 " pdb=" OD1 ASP C 66 " model vdw 1.736 3.040 nonbonded pdb=" OD1 ASP A 66 " pdb=" OG1 THR K 204 " model vdw 1.804 3.040 nonbonded pdb=" ND2 ASN A 62 " pdb=" O LEU K 200 " model vdw 1.965 3.120 nonbonded pdb=" N ASN B 62 " pdb=" NH2 ARG H 52 " model vdw 2.195 3.200 nonbonded pdb=" NH2 ARG B 100 " pdb=" OD2 ASP H 11 " model vdw 2.201 3.120 ... (remaining 151127 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 'B' 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' } 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 group one per residue 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: 3.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.680 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 41.660 Find NCS groups from input model: 0.590 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:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 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 : 0.003 0.031 19008 Z= 0.205 Angle : 0.522 5.523 25800 Z= 0.279 Chirality : 0.034 0.131 2952 Planarity : 0.006 0.071 3096 Dihedral : 13.371 60.712 6636 Min Nonbonded Distance : 1.736 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.14 % Allowed : 2.94 % Favored : 93.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.37 (0.17), residues: 2220 helix: 2.83 (0.11), residues: 1632 sheet: -1.84 (0.30), residues: 204 loop : -2.26 (0.26), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 77 HIS 0.003 0.001 HIS E 73 PHE 0.013 0.001 PHE G 31 TYR 0.005 0.001 TYR K 155 ARG 0.004 0.001 ARG F 52 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 661 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 597 time to evaluate : 2.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLN cc_start: 0.9310 (mt0) cc_final: 0.8788 (mt0) REVERT: A 61 GLU cc_start: 0.8814 (mm-30) cc_final: 0.7960 (mm-30) REVERT: B 48 GLN cc_start: 0.9515 (OUTLIER) cc_final: 0.8940 (tp40) REVERT: B 56 GLN cc_start: 0.9247 (mt0) cc_final: 0.8550 (mp10) REVERT: B 61 GLU cc_start: 0.8765 (mm-30) cc_final: 0.7878 (mm-30) REVERT: B 65 TYR cc_start: 0.9215 (t80) cc_final: 0.8982 (t80) REVERT: B 227 GLU cc_start: 0.8962 (mm-30) cc_final: 0.8737 (mm-30) REVERT: C 32 ARG cc_start: 0.9091 (ttm-80) cc_final: 0.8690 (ttm170) REVERT: C 46 ASP cc_start: 0.6950 (p0) cc_final: 0.6682 (p0) REVERT: C 76 PHE cc_start: 0.7676 (t80) cc_final: 0.7319 (t80) REVERT: C 164 ILE cc_start: 0.9268 (mm) cc_final: 0.8905 (pt) REVERT: C 210 ILE cc_start: 0.8713 (mt) cc_final: 0.8282 (mt) REVERT: D 22 LYS cc_start: 0.7785 (OUTLIER) cc_final: 0.6999 (tttm) REVERT: D 61 GLU cc_start: 0.7830 (mm-30) cc_final: 0.6588 (mm-30) REVERT: D 86 VAL cc_start: 0.8878 (t) cc_final: 0.8661 (t) REVERT: D 164 ILE cc_start: 0.8755 (mm) cc_final: 0.8370 (pt) REVERT: D 196 VAL cc_start: 0.5985 (p) cc_final: 0.5352 (t) REVERT: E 22 LYS cc_start: 0.7438 (OUTLIER) cc_final: 0.6676 (ttmt) REVERT: E 61 GLU cc_start: 0.8306 (mm-30) cc_final: 0.7377 (mm-30) REVERT: E 65 TYR cc_start: 0.8241 (t80) cc_final: 0.7501 (t80) REVERT: F 8 LYS cc_start: 0.9562 (pttp) cc_final: 0.9356 (ptpp) REVERT: F 65 TYR cc_start: 0.8697 (t80) cc_final: 0.8198 (t80) REVERT: F 162 LYS cc_start: 0.7626 (ttmm) cc_final: 0.6971 (mttm) REVERT: F 173 GLN cc_start: 0.9063 (tm-30) cc_final: 0.8798 (tm-30) REVERT: F 197 ASP cc_start: 0.9033 (m-30) cc_final: 0.8511 (m-30) REVERT: F 205 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7944 (mt-10) REVERT: F 227 GLU cc_start: 0.8383 (mm-30) cc_final: 0.8038 (mm-30) REVERT: G 22 LYS cc_start: 0.8128 (OUTLIER) cc_final: 0.7294 (pttm) REVERT: G 25 LEU cc_start: 0.9447 (mt) cc_final: 0.9209 (pp) REVERT: G 154 THR cc_start: 0.7582 (p) cc_final: 0.7042 (p) REVERT: G 199 PHE cc_start: 0.7316 (m-80) cc_final: 0.5949 (m-80) REVERT: G 213 MET cc_start: 0.7698 (mmp) cc_final: 0.6815 (mmp) REVERT: H 61 GLU cc_start: 0.7204 (mm-30) cc_final: 0.6866 (mm-30) REVERT: H 88 THR cc_start: 0.7799 (p) cc_final: 0.7315 (p) REVERT: H 166 GLU cc_start: 0.9047 (tp30) cc_final: 0.8476 (tp30) REVERT: H 205 GLU cc_start: 0.7549 (OUTLIER) cc_final: 0.6857 (mp0) REVERT: H 227 GLU cc_start: 0.8395 (mm-30) cc_final: 0.7919 (mm-30) REVERT: I 71 ILE cc_start: 0.8601 (tp) cc_final: 0.7946 (tt) REVERT: I 206 LYS cc_start: 0.8422 (mttm) cc_final: 0.8112 (mptt) REVERT: J 71 ILE cc_start: 0.7836 (tp) cc_final: 0.7533 (tt) REVERT: J 217 SER cc_start: 0.9108 (m) cc_final: 0.8707 (p) REVERT: J 231 VAL cc_start: 0.9085 (t) cc_final: 0.8774 (t) REVERT: K 227 GLU cc_start: 0.8790 (mm-30) cc_final: 0.8561 (mm-30) REVERT: L 80 GLN cc_start: 0.8550 (tt0) cc_final: 0.8254 (tm-30) REVERT: L 156 ILE cc_start: 0.9380 (mm) cc_final: 0.9058 (mm) REVERT: L 188 LYS cc_start: 0.8828 (mmmm) cc_final: 0.8416 (mptt) REVERT: L 218 LEU cc_start: 0.9445 (mm) cc_final: 0.9239 (mm) REVERT: L 225 ILE cc_start: 0.9538 (mm) cc_final: 0.9323 (pt) outliers start: 64 outliers final: 11 residues processed: 632 average time/residue: 0.3310 time to fit residues: 305.5647 Evaluate side-chains 364 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 347 time to evaluate : 1.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 48 GLN Chi-restraints excluded: chain C residue 22 LYS Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain D residue 22 LYS Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain E residue 22 LYS Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain F residue 22 LYS Chi-restraints excluded: chain F residue 205 GLU Chi-restraints excluded: chain G residue 22 LYS Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 52 ARG Chi-restraints excluded: chain H residue 205 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 3.9990 chunk 163 optimal weight: 20.0000 chunk 90 optimal weight: 3.9990 chunk 55 optimal weight: 40.0000 chunk 110 optimal weight: 8.9990 chunk 87 optimal weight: 0.8980 chunk 169 optimal weight: 0.8980 chunk 65 optimal weight: 20.0000 chunk 102 optimal weight: 6.9990 chunk 126 optimal weight: 20.0000 chunk 196 optimal weight: 6.9990 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN A 57 GLN ** B 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 GLN ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 54 ASN D 57 GLN D 80 GLN G 195 GLN H 14 GLN H 80 GLN ** H 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 62 ASN ** J 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 224 ASN K 48 GLN K 56 GLN K 73 HIS ** K 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 173 GLN ** L 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 224 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.3289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 19008 Z= 0.240 Angle : 0.646 10.845 25800 Z= 0.322 Chirality : 0.040 0.226 2952 Planarity : 0.004 0.051 3096 Dihedral : 5.271 49.322 2483 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 3.48 % Allowed : 14.36 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.27 (0.17), residues: 2220 helix: 2.57 (0.11), residues: 1668 sheet: -1.61 (0.33), residues: 204 loop : -2.00 (0.31), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP J 24 HIS 0.007 0.001 HIS G 73 PHE 0.027 0.002 PHE G 165 TYR 0.018 0.001 TYR D 91 ARG 0.007 0.001 ARG F 202 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 384 time to evaluate : 2.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLN cc_start: 0.9282 (mt0) cc_final: 0.8754 (mt0) REVERT: A 61 GLU cc_start: 0.8524 (mm-30) cc_final: 0.8307 (mm-30) REVERT: A 91 TYR cc_start: 0.8517 (t80) cc_final: 0.8270 (t80) REVERT: B 48 GLN cc_start: 0.9558 (OUTLIER) cc_final: 0.9060 (tp40) REVERT: B 61 GLU cc_start: 0.8320 (mm-30) cc_final: 0.7848 (mm-30) REVERT: B 65 TYR cc_start: 0.9230 (t80) cc_final: 0.8984 (t80) REVERT: B 91 TYR cc_start: 0.8402 (t80) cc_final: 0.8158 (t80) REVERT: C 46 ASP cc_start: 0.7203 (p0) cc_final: 0.6898 (p0) REVERT: C 61 GLU cc_start: 0.7848 (mp0) cc_final: 0.7482 (mm-30) REVERT: C 164 ILE cc_start: 0.9322 (mm) cc_final: 0.8981 (pt) REVERT: D 41 GLU cc_start: 0.8034 (tm-30) cc_final: 0.7717 (mt-10) REVERT: D 53 CYS cc_start: 0.5158 (OUTLIER) cc_final: 0.3904 (p) REVERT: D 164 ILE cc_start: 0.8900 (mm) cc_final: 0.8479 (pt) REVERT: E 22 LYS cc_start: 0.7813 (OUTLIER) cc_final: 0.7303 (mttp) REVERT: E 47 GLU cc_start: 0.8143 (tp30) cc_final: 0.7154 (tp30) REVERT: E 56 GLN cc_start: 0.9381 (mt0) cc_final: 0.9034 (mt0) REVERT: F 52 ARG cc_start: 0.7366 (mtm-85) cc_final: 0.6950 (mtm-85) REVERT: F 56 GLN cc_start: 0.8498 (pt0) cc_final: 0.7924 (pt0) REVERT: F 173 GLN cc_start: 0.9317 (tm-30) cc_final: 0.8796 (tm-30) REVERT: F 227 GLU cc_start: 0.8638 (mm-30) cc_final: 0.8206 (mm-30) REVERT: G 25 LEU cc_start: 0.9494 (mt) cc_final: 0.9207 (pp) REVERT: G 63 VAL cc_start: 0.9221 (m) cc_final: 0.9019 (p) REVERT: H 41 GLU cc_start: 0.8573 (tp30) cc_final: 0.8188 (tm-30) REVERT: H 56 GLN cc_start: 0.9297 (tt0) cc_final: 0.9089 (tt0) REVERT: H 99 MET cc_start: 0.8907 (mmp) cc_final: 0.8285 (mmp) REVERT: H 166 GLU cc_start: 0.9226 (tp30) cc_final: 0.8846 (tp30) REVERT: H 173 GLN cc_start: 0.8994 (tm-30) cc_final: 0.8719 (tm-30) REVERT: H 205 GLU cc_start: 0.8209 (mt-10) cc_final: 0.7571 (mp0) REVERT: I 188 LYS cc_start: 0.9031 (mmmm) cc_final: 0.8761 (mmmm) REVERT: J 56 GLN cc_start: 0.8676 (mt0) cc_final: 0.8379 (mt0) REVERT: J 212 PHE cc_start: 0.8959 (OUTLIER) cc_final: 0.8515 (t80) REVERT: K 173 GLN cc_start: 0.9188 (tm-30) cc_final: 0.8606 (pp30) REVERT: K 227 GLU cc_start: 0.8850 (mm-30) cc_final: 0.8644 (mm-30) REVERT: L 67 LYS cc_start: 0.8925 (tppt) cc_final: 0.8708 (ttmm) REVERT: L 80 GLN cc_start: 0.8832 (tt0) cc_final: 0.8306 (tt0) REVERT: L 188 LYS cc_start: 0.9039 (mmmm) cc_final: 0.8592 (mptt) REVERT: L 218 LEU cc_start: 0.9574 (mm) cc_final: 0.9322 (mm) outliers start: 71 outliers final: 42 residues processed: 429 average time/residue: 0.3134 time to fit residues: 203.2118 Evaluate side-chains 365 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 319 time to evaluate : 2.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 48 GLN Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 161 PHE Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 53 CYS Chi-restraints excluded: chain E residue 16 TYR Chi-restraints excluded: chain E residue 22 LYS Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 220 SER Chi-restraints excluded: chain F residue 31 PHE Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 71 ILE Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain G residue 156 ILE Chi-restraints excluded: chain G residue 160 LEU Chi-restraints excluded: chain G residue 182 SER Chi-restraints excluded: chain H residue 16 TYR Chi-restraints excluded: chain H residue 35 LEU Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 71 ILE Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain J residue 30 ILE Chi-restraints excluded: chain J residue 78 VAL Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 90 LEU Chi-restraints excluded: chain J residue 212 PHE Chi-restraints excluded: chain J residue 213 MET Chi-restraints excluded: chain J residue 223 LEU Chi-restraints excluded: chain J residue 224 ASN Chi-restraints excluded: chain K residue 31 PHE Chi-restraints excluded: chain K residue 48 GLN Chi-restraints excluded: chain K residue 88 THR Chi-restraints excluded: chain L residue 23 VAL Chi-restraints excluded: chain L residue 171 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 109 optimal weight: 50.0000 chunk 60 optimal weight: 2.9990 chunk 163 optimal weight: 20.0000 chunk 133 optimal weight: 10.0000 chunk 54 optimal weight: 50.0000 chunk 196 optimal weight: 1.9990 chunk 212 optimal weight: 7.9990 chunk 175 optimal weight: 20.0000 chunk 194 optimal weight: 8.9990 chunk 66 optimal weight: 5.9990 chunk 157 optimal weight: 20.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 HIS ** A 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 224 ASN B 48 GLN B 54 ASN ** B 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 54 ASN D 80 GLN ** D 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 48 GLN F 54 ASN ** G 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 54 ASN ** I 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 194 HIS ** L 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.5823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.110 19008 Z= 0.345 Angle : 0.689 11.364 25800 Z= 0.359 Chirality : 0.042 0.293 2952 Planarity : 0.005 0.068 3096 Dihedral : 4.992 59.129 2457 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 5.10 % Allowed : 17.01 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.17), residues: 2220 helix: 2.37 (0.11), residues: 1668 sheet: -1.90 (0.32), residues: 204 loop : -1.96 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP I 44 HIS 0.007 0.002 HIS H 194 PHE 0.037 0.002 PHE C 212 TYR 0.028 0.002 TYR E 65 ARG 0.006 0.001 ARG E 32 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 312 time to evaluate : 3.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ASP cc_start: 0.8499 (p0) cc_final: 0.7899 (p0) REVERT: A 61 GLU cc_start: 0.8553 (mm-30) cc_final: 0.8097 (tp30) REVERT: A 91 TYR cc_start: 0.8629 (t80) cc_final: 0.8227 (t80) REVERT: B 46 ASP cc_start: 0.8506 (p0) cc_final: 0.8006 (p0) REVERT: B 56 GLN cc_start: 0.9451 (mt0) cc_final: 0.9035 (mt0) REVERT: C 38 THR cc_start: 0.8922 (t) cc_final: 0.8544 (t) REVERT: C 179 PHE cc_start: 0.8209 (m-80) cc_final: 0.7866 (m-80) REVERT: D 41 GLU cc_start: 0.8286 (tm-30) cc_final: 0.8042 (mt-10) REVERT: D 47 GLU cc_start: 0.7583 (mt-10) cc_final: 0.7348 (mt-10) REVERT: E 47 GLU cc_start: 0.8865 (tp30) cc_final: 0.8523 (tp30) REVERT: E 56 GLN cc_start: 0.9487 (mt0) cc_final: 0.9199 (mt0) REVERT: E 65 TYR cc_start: 0.8893 (t80) cc_final: 0.8500 (t80) REVERT: F 26 SER cc_start: 0.8589 (OUTLIER) cc_final: 0.8359 (m) REVERT: F 56 GLN cc_start: 0.9122 (pt0) cc_final: 0.8605 (pt0) REVERT: F 173 GLN cc_start: 0.9580 (tm-30) cc_final: 0.8917 (tm-30) REVERT: F 195 GLN cc_start: 0.9161 (OUTLIER) cc_final: 0.8909 (mp10) REVERT: F 205 GLU cc_start: 0.8889 (mt-10) cc_final: 0.8457 (mt-10) REVERT: F 227 GLU cc_start: 0.8917 (mm-30) cc_final: 0.8577 (mm-30) REVERT: G 41 GLU cc_start: 0.8553 (pp20) cc_final: 0.8247 (pp20) REVERT: G 66 ASP cc_start: 0.9079 (OUTLIER) cc_final: 0.8826 (m-30) REVERT: G 165 PHE cc_start: 0.8261 (m-80) cc_final: 0.7892 (m-80) REVERT: H 41 GLU cc_start: 0.8765 (tp30) cc_final: 0.8481 (tm-30) REVERT: H 61 GLU cc_start: 0.8703 (mm-30) cc_final: 0.8451 (tp30) REVERT: H 166 GLU cc_start: 0.9343 (tp30) cc_final: 0.9042 (tp30) REVERT: H 173 GLN cc_start: 0.9298 (tm-30) cc_final: 0.9026 (tm-30) REVERT: J 56 GLN cc_start: 0.9043 (mt0) cc_final: 0.8507 (mt0) REVERT: J 165 PHE cc_start: 0.8688 (m-10) cc_final: 0.8461 (m-10) REVERT: K 173 GLN cc_start: 0.9164 (tm-30) cc_final: 0.8736 (tm-30) REVERT: K 227 GLU cc_start: 0.9054 (mm-30) cc_final: 0.8828 (mm-30) REVERT: L 48 GLN cc_start: 0.8277 (pm20) cc_final: 0.7733 (tt0) outliers start: 104 outliers final: 63 residues processed: 385 average time/residue: 0.3116 time to fit residues: 181.3820 Evaluate side-chains 331 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 265 time to evaluate : 2.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 161 PHE Chi-restraints excluded: chain D residue 16 TYR Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 53 CYS Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain E residue 16 TYR Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 81 ILE Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 31 PHE Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 38 THR Chi-restraints excluded: chain F residue 49 SER Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 195 GLN Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 55 THR Chi-restraints excluded: chain G residue 66 ASP Chi-restraints excluded: chain G residue 71 ILE Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 160 LEU Chi-restraints excluded: chain G residue 182 SER Chi-restraints excluded: chain H residue 16 TYR Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 35 LEU Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 66 ASP Chi-restraints excluded: chain H residue 71 ILE Chi-restraints excluded: chain I residue 16 TYR Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 71 ILE Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain I residue 90 LEU Chi-restraints excluded: chain J residue 16 TYR Chi-restraints excluded: chain J residue 86 VAL Chi-restraints excluded: chain J residue 89 LEU Chi-restraints excluded: chain J residue 90 LEU Chi-restraints excluded: chain J residue 212 PHE Chi-restraints excluded: chain K residue 31 PHE Chi-restraints excluded: chain K residue 47 GLU Chi-restraints excluded: chain K residue 68 SER Chi-restraints excluded: chain K residue 78 VAL Chi-restraints excluded: chain K residue 88 THR Chi-restraints excluded: chain K residue 184 VAL Chi-restraints excluded: chain K residue 190 ASP Chi-restraints excluded: chain K residue 223 LEU Chi-restraints excluded: chain L residue 23 VAL Chi-restraints excluded: chain L residue 55 THR Chi-restraints excluded: chain L residue 83 PHE Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain L residue 171 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 194 optimal weight: 7.9990 chunk 147 optimal weight: 6.9990 chunk 101 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 131 optimal weight: 0.0570 chunk 197 optimal weight: 10.0000 chunk 208 optimal weight: 6.9990 chunk 103 optimal weight: 3.9990 chunk 186 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 overall best weight: 2.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 54 ASN F 54 ASN H 56 GLN ** H 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 56 GLN I 224 ASN K 195 GLN ** K 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 80 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.6308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19008 Z= 0.182 Angle : 0.600 12.775 25800 Z= 0.296 Chirality : 0.037 0.187 2952 Planarity : 0.004 0.037 3096 Dihedral : 4.574 44.704 2448 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 4.26 % Allowed : 19.26 % Favored : 76.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.35 (0.17), residues: 2220 helix: 2.68 (0.11), residues: 1668 sheet: -1.85 (0.33), residues: 204 loop : -2.05 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP J 24 HIS 0.005 0.001 HIS G 73 PHE 0.033 0.001 PHE G 165 TYR 0.024 0.001 TYR D 65 ARG 0.006 0.000 ARG F 52 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 307 time to evaluate : 2.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 91 TYR cc_start: 0.7860 (t80) cc_final: 0.7489 (t80) REVERT: D 188 LYS cc_start: 0.8994 (mmmm) cc_final: 0.8606 (mmmm) REVERT: E 56 GLN cc_start: 0.9464 (mt0) cc_final: 0.9034 (mt0) REVERT: F 52 ARG cc_start: 0.7920 (mtm110) cc_final: 0.7603 (mtm110) REVERT: F 56 GLN cc_start: 0.9082 (pt0) cc_final: 0.8843 (pt0) REVERT: F 173 GLN cc_start: 0.9552 (tm-30) cc_final: 0.8883 (tm-30) REVERT: F 195 GLN cc_start: 0.9065 (pm20) cc_final: 0.8713 (pt0) REVERT: F 227 GLU cc_start: 0.8999 (mm-30) cc_final: 0.8677 (mm-30) REVERT: G 41 GLU cc_start: 0.8532 (pp20) cc_final: 0.8295 (pp20) REVERT: G 47 GLU cc_start: 0.8216 (mp0) cc_final: 0.7817 (mp0) REVERT: G 66 ASP cc_start: 0.9067 (OUTLIER) cc_final: 0.8811 (m-30) REVERT: G 165 PHE cc_start: 0.8433 (m-80) cc_final: 0.7990 (m-80) REVERT: G 188 LYS cc_start: 0.9023 (mmtt) cc_final: 0.8701 (mmmm) REVERT: H 41 GLU cc_start: 0.8721 (tp30) cc_final: 0.8470 (tm-30) REVERT: H 61 GLU cc_start: 0.8675 (mm-30) cc_final: 0.8363 (mm-30) REVERT: H 65 TYR cc_start: 0.9297 (t80) cc_final: 0.9043 (t80) REVERT: H 99 MET cc_start: 0.8856 (mmp) cc_final: 0.8399 (mmp) REVERT: H 103 GLU cc_start: 0.8445 (mm-30) cc_final: 0.8244 (mm-30) REVERT: H 166 GLU cc_start: 0.9365 (tp30) cc_final: 0.9040 (tp30) REVERT: H 173 GLN cc_start: 0.9247 (tm-30) cc_final: 0.9034 (tm-30) REVERT: J 75 ARG cc_start: 0.9218 (mpp80) cc_final: 0.8767 (mmt90) REVERT: J 227 GLU cc_start: 0.9184 (mm-30) cc_final: 0.8954 (mm-30) REVERT: K 166 GLU cc_start: 0.9029 (tp30) cc_final: 0.8771 (tp30) REVERT: K 173 GLN cc_start: 0.9294 (tm-30) cc_final: 0.8845 (tm-30) REVERT: L 47 GLU cc_start: 0.8531 (pm20) cc_final: 0.8088 (pm20) REVERT: L 48 GLN cc_start: 0.8227 (pm20) cc_final: 0.7915 (tt0) outliers start: 87 outliers final: 55 residues processed: 363 average time/residue: 0.3160 time to fit residues: 171.5682 Evaluate side-chains 330 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 274 time to evaluate : 1.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 192 CYS Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 53 CYS Chi-restraints excluded: chain D residue 54 ASN Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain E residue 16 TYR Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 81 ILE Chi-restraints excluded: chain F residue 31 PHE Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 66 ASP Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 182 SER Chi-restraints excluded: chain H residue 16 TYR Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 35 LEU Chi-restraints excluded: chain H residue 71 ILE Chi-restraints excluded: chain I residue 16 TYR Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 86 VAL Chi-restraints excluded: chain I residue 89 LEU Chi-restraints excluded: chain I residue 90 LEU Chi-restraints excluded: chain I residue 221 LEU Chi-restraints excluded: chain J residue 16 TYR Chi-restraints excluded: chain J residue 52 ARG Chi-restraints excluded: chain J residue 86 VAL Chi-restraints excluded: chain J residue 89 LEU Chi-restraints excluded: chain J residue 90 LEU Chi-restraints excluded: chain J residue 212 PHE Chi-restraints excluded: chain J residue 229 PHE Chi-restraints excluded: chain K residue 31 PHE Chi-restraints excluded: chain K residue 35 LEU Chi-restraints excluded: chain K residue 49 SER Chi-restraints excluded: chain K residue 81 ILE Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 184 VAL Chi-restraints excluded: chain K residue 190 ASP Chi-restraints excluded: chain L residue 23 VAL Chi-restraints excluded: chain L residue 80 GLN Chi-restraints excluded: chain L residue 171 LEU Chi-restraints excluded: chain L residue 184 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 173 optimal weight: 6.9990 chunk 118 optimal weight: 9.9990 chunk 3 optimal weight: 10.0000 chunk 155 optimal weight: 10.0000 chunk 86 optimal weight: 5.9990 chunk 178 optimal weight: 9.9990 chunk 144 optimal weight: 50.0000 chunk 0 optimal weight: 70.0000 chunk 106 optimal weight: 9.9990 chunk 187 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 224 ASN F 224 ASN G 224 ASN H 56 GLN H 194 HIS ** H 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 224 ASN ** K 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.7495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 19008 Z= 0.324 Angle : 0.648 11.548 25800 Z= 0.331 Chirality : 0.040 0.282 2952 Planarity : 0.004 0.045 3096 Dihedral : 4.702 51.996 2448 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 4.95 % Allowed : 20.25 % Favored : 74.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.29 (0.17), residues: 2220 helix: 2.64 (0.11), residues: 1668 sheet: -1.89 (0.34), residues: 204 loop : -2.13 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 77 HIS 0.006 0.001 HIS H 194 PHE 0.026 0.001 PHE G 165 TYR 0.016 0.001 TYR F 65 ARG 0.009 0.001 ARG D 52 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 276 time to evaluate : 2.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ASP cc_start: 0.8494 (p0) cc_final: 0.7994 (p0) REVERT: A 52 ARG cc_start: 0.8109 (mtm-85) cc_final: 0.7615 (mpp-170) REVERT: A 61 GLU cc_start: 0.8957 (tp30) cc_final: 0.8728 (mm-30) REVERT: B 56 GLN cc_start: 0.9538 (mt0) cc_final: 0.8424 (mt0) REVERT: D 41 GLU cc_start: 0.8135 (pm20) cc_final: 0.7902 (pm20) REVERT: D 56 GLN cc_start: 0.9396 (mt0) cc_final: 0.9178 (mt0) REVERT: D 61 GLU cc_start: 0.8866 (mm-30) cc_final: 0.8580 (mm-30) REVERT: D 91 TYR cc_start: 0.8403 (t80) cc_final: 0.8141 (t80) REVERT: D 188 LYS cc_start: 0.9194 (mmmm) cc_final: 0.8950 (mmmm) REVERT: E 56 GLN cc_start: 0.9424 (mt0) cc_final: 0.9176 (mt0) REVERT: F 56 GLN cc_start: 0.9381 (pt0) cc_final: 0.9150 (pt0) REVERT: F 61 GLU cc_start: 0.9057 (OUTLIER) cc_final: 0.8428 (mm-30) REVERT: F 91 TYR cc_start: 0.8155 (t80) cc_final: 0.7901 (t80) REVERT: F 173 GLN cc_start: 0.9610 (tm-30) cc_final: 0.8871 (tm-30) REVERT: F 195 GLN cc_start: 0.9226 (OUTLIER) cc_final: 0.8960 (mt0) REVERT: F 227 GLU cc_start: 0.9087 (mm-30) cc_final: 0.8792 (mm-30) REVERT: G 47 GLU cc_start: 0.8272 (mp0) cc_final: 0.8023 (pm20) REVERT: H 92 LEU cc_start: 0.9307 (OUTLIER) cc_final: 0.9020 (tt) REVERT: H 166 GLU cc_start: 0.9359 (tp30) cc_final: 0.9098 (tp30) REVERT: H 173 GLN cc_start: 0.9351 (tm-30) cc_final: 0.9095 (tm-30) REVERT: I 165 PHE cc_start: 0.8641 (m-80) cc_final: 0.8256 (m-80) REVERT: J 173 GLN cc_start: 0.9313 (tm-30) cc_final: 0.9009 (tm-30) REVERT: J 227 GLU cc_start: 0.9204 (mm-30) cc_final: 0.8981 (mm-30) REVERT: K 166 GLU cc_start: 0.9213 (tp30) cc_final: 0.8964 (tp30) REVERT: K 173 GLN cc_start: 0.9243 (tm-30) cc_final: 0.8893 (tm-30) REVERT: K 188 LYS cc_start: 0.9056 (tppt) cc_final: 0.8844 (tppt) REVERT: L 14 GLN cc_start: 0.8875 (pt0) cc_final: 0.8502 (pt0) REVERT: L 47 GLU cc_start: 0.8592 (pm20) cc_final: 0.8331 (pm20) REVERT: L 48 GLN cc_start: 0.8386 (pm20) cc_final: 0.8152 (tt0) REVERT: L 67 LYS cc_start: 0.9181 (tppt) cc_final: 0.8908 (tptp) REVERT: L 188 LYS cc_start: 0.9436 (mmmm) cc_final: 0.8869 (tppp) outliers start: 101 outliers final: 68 residues processed: 346 average time/residue: 0.3066 time to fit residues: 158.4840 Evaluate side-chains 325 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 254 time to evaluate : 1.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 161 PHE Chi-restraints excluded: chain C residue 192 CYS Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain D residue 16 TYR Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 53 CYS Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain E residue 16 TYR Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 31 PHE Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 81 ILE Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain E residue 229 PHE Chi-restraints excluded: chain F residue 31 PHE Chi-restraints excluded: chain F residue 49 SER Chi-restraints excluded: chain F residue 61 GLU Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 195 GLN Chi-restraints excluded: chain F residue 213 MET Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 55 THR Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain H residue 16 TYR Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 35 LEU Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 71 ILE Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain I residue 16 TYR Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain I residue 83 PHE Chi-restraints excluded: chain I residue 86 VAL Chi-restraints excluded: chain I residue 89 LEU Chi-restraints excluded: chain I residue 90 LEU Chi-restraints excluded: chain I residue 221 LEU Chi-restraints excluded: chain J residue 16 TYR Chi-restraints excluded: chain J residue 52 ARG Chi-restraints excluded: chain J residue 86 VAL Chi-restraints excluded: chain J residue 90 LEU Chi-restraints excluded: chain J residue 212 PHE Chi-restraints excluded: chain J residue 229 PHE Chi-restraints excluded: chain K residue 31 PHE Chi-restraints excluded: chain K residue 35 LEU Chi-restraints excluded: chain K residue 49 SER Chi-restraints excluded: chain K residue 55 THR Chi-restraints excluded: chain K residue 78 VAL Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 184 VAL Chi-restraints excluded: chain K residue 190 ASP Chi-restraints excluded: chain L residue 23 VAL Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain L residue 171 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 70 optimal weight: 1.9990 chunk 188 optimal weight: 6.9990 chunk 41 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 208 optimal weight: 6.9990 chunk 173 optimal weight: 8.9990 chunk 96 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 69 optimal weight: 6.9990 chunk 109 optimal weight: 50.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: