Starting phenix.real_space_refine on Sat Jun 28 08:15:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tum_41625/06_2025/8tum_41625.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tum_41625/06_2025/8tum_41625.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tum_41625/06_2025/8tum_41625.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tum_41625/06_2025/8tum_41625.map" model { file = "/net/cci-nas-00/data/ceres_data/8tum_41625/06_2025/8tum_41625.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tum_41625/06_2025/8tum_41625.cif" } resolution = 3.6 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= -0.007 sd= 0.042 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: 5 Type Number sf(0) Gaussians S 64 5.16 5 C 10512 2.51 5 N 2736 2.21 5 O 3376 1.98 5 H 17040 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 33728 Number of models: 1 Model: "" Number of chains: 16 Chain: "e" Number of atoms: 2108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2108 Classifications: {'peptide': 143} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 136} Chain: "f" Number of atoms: 2108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2108 Classifications: {'peptide': 143} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 136} Chain: "g" Number of atoms: 2108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2108 Classifications: {'peptide': 143} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 136} Chain: "h" Number of atoms: 2108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2108 Classifications: {'peptide': 143} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 136} Chain: "i" Number of atoms: 2108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2108 Classifications: {'peptide': 143} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 136} Chain: "j" Number of atoms: 2108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2108 Classifications: {'peptide': 143} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 136} Chain: "k" Number of atoms: 2108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2108 Classifications: {'peptide': 143} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 136} Chain: "l" Number of atoms: 2108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2108 Classifications: {'peptide': 143} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 136} Chain: "m" Number of atoms: 2108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2108 Classifications: {'peptide': 143} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 136} Chain: "n" Number of atoms: 2108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2108 Classifications: {'peptide': 143} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 136} Chain: "o" Number of atoms: 2108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2108 Classifications: {'peptide': 143} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 136} Chain: "p" Number of atoms: 2108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2108 Classifications: {'peptide': 143} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 136} Chain: "d" Number of atoms: 2108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2108 Classifications: {'peptide': 143} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 136} Chain: "c" Number of atoms: 2108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2108 Classifications: {'peptide': 143} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 136} Chain: "b" Number of atoms: 2108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2108 Classifications: {'peptide': 143} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 136} Chain: "a" Number of atoms: 2108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2108 Classifications: {'peptide': 143} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 136} Time building chain proxies: 18.10, per 1000 atoms: 0.54 Number of scatterers: 33728 At special positions: 0 Unit cell: (73.1, 73.1, 258, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 64 16.00 O 3376 8.00 N 2736 7.00 C 10512 6.00 H 17040 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS e 134 " - pdb=" SG CYS e 147 " distance=2.03 Simple disulfide: pdb=" SG CYS f 134 " - pdb=" SG CYS f 147 " distance=2.03 Simple disulfide: pdb=" SG CYS g 134 " - pdb=" SG CYS g 147 " distance=2.03 Simple disulfide: pdb=" SG CYS h 134 " - pdb=" SG CYS h 147 " distance=2.03 Simple disulfide: pdb=" SG CYS i 134 " - pdb=" SG CYS i 147 " distance=2.03 Simple disulfide: pdb=" SG CYS j 134 " - pdb=" SG CYS j 147 " distance=2.03 Simple disulfide: pdb=" SG CYS k 134 " - pdb=" SG CYS k 147 " distance=2.03 Simple disulfide: pdb=" SG CYS l 134 " - pdb=" SG CYS l 147 " distance=2.03 Simple disulfide: pdb=" SG CYS m 134 " - pdb=" SG CYS m 147 " distance=2.03 Simple disulfide: pdb=" SG CYS n 134 " - pdb=" SG CYS n 147 " distance=2.03 Simple disulfide: pdb=" SG CYS o 134 " - pdb=" SG CYS o 147 " distance=2.03 Simple disulfide: pdb=" SG CYS p 134 " - pdb=" SG CYS p 147 " distance=2.03 Simple disulfide: pdb=" SG CYS d 134 " - pdb=" SG CYS d 147 " distance=2.03 Simple disulfide: pdb=" SG CYS c 134 " - pdb=" SG CYS c 147 " distance=2.03 Simple disulfide: pdb=" SG CYS b 134 " - pdb=" SG CYS b 147 " distance=2.03 Simple disulfide: pdb=" SG CYS a 134 " - pdb=" SG CYS a 147 " 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: 11.03 Conformation dependent library (CDL) restraints added in 4.7 seconds 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4192 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 32 sheets defined 32.2% alpha, 17.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.98 Creating SS restraints... Processing helix chain 'e' and resid 8 through 23 removed outlier: 3.747A pdb=" N LEU e 12 " --> pdb=" O THR e 8 " (cutoff:3.500A) Processing helix chain 'e' and resid 31 through 47 removed outlier: 3.647A pdb=" N GLY e 39 " --> pdb=" O ALA e 35 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA e 44 " --> pdb=" O ALA e 40 " (cutoff:3.500A) Processing helix chain 'e' and resid 48 through 60 removed outlier: 3.988A pdb=" N THR e 52 " --> pdb=" O PRO e 48 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLY e 60 " --> pdb=" O SER e 56 " (cutoff:3.500A) Processing helix chain 'f' and resid 8 through 23 removed outlier: 3.747A pdb=" N LEU f 12 " --> pdb=" O THR f 8 " (cutoff:3.500A) Processing helix chain 'f' and resid 31 through 47 removed outlier: 3.647A pdb=" N GLY f 39 " --> pdb=" O ALA f 35 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA f 44 " --> pdb=" O ALA f 40 " (cutoff:3.500A) Processing helix chain 'f' and resid 48 through 60 removed outlier: 3.989A pdb=" N THR f 52 " --> pdb=" O PRO f 48 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLY f 60 " --> pdb=" O SER f 56 " (cutoff:3.500A) Processing helix chain 'g' and resid 8 through 23 removed outlier: 3.746A pdb=" N LEU g 12 " --> pdb=" O THR g 8 " (cutoff:3.500A) Processing helix chain 'g' and resid 31 through 47 removed outlier: 3.647A pdb=" N GLY g 39 " --> pdb=" O ALA g 35 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA g 44 " --> pdb=" O ALA g 40 " (cutoff:3.500A) Processing helix chain 'g' and resid 48 through 60 removed outlier: 3.988A pdb=" N THR g 52 " --> pdb=" O PRO g 48 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLY g 60 " --> pdb=" O SER g 56 " (cutoff:3.500A) Processing helix chain 'h' and resid 8 through 23 removed outlier: 3.747A pdb=" N LEU h 12 " --> pdb=" O THR h 8 " (cutoff:3.500A) Processing helix chain 'h' and resid 31 through 47 removed outlier: 3.646A pdb=" N GLY h 39 " --> pdb=" O ALA h 35 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA h 44 " --> pdb=" O ALA h 40 " (cutoff:3.500A) Processing helix chain 'h' and resid 48 through 60 removed outlier: 3.988A pdb=" N THR h 52 " --> pdb=" O PRO h 48 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLY h 60 " --> pdb=" O SER h 56 " (cutoff:3.500A) Processing helix chain 'i' and resid 8 through 23 removed outlier: 3.746A pdb=" N LEU i 12 " --> pdb=" O THR i 8 " (cutoff:3.500A) Processing helix chain 'i' and resid 31 through 47 removed outlier: 3.646A pdb=" N GLY i 39 " --> pdb=" O ALA i 35 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA i 44 " --> pdb=" O ALA i 40 " (cutoff:3.500A) Processing helix chain 'i' and resid 48 through 60 removed outlier: 3.988A pdb=" N THR i 52 " --> pdb=" O PRO i 48 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLY i 60 " --> pdb=" O SER i 56 " (cutoff:3.500A) Processing helix chain 'j' and resid 8 through 23 removed outlier: 3.747A pdb=" N LEU j 12 " --> pdb=" O THR j 8 " (cutoff:3.500A) Processing helix chain 'j' and resid 31 through 47 removed outlier: 3.647A pdb=" N GLY j 39 " --> pdb=" O ALA j 35 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA j 44 " --> pdb=" O ALA j 40 " (cutoff:3.500A) Processing helix chain 'j' and resid 48 through 60 removed outlier: 3.987A pdb=" N THR j 52 " --> pdb=" O PRO j 48 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLY j 60 " --> pdb=" O SER j 56 " (cutoff:3.500A) Processing helix chain 'k' and resid 8 through 23 removed outlier: 3.747A pdb=" N LEU k 12 " --> pdb=" O THR k 8 " (cutoff:3.500A) Processing helix chain 'k' and resid 31 through 47 removed outlier: 3.647A pdb=" N GLY k 39 " --> pdb=" O ALA k 35 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA k 44 " --> pdb=" O ALA k 40 " (cutoff:3.500A) Processing helix chain 'k' and resid 48 through 60 removed outlier: 3.989A pdb=" N THR k 52 " --> pdb=" O PRO k 48 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLY k 60 " --> pdb=" O SER k 56 " (cutoff:3.500A) Processing helix chain 'l' and resid 8 through 23 removed outlier: 3.747A pdb=" N LEU l 12 " --> pdb=" O THR l 8 " (cutoff:3.500A) Processing helix chain 'l' and resid 31 through 47 removed outlier: 3.647A pdb=" N GLY l 39 " --> pdb=" O ALA l 35 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA l 44 " --> pdb=" O ALA l 40 " (cutoff:3.500A) Processing helix chain 'l' and resid 48 through 60 removed outlier: 3.988A pdb=" N THR l 52 " --> pdb=" O PRO l 48 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLY l 60 " --> pdb=" O SER l 56 " (cutoff:3.500A) Processing helix chain 'm' and resid 8 through 23 removed outlier: 3.747A pdb=" N LEU m 12 " --> pdb=" O THR m 8 " (cutoff:3.500A) Processing helix chain 'm' and resid 31 through 47 removed outlier: 3.647A pdb=" N GLY m 39 " --> pdb=" O ALA m 35 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA m 44 " --> pdb=" O ALA m 40 " (cutoff:3.500A) Processing helix chain 'm' and resid 48 through 60 removed outlier: 3.988A pdb=" N THR m 52 " --> pdb=" O PRO m 48 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLY m 60 " --> pdb=" O SER m 56 " (cutoff:3.500A) Processing helix chain 'n' and resid 8 through 23 removed outlier: 3.747A pdb=" N LEU n 12 " --> pdb=" O THR n 8 " (cutoff:3.500A) Processing helix chain 'n' and resid 31 through 47 removed outlier: 3.647A pdb=" N GLY n 39 " --> pdb=" O ALA n 35 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA n 44 " --> pdb=" O ALA n 40 " (cutoff:3.500A) Processing helix chain 'n' and resid 48 through 60 removed outlier: 3.987A pdb=" N THR n 52 " --> pdb=" O PRO n 48 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLY n 60 " --> pdb=" O SER n 56 " (cutoff:3.500A) Processing helix chain 'o' and resid 8 through 23 removed outlier: 3.747A pdb=" N LEU o 12 " --> pdb=" O THR o 8 " (cutoff:3.500A) Processing helix chain 'o' and resid 31 through 47 removed outlier: 3.646A pdb=" N GLY o 39 " --> pdb=" O ALA o 35 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA o 44 " --> pdb=" O ALA o 40 " (cutoff:3.500A) Processing helix chain 'o' and resid 48 through 60 removed outlier: 3.988A pdb=" N THR o 52 " --> pdb=" O PRO o 48 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLY o 60 " --> pdb=" O SER o 56 " (cutoff:3.500A) Processing helix chain 'p' and resid 8 through 23 removed outlier: 3.747A pdb=" N LEU p 12 " --> pdb=" O THR p 8 " (cutoff:3.500A) Processing helix chain 'p' and resid 31 through 47 removed outlier: 3.646A pdb=" N GLY p 39 " --> pdb=" O ALA p 35 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA p 44 " --> pdb=" O ALA p 40 " (cutoff:3.500A) Processing helix chain 'p' and resid 48 through 60 removed outlier: 3.989A pdb=" N THR p 52 " --> pdb=" O PRO p 48 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLY p 60 " --> pdb=" O SER p 56 " (cutoff:3.500A) Processing helix chain 'd' and resid 8 through 23 removed outlier: 3.747A pdb=" N LEU d 12 " --> pdb=" O THR d 8 " (cutoff:3.500A) Processing helix chain 'd' and resid 31 through 47 removed outlier: 3.648A pdb=" N GLY d 39 " --> pdb=" O ALA d 35 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA d 44 " --> pdb=" O ALA d 40 " (cutoff:3.500A) Processing helix chain 'd' and resid 48 through 60 removed outlier: 3.988A pdb=" N THR d 52 " --> pdb=" O PRO d 48 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLY d 60 " --> pdb=" O SER d 56 " (cutoff:3.500A) Processing helix chain 'c' and resid 8 through 23 removed outlier: 3.747A pdb=" N LEU c 12 " --> pdb=" O THR c 8 " (cutoff:3.500A) Processing helix chain 'c' and resid 31 through 47 removed outlier: 3.647A pdb=" N GLY c 39 " --> pdb=" O ALA c 35 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA c 44 " --> pdb=" O ALA c 40 " (cutoff:3.500A) Processing helix chain 'c' and resid 48 through 60 removed outlier: 3.987A pdb=" N THR c 52 " --> pdb=" O PRO c 48 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLY c 60 " --> pdb=" O SER c 56 " (cutoff:3.500A) Processing helix chain 'b' and resid 8 through 23 removed outlier: 3.747A pdb=" N LEU b 12 " --> pdb=" O THR b 8 " (cutoff:3.500A) Processing helix chain 'b' and resid 31 through 47 removed outlier: 3.647A pdb=" N GLY b 39 " --> pdb=" O ALA b 35 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA b 44 " --> pdb=" O ALA b 40 " (cutoff:3.500A) Processing helix chain 'b' and resid 48 through 60 removed outlier: 3.987A pdb=" N THR b 52 " --> pdb=" O PRO b 48 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLY b 60 " --> pdb=" O SER b 56 " (cutoff:3.500A) Processing helix chain 'a' and resid 8 through 23 removed outlier: 3.747A pdb=" N LEU a 12 " --> pdb=" O THR a 8 " (cutoff:3.500A) Processing helix chain 'a' and resid 31 through 47 removed outlier: 3.647A pdb=" N GLY a 39 " --> pdb=" O ALA a 35 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA a 44 " --> pdb=" O ALA a 40 " (cutoff:3.500A) Processing helix chain 'a' and resid 48 through 60 removed outlier: 3.988A pdb=" N THR a 52 " --> pdb=" O PRO a 48 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLY a 60 " --> pdb=" O SER a 56 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'e' and resid 67 through 69 removed outlier: 7.511A pdb=" N LYS e 67 " --> pdb=" O VAL e 80 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'e' and resid 90 through 96 removed outlier: 3.728A pdb=" N ALA e 95 " --> pdb=" O ASP e 103 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ASP e 103 " --> pdb=" O ALA e 95 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'f' and resid 67 through 69 removed outlier: 7.511A pdb=" N LYS f 67 " --> pdb=" O VAL f 80 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'f' and resid 90 through 96 removed outlier: 3.729A pdb=" N ALA f 95 " --> pdb=" O ASP f 103 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ASP f 103 " --> pdb=" O ALA f 95 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'g' and resid 67 through 69 removed outlier: 7.511A pdb=" N LYS g 67 " --> pdb=" O VAL g 80 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'g' and resid 90 through 96 removed outlier: 3.729A pdb=" N ALA g 95 " --> pdb=" O ASP g 103 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ASP g 103 " --> pdb=" O ALA g 95 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'h' and resid 67 through 69 removed outlier: 7.511A pdb=" N LYS h 67 " --> pdb=" O VAL h 80 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'h' and resid 90 through 96 removed outlier: 3.729A pdb=" N ALA h 95 " --> pdb=" O ASP h 103 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ASP h 103 " --> pdb=" O ALA h 95 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'i' and resid 67 through 69 removed outlier: 7.512A pdb=" N LYS i 67 " --> pdb=" O VAL i 80 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'i' and resid 90 through 96 removed outlier: 3.729A pdb=" N ALA i 95 " --> pdb=" O ASP i 103 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ASP i 103 " --> pdb=" O ALA i 95 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'j' and resid 67 through 69 removed outlier: 7.511A pdb=" N LYS j 67 " --> pdb=" O VAL j 80 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'j' and resid 90 through 96 removed outlier: 3.728A pdb=" N ALA j 95 " --> pdb=" O ASP j 103 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ASP j 103 " --> pdb=" O ALA j 95 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'k' and resid 67 through 69 removed outlier: 7.511A pdb=" N LYS k 67 " --> pdb=" O VAL k 80 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'k' and resid 90 through 96 removed outlier: 3.729A pdb=" N ALA k 95 " --> pdb=" O ASP k 103 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ASP k 103 " --> pdb=" O ALA k 95 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'l' and resid 67 through 69 removed outlier: 7.511A pdb=" N LYS l 67 " --> pdb=" O VAL l 80 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'l' and resid 90 through 96 removed outlier: 3.728A pdb=" N ALA l 95 " --> pdb=" O ASP l 103 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ASP l 103 " --> pdb=" O ALA l 95 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'm' and resid 67 through 69 removed outlier: 7.512A pdb=" N LYS m 67 " --> pdb=" O VAL m 80 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'm' and resid 90 through 96 removed outlier: 3.728A pdb=" N ALA m 95 " --> pdb=" O ASP m 103 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ASP m 103 " --> pdb=" O ALA m 95 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'n' and resid 67 through 69 removed outlier: 7.511A pdb=" N LYS n 67 " --> pdb=" O VAL n 80 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'n' and resid 90 through 96 removed outlier: 3.729A pdb=" N ALA n 95 " --> pdb=" O ASP n 103 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ASP n 103 " --> pdb=" O ALA n 95 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'o' and resid 67 through 69 removed outlier: 7.511A pdb=" N LYS o 67 " --> pdb=" O VAL o 80 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'o' and resid 90 through 96 removed outlier: 3.729A pdb=" N ALA o 95 " --> pdb=" O ASP o 103 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ASP o 103 " --> pdb=" O ALA o 95 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'p' and resid 67 through 69 removed outlier: 7.511A pdb=" N LYS p 67 " --> pdb=" O VAL p 80 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'p' and resid 90 through 96 removed outlier: 3.729A pdb=" N ALA p 95 " --> pdb=" O ASP p 103 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ASP p 103 " --> pdb=" O ALA p 95 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'd' and resid 67 through 69 removed outlier: 7.512A pdb=" N LYS d 67 " --> pdb=" O VAL d 80 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'd' and resid 90 through 96 removed outlier: 3.729A pdb=" N ALA d 95 " --> pdb=" O ASP d 103 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ASP d 103 " --> pdb=" O ALA d 95 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'c' and resid 67 through 69 removed outlier: 7.511A pdb=" N LYS c 67 " --> pdb=" O VAL c 80 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'c' and resid 90 through 96 removed outlier: 3.729A pdb=" N ALA c 95 " --> pdb=" O ASP c 103 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ASP c 103 " --> pdb=" O ALA c 95 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'b' and resid 67 through 69 removed outlier: 7.511A pdb=" N LYS b 67 " --> pdb=" O VAL b 80 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'b' and resid 90 through 96 removed outlier: 3.728A pdb=" N ALA b 95 " --> pdb=" O ASP b 103 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ASP b 103 " --> pdb=" O ALA b 95 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'a' and resid 67 through 69 removed outlier: 7.511A pdb=" N LYS a 67 " --> pdb=" O VAL a 80 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'a' and resid 90 through 96 removed outlier: 3.729A pdb=" N ALA a 95 " --> pdb=" O ASP a 103 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ASP a 103 " --> pdb=" O ALA a 95 " (cutoff:3.500A) 688 hydrogen bonds defined for protein. 2016 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: 12.98 Time building geometry restraints manager: 12.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 17040 1.03 - 1.23: 0 1.23 - 1.42: 6480 1.42 - 1.61: 10336 1.61 - 1.81: 96 Bond restraints: 33952 Sorted by residual: bond pdb=" CA ALA d 23 " pdb=" C ALA d 23 " ideal model delta sigma weight residual 1.531 1.523 0.008 1.12e-02 7.97e+03 5.59e-01 bond pdb=" CA ALA g 23 " pdb=" C ALA g 23 " ideal model delta sigma weight residual 1.531 1.523 0.008 1.12e-02 7.97e+03 5.43e-01 bond pdb=" CA ALA j 23 " pdb=" C ALA j 23 " ideal model delta sigma weight residual 1.531 1.523 0.008 1.12e-02 7.97e+03 5.18e-01 bond pdb=" CA ALA e 23 " pdb=" C ALA e 23 " ideal model delta sigma weight residual 1.531 1.523 0.008 1.12e-02 7.97e+03 5.16e-01 bond pdb=" CA ALA h 23 " pdb=" C ALA h 23 " ideal model delta sigma weight residual 1.531 1.523 0.008 1.12e-02 7.97e+03 5.15e-01 ... (remaining 33947 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.75: 54645 0.75 - 1.50: 6476 1.50 - 2.25: 479 2.25 - 3.00: 48 3.00 - 3.75: 80 Bond angle restraints: 61728 Sorted by residual: angle pdb=" C ILE k 46 " pdb=" CA ILE k 46 " pdb=" CB ILE k 46 " ideal model delta sigma weight residual 111.88 109.27 2.61 1.37e+00 5.33e-01 3.64e+00 angle pdb=" C ILE n 46 " pdb=" CA ILE n 46 " pdb=" CB ILE n 46 " ideal model delta sigma weight residual 111.88 109.29 2.59 1.37e+00 5.33e-01 3.58e+00 angle pdb=" C ILE f 46 " pdb=" CA ILE f 46 " pdb=" CB ILE f 46 " ideal model delta sigma weight residual 111.88 109.29 2.59 1.37e+00 5.33e-01 3.57e+00 angle pdb=" C ILE p 46 " pdb=" CA ILE p 46 " pdb=" CB ILE p 46 " ideal model delta sigma weight residual 111.88 109.30 2.58 1.37e+00 5.33e-01 3.56e+00 angle pdb=" C ILE c 46 " pdb=" CA ILE c 46 " pdb=" CB ILE c 46 " ideal model delta sigma weight residual 111.88 109.30 2.58 1.37e+00 5.33e-01 3.55e+00 ... (remaining 61723 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.41: 14442 17.41 - 34.82: 910 34.82 - 52.23: 408 52.23 - 69.64: 144 69.64 - 87.05: 112 Dihedral angle restraints: 16016 sinusoidal: 8896 harmonic: 7120 Sorted by residual: dihedral pdb=" CB CYS a 134 " pdb=" SG CYS a 134 " pdb=" SG CYS a 147 " pdb=" CB CYS a 147 " ideal model delta sinusoidal sigma weight residual -86.00 -121.83 35.83 1 1.00e+01 1.00e-02 1.82e+01 dihedral pdb=" CB CYS k 134 " pdb=" SG CYS k 134 " pdb=" SG CYS k 147 " pdb=" CB CYS k 147 " ideal model delta sinusoidal sigma weight residual -86.00 -121.82 35.82 1 1.00e+01 1.00e-02 1.82e+01 dihedral pdb=" CB CYS g 134 " pdb=" SG CYS g 134 " pdb=" SG CYS g 147 " pdb=" CB CYS g 147 " ideal model delta sinusoidal sigma weight residual -86.00 -121.81 35.81 1 1.00e+01 1.00e-02 1.81e+01 ... (remaining 16013 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1950 0.026 - 0.053: 478 0.053 - 0.079: 156 0.079 - 0.106: 192 0.106 - 0.132: 136 Chirality restraints: 2912 Sorted by residual: chirality pdb=" CA ILE n 122 " pdb=" N ILE n 122 " pdb=" C ILE n 122 " pdb=" CB ILE n 122 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.36e-01 chirality pdb=" CA ILE e 122 " pdb=" N ILE e 122 " pdb=" C ILE e 122 " pdb=" CB ILE e 122 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.29e-01 chirality pdb=" CA ILE c 122 " pdb=" N ILE c 122 " pdb=" C ILE c 122 " pdb=" CB ILE c 122 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.24e-01 ... (remaining 2909 not shown) Planarity restraints: 5104 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER g 114 " -0.006 5.00e-02 4.00e+02 9.23e-03 1.36e-01 pdb=" N PRO g 115 " 0.016 5.00e-02 4.00e+02 pdb=" CA PRO g 115 " -0.005 5.00e-02 4.00e+02 pdb=" CD PRO g 115 " -0.005 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER l 114 " 0.006 5.00e-02 4.00e+02 9.22e-03 1.36e-01 pdb=" N PRO l 115 " -0.016 5.00e-02 4.00e+02 pdb=" CA PRO l 115 " 0.005 5.00e-02 4.00e+02 pdb=" CD PRO l 115 " 0.005 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER c 114 " -0.006 5.00e-02 4.00e+02 9.19e-03 1.35e-01 pdb=" N PRO c 115 " 0.016 5.00e-02 4.00e+02 pdb=" CA PRO c 115 " -0.005 5.00e-02 4.00e+02 pdb=" CD PRO c 115 " -0.005 5.00e-02 4.00e+02 ... (remaining 5101 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.31: 8332 2.31 - 2.88: 78332 2.88 - 3.46: 79227 3.46 - 4.03: 109860 4.03 - 4.60: 172181 Nonbonded interactions: 447932 Sorted by model distance: nonbonded pdb=" OE1 GLU g 77 " pdb=" HH TYR g 79 " model vdw 1.741 2.450 nonbonded pdb=" OE1 GLU k 77 " pdb=" HH TYR k 79 " model vdw 1.741 2.450 nonbonded pdb=" OE1 GLU o 77 " pdb=" HH TYR o 79 " model vdw 1.741 2.450 nonbonded pdb=" OE1 GLU a 77 " pdb=" HH TYR a 79 " model vdw 1.741 2.450 nonbonded pdb=" O GLY k 63 " pdb=" HG SER k 64 " model vdw 1.741 2.450 ... (remaining 447927 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: 0.18 Found NCS groups: ncs_group { reference = chain 'a' selection = chain 'c' selection = chain 'b' selection = chain 'e' selection = chain 'd' selection = chain 'g' selection = chain 'f' selection = chain 'i' selection = chain 'h' selection = chain 'k' selection = chain 'j' selection = chain 'm' selection = chain 'l' selection = chain 'o' selection = chain 'n' selection = chain 'p' } 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: 250.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.690 Extract box with map and model: 11.100 Check model and map are aligned: 0.260 Set scattering table: 0.360 Process input model: 78.340 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.210 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: 0.020 Load rotamer database and sin/cos tables:3.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 345.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6922 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 : 0.002 0.012 16928 Z= 0.082 Angle : 0.400 3.753 23088 Z= 0.218 Chirality : 0.042 0.132 2912 Planarity : 0.001 0.009 2928 Dihedral : 14.115 87.053 6016 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.06 % Favored : 87.94 % Rotamer: Outliers : 0.88 % Allowed : 8.85 % Favored : 90.27 % 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: -3.30 (0.14), residues: 2256 helix: -0.92 (0.16), residues: 704 sheet: -2.21 (0.16), residues: 400 loop : -3.08 (0.16), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP h 132 PHE 0.002 0.000 PHE i 142 TYR 0.001 0.000 TYR c 30 ARG 0.001 0.000 ARG a 126 Details of bonding type rmsd hydrogen bonds : bond 0.11508 ( 688) hydrogen bonds : angle 2.84269 ( 2016) SS BOND : bond 0.00044 ( 16) SS BOND : angle 0.16005 ( 32) covalent geometry : bond 0.00153 (16912) covalent geometry : angle 0.40034 (23056) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 743 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 727 time to evaluate : 3.144 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: 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: 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: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 0 residues processed: 728 average time/residue: 0.7522 time to fit residues: 799.2276 Evaluate side-chains 385 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 385 time to evaluate : 2.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 189 optimal weight: 0.9980 chunk 169 optimal weight: 4.9990 chunk 94 optimal weight: 7.9990 chunk 57 optimal weight: 4.9990 chunk 114 optimal weight: 4.9990 chunk 90 optimal weight: 0.0970 chunk 175 optimal weight: 5.9990 chunk 67 optimal weight: 5.9990 chunk 106 optimal weight: 5.9990 chunk 130 optimal weight: 3.9990 chunk 203 optimal weight: 1.9990 overall best weight: 2.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 31 GLN g 29 GLN g 31 GLN h 31 GLN i 29 GLN i 31 GLN ** d 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.068476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.056715 restraints weight = 165150.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.059623 restraints weight = 62900.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.061505 restraints weight = 31262.260| |-----------------------------------------------------------------------------| r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.4085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16928 Z= 0.148 Angle : 0.535 4.370 23088 Z= 0.277 Chirality : 0.044 0.144 2912 Planarity : 0.002 0.020 2928 Dihedral : 3.274 17.087 2384 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 0.77 % Allowed : 17.15 % Favored : 82.08 % 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: -1.77 (0.16), residues: 2256 helix: 0.47 (0.19), residues: 688 sheet: -1.27 (0.20), residues: 432 loop : -2.23 (0.16), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP n 132 PHE 0.003 0.000 PHE n 106 TYR 0.018 0.001 TYR g 79 ARG 0.002 0.000 ARG a 126 Details of bonding type rmsd hydrogen bonds : bond 0.03500 ( 688) hydrogen bonds : angle 3.26837 ( 2016) SS BOND : bond 0.00086 ( 16) SS BOND : angle 0.28106 ( 32) covalent geometry : bond 0.00333 (16912) covalent geometry : angle 0.53529 (23056) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 404 time to evaluate : 2.714 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: 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: 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: h 55 GLU cc_start: 0.8071 (tm-30) cc_final: 0.7581 (tm-30) REVERT: h 97 GLU cc_start: 0.8463 (tt0) cc_final: 0.8236 (tt0) REVERT: i 38 GLU cc_start: 0.8439 (mt-10) cc_final: 0.8216 (mt-10) REVERT: i 77 GLU cc_start: 0.8422 (mp0) cc_final: 0.8184 (mp0) REVERT: k 67 LYS cc_start: 0.9349 (mttt) cc_final: 0.9080 (mttp) REVERT: m 38 GLU cc_start: 0.8812 (mt-10) cc_final: 0.8597 (mt-10) REVERT: n 67 LYS cc_start: 0.9242 (mttt) cc_final: 0.8997 (mttm) REVERT: n 87 ASN cc_start: 0.8515 (t0) cc_final: 0.8049 (t0) REVERT: c 38 GLU cc_start: 0.8207 (mt-10) cc_final: 0.7933 (mt-10) REVERT: c 67 LYS cc_start: 0.9055 (mttm) cc_final: 0.8786 (mttp) REVERT: b 67 LYS cc_start: 0.9347 (mttt) cc_final: 0.9136 (mtmm) REVERT: a 38 GLU cc_start: 0.8443 (mt-10) cc_final: 0.8186 (mt-10) REVERT: a 141 MET cc_start: 0.7621 (ptp) cc_final: 0.6266 (mmt) outliers start: 14 outliers final: 10 residues processed: 412 average time/residue: 0.5776 time to fit residues: 368.3977 Evaluate side-chains 372 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 362 time to evaluate : 2.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain g residue 29 GLN Chi-restraints excluded: chain g residue 47 ASN Chi-restraints excluded: chain g residue 57 LEU Chi-restraints excluded: chain g residue 67 LYS Chi-restraints excluded: chain h residue 98 ASP Chi-restraints excluded: chain l residue 104 ILE Chi-restraints excluded: chain d residue 57 LEU Chi-restraints excluded: chain d residue 148 ASP Chi-restraints excluded: chain b residue 22 LEU Chi-restraints excluded: chain a residue 22 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 204 optimal weight: 5.9990 chunk 178 optimal weight: 0.9990 chunk 42 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 101 optimal weight: 6.9990 chunk 22 optimal weight: 4.9990 chunk 191 optimal weight: 4.9990 chunk 159 optimal weight: 8.9990 chunk 17 optimal weight: 6.9990 chunk 128 optimal weight: 0.5980 chunk 148 optimal weight: 4.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 29 GLN ** i 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 31 GLN m 31 GLN d 29 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.064043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.051424 restraints weight = 168878.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.054164 restraints weight = 62770.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.055945 restraints weight = 30635.788| |-----------------------------------------------------------------------------| r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8881 moved from start: 0.4766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16928 Z= 0.177 Angle : 0.517 4.806 23088 Z= 0.272 Chirality : 0.044 0.138 2912 Planarity : 0.002 0.023 2928 Dihedral : 3.331 13.143 2384 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 0.77 % Allowed : 16.10 % Favored : 83.13 % 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: -1.04 (0.17), residues: 2256 helix: 0.80 (0.19), residues: 688 sheet: -0.57 (0.23), residues: 432 loop : -1.71 (0.17), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP n 132 PHE 0.006 0.001 PHE p 7 TYR 0.017 0.001 TYR j 79 ARG 0.001 0.000 ARG h 126 Details of bonding type rmsd hydrogen bonds : bond 0.03467 ( 688) hydrogen bonds : angle 3.48427 ( 2016) SS BOND : bond 0.00207 ( 16) SS BOND : angle 0.28385 ( 32) covalent geometry : bond 0.00390 (16912) covalent geometry : angle 0.51722 (23056) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 348 time to evaluate : 2.699 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: 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: 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: g 47 ASN cc_start: 0.9419 (OUTLIER) cc_final: 0.9172 (t0) REVERT: h 55 GLU cc_start: 0.8471 (tm-30) cc_final: 0.8048 (tm-30) REVERT: h 97 GLU cc_start: 0.8511 (tt0) cc_final: 0.8282 (tt0) REVERT: i 55 GLU cc_start: 0.8334 (tm-30) cc_final: 0.8034 (tm-30) REVERT: i 77 GLU cc_start: 0.8455 (mp0) cc_final: 0.8210 (mp0) REVERT: k 67 LYS cc_start: 0.9357 (mttt) cc_final: 0.9137 (mttp) REVERT: m 38 GLU cc_start: 0.8791 (mt-10) cc_final: 0.8542 (mt-10) REVERT: m 103 ASP cc_start: 0.8783 (p0) cc_final: 0.8545 (p0) REVERT: o 38 GLU cc_start: 0.8852 (mt-10) cc_final: 0.8548 (mt-10) REVERT: o 57 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8805 (mm) REVERT: o 129 ASP cc_start: 0.8033 (p0) cc_final: 0.7821 (p0) REVERT: d 109 GLN cc_start: 0.8689 (mm-40) cc_final: 0.8481 (mm110) REVERT: c 38 GLU cc_start: 0.8196 (mt-10) cc_final: 0.7922 (mt-10) REVERT: c 67 LYS cc_start: 0.9107 (mttm) cc_final: 0.8818 (mttp) REVERT: a 38 GLU cc_start: 0.8488 (mt-10) cc_final: 0.8182 (mt-10) REVERT: a 141 MET cc_start: 0.7845 (ptp) cc_final: 0.6426 (mmt) outliers start: 14 outliers final: 9 residues processed: 356 average time/residue: 0.6069 time to fit residues: 339.7690 Evaluate side-chains 338 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 327 time to evaluate : 2.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain f residue 98 ASP Chi-restraints excluded: chain g residue 47 ASN Chi-restraints excluded: chain g residue 57 LEU Chi-restraints excluded: chain l residue 104 ILE Chi-restraints excluded: chain o residue 57 LEU Chi-restraints excluded: chain d residue 29 GLN Chi-restraints excluded: chain d residue 57 LEU Chi-restraints excluded: chain d residue 82 VAL Chi-restraints excluded: chain d residue 148 ASP Chi-restraints excluded: chain b residue 22 LEU Chi-restraints excluded: chain a residue 22 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 171 optimal weight: 0.8980 chunk 116 optimal weight: 4.9990 chunk 22 optimal weight: 5.9990 chunk 31 optimal weight: 7.9990 chunk 61 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 chunk 212 optimal weight: 7.9990 chunk 1 optimal weight: 4.9990 chunk 3 optimal weight: 7.9990 chunk 147 optimal weight: 5.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 29 GLN f 29 GLN j 31 GLN n 31 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.059840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.049609 restraints weight = 168637.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.052107 restraints weight = 62421.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.053661 restraints weight = 31208.264| |-----------------------------------------------------------------------------| r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8966 moved from start: 0.5342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 16928 Z= 0.235 Angle : 0.546 4.151 23088 Z= 0.292 Chirality : 0.045 0.139 2912 Planarity : 0.002 0.032 2928 Dihedral : 3.730 14.662 2384 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 3.26 % Allowed : 14.88 % Favored : 81.86 % 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: -0.70 (0.17), residues: 2256 helix: 0.61 (0.18), residues: 720 sheet: -0.35 (0.23), residues: 432 loop : -1.21 (0.18), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP n 132 PHE 0.006 0.001 PHE b 106 TYR 0.025 0.001 TYR a 79 ARG 0.001 0.000 ARG m 36 Details of bonding type rmsd hydrogen bonds : bond 0.03822 ( 688) hydrogen bonds : angle 3.74644 ( 2016) SS BOND : bond 0.00272 ( 16) SS BOND : angle 0.29127 ( 32) covalent geometry : bond 0.00509 (16912) covalent geometry : angle 0.54626 (23056) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 328 time to evaluate : 2.692 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: 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: 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: h 55 GLU cc_start: 0.8592 (tm-30) cc_final: 0.8229 (tm-30) REVERT: h 64 SER cc_start: 0.9467 (OUTLIER) cc_final: 0.9255 (p) REVERT: i 50 LYS cc_start: 0.9607 (mtmp) cc_final: 0.9354 (mtpp) REVERT: i 55 GLU cc_start: 0.8508 (tm-30) cc_final: 0.8158 (tm-30) REVERT: i 68 ILE cc_start: 0.9023 (OUTLIER) cc_final: 0.8818 (pp) REVERT: i 77 GLU cc_start: 0.8444 (mp0) cc_final: 0.8224 (mp0) REVERT: i 141 MET cc_start: 0.9193 (ptp) cc_final: 0.8948 (ptp) REVERT: j 7 PHE cc_start: 0.9066 (OUTLIER) cc_final: 0.8227 (t80) REVERT: k 7 PHE cc_start: 0.9047 (OUTLIER) cc_final: 0.8053 (t80) REVERT: k 67 LYS cc_start: 0.9330 (mttt) cc_final: 0.9125 (mttp) REVERT: k 113 SER cc_start: 0.9281 (m) cc_final: 0.9057 (m) REVERT: l 7 PHE cc_start: 0.8981 (OUTLIER) cc_final: 0.7990 (t80) REVERT: m 7 PHE cc_start: 0.9016 (OUTLIER) cc_final: 0.8169 (t80) REVERT: m 38 GLU cc_start: 0.8778 (mt-10) cc_final: 0.8476 (mt-10) REVERT: m 55 GLU cc_start: 0.8681 (tm-30) cc_final: 0.8383 (tm-30) REVERT: m 103 ASP cc_start: 0.8806 (p0) cc_final: 0.8582 (p0) REVERT: n 7 PHE cc_start: 0.9023 (OUTLIER) cc_final: 0.8341 (t80) REVERT: n 135 LYS cc_start: 0.8716 (mtmm) cc_final: 0.8451 (mtmm) REVERT: o 7 PHE cc_start: 0.9139 (OUTLIER) cc_final: 0.8627 (t80) REVERT: p 7 PHE cc_start: 0.9151 (OUTLIER) cc_final: 0.8586 (t80) REVERT: p 11 GLU cc_start: 0.8662 (pt0) cc_final: 0.8461 (pt0) REVERT: d 11 GLU cc_start: 0.9165 (tt0) cc_final: 0.8785 (pt0) REVERT: d 29 GLN cc_start: 0.9310 (OUTLIER) cc_final: 0.8397 (tp40) REVERT: d 38 GLU cc_start: 0.8430 (mt-10) cc_final: 0.8227 (mt-10) REVERT: d 97 GLU cc_start: 0.8760 (tt0) cc_final: 0.8286 (tt0) REVERT: c 67 LYS cc_start: 0.9135 (mttm) cc_final: 0.8849 (mttp) REVERT: b 103 ASP cc_start: 0.9199 (p0) cc_final: 0.8955 (p0) REVERT: a 38 GLU cc_start: 0.8462 (mt-10) cc_final: 0.8137 (mt-10) REVERT: a 141 MET cc_start: 0.8037 (ptp) cc_final: 0.6745 (mmt) outliers start: 59 outliers final: 16 residues processed: 381 average time/residue: 0.5821 time to fit residues: 346.3447 Evaluate side-chains 341 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 315 time to evaluate : 2.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain f residue 98 ASP Chi-restraints excluded: chain g residue 57 LEU Chi-restraints excluded: chain h residue 64 SER Chi-restraints excluded: chain i residue 34 VAL Chi-restraints excluded: chain i residue 68 ILE Chi-restraints excluded: chain j residue 7 PHE Chi-restraints excluded: chain k residue 7 PHE Chi-restraints excluded: chain l residue 7 PHE Chi-restraints excluded: chain l residue 94 VAL Chi-restraints excluded: chain l residue 104 ILE Chi-restraints excluded: chain m residue 7 PHE Chi-restraints excluded: chain n residue 7 PHE Chi-restraints excluded: chain o residue 7 PHE Chi-restraints excluded: chain o residue 34 VAL Chi-restraints excluded: chain p residue 7 PHE Chi-restraints excluded: chain p residue 34 VAL Chi-restraints excluded: chain d residue 29 GLN Chi-restraints excluded: chain d residue 34 VAL Chi-restraints excluded: chain d residue 82 VAL Chi-restraints excluded: chain d residue 148 ASP Chi-restraints excluded: chain c residue 99 SER Chi-restraints excluded: chain b residue 22 LEU Chi-restraints excluded: chain b residue 34 VAL Chi-restraints excluded: chain a residue 22 LEU Chi-restraints excluded: chain a residue 34 VAL Chi-restraints excluded: chain a residue 82 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 20 optimal weight: 2.9990 chunk 161 optimal weight: 8.9990 chunk 81 optimal weight: 5.9990 chunk 91 optimal weight: 5.9990 chunk 143 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 chunk 110 optimal weight: 0.9990 chunk 96 optimal weight: 5.9990 chunk 83 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 128 optimal weight: 0.9980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 29 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.062489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.050057 restraints weight = 169963.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.052706 restraints weight = 62599.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.054381 restraints weight = 30621.870| |-----------------------------------------------------------------------------| r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8932 moved from start: 0.5550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 16928 Z= 0.121 Angle : 0.505 4.525 23088 Z= 0.262 Chirality : 0.044 0.153 2912 Planarity : 0.002 0.023 2928 Dihedral : 3.627 12.994 2384 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 1.99 % Allowed : 15.49 % Favored : 82.52 % 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: -0.26 (0.17), residues: 2256 helix: 1.25 (0.18), residues: 704 sheet: -0.17 (0.23), residues: 432 loop : -1.10 (0.18), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP k 132 PHE 0.004 0.000 PHE k 7 TYR 0.022 0.001 TYR n 79 ARG 0.002 0.000 ARG o 36 Details of bonding type rmsd hydrogen bonds : bond 0.03269 ( 688) hydrogen bonds : angle 3.49319 ( 2016) SS BOND : bond 0.00217 ( 16) SS BOND : angle 0.26126 ( 32) covalent geometry : bond 0.00270 (16912) covalent geometry : angle 0.50573 (23056) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 348 time to evaluate : 2.638 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: 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: 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: e 79 TYR cc_start: 0.8974 (m-80) cc_final: 0.8728 (m-80) REVERT: h 55 GLU cc_start: 0.8627 (tm-30) cc_final: 0.8243 (tm-30) REVERT: h 64 SER cc_start: 0.9413 (OUTLIER) cc_final: 0.9207 (p) REVERT: i 50 LYS cc_start: 0.9604 (mtmp) cc_final: 0.9341 (mtpp) REVERT: i 55 GLU cc_start: 0.8528 (tm-30) cc_final: 0.8145 (tm-30) REVERT: i 141 MET cc_start: 0.9171 (ptp) cc_final: 0.8967 (ptp) REVERT: j 7 PHE cc_start: 0.9079 (OUTLIER) cc_final: 0.8295 (t80) REVERT: k 7 PHE cc_start: 0.9035 (OUTLIER) cc_final: 0.8106 (t80) REVERT: k 65 LYS cc_start: 0.8868 (mttp) cc_final: 0.8644 (mttp) REVERT: k 67 LYS cc_start: 0.9313 (mttt) cc_final: 0.9113 (mttp) REVERT: k 113 SER cc_start: 0.9242 (m) cc_final: 0.9017 (m) REVERT: l 7 PHE cc_start: 0.8952 (OUTLIER) cc_final: 0.7870 (t80) REVERT: m 7 PHE cc_start: 0.9003 (OUTLIER) cc_final: 0.8090 (t80) REVERT: m 38 GLU cc_start: 0.8785 (mt-10) cc_final: 0.8336 (mp0) REVERT: m 55 GLU cc_start: 0.8726 (tm-30) cc_final: 0.8380 (tm-30) REVERT: n 7 PHE cc_start: 0.9026 (OUTLIER) cc_final: 0.8311 (t80) REVERT: o 7 PHE cc_start: 0.9147 (OUTLIER) cc_final: 0.8568 (t80) REVERT: p 7 PHE cc_start: 0.9088 (OUTLIER) cc_final: 0.8520 (t80) REVERT: p 11 GLU cc_start: 0.8545 (pt0) cc_final: 0.8318 (pt0) REVERT: d 29 GLN cc_start: 0.9170 (tt0) cc_final: 0.8468 (tp40) REVERT: d 97 GLU cc_start: 0.8732 (tt0) cc_final: 0.8240 (tt0) REVERT: d 109 GLN cc_start: 0.8648 (mm-40) cc_final: 0.8397 (mm110) REVERT: c 38 GLU cc_start: 0.8207 (mt-10) cc_final: 0.7994 (mt-10) REVERT: c 67 LYS cc_start: 0.9123 (mttm) cc_final: 0.8839 (mttp) REVERT: a 38 GLU cc_start: 0.8508 (mt-10) cc_final: 0.8160 (mt-10) REVERT: a 109 GLN cc_start: 0.8633 (mm-40) cc_final: 0.8430 (mm110) REVERT: a 141 MET cc_start: 0.8015 (ptp) cc_final: 0.6800 (mmt) outliers start: 36 outliers final: 15 residues processed: 380 average time/residue: 0.5827 time to fit residues: 344.0651 Evaluate side-chains 347 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 324 time to evaluate : 2.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 34 VAL Chi-restraints excluded: chain g residue 57 LEU Chi-restraints excluded: chain h residue 64 SER Chi-restraints excluded: chain i residue 34 VAL Chi-restraints excluded: chain j residue 7 PHE Chi-restraints excluded: chain j residue 94 VAL Chi-restraints excluded: chain k residue 7 PHE Chi-restraints excluded: chain l residue 7 PHE Chi-restraints excluded: chain l residue 104 ILE Chi-restraints excluded: chain m residue 7 PHE Chi-restraints excluded: chain n residue 7 PHE Chi-restraints excluded: chain o residue 7 PHE Chi-restraints excluded: chain o residue 57 LEU Chi-restraints excluded: chain p residue 7 PHE Chi-restraints excluded: chain p residue 34 VAL Chi-restraints excluded: chain p residue 94 VAL Chi-restraints excluded: chain d residue 34 VAL Chi-restraints excluded: chain d residue 148 ASP Chi-restraints excluded: chain c residue 99 SER Chi-restraints excluded: chain b residue 22 LEU Chi-restraints excluded: chain b residue 34 VAL Chi-restraints excluded: chain a residue 22 LEU Chi-restraints excluded: chain a residue 34 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 119 optimal weight: 7.9990 chunk 80 optimal weight: 6.9990 chunk 97 optimal weight: 6.9990 chunk 34 optimal weight: 0.0770 chunk 88 optimal weight: 4.9990 chunk 54 optimal weight: 0.9990 chunk 153 optimal weight: 6.9990 chunk 12 optimal weight: 0.6980 chunk 113 optimal weight: 0.8980 chunk 31 optimal weight: 7.9990 chunk 192 optimal weight: 7.9990 overall best weight: 1.5342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.063963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.052687 restraints weight = 170455.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.055369 restraints weight = 63832.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.057105 restraints weight = 31174.984| |-----------------------------------------------------------------------------| r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8907 moved from start: 0.5674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 16928 Z= 0.106 Angle : 0.499 5.522 23088 Z= 0.257 Chirality : 0.044 0.144 2912 Planarity : 0.002 0.021 2928 Dihedral : 3.538 11.835 2384 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 1.49 % Allowed : 16.26 % Favored : 82.25 % 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: 0.04 (0.17), residues: 2256 helix: 1.63 (0.18), residues: 704 sheet: 0.04 (0.23), residues: 432 loop : -1.04 (0.18), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP n 132 PHE 0.003 0.000 PHE k 7 TYR 0.013 0.001 TYR g 79 ARG 0.001 0.000 ARG n 36 Details of bonding type rmsd hydrogen bonds : bond 0.03090 ( 688) hydrogen bonds : angle 3.39005 ( 2016) SS BOND : bond 0.00205 ( 16) SS BOND : angle 0.28119 ( 32) covalent geometry : bond 0.00242 (16912) covalent geometry : angle 0.49967 (23056) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 338 time to evaluate : 2.989 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: 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: 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: h 55 GLU cc_start: 0.8638 (tm-30) cc_final: 0.8252 (tm-30) REVERT: i 50 LYS cc_start: 0.9601 (mtmp) cc_final: 0.9227 (mtpp) REVERT: i 55 GLU cc_start: 0.8520 (tm-30) cc_final: 0.8120 (tm-30) REVERT: j 7 PHE cc_start: 0.9120 (OUTLIER) cc_final: 0.8273 (t80) REVERT: k 7 PHE cc_start: 0.9079 (OUTLIER) cc_final: 0.8067 (t80) REVERT: k 65 LYS cc_start: 0.8897 (mttp) cc_final: 0.8629 (mttp) REVERT: k 67 LYS cc_start: 0.9313 (mttt) cc_final: 0.9108 (mttp) REVERT: k 113 SER cc_start: 0.9221 (m) cc_final: 0.8976 (m) REVERT: l 7 PHE cc_start: 0.8986 (OUTLIER) cc_final: 0.7907 (t80) REVERT: m 7 PHE cc_start: 0.9027 (OUTLIER) cc_final: 0.8148 (t80) REVERT: m 55 GLU cc_start: 0.8757 (tm-30) cc_final: 0.8400 (tm-30) REVERT: n 7 PHE cc_start: 0.9022 (OUTLIER) cc_final: 0.8294 (t80) REVERT: n 55 GLU cc_start: 0.8588 (tt0) cc_final: 0.8377 (tm-30) REVERT: o 7 PHE cc_start: 0.9173 (OUTLIER) cc_final: 0.8510 (t80) REVERT: p 7 PHE cc_start: 0.9067 (OUTLIER) cc_final: 0.8467 (t80) REVERT: p 11 GLU cc_start: 0.8563 (pt0) cc_final: 0.8299 (pt0) REVERT: d 29 GLN cc_start: 0.9135 (tt0) cc_final: 0.8426 (tp40) REVERT: d 97 GLU cc_start: 0.8714 (tt0) cc_final: 0.8224 (tt0) REVERT: d 109 GLN cc_start: 0.8645 (mm-40) cc_final: 0.8397 (mm110) REVERT: c 38 GLU cc_start: 0.8228 (mt-10) cc_final: 0.8016 (mt-10) REVERT: c 67 LYS cc_start: 0.9097 (mttm) cc_final: 0.8794 (mttp) REVERT: b 67 LYS cc_start: 0.9288 (mttt) cc_final: 0.9046 (mtmm) REVERT: a 38 GLU cc_start: 0.8545 (mt-10) cc_final: 0.8175 (mt-10) REVERT: a 141 MET cc_start: 0.7948 (ptp) cc_final: 0.6778 (mmt) outliers start: 27 outliers final: 14 residues processed: 360 average time/residue: 0.5992 time to fit residues: 337.0453 Evaluate side-chains 339 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 318 time to evaluate : 2.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain f residue 57 LEU Chi-restraints excluded: chain f residue 98 ASP Chi-restraints excluded: chain g residue 57 LEU Chi-restraints excluded: chain i residue 34 VAL Chi-restraints excluded: chain j residue 7 PHE Chi-restraints excluded: chain j residue 94 VAL Chi-restraints excluded: chain k residue 7 PHE Chi-restraints excluded: chain l residue 7 PHE Chi-restraints excluded: chain l residue 89 LEU Chi-restraints excluded: chain l residue 104 ILE Chi-restraints excluded: chain m residue 7 PHE Chi-restraints excluded: chain n residue 7 PHE Chi-restraints excluded: chain o residue 7 PHE Chi-restraints excluded: chain o residue 57 LEU Chi-restraints excluded: chain p residue 7 PHE Chi-restraints excluded: chain p residue 34 VAL Chi-restraints excluded: chain p residue 68 ILE Chi-restraints excluded: chain d residue 148 ASP Chi-restraints excluded: chain c residue 34 VAL Chi-restraints excluded: chain b residue 22 LEU Chi-restraints excluded: chain a residue 22 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 73 optimal weight: 5.9990 chunk 208 optimal weight: 3.9990 chunk 90 optimal weight: 0.6980 chunk 170 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 chunk 40 optimal weight: 0.8980 chunk 116 optimal weight: 3.9990 chunk 174 optimal weight: 2.9990 chunk 31 optimal weight: 7.9990 chunk 111 optimal weight: 0.4980 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: n 29 GLN c 29 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.061260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.051010 restraints weight = 167778.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.053566 restraints weight = 62204.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.055215 restraints weight = 30809.746| |-----------------------------------------------------------------------------| r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8937 moved from start: 0.5811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16928 Z= 0.115 Angle : 0.502 5.753 23088 Z= 0.259 Chirality : 0.044 0.140 2912 Planarity : 0.002 0.021 2928 Dihedral : 3.537 12.201 2384 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 1.94 % Allowed : 16.04 % Favored : 82.02 % 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: 0.29 (0.17), residues: 2256 helix: 1.93 (0.18), residues: 704 sheet: 0.19 (0.23), residues: 432 loop : -0.97 (0.18), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP o 132 PHE 0.005 0.000 PHE o 7 TYR 0.010 0.001 TYR g 79 ARG 0.002 0.000 ARG o 36 Details of bonding type rmsd hydrogen bonds : bond 0.03096 ( 688) hydrogen bonds : angle 3.38149 ( 2016) SS BOND : bond 0.00215 ( 16) SS BOND : angle 0.30121 ( 32) covalent geometry : bond 0.00262 (16912) covalent geometry : angle 0.50221 (23056) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 333 time to evaluate : 2.778 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: 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: 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: h 7 PHE cc_start: 0.9322 (OUTLIER) cc_final: 0.8427 (t80) REVERT: h 55 GLU cc_start: 0.8670 (tm-30) cc_final: 0.8311 (tm-30) REVERT: i 7 PHE cc_start: 0.9234 (OUTLIER) cc_final: 0.8009 (t80) REVERT: i 55 GLU cc_start: 0.8525 (tm-30) cc_final: 0.8153 (tm-30) REVERT: j 7 PHE cc_start: 0.9105 (OUTLIER) cc_final: 0.8302 (t80) REVERT: k 7 PHE cc_start: 0.9091 (OUTLIER) cc_final: 0.8136 (t80) REVERT: k 113 SER cc_start: 0.9230 (m) cc_final: 0.8992 (m) REVERT: l 7 PHE cc_start: 0.8979 (OUTLIER) cc_final: 0.7687 (t80) REVERT: l 11 GLU cc_start: 0.8637 (pt0) cc_final: 0.8433 (pt0) REVERT: m 7 PHE cc_start: 0.9050 (OUTLIER) cc_final: 0.8116 (t80) REVERT: m 55 GLU cc_start: 0.8709 (tm-30) cc_final: 0.8390 (tm-30) REVERT: m 103 ASP cc_start: 0.8802 (p0) cc_final: 0.8569 (p0) REVERT: n 7 PHE cc_start: 0.8981 (OUTLIER) cc_final: 0.8303 (t80) REVERT: o 7 PHE cc_start: 0.9119 (OUTLIER) cc_final: 0.8504 (t80) REVERT: p 7 PHE cc_start: 0.9059 (OUTLIER) cc_final: 0.8482 (t80) REVERT: p 11 GLU cc_start: 0.8506 (pt0) cc_final: 0.8243 (pt0) REVERT: d 29 GLN cc_start: 0.9078 (tt0) cc_final: 0.8354 (tp40) REVERT: d 97 GLU cc_start: 0.8697 (tt0) cc_final: 0.8236 (tt0) REVERT: d 109 GLN cc_start: 0.8617 (mm-40) cc_final: 0.8391 (mm110) REVERT: c 67 LYS cc_start: 0.9146 (mttm) cc_final: 0.8839 (mttp) REVERT: c 148 ASP cc_start: 0.8903 (p0) cc_final: 0.8656 (p0) REVERT: a 38 GLU cc_start: 0.8543 (mt-10) cc_final: 0.8164 (mt-10) REVERT: a 141 MET cc_start: 0.7948 (ptp) cc_final: 0.6858 (mmt) outliers start: 35 outliers final: 20 residues processed: 360 average time/residue: 0.6140 time to fit residues: 344.7899 Evaluate side-chains 348 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 319 time to evaluate : 2.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 34 VAL Chi-restraints excluded: chain f residue 22 LEU Chi-restraints excluded: chain f residue 57 LEU Chi-restraints excluded: chain f residue 98 ASP Chi-restraints excluded: chain g residue 57 LEU Chi-restraints excluded: chain h residue 7 PHE Chi-restraints excluded: chain i residue 7 PHE Chi-restraints excluded: chain i residue 34 VAL Chi-restraints excluded: chain j residue 7 PHE Chi-restraints excluded: chain j residue 94 VAL Chi-restraints excluded: chain k residue 7 PHE Chi-restraints excluded: chain l residue 7 PHE Chi-restraints excluded: chain l residue 104 ILE Chi-restraints excluded: chain m residue 7 PHE Chi-restraints excluded: chain n residue 7 PHE Chi-restraints excluded: chain o residue 7 PHE Chi-restraints excluded: chain o residue 34 VAL Chi-restraints excluded: chain o residue 57 LEU Chi-restraints excluded: chain p residue 7 PHE Chi-restraints excluded: chain p residue 34 VAL Chi-restraints excluded: chain p residue 43 LEU Chi-restraints excluded: chain p residue 94 VAL Chi-restraints excluded: chain d residue 34 VAL Chi-restraints excluded: chain d residue 148 ASP Chi-restraints excluded: chain c residue 68 ILE Chi-restraints excluded: chain c residue 99 SER Chi-restraints excluded: chain b residue 34 VAL Chi-restraints excluded: chain a residue 22 LEU Chi-restraints excluded: chain a residue 34 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 172 optimal weight: 0.4980 chunk 65 optimal weight: 6.9990 chunk 137 optimal weight: 8.9990 chunk 148 optimal weight: 4.9990 chunk 140 optimal weight: 3.9990 chunk 204 optimal weight: 7.9990 chunk 98 optimal weight: 5.9990 chunk 186 optimal weight: 4.9990 chunk 111 optimal weight: 6.9990 chunk 94 optimal weight: 5.9990 chunk 178 optimal weight: 0.8980 overall best weight: 3.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 29 GLN f 29 GLN g 29 GLN o 29 GLN d 29 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.059995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.049819 restraints weight = 168799.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.052358 restraints weight = 62371.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.053907 restraints weight = 30700.412| |-----------------------------------------------------------------------------| r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8981 moved from start: 0.6064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 16928 Z= 0.177 Angle : 0.533 5.993 23088 Z= 0.278 Chirality : 0.044 0.137 2912 Planarity : 0.002 0.026 2928 Dihedral : 3.731 13.878 2384 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 2.16 % Allowed : 16.26 % Favored : 81.58 % 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: 0.31 (0.17), residues: 2256 helix: 1.82 (0.18), residues: 720 sheet: 0.26 (0.23), residues: 432 loop : -0.93 (0.18), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP h 132 PHE 0.005 0.001 PHE b 106 TYR 0.013 0.001 TYR g 79 ARG 0.003 0.000 ARG n 59 Details of bonding type rmsd hydrogen bonds : bond 0.03484 ( 688) hydrogen bonds : angle 3.54914 ( 2016) SS BOND : bond 0.00254 ( 16) SS BOND : angle 0.34682 ( 32) covalent geometry : bond 0.00391 (16912) covalent geometry : angle 0.53349 (23056) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 314 time to evaluate : 2.954 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: 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: 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: e 29 GLN cc_start: 0.8806 (OUTLIER) cc_final: 0.8465 (tt0) REVERT: h 7 PHE cc_start: 0.9347 (OUTLIER) cc_final: 0.8492 (t80) REVERT: h 55 GLU cc_start: 0.8745 (tm-30) cc_final: 0.8357 (tm-30) REVERT: h 97 GLU cc_start: 0.8344 (tt0) cc_final: 0.8096 (tt0) REVERT: i 7 PHE cc_start: 0.9290 (OUTLIER) cc_final: 0.8159 (t80) REVERT: i 55 GLU cc_start: 0.8608 (tm-30) cc_final: 0.8248 (tm-30) REVERT: j 7 PHE cc_start: 0.9120 (OUTLIER) cc_final: 0.8337 (t80) REVERT: k 7 PHE cc_start: 0.9118 (OUTLIER) cc_final: 0.8176 (t80) REVERT: k 113 SER cc_start: 0.9314 (m) cc_final: 0.9091 (m) REVERT: l 7 PHE cc_start: 0.9033 (OUTLIER) cc_final: 0.7876 (t80) REVERT: l 67 LYS cc_start: 0.9197 (mttp) cc_final: 0.8685 (mmtp) REVERT: m 7 PHE cc_start: 0.9069 (OUTLIER) cc_final: 0.8192 (t80) REVERT: m 55 GLU cc_start: 0.8727 (tm-30) cc_final: 0.8380 (tm-30) REVERT: n 7 PHE cc_start: 0.9019 (OUTLIER) cc_final: 0.8372 (t80) REVERT: o 7 PHE cc_start: 0.9123 (OUTLIER) cc_final: 0.8560 (t80) REVERT: p 7 PHE cc_start: 0.9096 (OUTLIER) cc_final: 0.8561 (t80) REVERT: p 11 GLU cc_start: 0.8464 (pt0) cc_final: 0.8198 (pt0) REVERT: d 29 GLN cc_start: 0.8947 (OUTLIER) cc_final: 0.8245 (tp40) REVERT: d 97 GLU cc_start: 0.8740 (tt0) cc_final: 0.8279 (tt0) REVERT: d 109 GLN cc_start: 0.8618 (mm-40) cc_final: 0.8396 (mm110) REVERT: c 67 LYS cc_start: 0.9156 (mttm) cc_final: 0.8871 (mttp) REVERT: c 148 ASP cc_start: 0.8954 (p0) cc_final: 0.8713 (p0) REVERT: a 141 MET cc_start: 0.7948 (ptp) cc_final: 0.7109 (mmt) outliers start: 39 outliers final: 21 residues processed: 343 average time/residue: 0.5793 time to fit residues: 311.4345 Evaluate side-chains 340 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 308 time to evaluate : 2.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 29 GLN Chi-restraints excluded: chain e residue 34 VAL Chi-restraints excluded: chain f residue 22 LEU Chi-restraints excluded: chain f residue 29 GLN Chi-restraints excluded: chain f residue 57 LEU Chi-restraints excluded: chain f residue 98 ASP Chi-restraints excluded: chain g residue 57 LEU Chi-restraints excluded: chain h residue 7 PHE Chi-restraints excluded: chain i residue 7 PHE Chi-restraints excluded: chain i residue 34 VAL Chi-restraints excluded: chain j residue 7 PHE Chi-restraints excluded: chain j residue 94 VAL Chi-restraints excluded: chain k residue 7 PHE Chi-restraints excluded: chain l residue 7 PHE Chi-restraints excluded: chain l residue 104 ILE Chi-restraints excluded: chain m residue 7 PHE Chi-restraints excluded: chain n residue 7 PHE Chi-restraints excluded: chain o residue 7 PHE Chi-restraints excluded: chain o residue 34 VAL Chi-restraints excluded: chain o residue 57 LEU Chi-restraints excluded: chain p residue 7 PHE Chi-restraints excluded: chain p residue 34 VAL Chi-restraints excluded: chain p residue 43 LEU Chi-restraints excluded: chain d residue 29 GLN Chi-restraints excluded: chain d residue 34 VAL Chi-restraints excluded: chain d residue 79 TYR Chi-restraints excluded: chain d residue 148 ASP Chi-restraints excluded: chain c residue 34 VAL Chi-restraints excluded: chain c residue 68 ILE Chi-restraints excluded: chain c residue 99 SER Chi-restraints excluded: chain b residue 34 VAL Chi-restraints excluded: chain a residue 34 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 206 optimal weight: 7.9990 chunk 86 optimal weight: 4.9990 chunk 90 optimal weight: 0.9990 chunk 118 optimal weight: 7.9990 chunk 106 optimal weight: 0.8980 chunk 53 optimal weight: 4.9990 chunk 149 optimal weight: 0.9980 chunk 217 optimal weight: 6.9990 chunk 36 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 184 optimal weight: 1.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.061855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.051850 restraints weight = 168059.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.054424 restraints weight = 60835.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.055968 restraints weight = 29601.776| |-----------------------------------------------------------------------------| r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8961 moved from start: 0.6100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16928 Z= 0.115 Angle : 0.525 6.306 23088 Z= 0.269 Chirality : 0.044 0.142 2912 Planarity : 0.002 0.020 2928 Dihedral : 3.672 12.898 2384 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 1.55 % Allowed : 17.37 % Favored : 81.08 % 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: 0.49 (0.17), residues: 2256 helix: 2.02 (0.18), residues: 720 sheet: 0.41 (0.23), residues: 432 loop : -0.88 (0.18), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP h 132 PHE 0.003 0.000 PHE b 106 TYR 0.011 0.001 TYR g 79 ARG 0.002 0.000 ARG n 59 Details of bonding type rmsd hydrogen bonds : bond 0.03236 ( 688) hydrogen bonds : angle 3.44401 ( 2016) SS BOND : bond 0.00218 ( 16) SS BOND : angle 0.29220 ( 32) covalent geometry : bond 0.00263 (16912) covalent geometry : angle 0.52496 (23056) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 318 time to evaluate : 2.720 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: 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: 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: g 7 PHE cc_start: 0.9304 (OUTLIER) cc_final: 0.8783 (t80) REVERT: h 7 PHE cc_start: 0.9334 (OUTLIER) cc_final: 0.8489 (t80) REVERT: h 55 GLU cc_start: 0.8753 (tm-30) cc_final: 0.8364 (tm-30) REVERT: h 97 GLU cc_start: 0.8343 (tt0) cc_final: 0.8078 (tt0) REVERT: i 7 PHE cc_start: 0.9279 (OUTLIER) cc_final: 0.8055 (t80) REVERT: i 55 GLU cc_start: 0.8608 (tm-30) cc_final: 0.8239 (tm-30) REVERT: j 7 PHE cc_start: 0.9120 (OUTLIER) cc_final: 0.8345 (t80) REVERT: k 7 PHE cc_start: 0.9108 (OUTLIER) cc_final: 0.8091 (t80) REVERT: k 113 SER cc_start: 0.9294 (m) cc_final: 0.9061 (m) REVERT: l 7 PHE cc_start: 0.9013 (OUTLIER) cc_final: 0.7770 (t80) REVERT: l 55 GLU cc_start: 0.8828 (tm-30) cc_final: 0.8562 (tm-30) REVERT: m 7 PHE cc_start: 0.9057 (OUTLIER) cc_final: 0.8193 (t80) REVERT: m 55 GLU cc_start: 0.8732 (tm-30) cc_final: 0.8395 (tm-30) REVERT: m 57 LEU cc_start: 0.9105 (OUTLIER) cc_final: 0.8856 (mm) REVERT: n 7 PHE cc_start: 0.8995 (OUTLIER) cc_final: 0.8372 (t80) REVERT: o 7 PHE cc_start: 0.9123 (OUTLIER) cc_final: 0.8556 (t80) REVERT: o 57 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.9012 (mm) REVERT: p 7 PHE cc_start: 0.9095 (OUTLIER) cc_final: 0.8574 (t80) REVERT: p 11 GLU cc_start: 0.8442 (pt0) cc_final: 0.8166 (pt0) REVERT: p 50 LYS cc_start: 0.9763 (mtmt) cc_final: 0.9497 (mtpp) REVERT: d 29 GLN cc_start: 0.9185 (tt0) cc_final: 0.8393 (tp40) REVERT: d 97 GLU cc_start: 0.8719 (tt0) cc_final: 0.8277 (tt0) REVERT: d 109 GLN cc_start: 0.8602 (mm-40) cc_final: 0.8383 (mm110) REVERT: c 67 LYS cc_start: 0.9138 (mttm) cc_final: 0.8863 (mttp) REVERT: c 148 ASP cc_start: 0.8978 (p0) cc_final: 0.8722 (p0) REVERT: a 141 MET cc_start: 0.8005 (ptp) cc_final: 0.7076 (mmt) outliers start: 28 outliers final: 16 residues processed: 343 average time/residue: 0.5870 time to fit residues: 315.1496 Evaluate side-chains 341 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 313 time to evaluate : 2.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 34 VAL Chi-restraints excluded: chain f residue 57 LEU Chi-restraints excluded: chain f residue 98 ASP Chi-restraints excluded: chain g residue 7 PHE Chi-restraints excluded: chain g residue 57 LEU Chi-restraints excluded: chain h residue 7 PHE Chi-restraints excluded: chain i residue 7 PHE Chi-restraints excluded: chain j residue 7 PHE Chi-restraints excluded: chain j residue 94 VAL Chi-restraints excluded: chain k residue 7 PHE Chi-restraints excluded: chain l residue 7 PHE Chi-restraints excluded: chain l residue 89 LEU Chi-restraints excluded: chain l residue 104 ILE Chi-restraints excluded: chain m residue 7 PHE Chi-restraints excluded: chain m residue 57 LEU Chi-restraints excluded: chain n residue 7 PHE Chi-restraints excluded: chain o residue 7 PHE Chi-restraints excluded: chain o residue 34 VAL Chi-restraints excluded: chain o residue 57 LEU Chi-restraints excluded: chain p residue 7 PHE Chi-restraints excluded: chain p residue 34 VAL Chi-restraints excluded: chain p residue 43 LEU Chi-restraints excluded: chain d residue 34 VAL Chi-restraints excluded: chain c residue 34 VAL Chi-restraints excluded: chain c residue 68 ILE Chi-restraints excluded: chain c residue 99 SER Chi-restraints excluded: chain b residue 34 VAL Chi-restraints excluded: chain a residue 34 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 74 optimal weight: 0.5980 chunk 108 optimal weight: 5.9990 chunk 126 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 183 optimal weight: 1.9990 chunk 95 optimal weight: 7.9990 chunk 105 optimal weight: 6.9990 chunk 79 optimal weight: 0.9980 chunk 124 optimal weight: 6.9990 chunk 121 optimal weight: 0.8980 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.061921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.052008 restraints weight = 167516.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.054553 restraints weight = 61305.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.056069 restraints weight = 30009.654| |-----------------------------------------------------------------------------| r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8964 moved from start: 0.6172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 16928 Z= 0.121 Angle : 0.527 6.596 23088 Z= 0.270 Chirality : 0.044 0.141 2912 Planarity : 0.002 0.021 2928 Dihedral : 3.633 13.031 2384 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 1.55 % Allowed : 17.31 % Favored : 81.14 % 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: 0.58 (0.17), residues: 2256 helix: 2.14 (0.18), residues: 720 sheet: 0.50 (0.23), residues: 432 loop : -0.88 (0.18), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP h 132 PHE 0.004 0.000 PHE b 106 TYR 0.011 0.001 TYR g 79 ARG 0.001 0.000 ARG n 59 Details of bonding type rmsd hydrogen bonds : bond 0.03192 ( 688) hydrogen bonds : angle 3.46408 ( 2016) SS BOND : bond 0.00223 ( 16) SS BOND : angle 0.31789 ( 32) covalent geometry : bond 0.00278 (16912) covalent geometry : angle 0.52685 (23056) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 324 time to evaluate : 2.786 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: 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: 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: g 7 PHE cc_start: 0.9295 (OUTLIER) cc_final: 0.8804 (t80) REVERT: h 7 PHE cc_start: 0.9336 (OUTLIER) cc_final: 0.8512 (t80) REVERT: h 55 GLU cc_start: 0.8754 (tm-30) cc_final: 0.8376 (tm-30) REVERT: h 97 GLU cc_start: 0.8335 (tt0) cc_final: 0.8076 (tt0) REVERT: i 7 PHE cc_start: 0.9289 (OUTLIER) cc_final: 0.8133 (t80) REVERT: i 55 GLU cc_start: 0.8617 (tm-30) cc_final: 0.8240 (tm-30) REVERT: j 7 PHE cc_start: 0.9118 (OUTLIER) cc_final: 0.8347 (t80) REVERT: k 7 PHE cc_start: 0.9125 (OUTLIER) cc_final: 0.8182 (t80) REVERT: k 113 SER cc_start: 0.9274 (m) cc_final: 0.9039 (m) REVERT: l 7 PHE cc_start: 0.9009 (OUTLIER) cc_final: 0.7858 (t80) REVERT: l 55 GLU cc_start: 0.8787 (tm-30) cc_final: 0.8526 (tm-30) REVERT: m 7 PHE cc_start: 0.9056 (OUTLIER) cc_final: 0.8127 (t80) REVERT: m 55 GLU cc_start: 0.8734 (tm-30) cc_final: 0.8398 (tm-30) REVERT: m 57 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8873 (mm) REVERT: n 7 PHE cc_start: 0.9029 (OUTLIER) cc_final: 0.8383 (t80) REVERT: o 7 PHE cc_start: 0.9105 (OUTLIER) cc_final: 0.8471 (t80) REVERT: o 57 LEU cc_start: 0.9262 (OUTLIER) cc_final: 0.9058 (mm) REVERT: p 7 PHE cc_start: 0.9093 (OUTLIER) cc_final: 0.8552 (t80) REVERT: p 11 GLU cc_start: 0.8431 (pt0) cc_final: 0.8156 (pt0) REVERT: d 29 GLN cc_start: 0.9175 (tt0) cc_final: 0.8385 (tp40) REVERT: d 97 GLU cc_start: 0.8707 (tt0) cc_final: 0.8257 (tt0) REVERT: d 109 GLN cc_start: 0.8557 (mm-40) cc_final: 0.8354 (mm110) REVERT: c 67 LYS cc_start: 0.9146 (mttm) cc_final: 0.8873 (mttp) REVERT: c 148 ASP cc_start: 0.8960 (p0) cc_final: 0.8718 (p0) REVERT: a 141 MET cc_start: 0.7957 (ptp) cc_final: 0.7075 (mmt) outliers start: 28 outliers final: 16 residues processed: 348 average time/residue: 0.6038 time to fit residues: 330.5963 Evaluate side-chains 342 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 314 time to evaluate : 2.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 34 VAL Chi-restraints excluded: chain f residue 22 LEU Chi-restraints excluded: chain f residue 57 LEU Chi-restraints excluded: chain f residue 98 ASP Chi-restraints excluded: chain g residue 7 PHE Chi-restraints excluded: chain g residue 57 LEU Chi-restraints excluded: chain h residue 7 PHE Chi-restraints excluded: chain i residue 7 PHE Chi-restraints excluded: chain j residue 7 PHE Chi-restraints excluded: chain j residue 94 VAL Chi-restraints excluded: chain k residue 7 PHE Chi-restraints excluded: chain l residue 7 PHE Chi-restraints excluded: chain l residue 89 LEU Chi-restraints excluded: chain l residue 104 ILE Chi-restraints excluded: chain m residue 7 PHE Chi-restraints excluded: chain m residue 57 LEU Chi-restraints excluded: chain n residue 7 PHE Chi-restraints excluded: chain o residue 7 PHE Chi-restraints excluded: chain o residue 34 VAL Chi-restraints excluded: chain o residue 57 LEU Chi-restraints excluded: chain p residue 7 PHE Chi-restraints excluded: chain p residue 34 VAL Chi-restraints excluded: chain p residue 43 LEU Chi-restraints excluded: chain d residue 34 VAL Chi-restraints excluded: chain c residue 68 ILE Chi-restraints excluded: chain c residue 99 SER Chi-restraints excluded: chain b residue 34 VAL Chi-restraints excluded: chain a residue 34 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 79 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 87 optimal weight: 7.9990 chunk 146 optimal weight: 5.9990 chunk 182 optimal weight: 0.1980 chunk 192 optimal weight: 3.9990 chunk 152 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 134 optimal weight: 6.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.062532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.052583 restraints weight = 167799.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.055174 restraints weight = 61240.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.056787 restraints weight = 29727.818| |-----------------------------------------------------------------------------| r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8951 moved from start: 0.6230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 16928 Z= 0.103 Angle : 0.521 6.790 23088 Z= 0.264 Chirality : 0.044 0.140 2912 Planarity : 0.002 0.021 2928 Dihedral : 3.575 12.827 2384 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 1.49 % Allowed : 17.81 % Favored : 80.70 % 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: 0.73 (0.17), residues: 2256 helix: 2.33 (0.18), residues: 720 sheet: 0.63 (0.23), residues: 432 loop : -0.86 (0.18), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP h 132 PHE 0.003 0.000 PHE b 106 TYR 0.010 0.001 TYR g 79 ARG 0.001 0.000 ARG m 36 Details of bonding type rmsd hydrogen bonds : bond 0.03044 ( 688) hydrogen bonds : angle 3.39081 ( 2016) SS BOND : bond 0.00207 ( 16) SS BOND : angle 0.30528 ( 32) covalent geometry : bond 0.00240 (16912) covalent geometry : angle 0.52097 (23056) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10403.89 seconds wall clock time: 181 minutes 17.86 seconds (10877.86 seconds total)