Starting phenix.real_space_refine on Tue Aug 26 03:00:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tum_41625/08_2025/8tum_41625.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tum_41625/08_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_41625/08_2025/8tum_41625.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tum_41625/08_2025/8tum_41625.map" model { file = "/net/cci-nas-00/data/ceres_data/8tum_41625/08_2025/8tum_41625.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tum_41625/08_2025/8tum_41625.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 5.72, per 1000 atoms: 0.17 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: 2.40 Conformation dependent library (CDL) restraints added in 743.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.69 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: 7.07 Time building geometry restraints manager: 3.37 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: 0.08 Found NCS groups: ncs_group { reference = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'd' selection = chain 'c' selection = chain 'b' selection = chain 'a' } 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: 4.200 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: 0.160 Extract box with map and model: 0.340 Check model and map are aligned: 0.090 Set scattering table: 0.050 Process input model: 26.810 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.540 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.001 0.000 ARG a 126 TYR 0.001 0.000 TYR c 30 PHE 0.002 0.000 PHE i 142 TRP 0.001 0.000 TRP h 132 Details of bonding type rmsd covalent geometry : bond 0.00153 (16912) covalent geometry : angle 0.40034 (23056) SS BOND : bond 0.00044 ( 16) SS BOND : angle 0.16005 ( 32) hydrogen bonds : bond 0.11508 ( 688) hydrogen bonds : angle 2.84269 ( 2016) *********************** 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 : 0.854 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 outliers start: 16 outliers final: 0 residues processed: 728 average time/residue: 0.2885 time to fit residues: 306.5883 Evaluate side-chains 382 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 382 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 216 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 4.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.1980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 6.9990 chunk 200 optimal weight: 4.9990 chunk 212 optimal weight: 2.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 31 GLN g 31 GLN h 31 GLN i 29 GLN i 31 GLN o 87 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.068439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.056547 restraints weight = 165236.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.059457 restraints weight = 62912.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.061380 restraints weight = 31135.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.062564 restraints weight = 18069.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.063263 restraints weight = 11881.323| |-----------------------------------------------------------------------------| r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.4131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16928 Z= 0.147 Angle : 0.540 4.674 23088 Z= 0.279 Chirality : 0.044 0.149 2912 Planarity : 0.002 0.020 2928 Dihedral : 3.329 18.119 2384 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 0.72 % Allowed : 16.87 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.75 (0.16), residues: 2256 helix: 0.48 (0.19), residues: 688 sheet: -1.26 (0.20), residues: 432 loop : -2.22 (0.16), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG a 126 TYR 0.015 0.001 TYR j 79 PHE 0.004 0.000 PHE a 7 TRP 0.007 0.001 TRP n 132 Details of bonding type rmsd covalent geometry : bond 0.00331 (16912) covalent geometry : angle 0.53979 (23056) SS BOND : bond 0.00102 ( 16) SS BOND : angle 0.28844 ( 32) hydrogen bonds : bond 0.03509 ( 688) hydrogen bonds : angle 3.29722 ( 2016) *********************** 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 416 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 403 time to evaluate : 0.692 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: symmetry clash revert: symmetry clash REVERT: h 97 GLU cc_start: 0.8480 (tt0) cc_final: 0.8246 (tt0) REVERT: i 38 GLU cc_start: 0.8503 (mt-10) cc_final: 0.8289 (mt-10) REVERT: i 77 GLU cc_start: 0.8437 (mp0) cc_final: 0.8188 (mp0) REVERT: k 67 LYS cc_start: 0.9348 (mttt) cc_final: 0.9086 (mttp) REVERT: n 67 LYS cc_start: 0.9247 (mttt) cc_final: 0.9011 (mttm) REVERT: n 87 ASN cc_start: 0.8508 (t0) cc_final: 0.8036 (t0) REVERT: c 67 LYS cc_start: 0.9064 (mttm) cc_final: 0.8789 (mttp) REVERT: c 83 GLU cc_start: 0.8468 (mp0) cc_final: 0.8264 (mm-30) REVERT: a 141 MET cc_start: 0.7602 (ptp) cc_final: 0.6242 (mmt) outliers start: 13 outliers final: 9 residues processed: 411 average time/residue: 0.2317 time to fit residues: 150.2574 Evaluate side-chains 373 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 364 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain g residue 47 ASN Chi-restraints excluded: chain g residue 57 LEU Chi-restraints excluded: chain h residue 98 ASP Chi-restraints excluded: chain l residue 104 ILE Chi-restraints excluded: chain n residue 114 SER Chi-restraints excluded: chain d residue 57 LEU Chi-restraints excluded: chain b residue 22 LEU Chi-restraints excluded: chain a residue 22 LEU Chi-restraints excluded: chain a residue 82 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 220 optimal weight: 2.9990 chunk 130 optimal weight: 5.9990 chunk 56 optimal weight: 5.9990 chunk 202 optimal weight: 3.9990 chunk 147 optimal weight: 10.0000 chunk 57 optimal weight: 0.9990 chunk 87 optimal weight: 6.9990 chunk 112 optimal weight: 3.9990 chunk 205 optimal weight: 4.9990 chunk 38 optimal weight: 7.9990 chunk 103 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: j 31 GLN m 31 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.063618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.051082 restraints weight = 169464.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.053791 restraints weight = 62792.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.055543 restraints weight = 30822.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.056607 restraints weight = 18276.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.057251 restraints weight = 12376.966| |-----------------------------------------------------------------------------| r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8860 moved from start: 0.4824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16928 Z= 0.193 Angle : 0.524 4.653 23088 Z= 0.277 Chirality : 0.044 0.136 2912 Planarity : 0.002 0.022 2928 Dihedral : 3.359 12.639 2384 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 0.77 % Allowed : 16.32 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.05 (0.17), residues: 2256 helix: 0.76 (0.18), residues: 688 sheet: -0.53 (0.23), residues: 432 loop : -1.72 (0.17), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG k 36 TYR 0.018 0.001 TYR j 79 PHE 0.010 0.001 PHE p 7 TRP 0.004 0.001 TRP n 132 Details of bonding type rmsd covalent geometry : bond 0.00422 (16912) covalent geometry : angle 0.52417 (23056) SS BOND : bond 0.00217 ( 16) SS BOND : angle 0.29917 ( 32) hydrogen bonds : bond 0.03560 ( 688) hydrogen bonds : angle 3.54217 ( 2016) *********************** 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 363 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 349 time to evaluate : 0.828 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 47 ASN cc_start: 0.9411 (OUTLIER) cc_final: 0.9171 (t0) REVERT: i 77 GLU cc_start: 0.8443 (mp0) cc_final: 0.8157 (mp0) REVERT: k 67 LYS cc_start: 0.9359 (mttt) cc_final: 0.9122 (mttp) REVERT: m 103 ASP cc_start: 0.8797 (p0) cc_final: 0.8550 (p0) REVERT: n 67 LYS cc_start: 0.9255 (mttt) cc_final: 0.8990 (mttm) REVERT: o 38 GLU cc_start: 0.8848 (mt-10) cc_final: 0.8643 (mt-10) REVERT: o 57 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8844 (mm) REVERT: o 129 ASP cc_start: 0.8007 (p0) cc_final: 0.7797 (p0) REVERT: d 97 GLU cc_start: 0.8681 (tt0) cc_final: 0.8179 (tt0) REVERT: d 109 GLN cc_start: 0.8674 (mm-40) cc_final: 0.8473 (mm110) REVERT: c 38 GLU cc_start: 0.8240 (mt-10) cc_final: 0.7995 (mt-10) REVERT: c 67 LYS cc_start: 0.9081 (mttm) cc_final: 0.8794 (mttp) REVERT: a 77 GLU cc_start: 0.8531 (mp0) cc_final: 0.8252 (mp0) REVERT: a 141 MET cc_start: 0.7847 (ptp) cc_final: 0.6444 (mmt) outliers start: 14 outliers final: 9 residues processed: 358 average time/residue: 0.2396 time to fit residues: 135.0074 Evaluate side-chains 333 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 322 time to evaluate : 0.849 ------------------------------------------------------------------------------- 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 n residue 114 SER Chi-restraints excluded: chain o residue 57 LEU 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 128 optimal weight: 0.0970 chunk 107 optimal weight: 0.9990 chunk 193 optimal weight: 5.9990 chunk 42 optimal weight: 0.9980 chunk 67 optimal weight: 4.9990 chunk 168 optimal weight: 7.9990 chunk 51 optimal weight: 8.9990 chunk 223 optimal weight: 6.9990 chunk 201 optimal weight: 8.9990 chunk 50 optimal weight: 4.9990 chunk 64 optimal weight: 5.9990 overall best weight: 2.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 29 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.063219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.050699 restraints weight = 168573.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.053405 restraints weight = 62365.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.055097 restraints weight = 30416.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.056146 restraints weight = 18283.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.056813 restraints weight = 12394.638| |-----------------------------------------------------------------------------| r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8882 moved from start: 0.5096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16928 Z= 0.139 Angle : 0.499 4.296 23088 Z= 0.259 Chirality : 0.044 0.139 2912 Planarity : 0.002 0.024 2928 Dihedral : 3.413 11.743 2384 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.38 % Allowed : 15.38 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.60 (0.17), residues: 2256 helix: 1.00 (0.18), residues: 704 sheet: -0.29 (0.23), residues: 432 loop : -1.37 (0.18), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG m 36 TYR 0.015 0.001 TYR j 79 PHE 0.005 0.001 PHE m 7 TRP 0.003 0.001 TRP n 132 Details of bonding type rmsd covalent geometry : bond 0.00309 (16912) covalent geometry : angle 0.49955 (23056) SS BOND : bond 0.00207 ( 16) SS BOND : angle 0.26205 ( 32) hydrogen bonds : bond 0.03267 ( 688) hydrogen bonds : angle 3.46893 ( 2016) *********************** 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 389 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 346 time to evaluate : 0.886 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: f 97 GLU cc_start: 0.7752 (mp0) cc_final: 0.7542 (mp0) REVERT: i 50 LYS cc_start: 0.9582 (mtmp) cc_final: 0.9338 (mtpp) REVERT: i 77 GLU cc_start: 0.8405 (mp0) cc_final: 0.8148 (mp0) REVERT: i 141 MET cc_start: 0.9200 (ptp) cc_final: 0.8976 (ptp) REVERT: j 7 PHE cc_start: 0.9028 (OUTLIER) cc_final: 0.8247 (t80) REVERT: j 55 GLU cc_start: 0.8380 (tm-30) cc_final: 0.8157 (tm-30) REVERT: k 7 PHE cc_start: 0.8975 (OUTLIER) cc_final: 0.7969 (t80) REVERT: k 65 LYS cc_start: 0.8821 (mttp) cc_final: 0.8562 (mttp) REVERT: k 67 LYS cc_start: 0.9344 (mttt) cc_final: 0.9127 (mttp) REVERT: l 7 PHE cc_start: 0.8915 (OUTLIER) cc_final: 0.7847 (t80) REVERT: l 77 GLU cc_start: 0.8393 (mp0) cc_final: 0.8000 (mp0) REVERT: m 7 PHE cc_start: 0.8926 (OUTLIER) cc_final: 0.8086 (t80) REVERT: m 103 ASP cc_start: 0.8800 (p0) cc_final: 0.8557 (p0) REVERT: n 7 PHE cc_start: 0.8976 (OUTLIER) cc_final: 0.8259 (t80) REVERT: n 135 LYS cc_start: 0.8659 (mtmm) cc_final: 0.8412 (mtmm) REVERT: o 7 PHE cc_start: 0.9074 (OUTLIER) cc_final: 0.8426 (t80) REVERT: o 38 GLU cc_start: 0.8860 (mt-10) cc_final: 0.8659 (mt-10) REVERT: p 7 PHE cc_start: 0.9102 (OUTLIER) cc_final: 0.8483 (t80) REVERT: d 11 GLU cc_start: 0.9100 (tt0) cc_final: 0.8605 (pt0) REVERT: d 97 GLU cc_start: 0.8708 (tt0) cc_final: 0.8218 (tt0) REVERT: c 67 LYS cc_start: 0.9108 (mttm) cc_final: 0.8797 (mttp) REVERT: a 77 GLU cc_start: 0.8535 (mp0) cc_final: 0.8250 (mp0) REVERT: a 141 MET cc_start: 0.8096 (ptp) cc_final: 0.6646 (mmt) outliers start: 43 outliers final: 9 residues processed: 386 average time/residue: 0.2536 time to fit residues: 154.6242 Evaluate side-chains 346 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 330 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain g residue 57 LEU 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 104 ILE Chi-restraints excluded: chain m residue 7 PHE Chi-restraints excluded: chain n residue 7 PHE Chi-restraints excluded: chain n residue 114 SER Chi-restraints excluded: chain o residue 7 PHE Chi-restraints excluded: chain p residue 7 PHE Chi-restraints excluded: chain p 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 a residue 22 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 96 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 180 optimal weight: 0.7980 chunk 132 optimal weight: 3.9990 chunk 130 optimal weight: 4.9990 chunk 211 optimal weight: 10.0000 chunk 53 optimal weight: 6.9990 chunk 19 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 88 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 = 0.3179 r_free = 0.3179 target = 0.064024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.052695 restraints weight = 170732.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.055401 restraints weight = 63549.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.057144 restraints weight = 30801.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.058222 restraints weight = 17979.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.058872 restraints weight = 11951.316| |-----------------------------------------------------------------------------| r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8892 moved from start: 0.5385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 16928 Z= 0.121 Angle : 0.503 6.528 23088 Z= 0.260 Chirality : 0.044 0.141 2912 Planarity : 0.002 0.024 2928 Dihedral : 3.448 15.473 2384 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 1.83 % Allowed : 15.93 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.22 (0.17), residues: 2256 helix: 1.40 (0.18), residues: 704 sheet: -0.14 (0.23), residues: 432 loop : -1.17 (0.18), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG o 36 TYR 0.021 0.001 TYR d 79 PHE 0.004 0.001 PHE l 7 TRP 0.002 0.000 TRP n 132 Details of bonding type rmsd covalent geometry : bond 0.00270 (16912) covalent geometry : angle 0.50360 (23056) SS BOND : bond 0.00214 ( 16) SS BOND : angle 0.29034 ( 32) hydrogen bonds : bond 0.03134 ( 688) hydrogen bonds : angle 3.40150 ( 2016) *********************** 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 382 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 349 time to evaluate : 0.957 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: f 97 GLU cc_start: 0.7883 (mp0) cc_final: 0.7612 (mp0) REVERT: i 38 GLU cc_start: 0.8453 (mt-10) cc_final: 0.8244 (mt-10) REVERT: i 50 LYS cc_start: 0.9583 (mtmp) cc_final: 0.9317 (mtpp) REVERT: i 77 GLU cc_start: 0.8369 (mp0) cc_final: 0.8158 (mp0) REVERT: j 7 PHE cc_start: 0.9052 (OUTLIER) cc_final: 0.8226 (t80) REVERT: j 55 GLU cc_start: 0.8426 (tm-30) cc_final: 0.8201 (tm-30) REVERT: k 7 PHE cc_start: 0.8987 (OUTLIER) cc_final: 0.8083 (t80) REVERT: k 65 LYS cc_start: 0.8856 (mttp) cc_final: 0.8622 (mtmm) REVERT: l 7 PHE cc_start: 0.8900 (OUTLIER) cc_final: 0.7841 (t80) REVERT: m 7 PHE cc_start: 0.8951 (OUTLIER) cc_final: 0.8122 (t80) REVERT: m 38 GLU cc_start: 0.8802 (mt-10) cc_final: 0.8444 (mt-10) REVERT: m 103 ASP cc_start: 0.8795 (p0) cc_final: 0.8558 (p0) REVERT: n 7 PHE cc_start: 0.8993 (OUTLIER) cc_final: 0.8317 (t80) REVERT: o 7 PHE cc_start: 0.9040 (OUTLIER) cc_final: 0.8444 (t80) REVERT: o 38 GLU cc_start: 0.8859 (mt-10) cc_final: 0.8652 (mt-10) REVERT: p 7 PHE cc_start: 0.9047 (OUTLIER) cc_final: 0.8427 (t80) REVERT: d 11 GLU cc_start: 0.9108 (tt0) cc_final: 0.8576 (pt0) REVERT: d 97 GLU cc_start: 0.8685 (tt0) cc_final: 0.8211 (tt0) REVERT: d 109 GLN cc_start: 0.8619 (mm-40) cc_final: 0.8396 (mm110) REVERT: c 67 LYS cc_start: 0.9117 (mttm) cc_final: 0.8822 (mttp) REVERT: a 77 GLU cc_start: 0.8521 (mp0) cc_final: 0.8221 (mp0) REVERT: a 109 GLN cc_start: 0.8598 (mm-40) cc_final: 0.8395 (mm110) REVERT: a 141 MET cc_start: 0.7950 (ptp) cc_final: 0.6593 (mmt) outliers start: 33 outliers final: 16 residues processed: 377 average time/residue: 0.2596 time to fit residues: 154.3325 Evaluate side-chains 355 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 332 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain f residue 98 ASP Chi-restraints excluded: chain g residue 57 LEU Chi-restraints excluded: chain g residue 94 VAL Chi-restraints excluded: chain i residue 34 VAL 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 104 ILE Chi-restraints excluded: chain m residue 7 PHE Chi-restraints excluded: chain n residue 7 PHE Chi-restraints excluded: chain n residue 114 SER 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 46 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 120 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 113 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 185 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 195 optimal weight: 5.9990 chunk 172 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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 = 0.3189 r_free = 0.3189 target = 0.062062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.051857 restraints weight = 164957.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.054433 restraints weight = 61190.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.056075 restraints weight = 29779.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.057022 restraints weight = 17408.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.057608 restraints weight = 11965.464| |-----------------------------------------------------------------------------| r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8917 moved from start: 0.5658 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= 0.151 Angle : 0.511 5.450 23088 Z= 0.266 Chirality : 0.044 0.141 2912 Planarity : 0.002 0.021 2928 Dihedral : 3.559 16.121 2384 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 1.94 % Allowed : 15.98 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.01 (0.17), residues: 2256 helix: 1.59 (0.18), residues: 704 sheet: 0.02 (0.23), residues: 432 loop : -1.04 (0.18), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG n 59 TYR 0.014 0.001 TYR d 79 PHE 0.004 0.001 PHE b 106 TRP 0.004 0.000 TRP p 132 Details of bonding type rmsd covalent geometry : bond 0.00332 (16912) covalent geometry : angle 0.51110 (23056) SS BOND : bond 0.00225 ( 16) SS BOND : angle 0.29308 ( 32) hydrogen bonds : bond 0.03285 ( 688) hydrogen bonds : angle 3.46687 ( 2016) *********************** 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 366 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 331 time to evaluate : 0.744 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: f 97 GLU cc_start: 0.8024 (mp0) cc_final: 0.7718 (mp0) REVERT: i 50 LYS cc_start: 0.9603 (mtmp) cc_final: 0.9332 (mtpp) REVERT: j 7 PHE cc_start: 0.9083 (OUTLIER) cc_final: 0.8226 (t80) REVERT: j 55 GLU cc_start: 0.8517 (tm-30) cc_final: 0.8259 (tm-30) REVERT: k 7 PHE cc_start: 0.9022 (OUTLIER) cc_final: 0.8014 (t80) REVERT: k 113 SER cc_start: 0.9232 (m) cc_final: 0.8989 (m) REVERT: l 7 PHE cc_start: 0.8970 (OUTLIER) cc_final: 0.7871 (t80) REVERT: m 7 PHE cc_start: 0.9006 (OUTLIER) cc_final: 0.8089 (t80) REVERT: m 103 ASP cc_start: 0.8793 (p0) cc_final: 0.8590 (p0) REVERT: n 7 PHE cc_start: 0.9022 (OUTLIER) cc_final: 0.8303 (t80) REVERT: o 7 PHE cc_start: 0.9111 (OUTLIER) cc_final: 0.8535 (t80) REVERT: o 38 GLU cc_start: 0.8858 (mt-10) cc_final: 0.8637 (mt-10) REVERT: p 7 PHE cc_start: 0.9077 (OUTLIER) cc_final: 0.8466 (t80) REVERT: d 97 GLU cc_start: 0.8699 (tt0) cc_final: 0.8236 (tt0) REVERT: d 109 GLN cc_start: 0.8623 (mm-40) cc_final: 0.8392 (mm110) REVERT: c 67 LYS cc_start: 0.9129 (mttm) cc_final: 0.8824 (mttp) REVERT: a 77 GLU cc_start: 0.8533 (mp0) cc_final: 0.8229 (mp0) REVERT: a 141 MET cc_start: 0.7955 (ptp) cc_final: 0.6791 (mmt) outliers start: 35 outliers final: 19 residues processed: 358 average time/residue: 0.2575 time to fit residues: 145.7356 Evaluate side-chains 343 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 317 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain f residue 22 LEU Chi-restraints excluded: chain f residue 98 ASP Chi-restraints excluded: chain g residue 57 LEU 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 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 n residue 114 SER 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 68 ILE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 165 optimal weight: 8.9990 chunk 221 optimal weight: 4.9990 chunk 211 optimal weight: 0.9990 chunk 68 optimal weight: 4.9990 chunk 183 optimal weight: 0.6980 chunk 64 optimal weight: 6.9990 chunk 149 optimal weight: 0.9980 chunk 104 optimal weight: 0.2980 chunk 124 optimal weight: 2.9990 chunk 118 optimal weight: 5.9990 chunk 105 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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 = 0.3229 r_free = 0.3229 target = 0.065053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.054318 restraints weight = 164178.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.057046 restraints weight = 60335.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.058800 restraints weight = 28960.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.059831 restraints weight = 16698.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.060435 restraints weight = 11124.047| |-----------------------------------------------------------------------------| r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8879 moved from start: 0.5693 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= 0.087 Angle : 0.496 6.072 23088 Z= 0.253 Chirality : 0.044 0.144 2912 Planarity : 0.002 0.022 2928 Dihedral : 3.409 15.168 2384 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 1.55 % Allowed : 16.76 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.35 (0.17), residues: 2256 helix: 2.04 (0.19), residues: 704 sheet: 0.21 (0.23), residues: 432 loop : -0.96 (0.18), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG p 36 TYR 0.011 0.001 TYR d 79 PHE 0.003 0.000 PHE m 7 TRP 0.003 0.001 TRP p 132 Details of bonding type rmsd covalent geometry : bond 0.00204 (16912) covalent geometry : angle 0.49662 (23056) SS BOND : bond 0.00174 ( 16) SS BOND : angle 0.28009 ( 32) hydrogen bonds : bond 0.02872 ( 688) hydrogen bonds : angle 3.25156 ( 2016) *********************** 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 381 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 353 time to evaluate : 0.976 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: f 97 GLU cc_start: 0.8062 (mp0) cc_final: 0.7731 (mp0) REVERT: h 50 LYS cc_start: 0.9580 (mtmp) cc_final: 0.9324 (mtpp) REVERT: h 97 GLU cc_start: 0.8359 (tt0) cc_final: 0.8075 (tt0) REVERT: i 38 GLU cc_start: 0.8500 (mt-10) cc_final: 0.8286 (mt-10) REVERT: i 50 LYS cc_start: 0.9588 (mtmp) cc_final: 0.9194 (mtpp) REVERT: j 7 PHE cc_start: 0.9061 (OUTLIER) cc_final: 0.8214 (t80) REVERT: j 55 GLU cc_start: 0.8522 (tm-30) cc_final: 0.8214 (tm-30) REVERT: k 7 PHE cc_start: 0.9040 (OUTLIER) cc_final: 0.7987 (t80) REVERT: k 113 SER cc_start: 0.9134 (m) cc_final: 0.8859 (m) REVERT: l 7 PHE cc_start: 0.8944 (OUTLIER) cc_final: 0.7596 (t80) REVERT: l 11 GLU cc_start: 0.8633 (pt0) cc_final: 0.8431 (pt0) REVERT: m 7 PHE cc_start: 0.9004 (OUTLIER) cc_final: 0.7994 (t80) REVERT: m 103 ASP cc_start: 0.8798 (p0) cc_final: 0.8568 (p0) REVERT: n 7 PHE cc_start: 0.9006 (OUTLIER) cc_final: 0.8280 (t80) REVERT: o 7 PHE cc_start: 0.9092 (OUTLIER) cc_final: 0.8428 (t80) REVERT: p 7 PHE cc_start: 0.9046 (OUTLIER) cc_final: 0.8354 (t80) REVERT: d 97 GLU cc_start: 0.8653 (tt0) cc_final: 0.8184 (tt0) REVERT: d 109 GLN cc_start: 0.8605 (mm-40) cc_final: 0.8384 (mm110) REVERT: c 67 LYS cc_start: 0.9107 (mttm) cc_final: 0.8785 (mttp) REVERT: a 77 GLU cc_start: 0.8504 (mp0) cc_final: 0.8219 (mp0) REVERT: a 141 MET cc_start: 0.7854 (ptp) cc_final: 0.6697 (mmt) outliers start: 28 outliers final: 17 residues processed: 373 average time/residue: 0.2535 time to fit residues: 148.8225 Evaluate side-chains 358 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 334 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain f residue 9 LEU Chi-restraints excluded: chain f residue 22 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 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 43 LEU Chi-restraints excluded: chain p residue 68 ILE 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 b residue 34 VAL Chi-restraints excluded: chain b residue 98 ASP 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 101 optimal weight: 6.9990 chunk 133 optimal weight: 8.9990 chunk 183 optimal weight: 0.9980 chunk 168 optimal weight: 6.9990 chunk 93 optimal weight: 0.0070 chunk 192 optimal weight: 7.9990 chunk 45 optimal weight: 7.9990 chunk 57 optimal weight: 4.9990 chunk 206 optimal weight: 7.9990 chunk 161 optimal weight: 0.5980 chunk 9 optimal weight: 8.9990 overall best weight: 2.7202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 29 GLN n 29 GLN c 29 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.061827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.051776 restraints weight = 165338.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.054297 restraints weight = 61585.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.055844 restraints weight = 30091.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.056807 restraints weight = 17922.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.057367 restraints weight = 12244.995| |-----------------------------------------------------------------------------| r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8931 moved from start: 0.5930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16928 Z= 0.155 Angle : 0.522 5.884 23088 Z= 0.270 Chirality : 0.044 0.141 2912 Planarity : 0.002 0.021 2928 Dihedral : 3.560 14.619 2384 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 1.83 % Allowed : 17.20 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.45 (0.17), residues: 2256 helix: 1.94 (0.19), residues: 720 sheet: 0.36 (0.23), residues: 432 loop : -0.85 (0.18), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG p 36 TYR 0.017 0.001 TYR a 79 PHE 0.004 0.001 PHE b 106 TRP 0.002 0.000 TRP g 132 Details of bonding type rmsd covalent geometry : bond 0.00347 (16912) covalent geometry : angle 0.52242 (23056) SS BOND : bond 0.00231 ( 16) SS BOND : angle 0.32866 ( 32) hydrogen bonds : bond 0.03315 ( 688) hydrogen bonds : angle 3.45029 ( 2016) *********************** 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 354 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 321 time to evaluate : 0.729 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: e 79 TYR cc_start: 0.9067 (m-80) cc_final: 0.8724 (m-80) REVERT: h 97 GLU cc_start: 0.8364 (tt0) cc_final: 0.8102 (tt0) REVERT: j 7 PHE cc_start: 0.9120 (OUTLIER) cc_final: 0.8318 (t80) REVERT: j 55 GLU cc_start: 0.8594 (tm-30) cc_final: 0.8287 (tm-30) REVERT: k 7 PHE cc_start: 0.9084 (OUTLIER) cc_final: 0.8073 (t80) REVERT: k 113 SER cc_start: 0.9216 (m) cc_final: 0.8982 (m) REVERT: l 7 PHE cc_start: 0.9001 (OUTLIER) cc_final: 0.7763 (t80) REVERT: m 7 PHE cc_start: 0.9033 (OUTLIER) cc_final: 0.8101 (t80) REVERT: m 103 ASP cc_start: 0.8821 (p0) cc_final: 0.8591 (p0) REVERT: n 7 PHE cc_start: 0.9029 (OUTLIER) cc_final: 0.8335 (t80) REVERT: o 7 PHE cc_start: 0.9112 (OUTLIER) cc_final: 0.8504 (t80) REVERT: p 7 PHE cc_start: 0.9071 (OUTLIER) cc_final: 0.8477 (t80) REVERT: d 97 GLU cc_start: 0.8692 (tt0) cc_final: 0.8239 (tt0) REVERT: d 109 GLN cc_start: 0.8631 (mm-40) cc_final: 0.8407 (mm110) REVERT: d 135 LYS cc_start: 0.8646 (mmmm) cc_final: 0.8443 (mmmm) REVERT: c 67 LYS cc_start: 0.9151 (mttm) cc_final: 0.8870 (mttp) REVERT: c 148 ASP cc_start: 0.8898 (p0) cc_final: 0.8680 (p0) REVERT: a 38 GLU cc_start: 0.8625 (mt-10) cc_final: 0.8317 (mt-10) REVERT: a 77 GLU cc_start: 0.8517 (mp0) cc_final: 0.8234 (mp0) REVERT: a 141 MET cc_start: 0.7877 (ptp) cc_final: 0.6830 (mmt) outliers start: 33 outliers final: 18 residues processed: 345 average time/residue: 0.2276 time to fit residues: 124.1992 Evaluate side-chains 338 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 313 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 34 VAL Chi-restraints excluded: chain f residue 9 LEU Chi-restraints excluded: chain f residue 29 GLN Chi-restraints excluded: chain f residue 98 ASP Chi-restraints excluded: chain g residue 57 LEU 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 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 68 ILE 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 34 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 84 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 136 optimal weight: 5.9990 chunk 117 optimal weight: 4.9990 chunk 156 optimal weight: 0.5980 chunk 62 optimal weight: 0.9990 chunk 195 optimal weight: 5.9990 chunk 96 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 chunk 167 optimal weight: 0.6980 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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 = 0.3154 r_free = 0.3154 target = 0.061914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.051227 restraints weight = 167408.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.053889 restraints weight = 62851.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.055606 restraints weight = 31307.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.056603 restraints weight = 18365.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.057164 restraints weight = 12558.634| |-----------------------------------------------------------------------------| r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8916 moved from start: 0.5958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 16928 Z= 0.091 Angle : 0.516 6.336 23088 Z= 0.261 Chirality : 0.044 0.143 2912 Planarity : 0.002 0.021 2928 Dihedral : 3.451 14.774 2384 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 1.33 % Allowed : 17.59 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.67 (0.17), residues: 2256 helix: 2.35 (0.18), residues: 704 sheet: 0.54 (0.23), residues: 432 loop : -0.87 (0.18), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG p 36 TYR 0.016 0.001 TYR f 30 PHE 0.003 0.000 PHE e 106 TRP 0.006 0.001 TRP h 132 Details of bonding type rmsd covalent geometry : bond 0.00214 (16912) covalent geometry : angle 0.51673 (23056) SS BOND : bond 0.00184 ( 16) SS BOND : angle 0.27377 ( 32) hydrogen bonds : bond 0.02985 ( 688) hydrogen bonds : angle 3.27630 ( 2016) *********************** 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 361 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 337 time to evaluate : 0.859 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: f 97 GLU cc_start: 0.7865 (mp0) cc_final: 0.7641 (mp0) REVERT: h 97 GLU cc_start: 0.8289 (tt0) cc_final: 0.8021 (tt0) REVERT: i 83 GLU cc_start: 0.8153 (mp0) cc_final: 0.7896 (mp0) REVERT: j 7 PHE cc_start: 0.9079 (OUTLIER) cc_final: 0.8295 (t80) REVERT: j 55 GLU cc_start: 0.8581 (tm-30) cc_final: 0.8251 (tm-30) REVERT: k 7 PHE cc_start: 0.9070 (OUTLIER) cc_final: 0.8035 (t80) REVERT: k 113 SER cc_start: 0.9162 (m) cc_final: 0.8918 (m) REVERT: l 7 PHE cc_start: 0.8967 (OUTLIER) cc_final: 0.7778 (t80) REVERT: m 7 PHE cc_start: 0.9006 (OUTLIER) cc_final: 0.8079 (t80) REVERT: m 57 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8889 (mm) REVERT: m 103 ASP cc_start: 0.8771 (p0) cc_final: 0.8559 (p0) REVERT: n 7 PHE cc_start: 0.8995 (OUTLIER) cc_final: 0.8285 (t80) REVERT: o 7 PHE cc_start: 0.9067 (OUTLIER) cc_final: 0.8468 (t80) REVERT: p 7 PHE cc_start: 0.9007 (OUTLIER) cc_final: 0.8330 (t80) REVERT: d 97 GLU cc_start: 0.8626 (tt0) cc_final: 0.8183 (tt0) REVERT: d 135 LYS cc_start: 0.8661 (mmmm) cc_final: 0.8458 (mmmm) REVERT: c 67 LYS cc_start: 0.9145 (mttm) cc_final: 0.8863 (mttp) REVERT: c 148 ASP cc_start: 0.8873 (p0) cc_final: 0.8626 (p0) REVERT: a 141 MET cc_start: 0.7814 (ptp) cc_final: 0.6812 (mmt) outliers start: 24 outliers final: 15 residues processed: 356 average time/residue: 0.2406 time to fit residues: 135.5874 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 : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain f residue 9 LEU Chi-restraints excluded: chain f residue 98 ASP Chi-restraints excluded: chain g residue 57 LEU 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 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 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 68 ILE 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 34 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 12 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 213 optimal weight: 10.0000 chunk 200 optimal weight: 2.9990 chunk 158 optimal weight: 0.9990 chunk 117 optimal weight: 4.9990 chunk 125 optimal weight: 4.9990 chunk 145 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 chunk 178 optimal weight: 4.9990 chunk 19 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: o 29 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.061196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.050610 restraints weight = 170060.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.053137 restraints weight = 64527.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.054784 restraints weight = 31937.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.055771 restraints weight = 18853.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.056319 restraints weight = 12859.750| |-----------------------------------------------------------------------------| r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8961 moved from start: 0.6153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 16928 Z= 0.175 Angle : 0.544 6.405 23088 Z= 0.282 Chirality : 0.044 0.138 2912 Planarity : 0.002 0.020 2928 Dihedral : 3.663 14.038 2384 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 1.60 % Allowed : 17.48 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.62 (0.17), residues: 2256 helix: 2.13 (0.18), residues: 720 sheet: 0.59 (0.23), residues: 432 loop : -0.85 (0.18), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG o 36 TYR 0.021 0.001 TYR a 79 PHE 0.005 0.001 PHE b 106 TRP 0.004 0.001 TRP g 132 Details of bonding type rmsd covalent geometry : bond 0.00387 (16912) covalent geometry : angle 0.54459 (23056) SS BOND : bond 0.00241 ( 16) SS BOND : angle 0.33554 ( 32) hydrogen bonds : bond 0.03496 ( 688) hydrogen bonds : angle 3.52297 ( 2016) ********************** 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 339 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 310 time to evaluate : 0.975 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: e 29 GLN cc_start: 0.8789 (tt0) cc_final: 0.8350 (tt0) REVERT: g 83 GLU cc_start: 0.8087 (mp0) cc_final: 0.7878 (mp0) REVERT: h 7 PHE cc_start: 0.9338 (OUTLIER) cc_final: 0.8495 (t80) REVERT: h 97 GLU cc_start: 0.8332 (tt0) cc_final: 0.8091 (tt0) REVERT: i 7 PHE cc_start: 0.9276 (OUTLIER) cc_final: 0.8131 (t80) REVERT: i 83 GLU cc_start: 0.8136 (mp0) cc_final: 0.7890 (mp0) REVERT: j 7 PHE cc_start: 0.9117 (OUTLIER) cc_final: 0.8347 (t80) REVERT: j 55 GLU cc_start: 0.8657 (tm-30) cc_final: 0.8338 (tm-30) REVERT: k 7 PHE cc_start: 0.9087 (OUTLIER) cc_final: 0.8147 (t80) REVERT: k 113 SER cc_start: 0.9275 (m) cc_final: 0.9051 (m) REVERT: l 7 PHE cc_start: 0.9004 (OUTLIER) cc_final: 0.7870 (t80) REVERT: m 7 PHE cc_start: 0.9022 (OUTLIER) cc_final: 0.8152 (t80) REVERT: m 57 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8914 (mm) REVERT: n 7 PHE cc_start: 0.9014 (OUTLIER) cc_final: 0.8380 (t80) REVERT: o 7 PHE cc_start: 0.9102 (OUTLIER) cc_final: 0.8531 (t80) REVERT: o 57 LEU cc_start: 0.9257 (OUTLIER) cc_final: 0.9047 (mm) REVERT: p 7 PHE cc_start: 0.9066 (OUTLIER) cc_final: 0.8500 (t80) REVERT: d 97 GLU cc_start: 0.8687 (tt0) cc_final: 0.8244 (tt0) REVERT: d 135 LYS cc_start: 0.8707 (mmmm) cc_final: 0.8489 (mmmm) REVERT: c 67 LYS cc_start: 0.9157 (mttm) cc_final: 0.8887 (mttp) REVERT: c 148 ASP cc_start: 0.8938 (p0) cc_final: 0.8708 (p0) REVERT: a 38 GLU cc_start: 0.8583 (mt-10) cc_final: 0.8334 (mt-10) REVERT: a 141 MET cc_start: 0.7946 (ptp) cc_final: 0.6971 (mmt) outliers start: 29 outliers final: 13 residues processed: 335 average time/residue: 0.2773 time to fit residues: 147.2586 Evaluate side-chains 328 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 304 time to evaluate : 1.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 34 VAL 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 k residue 7 PHE Chi-restraints excluded: chain l residue 7 PHE 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 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 34 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 198 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 69 optimal weight: 0.9990 chunk 31 optimal weight: 7.9990 chunk 50 optimal weight: 5.9990 chunk 210 optimal weight: 0.8980 chunk 215 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 138 optimal weight: 5.9990 chunk 118 optimal weight: 4.9990 chunk 88 optimal weight: 0.3980 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** i 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.063163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.053098 restraints weight = 166844.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.055715 restraints weight = 61098.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.057332 restraints weight = 29890.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.058253 restraints weight = 17426.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.058774 restraints weight = 12071.463| |-----------------------------------------------------------------------------| r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8938 moved from start: 0.6198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16928 Z= 0.112 Angle : 0.528 6.712 23088 Z= 0.268 Chirality : 0.044 0.143 2912 Planarity : 0.002 0.021 2928 Dihedral : 3.577 15.364 2384 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 1.16 % Allowed : 18.20 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.75 (0.17), residues: 2256 helix: 2.31 (0.18), residues: 720 sheet: 0.66 (0.23), residues: 432 loop : -0.84 (0.18), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG o 36 TYR 0.014 0.001 TYR a 79 PHE 0.003 0.000 PHE b 106 TRP 0.004 0.000 TRP h 132 Details of bonding type rmsd covalent geometry : bond 0.00256 (16912) covalent geometry : angle 0.52804 (23056) SS BOND : bond 0.00213 ( 16) SS BOND : angle 0.32180 ( 32) hydrogen bonds : bond 0.03129 ( 688) hydrogen bonds : angle 3.37742 ( 2016) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4718.56 seconds wall clock time: 81 minutes 28.39 seconds (4888.39 seconds total)