Starting phenix.real_space_refine on Fri May 30 00:13:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tum_41625/05_2025/8tum_41625.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tum_41625/05_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_41625/05_2025/8tum_41625.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tum_41625/05_2025/8tum_41625.map" model { file = "/net/cci-nas-00/data/ceres_data/8tum_41625/05_2025/8tum_41625.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tum_41625/05_2025/8tum_41625.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.007 sd= 0.042 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 64 5.16 5 C 10512 2.51 5 N 2736 2.21 5 O 3376 1.98 5 H 17040 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 33728 Number of models: 1 Model: "" Number of chains: 16 Chain: "e" Number of atoms: 2108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2108 Classifications: {'peptide': 143} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 136} Chain: "f" Number of atoms: 2108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2108 Classifications: {'peptide': 143} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 136} Chain: "g" Number of atoms: 2108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2108 Classifications: {'peptide': 143} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 136} Chain: "h" Number of atoms: 2108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2108 Classifications: {'peptide': 143} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 136} Chain: "i" Number of atoms: 2108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2108 Classifications: {'peptide': 143} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 136} Chain: "j" Number of atoms: 2108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2108 Classifications: {'peptide': 143} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 136} Chain: "k" Number of atoms: 2108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2108 Classifications: {'peptide': 143} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 136} Chain: "l" Number of atoms: 2108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2108 Classifications: {'peptide': 143} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 136} Chain: "m" Number of atoms: 2108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2108 Classifications: {'peptide': 143} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 136} Chain: "n" Number of atoms: 2108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2108 Classifications: {'peptide': 143} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 136} Chain: "o" Number of atoms: 2108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2108 Classifications: {'peptide': 143} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 136} Chain: "p" Number of atoms: 2108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2108 Classifications: {'peptide': 143} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 136} Chain: "d" Number of atoms: 2108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2108 Classifications: {'peptide': 143} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 136} Chain: "c" Number of atoms: 2108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2108 Classifications: {'peptide': 143} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 136} Chain: "b" Number of atoms: 2108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2108 Classifications: {'peptide': 143} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 136} Chain: "a" Number of atoms: 2108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2108 Classifications: {'peptide': 143} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 136} Time building chain proxies: 16.42, per 1000 atoms: 0.49 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: 9.27 Conformation dependent library (CDL) restraints added in 2.9 seconds 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4192 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 32 sheets defined 32.2% alpha, 17.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.04 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: 11.97 Time building geometry restraints manager: 10.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 17040 1.03 - 1.23: 0 1.23 - 1.42: 6480 1.42 - 1.61: 10336 1.61 - 1.81: 96 Bond restraints: 33952 Sorted by residual: bond pdb=" CA ALA d 23 " pdb=" C ALA d 23 " ideal model delta sigma weight residual 1.531 1.523 0.008 1.12e-02 7.97e+03 5.59e-01 bond pdb=" CA ALA g 23 " pdb=" C ALA g 23 " ideal model delta sigma weight residual 1.531 1.523 0.008 1.12e-02 7.97e+03 5.43e-01 bond pdb=" CA ALA j 23 " pdb=" C ALA j 23 " ideal model delta sigma weight residual 1.531 1.523 0.008 1.12e-02 7.97e+03 5.18e-01 bond pdb=" CA ALA e 23 " pdb=" C ALA e 23 " ideal model delta sigma weight residual 1.531 1.523 0.008 1.12e-02 7.97e+03 5.16e-01 bond pdb=" CA ALA h 23 " pdb=" C ALA h 23 " ideal model delta sigma weight residual 1.531 1.523 0.008 1.12e-02 7.97e+03 5.15e-01 ... (remaining 33947 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.75: 54645 0.75 - 1.50: 6476 1.50 - 2.25: 479 2.25 - 3.00: 48 3.00 - 3.75: 80 Bond angle restraints: 61728 Sorted by residual: angle pdb=" C ILE k 46 " pdb=" CA ILE k 46 " pdb=" CB ILE k 46 " ideal model delta sigma weight residual 111.88 109.27 2.61 1.37e+00 5.33e-01 3.64e+00 angle pdb=" C ILE n 46 " pdb=" CA ILE n 46 " pdb=" CB ILE n 46 " ideal model delta sigma weight residual 111.88 109.29 2.59 1.37e+00 5.33e-01 3.58e+00 angle pdb=" C ILE f 46 " pdb=" CA ILE f 46 " pdb=" CB ILE f 46 " ideal model delta sigma weight residual 111.88 109.29 2.59 1.37e+00 5.33e-01 3.57e+00 angle pdb=" C ILE p 46 " pdb=" CA ILE p 46 " pdb=" CB ILE p 46 " ideal model delta sigma weight residual 111.88 109.30 2.58 1.37e+00 5.33e-01 3.56e+00 angle pdb=" C ILE c 46 " pdb=" CA ILE c 46 " pdb=" CB ILE c 46 " ideal model delta sigma weight residual 111.88 109.30 2.58 1.37e+00 5.33e-01 3.55e+00 ... (remaining 61723 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.41: 14442 17.41 - 34.82: 910 34.82 - 52.23: 408 52.23 - 69.64: 144 69.64 - 87.05: 112 Dihedral angle restraints: 16016 sinusoidal: 8896 harmonic: 7120 Sorted by residual: dihedral pdb=" CB CYS a 134 " pdb=" SG CYS a 134 " pdb=" SG CYS a 147 " pdb=" CB CYS a 147 " ideal model delta sinusoidal sigma weight residual -86.00 -121.83 35.83 1 1.00e+01 1.00e-02 1.82e+01 dihedral pdb=" CB CYS k 134 " pdb=" SG CYS k 134 " pdb=" SG CYS k 147 " pdb=" CB CYS k 147 " ideal model delta sinusoidal sigma weight residual -86.00 -121.82 35.82 1 1.00e+01 1.00e-02 1.82e+01 dihedral pdb=" CB CYS g 134 " pdb=" SG CYS g 134 " pdb=" SG CYS g 147 " pdb=" CB CYS g 147 " ideal model delta sinusoidal sigma weight residual -86.00 -121.81 35.81 1 1.00e+01 1.00e-02 1.81e+01 ... (remaining 16013 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1950 0.026 - 0.053: 478 0.053 - 0.079: 156 0.079 - 0.106: 192 0.106 - 0.132: 136 Chirality restraints: 2912 Sorted by residual: chirality pdb=" CA ILE n 122 " pdb=" N ILE n 122 " pdb=" C ILE n 122 " pdb=" CB ILE n 122 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.36e-01 chirality pdb=" CA ILE e 122 " pdb=" N ILE e 122 " pdb=" C ILE e 122 " pdb=" CB ILE e 122 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.29e-01 chirality pdb=" CA ILE c 122 " pdb=" N ILE c 122 " pdb=" C ILE c 122 " pdb=" CB ILE c 122 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.24e-01 ... (remaining 2909 not shown) Planarity restraints: 5104 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER g 114 " -0.006 5.00e-02 4.00e+02 9.23e-03 1.36e-01 pdb=" N PRO g 115 " 0.016 5.00e-02 4.00e+02 pdb=" CA PRO g 115 " -0.005 5.00e-02 4.00e+02 pdb=" CD PRO g 115 " -0.005 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER l 114 " 0.006 5.00e-02 4.00e+02 9.22e-03 1.36e-01 pdb=" N PRO l 115 " -0.016 5.00e-02 4.00e+02 pdb=" CA PRO l 115 " 0.005 5.00e-02 4.00e+02 pdb=" CD PRO l 115 " 0.005 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER c 114 " -0.006 5.00e-02 4.00e+02 9.19e-03 1.35e-01 pdb=" N PRO c 115 " 0.016 5.00e-02 4.00e+02 pdb=" CA PRO c 115 " -0.005 5.00e-02 4.00e+02 pdb=" CD PRO c 115 " -0.005 5.00e-02 4.00e+02 ... (remaining 5101 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.31: 8332 2.31 - 2.88: 78332 2.88 - 3.46: 79227 3.46 - 4.03: 109860 4.03 - 4.60: 172181 Nonbonded interactions: 447932 Sorted by model distance: nonbonded pdb=" OE1 GLU g 77 " pdb=" HH TYR g 79 " model vdw 1.741 2.450 nonbonded pdb=" OE1 GLU k 77 " pdb=" HH TYR k 79 " model vdw 1.741 2.450 nonbonded pdb=" OE1 GLU o 77 " pdb=" HH TYR o 79 " model vdw 1.741 2.450 nonbonded pdb=" OE1 GLU a 77 " pdb=" HH TYR a 79 " model vdw 1.741 2.450 nonbonded pdb=" O GLY k 63 " pdb=" HG SER k 64 " model vdw 1.741 2.450 ... (remaining 447927 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.18 Found NCS groups: ncs_group { reference = chain 'a' selection = chain 'c' selection = chain 'b' selection = chain 'e' selection = chain 'd' selection = chain 'g' selection = chain 'f' selection = chain 'i' selection = chain 'h' selection = chain 'k' selection = chain 'j' selection = chain 'm' selection = chain 'l' selection = chain 'o' selection = chain 'n' selection = chain 'p' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.660 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: 0.590 Extract box with map and model: 1.360 Check model and map are aligned: 0.230 Set scattering table: 0.330 Process input model: 69.030 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.150 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6922 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.012 16928 Z= 0.082 Angle : 0.400 3.753 23088 Z= 0.218 Chirality : 0.042 0.132 2912 Planarity : 0.001 0.009 2928 Dihedral : 14.115 87.053 6016 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.06 % Favored : 87.94 % Rotamer: Outliers : 0.88 % Allowed : 8.85 % Favored : 90.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.30 (0.14), residues: 2256 helix: -0.92 (0.16), residues: 704 sheet: -2.21 (0.16), residues: 400 loop : -3.08 (0.16), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP h 132 PHE 0.002 0.000 PHE i 142 TYR 0.001 0.000 TYR c 30 ARG 0.001 0.000 ARG a 126 Details of bonding type rmsd hydrogen bonds : bond 0.11508 ( 688) hydrogen bonds : angle 2.84269 ( 2016) SS BOND : bond 0.00044 ( 16) SS BOND : angle 0.16005 ( 32) covalent geometry : bond 0.00153 (16912) covalent geometry : angle 0.40034 (23056) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 743 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 727 time to evaluate : 2.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 0 residues processed: 728 average time/residue: 0.7072 time to fit residues: 750.9557 Evaluate side-chains 385 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 385 time to evaluate : 2.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 189 optimal weight: 0.9980 chunk 169 optimal weight: 4.9990 chunk 94 optimal weight: 7.9990 chunk 57 optimal weight: 4.9990 chunk 114 optimal weight: 4.9990 chunk 90 optimal weight: 0.0970 chunk 175 optimal weight: 5.9990 chunk 67 optimal weight: 5.9990 chunk 106 optimal weight: 5.9990 chunk 130 optimal weight: 3.9990 chunk 203 optimal weight: 1.9990 overall best weight: 2.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 31 GLN g 29 GLN g 31 GLN h 31 GLN i 29 GLN i 31 GLN ** d 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.068476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.056715 restraints weight = 165150.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.059623 restraints weight = 62902.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.061505 restraints weight = 31255.052| |-----------------------------------------------------------------------------| r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.4085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16928 Z= 0.148 Angle : 0.535 4.370 23088 Z= 0.277 Chirality : 0.044 0.144 2912 Planarity : 0.002 0.020 2928 Dihedral : 3.274 17.087 2384 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 0.77 % Allowed : 17.15 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.16), residues: 2256 helix: 0.47 (0.19), residues: 688 sheet: -1.27 (0.20), residues: 432 loop : -2.23 (0.16), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP n 132 PHE 0.003 0.000 PHE n 106 TYR 0.018 0.001 TYR g 79 ARG 0.002 0.000 ARG a 126 Details of bonding type rmsd hydrogen bonds : bond 0.03500 ( 688) hydrogen bonds : angle 3.26837 ( 2016) SS BOND : bond 0.00086 ( 16) SS BOND : angle 0.28106 ( 32) covalent geometry : bond 0.00333 (16912) covalent geometry : angle 0.53529 (23056) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 404 time to evaluate : 2.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: h 55 GLU cc_start: 0.8071 (tm-30) cc_final: 0.7581 (tm-30) REVERT: h 97 GLU cc_start: 0.8463 (tt0) cc_final: 0.8236 (tt0) REVERT: i 38 GLU cc_start: 0.8439 (mt-10) cc_final: 0.8217 (mt-10) REVERT: i 77 GLU cc_start: 0.8422 (mp0) cc_final: 0.8184 (mp0) REVERT: k 67 LYS cc_start: 0.9349 (mttt) cc_final: 0.9080 (mttp) REVERT: m 38 GLU cc_start: 0.8811 (mt-10) cc_final: 0.8597 (mt-10) REVERT: n 67 LYS cc_start: 0.9242 (mttt) cc_final: 0.8997 (mttm) REVERT: n 87 ASN cc_start: 0.8516 (t0) cc_final: 0.8049 (t0) REVERT: c 38 GLU cc_start: 0.8207 (mt-10) cc_final: 0.7933 (mt-10) REVERT: c 67 LYS cc_start: 0.9055 (mttm) cc_final: 0.8786 (mttp) REVERT: b 67 LYS cc_start: 0.9347 (mttt) cc_final: 0.9136 (mtmm) REVERT: a 38 GLU cc_start: 0.8442 (mt-10) cc_final: 0.8187 (mt-10) REVERT: a 141 MET cc_start: 0.7621 (ptp) cc_final: 0.6266 (mmt) outliers start: 14 outliers final: 10 residues processed: 412 average time/residue: 0.5677 time to fit residues: 362.6855 Evaluate side-chains 372 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 362 time to evaluate : 2.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain g residue 29 GLN Chi-restraints excluded: chain g residue 47 ASN Chi-restraints excluded: chain g residue 57 LEU Chi-restraints excluded: chain g residue 67 LYS Chi-restraints excluded: chain h residue 98 ASP Chi-restraints excluded: chain l residue 104 ILE Chi-restraints excluded: chain d residue 57 LEU Chi-restraints excluded: chain d residue 148 ASP Chi-restraints excluded: chain b residue 22 LEU Chi-restraints excluded: chain a residue 22 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 204 optimal weight: 5.9990 chunk 178 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 chunk 101 optimal weight: 6.9990 chunk 22 optimal weight: 4.9990 chunk 191 optimal weight: 4.9990 chunk 159 optimal weight: 8.9990 chunk 17 optimal weight: 6.9990 chunk 128 optimal weight: 0.9980 chunk 148 optimal weight: 5.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- 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** j 31 GLN l 31 GLN m 31 GLN n 31 GLN d 29 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.062774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.050212 restraints weight = 170226.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.052880 restraints weight = 63112.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.054610 restraints weight = 31133.722| |-----------------------------------------------------------------------------| r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8928 moved from start: 0.4998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 16928 Z= 0.212 Angle : 0.542 4.785 23088 Z= 0.290 Chirality : 0.045 0.137 2912 Planarity : 0.002 0.023 2928 Dihedral : 3.552 13.450 2384 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 1.22 % Allowed : 15.87 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.17), residues: 2256 helix: 0.71 (0.18), residues: 688 sheet: -0.50 (0.23), residues: 432 loop : -1.66 (0.17), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP n 132 PHE 0.012 0.001 PHE p 7 TYR 0.020 0.001 TYR g 30 ARG 0.002 0.000 ARG h 126 Details of bonding type rmsd hydrogen bonds : bond 0.03788 ( 688) hydrogen bonds : angle 3.63818 ( 2016) SS BOND : bond 0.00251 ( 16) SS BOND : angle 0.31383 ( 32) covalent geometry : bond 0.00462 (16912) covalent geometry : angle 0.54259 (23056) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 341 time to evaluate : 2.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: g 47 ASN cc_start: 0.9447 (OUTLIER) cc_final: 0.9219 (t0) REVERT: i 55 GLU cc_start: 0.8411 (tm-30) cc_final: 0.8103 (tm-30) REVERT: i 77 GLU cc_start: 0.8428 (mp0) cc_final: 0.8185 (mp0) REVERT: j 55 GLU cc_start: 0.8334 (tm-30) cc_final: 0.8108 (tm-30) REVERT: k 65 LYS cc_start: 0.8821 (mttp) cc_final: 0.8576 (mttp) REVERT: k 67 LYS cc_start: 0.9338 (mttt) cc_final: 0.9122 (mttp) REVERT: m 38 GLU cc_start: 0.8773 (mt-10) cc_final: 0.8507 (mt-10) REVERT: m 55 GLU cc_start: 0.8629 (tm-30) cc_final: 0.8274 (tm-30) REVERT: m 103 ASP cc_start: 0.8769 (p0) cc_final: 0.8520 (p0) REVERT: o 55 GLU cc_start: 0.8691 (tt0) cc_final: 0.8486 (tm-30) REVERT: o 57 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8856 (mm) REVERT: d 97 GLU cc_start: 0.8719 (tt0) cc_final: 0.8227 (tt0) REVERT: c 38 GLU cc_start: 0.8161 (mt-10) cc_final: 0.7895 (mt-10) REVERT: c 67 LYS cc_start: 0.9116 (mttm) cc_final: 0.8812 (mttp) REVERT: b 103 ASP cc_start: 0.9194 (p0) cc_final: 0.8939 (p0) REVERT: a 141 MET cc_start: 0.8054 (ptp) cc_final: 0.6563 (mmt) outliers start: 22 outliers final: 13 residues processed: 358 average time/residue: 0.5680 time to fit residues: 320.1247 Evaluate side-chains 333 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 318 time to evaluate : 2.468 ------------------------------------------------------------------------------- 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 i residue 34 VAL Chi-restraints excluded: chain l residue 104 ILE Chi-restraints excluded: chain o residue 57 LEU Chi-restraints excluded: chain p residue 34 VAL Chi-restraints excluded: chain d residue 29 GLN Chi-restraints excluded: chain d residue 57 LEU Chi-restraints excluded: chain d residue 82 VAL Chi-restraints excluded: chain d residue 148 ASP Chi-restraints excluded: chain c residue 99 SER 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 171 optimal weight: 8.9990 chunk 116 optimal weight: 4.9990 chunk 22 optimal weight: 0.9980 chunk 31 optimal weight: 6.9990 chunk 61 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 212 optimal weight: 7.9990 chunk 1 optimal weight: 4.9990 chunk 3 optimal weight: 7.9990 chunk 147 optimal weight: 7.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 29 GLN f 29 GLN ** i 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.060169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.049941 restraints weight = 168050.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.052508 restraints weight = 62152.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.054115 restraints weight = 30679.462| |-----------------------------------------------------------------------------| r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8971 moved from start: 0.5379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16928 Z= 0.200 Angle : 0.526 4.098 23088 Z= 0.279 Chirality : 0.045 0.140 2912 Planarity : 0.002 0.026 2928 Dihedral : 3.682 14.093 2384 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 2.27 % Allowed : 16.32 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.17), residues: 2256 helix: 0.70 (0.18), residues: 720 sheet: -0.32 (0.23), residues: 432 loop : -1.21 (0.18), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP n 132 PHE 0.007 0.001 PHE p 7 TYR 0.015 0.001 TYR g 79 ARG 0.001 0.000 ARG k 36 Details of bonding type rmsd hydrogen bonds : bond 0.03579 ( 688) hydrogen bonds : angle 3.66293 ( 2016) SS BOND : bond 0.00262 ( 16) SS BOND : angle 0.27698 ( 32) covalent geometry : bond 0.00434 (16912) covalent geometry : angle 0.52611 (23056) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 329 time to evaluate : 2.450 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: i 50 LYS cc_start: 0.9601 (mtmp) cc_final: 0.9352 (mtpp) REVERT: i 55 GLU cc_start: 0.8494 (tm-30) cc_final: 0.8151 (tm-30) REVERT: i 68 ILE cc_start: 0.9020 (OUTLIER) cc_final: 0.8814 (pp) REVERT: i 141 MET cc_start: 0.9123 (ptp) cc_final: 0.8897 (ptp) REVERT: j 7 PHE cc_start: 0.9063 (OUTLIER) cc_final: 0.8248 (t80) REVERT: j 55 GLU cc_start: 0.8422 (tm-30) cc_final: 0.8178 (tm-30) REVERT: k 7 PHE cc_start: 0.9047 (OUTLIER) cc_final: 0.8133 (t80) REVERT: k 65 LYS cc_start: 0.8819 (mttp) cc_final: 0.8611 (mttp) REVERT: k 113 SER cc_start: 0.9272 (m) cc_final: 0.9063 (m) REVERT: l 7 PHE cc_start: 0.8974 (OUTLIER) cc_final: 0.7793 (t80) REVERT: m 7 PHE cc_start: 0.8975 (OUTLIER) cc_final: 0.8162 (t80) REVERT: m 38 GLU cc_start: 0.8717 (mt-10) cc_final: 0.8369 (mp0) REVERT: m 55 GLU cc_start: 0.8661 (tm-30) cc_final: 0.8317 (tm-30) REVERT: n 7 PHE cc_start: 0.8993 (OUTLIER) cc_final: 0.8329 (t80) REVERT: o 7 PHE cc_start: 0.9132 (OUTLIER) cc_final: 0.8647 (t80) REVERT: p 7 PHE cc_start: 0.9044 (OUTLIER) cc_final: 0.8498 (t80) REVERT: d 29 GLN cc_start: 0.9329 (OUTLIER) cc_final: 0.8981 (pp30) REVERT: d 38 GLU cc_start: 0.8419 (mt-10) cc_final: 0.8188 (mt-10) REVERT: d 97 GLU cc_start: 0.8725 (tt0) cc_final: 0.8282 (tt0) REVERT: c 67 LYS cc_start: 0.9151 (mttm) cc_final: 0.8868 (mttp) REVERT: b 103 ASP cc_start: 0.9182 (p0) cc_final: 0.8931 (p0) REVERT: a 103 ASP cc_start: 0.9156 (p0) cc_final: 0.8825 (p0) REVERT: a 141 MET cc_start: 0.8018 (ptp) cc_final: 0.6746 (mmt) outliers start: 41 outliers final: 13 residues processed: 365 average time/residue: 0.5710 time to fit residues: 323.3302 Evaluate side-chains 340 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 318 time to evaluate : 2.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain f residue 98 ASP Chi-restraints excluded: chain g residue 57 LEU Chi-restraints excluded: chain i residue 68 ILE Chi-restraints excluded: chain j residue 7 PHE Chi-restraints excluded: chain k residue 7 PHE Chi-restraints excluded: chain l residue 7 PHE Chi-restraints excluded: chain l residue 94 VAL Chi-restraints excluded: chain l residue 104 ILE Chi-restraints excluded: chain m residue 7 PHE Chi-restraints excluded: chain n residue 7 PHE Chi-restraints excluded: chain o residue 7 PHE Chi-restraints excluded: chain o residue 34 VAL Chi-restraints excluded: chain p residue 7 PHE Chi-restraints excluded: chain p residue 34 VAL Chi-restraints excluded: chain d residue 29 GLN Chi-restraints excluded: chain d residue 34 VAL Chi-restraints excluded: chain d residue 82 VAL Chi-restraints excluded: chain d residue 148 ASP Chi-restraints excluded: chain 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 20 optimal weight: 1.9990 chunk 161 optimal weight: 8.9990 chunk 81 optimal weight: 5.9990 chunk 91 optimal weight: 0.3980 chunk 143 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 110 optimal weight: 1.9990 chunk 96 optimal weight: 5.9990 chunk 83 optimal weight: 3.9990 chunk 60 optimal weight: 0.0980 chunk 128 optimal weight: 0.4980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 29 GLN i 29 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.064183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.052772 restraints weight = 169540.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.055489 restraints weight = 63440.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.057229 restraints weight = 30918.017| |-----------------------------------------------------------------------------| r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8897 moved from start: 0.5473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 16928 Z= 0.090 Angle : 0.489 4.809 23088 Z= 0.250 Chirality : 0.044 0.147 2912 Planarity : 0.002 0.025 2928 Dihedral : 3.476 11.636 2384 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.16 % Allowed : 15.76 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.17), residues: 2256 helix: 1.45 (0.18), residues: 704 sheet: -0.10 (0.23), residues: 432 loop : -1.12 (0.18), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP j 132 PHE 0.003 0.000 PHE l 7 TYR 0.018 0.001 TYR n 79 ARG 0.003 0.000 ARG o 36 Details of bonding type rmsd hydrogen bonds : bond 0.02954 ( 688) hydrogen bonds : angle 3.34271 ( 2016) SS BOND : bond 0.00191 ( 16) SS BOND : angle 0.26451 ( 32) covalent geometry : bond 0.00207 (16912) covalent geometry : angle 0.48893 (23056) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 356 time to evaluate : 2.559 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: g 64 SER cc_start: 0.9558 (OUTLIER) cc_final: 0.9354 (p) REVERT: i 38 GLU cc_start: 0.8483 (mt-10) cc_final: 0.8274 (mt-10) REVERT: i 50 LYS cc_start: 0.9586 (mtmp) cc_final: 0.9201 (mtpp) REVERT: i 55 GLU cc_start: 0.8497 (tm-30) cc_final: 0.8102 (tm-30) REVERT: j 7 PHE cc_start: 0.9069 (OUTLIER) cc_final: 0.8232 (t80) REVERT: j 55 GLU cc_start: 0.8468 (tm-30) cc_final: 0.8201 (tm-30) REVERT: k 7 PHE cc_start: 0.9056 (OUTLIER) cc_final: 0.8020 (t80) REVERT: k 113 SER cc_start: 0.9187 (m) cc_final: 0.8938 (m) REVERT: l 7 PHE cc_start: 0.8991 (OUTLIER) cc_final: 0.7767 (t80) REVERT: m 7 PHE cc_start: 0.9016 (OUTLIER) cc_final: 0.8089 (t80) REVERT: m 38 GLU cc_start: 0.8810 (mt-10) cc_final: 0.8414 (mp0) REVERT: m 55 GLU cc_start: 0.8721 (tm-30) cc_final: 0.8351 (tm-30) REVERT: n 7 PHE cc_start: 0.9016 (OUTLIER) cc_final: 0.8268 (t80) REVERT: o 7 PHE cc_start: 0.9151 (OUTLIER) cc_final: 0.8455 (t80) REVERT: o 57 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8829 (mm) REVERT: p 7 PHE cc_start: 0.9041 (OUTLIER) cc_final: 0.8384 (t80) REVERT: d 11 GLU cc_start: 0.9093 (tt0) cc_final: 0.8758 (pt0) REVERT: d 29 GLN cc_start: 0.9156 (tt0) cc_final: 0.8429 (tp40) REVERT: d 97 GLU cc_start: 0.8687 (tt0) cc_final: 0.8201 (tt0) REVERT: c 38 GLU cc_start: 0.8212 (mt-10) cc_final: 0.7994 (mt-10) REVERT: c 67 LYS cc_start: 0.9101 (mttm) cc_final: 0.8803 (mttp) REVERT: a 109 GLN cc_start: 0.8615 (mm-40) cc_final: 0.8408 (mm110) REVERT: a 141 MET cc_start: 0.7963 (ptp) cc_final: 0.6742 (mmt) outliers start: 39 outliers final: 9 residues processed: 390 average time/residue: 0.5586 time to fit residues: 340.7614 Evaluate side-chains 347 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 329 time to evaluate : 2.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 34 VAL Chi-restraints excluded: chain g residue 57 LEU Chi-restraints excluded: chain g residue 64 SER 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 d residue 34 VAL Chi-restraints excluded: chain b residue 22 LEU Chi-restraints excluded: chain b residue 34 VAL Chi-restraints excluded: chain a residue 22 LEU Chi-restraints excluded: chain a residue 34 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 119 optimal weight: 7.9990 chunk 80 optimal weight: 7.9990 chunk 97 optimal weight: 7.9990 chunk 34 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 chunk 54 optimal weight: 0.8980 chunk 153 optimal weight: 2.9990 chunk 12 optimal weight: 0.0770 chunk 113 optimal weight: 1.9990 chunk 31 optimal weight: 8.9990 chunk 192 optimal weight: 6.9990 overall best weight: 1.9944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 29 GLN i 29 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.062832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.050454 restraints weight = 169567.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.053099 restraints weight = 63038.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.054851 restraints weight = 30644.910| |-----------------------------------------------------------------------------| r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8932 moved from start: 0.5713 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= 0.123 Angle : 0.504 5.612 23088 Z= 0.260 Chirality : 0.044 0.141 2912 Planarity : 0.002 0.022 2928 Dihedral : 3.512 14.930 2384 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 1.88 % Allowed : 16.26 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.17), residues: 2256 helix: 1.68 (0.18), residues: 704 sheet: 0.06 (0.23), residues: 432 loop : -1.02 (0.18), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP o 132 PHE 0.003 0.000 PHE b 106 TYR 0.012 0.001 TYR g 79 ARG 0.001 0.000 ARG n 36 Details of bonding type rmsd hydrogen bonds : bond 0.03162 ( 688) hydrogen bonds : angle 3.41991 ( 2016) SS BOND : bond 0.00218 ( 16) SS BOND : angle 0.30032 ( 32) covalent geometry : bond 0.00281 (16912) covalent geometry : angle 0.50375 (23056) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 327 time to evaluate : 2.599 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: e 79 TYR cc_start: 0.8985 (m-80) cc_final: 0.8678 (m-80) REVERT: i 55 GLU cc_start: 0.8495 (tm-30) cc_final: 0.8115 (tm-30) REVERT: j 7 PHE cc_start: 0.9104 (OUTLIER) cc_final: 0.8299 (t80) REVERT: j 55 GLU cc_start: 0.8501 (tm-30) cc_final: 0.8230 (tm-30) REVERT: k 7 PHE cc_start: 0.9096 (OUTLIER) cc_final: 0.8144 (t80) REVERT: k 113 SER cc_start: 0.9230 (m) cc_final: 0.8992 (m) REVERT: l 7 PHE cc_start: 0.9002 (OUTLIER) cc_final: 0.7989 (t80) REVERT: m 7 PHE cc_start: 0.9031 (OUTLIER) cc_final: 0.8157 (t80) REVERT: m 38 GLU cc_start: 0.8765 (mt-10) cc_final: 0.8457 (mt-10) REVERT: m 55 GLU cc_start: 0.8741 (tm-30) cc_final: 0.8384 (tm-30) REVERT: m 103 ASP cc_start: 0.8790 (p0) cc_final: 0.8574 (p0) REVERT: n 7 PHE cc_start: 0.8988 (OUTLIER) cc_final: 0.8313 (t80) REVERT: o 7 PHE cc_start: 0.9128 (OUTLIER) cc_final: 0.8523 (t80) REVERT: o 57 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8905 (mm) REVERT: p 7 PHE cc_start: 0.9054 (OUTLIER) cc_final: 0.8437 (t80) REVERT: d 29 GLN cc_start: 0.9109 (tt0) cc_final: 0.8430 (tp40) REVERT: d 38 GLU cc_start: 0.8502 (mt-10) cc_final: 0.8277 (mt-10) REVERT: d 97 GLU cc_start: 0.8708 (tt0) cc_final: 0.8222 (tt0) REVERT: c 38 GLU cc_start: 0.8254 (mt-10) cc_final: 0.8053 (mt-10) REVERT: c 67 LYS cc_start: 0.9143 (mttm) cc_final: 0.8861 (mttp) REVERT: a 141 MET cc_start: 0.7963 (ptp) cc_final: 0.6831 (mmt) outliers start: 34 outliers final: 12 residues processed: 354 average time/residue: 0.5746 time to fit residues: 318.3608 Evaluate side-chains 331 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 311 time to evaluate : 2.533 ------------------------------------------------------------------------------- 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 j residue 7 PHE Chi-restraints excluded: chain j residue 94 VAL Chi-restraints excluded: chain k residue 7 PHE Chi-restraints excluded: chain l residue 7 PHE Chi-restraints excluded: chain l residue 89 LEU Chi-restraints excluded: chain l residue 104 ILE Chi-restraints excluded: chain m residue 7 PHE Chi-restraints excluded: chain n residue 7 PHE Chi-restraints excluded: chain o residue 7 PHE Chi-restraints excluded: chain o residue 57 LEU Chi-restraints excluded: chain p residue 7 PHE Chi-restraints excluded: chain p residue 34 VAL Chi-restraints excluded: chain p residue 94 VAL Chi-restraints excluded: chain d residue 34 VAL Chi-restraints excluded: chain b residue 22 LEU Chi-restraints excluded: chain b residue 34 VAL 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 73 optimal weight: 5.9990 chunk 208 optimal weight: 10.0000 chunk 90 optimal weight: 4.9990 chunk 170 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 chunk 40 optimal weight: 0.9990 chunk 116 optimal weight: 3.9990 chunk 174 optimal weight: 2.9990 chunk 31 optimal weight: 8.9990 chunk 111 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 29 GLN g 29 GLN n 29 GLN o 29 GLN d 29 GLN c 29 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.061485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.049170 restraints weight = 173829.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.051712 restraints weight = 64085.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.053365 restraints weight = 31560.262| |-----------------------------------------------------------------------------| r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8970 moved from start: 0.6026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 16928 Z= 0.200 Angle : 0.538 4.819 23088 Z= 0.284 Chirality : 0.045 0.138 2912 Planarity : 0.002 0.019 2928 Dihedral : 3.809 16.771 2384 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 2.16 % Allowed : 16.54 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.17), residues: 2256 helix: 1.58 (0.18), residues: 720 sheet: 0.12 (0.23), residues: 432 loop : -0.94 (0.18), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP g 132 PHE 0.005 0.001 PHE b 106 TYR 0.014 0.001 TYR g 79 ARG 0.001 0.000 ARG j 36 Details of bonding type rmsd hydrogen bonds : bond 0.03629 ( 688) hydrogen bonds : angle 3.64245 ( 2016) SS BOND : bond 0.00269 ( 16) SS BOND : angle 0.34696 ( 32) covalent geometry : bond 0.00438 (16912) covalent geometry : angle 0.53820 (23056) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 309 time to evaluate : 2.491 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: e 29 GLN cc_start: 0.8824 (OUTLIER) cc_final: 0.8422 (tt0) REVERT: h 7 PHE cc_start: 0.9355 (OUTLIER) cc_final: 0.8566 (t80) REVERT: i 7 PHE cc_start: 0.9302 (OUTLIER) cc_final: 0.8129 (t80) REVERT: i 38 GLU cc_start: 0.8524 (mt-10) cc_final: 0.8323 (mt-10) REVERT: i 55 GLU cc_start: 0.8621 (tm-30) cc_final: 0.8255 (tm-30) REVERT: i 83 GLU cc_start: 0.8294 (mp0) cc_final: 0.8038 (mp0) REVERT: j 7 PHE cc_start: 0.9156 (OUTLIER) cc_final: 0.8361 (t80) REVERT: j 55 GLU cc_start: 0.8614 (tm-30) cc_final: 0.8310 (tm-30) REVERT: k 7 PHE cc_start: 0.9164 (OUTLIER) cc_final: 0.7997 (t80) REVERT: k 113 SER cc_start: 0.9323 (m) cc_final: 0.9097 (m) REVERT: l 7 PHE cc_start: 0.9033 (OUTLIER) cc_final: 0.8020 (t80) REVERT: l 67 LYS cc_start: 0.9203 (mttp) cc_final: 0.8635 (mmtp) REVERT: m 7 PHE cc_start: 0.9077 (OUTLIER) cc_final: 0.8176 (t80) REVERT: m 55 GLU cc_start: 0.8769 (tm-30) cc_final: 0.8440 (tm-30) REVERT: n 7 PHE cc_start: 0.9114 (OUTLIER) cc_final: 0.8437 (t80) REVERT: n 67 LYS cc_start: 0.9196 (mttt) cc_final: 0.8925 (mmtp) REVERT: o 7 PHE cc_start: 0.9188 (OUTLIER) cc_final: 0.8626 (t80) REVERT: o 57 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8941 (mm) REVERT: p 7 PHE cc_start: 0.9131 (OUTLIER) cc_final: 0.8581 (t80) REVERT: d 29 GLN cc_start: 0.8988 (OUTLIER) cc_final: 0.8356 (tp40) REVERT: d 97 GLU cc_start: 0.8769 (tt0) cc_final: 0.8307 (tt0) REVERT: c 67 LYS cc_start: 0.9139 (mttm) cc_final: 0.8807 (mttp) REVERT: c 148 ASP cc_start: 0.8949 (p0) cc_final: 0.8705 (p0) REVERT: a 141 MET cc_start: 0.8006 (ptp) cc_final: 0.7031 (mmt) outliers start: 39 outliers final: 17 residues processed: 338 average time/residue: 0.5663 time to fit residues: 299.4033 Evaluate side-chains 328 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 299 time to evaluate : 2.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 29 GLN Chi-restraints excluded: chain e residue 34 VAL Chi-restraints excluded: chain f residue 22 LEU Chi-restraints excluded: chain f residue 98 ASP Chi-restraints excluded: chain g residue 57 LEU Chi-restraints excluded: chain h residue 7 PHE Chi-restraints excluded: chain i residue 7 PHE Chi-restraints excluded: chain i residue 34 VAL Chi-restraints excluded: chain j residue 7 PHE Chi-restraints excluded: chain j residue 94 VAL Chi-restraints excluded: chain k residue 7 PHE Chi-restraints excluded: chain l residue 7 PHE Chi-restraints excluded: chain l residue 104 ILE Chi-restraints excluded: chain m residue 7 PHE Chi-restraints excluded: chain n residue 7 PHE Chi-restraints excluded: chain o residue 7 PHE Chi-restraints excluded: chain o residue 34 VAL Chi-restraints excluded: chain o residue 57 LEU Chi-restraints excluded: chain p residue 7 PHE Chi-restraints excluded: chain p residue 34 VAL Chi-restraints excluded: chain p residue 94 VAL Chi-restraints excluded: chain d residue 29 GLN Chi-restraints excluded: chain d residue 34 VAL Chi-restraints excluded: chain d residue 148 ASP Chi-restraints excluded: chain c residue 34 VAL Chi-restraints excluded: chain c residue 68 ILE Chi-restraints excluded: chain c residue 99 SER Chi-restraints excluded: chain b residue 34 VAL Chi-restraints excluded: chain a residue 34 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 172 optimal weight: 0.9990 chunk 65 optimal weight: 5.9990 chunk 137 optimal weight: 8.9990 chunk 148 optimal weight: 0.4980 chunk 140 optimal weight: 3.9990 chunk 204 optimal weight: 6.9990 chunk 98 optimal weight: 3.9990 chunk 186 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 178 optimal weight: 4.9990 overall best weight: 2.4988 ------------------------------------------------------------------------------- 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 = 0.3120 r_free = 0.3120 target = 0.062061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.049766 restraints weight = 172076.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.052361 restraints weight = 63297.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.053985 restraints weight = 30695.513| |-----------------------------------------------------------------------------| r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8958 moved from start: 0.6112 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= 0.146 Angle : 0.532 5.831 23088 Z= 0.275 Chirality : 0.044 0.141 2912 Planarity : 0.002 0.022 2928 Dihedral : 3.777 16.348 2384 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 1.88 % Allowed : 17.37 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.17), residues: 2256 helix: 1.80 (0.18), residues: 720 sheet: 0.21 (0.23), residues: 432 loop : -0.90 (0.18), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP h 132 PHE 0.004 0.001 PHE l 7 TYR 0.012 0.001 TYR g 79 ARG 0.002 0.000 ARG n 59 Details of bonding type rmsd hydrogen bonds : bond 0.03424 ( 688) hydrogen bonds : angle 3.54353 ( 2016) SS BOND : bond 0.00238 ( 16) SS BOND : angle 0.30554 ( 32) covalent geometry : bond 0.00324 (16912) covalent geometry : angle 0.53178 (23056) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 315 time to evaluate : 2.815 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: h 7 PHE cc_start: 0.9348 (OUTLIER) cc_final: 0.8472 (t80) REVERT: i 7 PHE cc_start: 0.9307 (OUTLIER) cc_final: 0.8075 (t80) REVERT: i 55 GLU cc_start: 0.8637 (tm-30) cc_final: 0.8271 (tm-30) REVERT: i 83 GLU cc_start: 0.8270 (mp0) cc_final: 0.7991 (mp0) REVERT: j 7 PHE cc_start: 0.9166 (OUTLIER) cc_final: 0.8385 (t80) REVERT: j 55 GLU cc_start: 0.8629 (tm-30) cc_final: 0.8303 (tm-30) REVERT: k 7 PHE cc_start: 0.9158 (OUTLIER) cc_final: 0.8086 (t80) REVERT: k 113 SER cc_start: 0.9305 (m) cc_final: 0.9085 (m) REVERT: l 7 PHE cc_start: 0.9032 (OUTLIER) cc_final: 0.7994 (t80) REVERT: l 67 LYS cc_start: 0.9203 (mttp) cc_final: 0.8656 (mmtp) REVERT: m 7 PHE cc_start: 0.9078 (OUTLIER) cc_final: 0.8190 (t80) REVERT: m 55 GLU cc_start: 0.8773 (tm-30) cc_final: 0.8431 (tm-30) REVERT: n 7 PHE cc_start: 0.9108 (OUTLIER) cc_final: 0.8463 (t80) REVERT: o 7 PHE cc_start: 0.9190 (OUTLIER) cc_final: 0.8630 (t80) REVERT: o 57 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8998 (mm) REVERT: p 7 PHE cc_start: 0.9124 (OUTLIER) cc_final: 0.8537 (t80) REVERT: d 29 GLN cc_start: 0.9179 (tt0) cc_final: 0.8262 (tp40) REVERT: d 97 GLU cc_start: 0.8760 (tt0) cc_final: 0.8286 (tt0) REVERT: c 67 LYS cc_start: 0.9125 (mttm) cc_final: 0.8851 (mttp) REVERT: c 148 ASP cc_start: 0.8989 (p0) cc_final: 0.8736 (p0) REVERT: a 38 GLU cc_start: 0.8580 (mt-10) cc_final: 0.8355 (mt-10) REVERT: a 141 MET cc_start: 0.7989 (ptp) cc_final: 0.7142 (mmt) outliers start: 34 outliers final: 21 residues processed: 342 average time/residue: 0.5731 time to fit residues: 308.3447 Evaluate side-chains 338 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 307 time to evaluate : 2.563 ------------------------------------------------------------------------------- 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 22 LEU Chi-restraints excluded: chain f residue 98 ASP Chi-restraints excluded: chain g residue 57 LEU Chi-restraints excluded: chain h residue 7 PHE Chi-restraints excluded: chain i residue 7 PHE Chi-restraints excluded: chain i residue 34 VAL Chi-restraints excluded: chain j residue 7 PHE Chi-restraints excluded: chain j residue 94 VAL Chi-restraints excluded: chain k residue 7 PHE Chi-restraints excluded: chain l residue 7 PHE Chi-restraints excluded: chain l residue 89 LEU Chi-restraints excluded: chain l residue 94 VAL Chi-restraints excluded: chain l residue 104 ILE Chi-restraints excluded: chain m residue 7 PHE Chi-restraints excluded: chain n residue 7 PHE Chi-restraints excluded: chain o residue 7 PHE Chi-restraints excluded: chain o residue 34 VAL Chi-restraints excluded: chain 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 c residue 22 LEU Chi-restraints excluded: chain c residue 34 VAL Chi-restraints excluded: chain c residue 68 ILE Chi-restraints excluded: chain c residue 99 SER Chi-restraints excluded: chain b residue 34 VAL Chi-restraints excluded: chain a residue 34 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 206 optimal weight: 6.9990 chunk 86 optimal weight: 4.9990 chunk 90 optimal weight: 0.4980 chunk 118 optimal weight: 3.9990 chunk 106 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 149 optimal weight: 0.7980 chunk 217 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 184 optimal weight: 0.0970 overall best weight: 0.6578 ------------------------------------------------------------------------------- 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 = 0.3195 r_free = 0.3195 target = 0.064856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.052191 restraints weight = 169605.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.054836 restraints weight = 61733.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.056515 restraints weight = 30078.236| |-----------------------------------------------------------------------------| r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8912 moved from start: 0.6088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 16928 Z= 0.092 Angle : 0.511 6.350 23088 Z= 0.258 Chirality : 0.044 0.145 2912 Planarity : 0.002 0.022 2928 Dihedral : 3.522 16.468 2384 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 1.16 % Allowed : 17.75 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.17), residues: 2256 helix: 2.20 (0.18), residues: 720 sheet: 0.47 (0.23), residues: 432 loop : -0.86 (0.18), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP h 132 PHE 0.003 0.000 PHE e 106 TYR 0.011 0.001 TYR g 79 ARG 0.001 0.000 ARG k 59 Details of bonding type rmsd hydrogen bonds : bond 0.02848 ( 688) hydrogen bonds : angle 3.29590 ( 2016) SS BOND : bond 0.00192 ( 16) SS BOND : angle 0.30345 ( 32) covalent geometry : bond 0.00212 (16912) covalent geometry : angle 0.51117 (23056) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 340 time to evaluate : 2.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: e 79 TYR cc_start: 0.9068 (m-80) cc_final: 0.8768 (m-80) REVERT: g 7 PHE cc_start: 0.9323 (OUTLIER) cc_final: 0.8805 (t80) REVERT: g 77 GLU cc_start: 0.8037 (mp0) cc_final: 0.7626 (mp0) REVERT: h 97 GLU cc_start: 0.8384 (tt0) cc_final: 0.8082 (tt0) REVERT: i 55 GLU cc_start: 0.8606 (tm-30) cc_final: 0.8222 (tm-30) REVERT: i 83 GLU cc_start: 0.8268 (mp0) cc_final: 0.7971 (mp0) REVERT: j 7 PHE cc_start: 0.9162 (OUTLIER) cc_final: 0.8327 (t80) REVERT: j 55 GLU cc_start: 0.8616 (tm-30) cc_final: 0.8264 (tm-30) REVERT: k 7 PHE cc_start: 0.9145 (OUTLIER) cc_final: 0.7921 (t80) REVERT: k 113 SER cc_start: 0.9229 (m) cc_final: 0.8950 (m) REVERT: l 7 PHE cc_start: 0.9020 (OUTLIER) cc_final: 0.8042 (t80) REVERT: m 7 PHE cc_start: 0.9067 (OUTLIER) cc_final: 0.8099 (t80) REVERT: m 55 GLU cc_start: 0.8759 (tm-30) cc_final: 0.8414 (tm-30) REVERT: n 7 PHE cc_start: 0.9061 (OUTLIER) cc_final: 0.8320 (t80) REVERT: o 7 PHE cc_start: 0.9146 (OUTLIER) cc_final: 0.8486 (t80) REVERT: o 57 LEU cc_start: 0.9182 (OUTLIER) cc_final: 0.8974 (mm) REVERT: p 7 PHE cc_start: 0.9073 (OUTLIER) cc_final: 0.8400 (t80) REVERT: p 50 LYS cc_start: 0.9754 (mtmt) cc_final: 0.9436 (mtpp) REVERT: d 29 GLN cc_start: 0.9223 (tt0) cc_final: 0.8380 (tp40) REVERT: d 97 GLU cc_start: 0.8678 (tt0) cc_final: 0.8224 (tt0) REVERT: c 67 LYS cc_start: 0.9115 (mttm) cc_final: 0.8787 (mttp) REVERT: c 148 ASP cc_start: 0.8987 (p0) cc_final: 0.8762 (p0) REVERT: a 141 MET cc_start: 0.7986 (ptp) cc_final: 0.7040 (mmt) outliers start: 21 outliers final: 11 residues processed: 356 average time/residue: 0.5739 time to fit residues: 319.4127 Evaluate side-chains 341 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 321 time to evaluate : 2.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 34 VAL Chi-restraints excluded: chain f residue 22 LEU Chi-restraints excluded: chain f residue 98 ASP Chi-restraints excluded: chain g 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 l residue 89 LEU Chi-restraints excluded: chain l residue 104 ILE Chi-restraints excluded: chain m residue 7 PHE Chi-restraints excluded: chain n residue 7 PHE Chi-restraints excluded: chain o residue 7 PHE Chi-restraints excluded: chain o residue 57 LEU Chi-restraints excluded: chain p residue 7 PHE Chi-restraints excluded: chain p residue 43 LEU Chi-restraints excluded: chain p residue 94 VAL Chi-restraints excluded: chain d residue 34 VAL Chi-restraints excluded: chain c residue 68 ILE Chi-restraints excluded: chain c residue 99 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 74 optimal weight: 0.6980 chunk 108 optimal weight: 0.7980 chunk 126 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 183 optimal weight: 0.5980 chunk 95 optimal weight: 4.9990 chunk 105 optimal weight: 6.9990 chunk 79 optimal weight: 0.6980 chunk 124 optimal weight: 6.9990 chunk 121 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3203 r_free = 0.3203 target = 0.065244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.052631 restraints weight = 168900.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.055272 restraints weight = 61316.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.056944 restraints weight = 29815.882| |-----------------------------------------------------------------------------| r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8903 moved from start: 0.6135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 16928 Z= 0.091 Angle : 0.527 7.093 23088 Z= 0.264 Chirality : 0.044 0.140 2912 Planarity : 0.002 0.022 2928 Dihedral : 3.430 15.783 2384 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 1.11 % Allowed : 18.14 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.17), residues: 2256 helix: 2.40 (0.19), residues: 720 sheet: 0.74 (0.23), residues: 432 loop : -0.79 (0.18), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP h 132 PHE 0.003 0.000 PHE k 7 TYR 0.012 0.001 TYR a 79 ARG 0.001 0.000 ARG n 59 Details of bonding type rmsd hydrogen bonds : bond 0.02845 ( 688) hydrogen bonds : angle 3.25296 ( 2016) SS BOND : bond 0.00182 ( 16) SS BOND : angle 0.31105 ( 32) covalent geometry : bond 0.00214 (16912) covalent geometry : angle 0.52706 (23056) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 330 time to evaluate : 2.424 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: e 79 TYR cc_start: 0.9054 (m-80) cc_final: 0.8777 (m-80) REVERT: g 7 PHE cc_start: 0.9317 (OUTLIER) cc_final: 0.8728 (t80) REVERT: h 97 GLU cc_start: 0.8388 (tt0) cc_final: 0.8092 (tt0) REVERT: i 55 GLU cc_start: 0.8603 (tm-30) cc_final: 0.8207 (tm-30) REVERT: i 83 GLU cc_start: 0.8280 (mp0) cc_final: 0.7978 (mp0) REVERT: j 7 PHE cc_start: 0.9127 (OUTLIER) cc_final: 0.8290 (t80) REVERT: j 55 GLU cc_start: 0.8627 (tm-30) cc_final: 0.8278 (tm-30) REVERT: k 7 PHE cc_start: 0.9140 (OUTLIER) cc_final: 0.8031 (t80) REVERT: k 113 SER cc_start: 0.9143 (m) cc_final: 0.8867 (m) REVERT: l 7 PHE cc_start: 0.9022 (OUTLIER) cc_final: 0.7952 (t80) REVERT: l 55 GLU cc_start: 0.8812 (tm-30) cc_final: 0.8541 (tm-30) REVERT: m 7 PHE cc_start: 0.9063 (OUTLIER) cc_final: 0.8107 (t80) REVERT: m 55 GLU cc_start: 0.8763 (tm-30) cc_final: 0.8430 (tm-30) REVERT: n 7 PHE cc_start: 0.9040 (OUTLIER) cc_final: 0.8283 (t80) REVERT: o 7 PHE cc_start: 0.9140 (OUTLIER) cc_final: 0.8475 (t80) REVERT: p 7 PHE cc_start: 0.9072 (OUTLIER) cc_final: 0.8346 (t80) REVERT: d 29 GLN cc_start: 0.9206 (tt0) cc_final: 0.8392 (tp40) REVERT: d 97 GLU cc_start: 0.8653 (tt0) cc_final: 0.8217 (tt0) REVERT: c 67 LYS cc_start: 0.9136 (mttm) cc_final: 0.8805 (mttp) REVERT: c 148 ASP cc_start: 0.8991 (p0) cc_final: 0.8755 (p0) REVERT: a 141 MET cc_start: 0.7952 (ptp) cc_final: 0.7059 (mmt) outliers start: 20 outliers final: 9 residues processed: 345 average time/residue: 0.5579 time to fit residues: 301.8740 Evaluate side-chains 337 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 320 time to evaluate : 2.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain f residue 22 LEU Chi-restraints excluded: chain f residue 29 GLN Chi-restraints excluded: chain g 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 l residue 89 LEU Chi-restraints excluded: chain l residue 104 ILE Chi-restraints excluded: chain m residue 7 PHE Chi-restraints excluded: chain n residue 7 PHE Chi-restraints excluded: chain o residue 7 PHE Chi-restraints excluded: chain p residue 7 PHE Chi-restraints excluded: chain p residue 43 LEU Chi-restraints excluded: chain p residue 94 VAL Chi-restraints excluded: chain c residue 68 ILE Chi-restraints excluded: chain c residue 99 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 79 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 87 optimal weight: 6.9990 chunk 146 optimal weight: 7.9990 chunk 182 optimal weight: 6.9990 chunk 192 optimal weight: 4.9990 chunk 152 optimal weight: 1.9990 chunk 29 optimal weight: 0.4980 chunk 55 optimal weight: 0.4980 chunk 134 optimal weight: 6.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 = 0.3203 r_free = 0.3203 target = 0.065251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.052579 restraints weight = 170455.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.055249 restraints weight = 61976.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.056925 restraints weight = 30151.609| |-----------------------------------------------------------------------------| r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8908 moved from start: 0.6161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.201 16928 Z= 0.144 Angle : 0.709 59.200 23088 Z= 0.407 Chirality : 0.045 0.447 2912 Planarity : 0.002 0.021 2928 Dihedral : 3.447 15.769 2384 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 1.00 % Allowed : 18.31 % Favored : 80.70 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.17), residues: 2256 helix: 2.40 (0.19), residues: 720 sheet: 0.76 (0.23), residues: 432 loop : -0.78 (0.18), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP p 132 PHE 0.003 0.000 PHE m 7 TYR 0.010 0.001 TYR a 79 ARG 0.001 0.000 ARG n 59 Details of bonding type rmsd hydrogen bonds : bond 0.02856 ( 688) hydrogen bonds : angle 3.26678 ( 2016) SS BOND : bond 0.00167 ( 16) SS BOND : angle 0.29917 ( 32) covalent geometry : bond 0.00309 (16912) covalent geometry : angle 0.70981 (23056) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9363.98 seconds wall clock time: 162 minutes 33.99 seconds (9753.99 seconds total)