Starting phenix.real_space_refine on Fri Jul 26 11:35:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tum_41625/07_2024/8tum_41625.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tum_41625/07_2024/8tum_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tum_41625/07_2024/8tum_41625.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tum_41625/07_2024/8tum_41625.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tum_41625/07_2024/8tum_41625.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tum_41625/07_2024/8tum_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 Residue "e ASP 103": "OD1" <-> "OD2" Residue "f ASP 103": "OD1" <-> "OD2" Residue "g ASP 103": "OD1" <-> "OD2" Residue "h ASP 103": "OD1" <-> "OD2" Residue "i ASP 103": "OD1" <-> "OD2" Residue "j ASP 103": "OD1" <-> "OD2" Residue "k ASP 103": "OD1" <-> "OD2" Residue "l ASP 103": "OD1" <-> "OD2" Residue "m ASP 103": "OD1" <-> "OD2" Residue "n ASP 103": "OD1" <-> "OD2" Residue "o ASP 103": "OD1" <-> "OD2" Residue "p ASP 103": "OD1" <-> "OD2" Residue "d ASP 103": "OD1" <-> "OD2" Residue "c ASP 103": "OD1" <-> "OD2" Residue "b ASP 103": "OD1" <-> "OD2" Residue "a ASP 103": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 15.98, per 1000 atoms: 0.47 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 - 3.50 Amino acid : False - 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: 28.45 Conformation dependent library (CDL) restraints added in 4.0 seconds 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4192 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 32 sheets defined 32.2% alpha, 17.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.82 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: 11.67 Time building geometry restraints manager: 29.78 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: 101.07 - 107.65: 1372 107.65 - 114.23: 43009 114.23 - 120.81: 9421 120.81 - 127.39: 7798 127.39 - 133.98: 128 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 1.850 nonbonded pdb=" OE1 GLU k 77 " pdb=" HH TYR k 79 " model vdw 1.741 1.850 nonbonded pdb=" OE1 GLU o 77 " pdb=" HH TYR o 79 " model vdw 1.741 1.850 nonbonded pdb=" OE1 GLU a 77 " pdb=" HH TYR a 79 " model vdw 1.741 1.850 nonbonded pdb=" O GLY k 63 " pdb=" HG SER k 64 " model vdw 1.741 1.850 ... (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 Found NCS groups: ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' 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: 2.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.590 Extract box with map and model: 1.390 Check model and map are aligned: 0.240 Set scattering table: 0.320 Process input model: 107.850 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 116.580 ------------------------------------------------------------------------------- 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 16912 Z= 0.098 Angle : 0.400 3.753 23056 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 *********************** 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 fitting. rotamer outliers: 16 poor density : 727 time to evaluate : 2.747 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: 0.7200 time to fit residues: 768.5540 Evaluate side-chains 385 residues out of total 1808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 385 time to evaluate : 2.888 ------------------------------------------------------------------------------- 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: 2.9990 chunk 169 optimal weight: 4.9990 chunk 94 optimal weight: 7.9990 chunk 57 optimal weight: 3.9990 chunk 114 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 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: 0.8980 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 31 GLN g 29 GLN g 31 GLN h 31 GLN i 29 GLN i 31 GLN l 31 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.4272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 16912 Z= 0.265 Angle : 0.557 4.152 23056 Z= 0.289 Chirality : 0.044 0.141 2912 Planarity : 0.002 0.020 2928 Dihedral : 3.488 19.351 2384 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 1.49 % Allowed : 16.70 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.16), residues: 2256 helix: 0.33 (0.19), residues: 688 sheet: -1.05 (0.21), residues: 432 loop : -2.04 (0.17), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP n 132 PHE 0.005 0.001 PHE n 106 TYR 0.022 0.001 TYR g 79 ARG 0.002 0.000 ARG k 59 *********************** 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 415 residues out of total 1808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 388 time to evaluate : 2.749 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: c 103 ASP cc_start: 0.7215 (OUTLIER) cc_final: 0.6969 (p0) outliers start: 27 outliers final: 18 residues processed: 403 average time/residue: 0.5655 time to fit residues: 353.3827 Evaluate side-chains 363 residues out of total 1808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 344 time to evaluate : 2.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 58 SER Chi-restraints excluded: chain f residue 58 SER 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 l residue 56 SER Chi-restraints excluded: chain l residue 104 ILE Chi-restraints excluded: chain m residue 56 SER Chi-restraints excluded: chain m residue 103 ASP Chi-restraints excluded: chain d residue 57 LEU Chi-restraints excluded: chain d residue 58 SER Chi-restraints excluded: chain d residue 148 ASP Chi-restraints excluded: chain c residue 58 SER Chi-restraints excluded: chain c residue 103 ASP Chi-restraints excluded: chain b residue 22 LEU Chi-restraints excluded: chain b residue 58 SER Chi-restraints excluded: chain a residue 22 LEU Chi-restraints excluded: chain a residue 58 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 113 optimal weight: 0.9990 chunk 63 optimal weight: 4.9990 chunk 169 optimal weight: 0.5980 chunk 138 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 203 optimal weight: 6.9990 chunk 220 optimal weight: 0.9990 chunk 181 optimal weight: 0.5980 chunk 202 optimal weight: 0.9980 chunk 69 optimal weight: 5.9990 chunk 163 optimal weight: 7.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.4507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 16912 Z= 0.132 Angle : 0.468 4.957 23056 Z= 0.236 Chirality : 0.043 0.141 2912 Planarity : 0.002 0.024 2928 Dihedral : 3.038 11.826 2384 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 1.27 % Allowed : 17.64 % 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: -1.04 (0.16), residues: 2256 helix: 0.73 (0.19), residues: 688 sheet: -0.68 (0.21), residues: 432 loop : -1.61 (0.17), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP n 132 PHE 0.009 0.001 PHE m 7 TYR 0.017 0.001 TYR a 79 ARG 0.001 0.000 ARG k 59 *********************** 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 391 residues out of total 1808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 368 time to evaluate : 2.654 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: g 47 ASN cc_start: 0.7974 (OUTLIER) cc_final: 0.7641 (t0) REVERT: m 7 PHE cc_start: 0.7401 (OUTLIER) cc_final: 0.6797 (t80) REVERT: c 103 ASP cc_start: 0.7155 (OUTLIER) cc_final: 0.6919 (p0) outliers start: 23 outliers final: 16 residues processed: 384 average time/residue: 0.5596 time to fit residues: 335.3102 Evaluate side-chains 360 residues out of total 1808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 341 time to evaluate : 2.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 58 SER Chi-restraints excluded: chain f residue 58 SER Chi-restraints excluded: chain g residue 47 ASN Chi-restraints excluded: chain g residue 57 LEU Chi-restraints excluded: chain h residue 149 ASN Chi-restraints excluded: chain l residue 104 ILE Chi-restraints excluded: chain m residue 7 PHE Chi-restraints excluded: chain m residue 103 ASP Chi-restraints excluded: chain p residue 149 ASN Chi-restraints excluded: chain d residue 57 LEU Chi-restraints excluded: chain d residue 58 SER Chi-restraints excluded: chain d residue 148 ASP Chi-restraints excluded: chain c residue 58 SER Chi-restraints excluded: chain c residue 103 ASP Chi-restraints excluded: chain b residue 22 LEU Chi-restraints excluded: chain b residue 58 SER Chi-restraints excluded: chain a residue 22 LEU Chi-restraints excluded: chain a residue 58 SER Chi-restraints excluded: chain a residue 103 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 201 optimal weight: 8.9990 chunk 153 optimal weight: 3.9990 chunk 105 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 chunk 97 optimal weight: 0.8980 chunk 136 optimal weight: 6.9990 chunk 204 optimal weight: 6.9990 chunk 216 optimal weight: 2.9990 chunk 106 optimal weight: 5.9990 chunk 193 optimal weight: 7.9990 chunk 58 optimal weight: 6.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 29 GLN j 31 GLN d 29 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.5088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16912 Z= 0.241 Angle : 0.506 5.653 23056 Z= 0.264 Chirality : 0.043 0.142 2912 Planarity : 0.002 0.029 2928 Dihedral : 3.316 11.966 2384 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 2.38 % Allowed : 16.98 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.56 (0.16), residues: 2256 helix: 0.89 (0.18), residues: 688 sheet: -0.34 (0.22), residues: 432 loop : -1.16 (0.18), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP o 132 PHE 0.006 0.001 PHE m 7 TYR 0.026 0.001 TYR n 79 ARG 0.003 0.000 ARG o 126 *********************** 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 384 residues out of total 1808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 341 time to evaluate : 2.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: g 47 ASN cc_start: 0.8071 (OUTLIER) cc_final: 0.7777 (t0) REVERT: j 7 PHE cc_start: 0.7236 (OUTLIER) cc_final: 0.6828 (t80) REVERT: l 7 PHE cc_start: 0.7523 (OUTLIER) cc_final: 0.6831 (t80) REVERT: m 7 PHE cc_start: 0.7435 (OUTLIER) cc_final: 0.6872 (t80) REVERT: n 7 PHE cc_start: 0.7753 (OUTLIER) cc_final: 0.7215 (t80) REVERT: o 7 PHE cc_start: 0.7407 (OUTLIER) cc_final: 0.6987 (t80) REVERT: p 7 PHE cc_start: 0.7238 (OUTLIER) cc_final: 0.6973 (t80) outliers start: 43 outliers final: 20 residues processed: 372 average time/residue: 0.5764 time to fit residues: 337.4006 Evaluate side-chains 352 residues out of total 1808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 325 time to evaluate : 2.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 58 SER Chi-restraints excluded: chain f residue 58 SER 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 j residue 7 PHE Chi-restraints excluded: chain k residue 56 SER Chi-restraints excluded: chain l residue 7 PHE Chi-restraints excluded: chain l residue 56 SER Chi-restraints excluded: chain l residue 104 ILE Chi-restraints excluded: chain m residue 7 PHE Chi-restraints excluded: chain m residue 56 SER Chi-restraints excluded: chain m residue 103 ASP Chi-restraints excluded: chain n residue 7 PHE Chi-restraints excluded: chain n residue 57 LEU Chi-restraints excluded: chain o residue 7 PHE Chi-restraints excluded: chain p residue 7 PHE Chi-restraints excluded: chain p residue 34 VAL Chi-restraints excluded: chain p residue 149 ASN Chi-restraints excluded: chain d residue 58 SER Chi-restraints excluded: chain d residue 148 ASP Chi-restraints excluded: chain c residue 22 LEU Chi-restraints excluded: chain c residue 58 SER Chi-restraints excluded: chain c residue 103 ASP Chi-restraints excluded: chain b residue 58 SER Chi-restraints excluded: chain a residue 58 SER Chi-restraints excluded: chain a residue 103 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 180 optimal weight: 5.9990 chunk 122 optimal weight: 7.9990 chunk 3 optimal weight: 7.9990 chunk 161 optimal weight: 6.9990 chunk 89 optimal weight: 4.9990 chunk 184 optimal weight: 2.9990 chunk 149 optimal weight: 0.5980 chunk 0 optimal weight: 6.9990 chunk 110 optimal weight: 6.9990 chunk 194 optimal weight: 5.9990 chunk 54 optimal weight: 0.7980 overall best weight: 3.0786 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.5553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 16912 Z= 0.247 Angle : 0.508 5.098 23056 Z= 0.265 Chirality : 0.044 0.142 2912 Planarity : 0.002 0.032 2928 Dihedral : 3.511 12.155 2384 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 2.65 % Allowed : 17.48 % Favored : 79.87 % 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: -0.23 (0.17), residues: 2256 helix: 1.08 (0.18), residues: 704 sheet: -0.17 (0.22), residues: 432 loop : -0.91 (0.18), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP o 132 PHE 0.004 0.001 PHE b 106 TYR 0.024 0.001 TYR d 79 ARG 0.002 0.000 ARG o 126 *********************** 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 374 residues out of total 1808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 326 time to evaluate : 2.647 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: j 7 PHE cc_start: 0.7364 (OUTLIER) cc_final: 0.6909 (t80) REVERT: k 7 PHE cc_start: 0.7577 (OUTLIER) cc_final: 0.6918 (t80) REVERT: l 7 PHE cc_start: 0.7449 (OUTLIER) cc_final: 0.6749 (t80) REVERT: m 7 PHE cc_start: 0.7454 (OUTLIER) cc_final: 0.6960 (t80) REVERT: n 7 PHE cc_start: 0.7628 (OUTLIER) cc_final: 0.7179 (t80) REVERT: o 7 PHE cc_start: 0.7389 (OUTLIER) cc_final: 0.7076 (t80) REVERT: p 7 PHE cc_start: 0.7253 (OUTLIER) cc_final: 0.7013 (t80) outliers start: 48 outliers final: 28 residues processed: 362 average time/residue: 0.5707 time to fit residues: 324.0194 Evaluate side-chains 347 residues out of total 1808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 312 time to evaluate : 2.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 58 SER Chi-restraints excluded: chain f residue 58 SER Chi-restraints excluded: chain f residue 98 ASP Chi-restraints excluded: chain f residue 149 ASN Chi-restraints excluded: chain g residue 57 LEU Chi-restraints excluded: chain g residue 149 ASN Chi-restraints excluded: chain i residue 56 SER Chi-restraints excluded: chain j residue 7 PHE Chi-restraints excluded: chain j residue 56 SER Chi-restraints excluded: chain k residue 7 PHE Chi-restraints excluded: chain k residue 56 SER Chi-restraints excluded: chain l residue 7 PHE Chi-restraints excluded: chain l residue 56 SER Chi-restraints excluded: chain l residue 104 ILE Chi-restraints excluded: chain m residue 7 PHE Chi-restraints excluded: chain m residue 56 SER Chi-restraints excluded: chain m residue 103 ASP Chi-restraints excluded: chain n residue 7 PHE Chi-restraints excluded: chain n residue 57 LEU Chi-restraints excluded: chain o residue 7 PHE Chi-restraints excluded: chain o residue 149 ASN Chi-restraints excluded: chain p residue 7 PHE Chi-restraints excluded: chain p residue 34 VAL Chi-restraints excluded: chain p residue 68 ILE Chi-restraints excluded: chain p residue 149 ASN Chi-restraints excluded: chain d residue 58 SER Chi-restraints excluded: chain d residue 148 ASP Chi-restraints excluded: chain c residue 58 SER Chi-restraints excluded: chain c residue 99 SER Chi-restraints excluded: chain c residue 103 ASP Chi-restraints excluded: chain b residue 22 LEU Chi-restraints excluded: chain b residue 58 SER Chi-restraints excluded: chain a residue 37 SER Chi-restraints excluded: chain a residue 58 SER Chi-restraints excluded: chain a residue 103 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 72 optimal weight: 5.9990 chunk 194 optimal weight: 4.9990 chunk 42 optimal weight: 5.9990 chunk 127 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 216 optimal weight: 3.9990 chunk 179 optimal weight: 6.9990 chunk 100 optimal weight: 4.9990 chunk 18 optimal weight: 0.1980 chunk 71 optimal weight: 4.9990 chunk 113 optimal weight: 2.9990 overall best weight: 3.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 29 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.5812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 16912 Z= 0.264 Angle : 0.518 5.437 23056 Z= 0.271 Chirality : 0.044 0.144 2912 Planarity : 0.002 0.037 2928 Dihedral : 3.666 13.891 2384 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 3.15 % Allowed : 16.65 % Favored : 80.20 % 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: 1.23 (0.18), residues: 704 sheet: -0.09 (0.22), residues: 432 loop : -0.86 (0.18), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP i 132 PHE 0.004 0.001 PHE b 106 TYR 0.016 0.001 TYR g 79 ARG 0.002 0.000 ARG i 126 *********************** 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 372 residues out of total 1808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 315 time to evaluate : 2.515 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: j 7 PHE cc_start: 0.7502 (OUTLIER) cc_final: 0.6965 (t80) REVERT: k 7 PHE cc_start: 0.7684 (OUTLIER) cc_final: 0.7014 (t80) REVERT: l 7 PHE cc_start: 0.7528 (OUTLIER) cc_final: 0.6765 (t80) REVERT: m 7 PHE cc_start: 0.7512 (OUTLIER) cc_final: 0.6878 (t80) REVERT: n 7 PHE cc_start: 0.7661 (OUTLIER) cc_final: 0.7201 (t80) REVERT: o 7 PHE cc_start: 0.7422 (OUTLIER) cc_final: 0.7169 (t80) REVERT: o 94 VAL cc_start: 0.8127 (OUTLIER) cc_final: 0.7899 (p) REVERT: p 7 PHE cc_start: 0.7289 (OUTLIER) cc_final: 0.6990 (t80) outliers start: 57 outliers final: 35 residues processed: 359 average time/residue: 0.5522 time to fit residues: 310.6216 Evaluate side-chains 350 residues out of total 1808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 307 time to evaluate : 2.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 58 SER Chi-restraints excluded: chain f residue 58 SER Chi-restraints excluded: chain f residue 98 ASP Chi-restraints excluded: chain f residue 149 ASN Chi-restraints excluded: chain g residue 57 LEU Chi-restraints excluded: chain g residue 148 ASP Chi-restraints excluded: chain g residue 149 ASN Chi-restraints excluded: chain i residue 34 VAL Chi-restraints excluded: chain i residue 56 SER Chi-restraints excluded: chain j residue 7 PHE Chi-restraints excluded: chain j residue 56 SER Chi-restraints excluded: chain j residue 94 VAL Chi-restraints excluded: chain k residue 7 PHE Chi-restraints excluded: chain k residue 56 SER Chi-restraints excluded: chain l residue 7 PHE Chi-restraints excluded: chain l residue 56 SER 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 m residue 56 SER Chi-restraints excluded: chain m residue 103 ASP Chi-restraints excluded: chain n residue 7 PHE Chi-restraints excluded: chain o residue 7 PHE Chi-restraints excluded: chain o residue 94 VAL Chi-restraints excluded: chain p residue 7 PHE Chi-restraints excluded: chain p residue 34 VAL Chi-restraints excluded: chain p residue 68 ILE Chi-restraints excluded: chain p residue 94 VAL Chi-restraints excluded: chain p residue 149 ASN Chi-restraints excluded: chain d residue 34 VAL Chi-restraints excluded: chain d residue 58 SER Chi-restraints excluded: chain d residue 148 ASP Chi-restraints excluded: chain c residue 22 LEU Chi-restraints excluded: chain c residue 34 VAL Chi-restraints excluded: chain c residue 58 SER Chi-restraints excluded: chain c residue 99 SER Chi-restraints excluded: chain c residue 103 ASP Chi-restraints excluded: chain b residue 34 VAL Chi-restraints excluded: chain b residue 58 SER Chi-restraints excluded: chain a residue 34 VAL Chi-restraints excluded: chain a residue 37 SER Chi-restraints excluded: chain a residue 58 SER Chi-restraints excluded: chain a residue 103 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 208 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 123 optimal weight: 6.9990 chunk 158 optimal weight: 4.9990 chunk 122 optimal weight: 1.9990 chunk 182 optimal weight: 7.9990 chunk 121 optimal weight: 2.9990 chunk 215 optimal weight: 7.9990 chunk 135 optimal weight: 7.9990 chunk 131 optimal weight: 0.6980 chunk 99 optimal weight: 4.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- 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 ** p 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.5957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 16912 Z= 0.226 Angle : 0.508 5.617 23056 Z= 0.263 Chirality : 0.044 0.144 2912 Planarity : 0.002 0.038 2928 Dihedral : 3.664 13.572 2384 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 2.88 % Allowed : 17.48 % Favored : 79.65 % 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: 1.56 (0.18), residues: 704 sheet: 0.00 (0.22), residues: 432 loop : -0.79 (0.18), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP i 132 PHE 0.004 0.001 PHE b 106 TYR 0.008 0.001 TYR g 79 ARG 0.001 0.000 ARG n 59 *********************** 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 377 residues out of total 1808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 325 time to evaluate : 2.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: e 29 GLN cc_start: 0.6545 (OUTLIER) cc_final: 0.6319 (tt0) REVERT: h 7 PHE cc_start: 0.7890 (OUTLIER) cc_final: 0.7422 (t80) REVERT: j 7 PHE cc_start: 0.7527 (OUTLIER) cc_final: 0.6987 (t80) REVERT: k 7 PHE cc_start: 0.7715 (OUTLIER) cc_final: 0.7023 (t80) REVERT: l 7 PHE cc_start: 0.7516 (OUTLIER) cc_final: 0.6742 (t80) REVERT: m 7 PHE cc_start: 0.7513 (OUTLIER) cc_final: 0.6882 (t80) REVERT: n 7 PHE cc_start: 0.7666 (OUTLIER) cc_final: 0.7178 (t80) REVERT: o 7 PHE cc_start: 0.7547 (OUTLIER) cc_final: 0.7246 (t80) REVERT: o 94 VAL cc_start: 0.8143 (OUTLIER) cc_final: 0.7912 (p) REVERT: p 7 PHE cc_start: 0.7361 (OUTLIER) cc_final: 0.7121 (t80) outliers start: 52 outliers final: 31 residues processed: 364 average time/residue: 0.5804 time to fit residues: 331.6284 Evaluate side-chains 343 residues out of total 1808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 302 time to evaluate : 2.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 29 GLN Chi-restraints excluded: chain e residue 58 SER Chi-restraints excluded: chain f residue 29 GLN Chi-restraints excluded: chain f residue 58 SER Chi-restraints excluded: chain f residue 98 ASP Chi-restraints excluded: chain f residue 149 ASN Chi-restraints excluded: chain g residue 57 LEU Chi-restraints excluded: chain g residue 149 ASN Chi-restraints excluded: chain h residue 7 PHE Chi-restraints excluded: chain i residue 34 VAL Chi-restraints excluded: chain i residue 56 SER Chi-restraints excluded: chain j residue 7 PHE Chi-restraints excluded: chain j residue 56 SER Chi-restraints excluded: chain j residue 94 VAL Chi-restraints excluded: chain k residue 7 PHE Chi-restraints excluded: chain k residue 56 SER Chi-restraints excluded: chain l residue 7 PHE Chi-restraints excluded: chain l residue 56 SER Chi-restraints excluded: chain l residue 104 ILE Chi-restraints excluded: chain m residue 7 PHE Chi-restraints excluded: chain m residue 56 SER Chi-restraints excluded: chain m residue 103 ASP Chi-restraints excluded: chain n residue 7 PHE Chi-restraints excluded: chain o residue 7 PHE Chi-restraints excluded: chain o residue 94 VAL 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 149 ASN Chi-restraints excluded: chain d residue 34 VAL Chi-restraints excluded: chain d residue 58 SER Chi-restraints excluded: chain d residue 148 ASP Chi-restraints excluded: chain c residue 34 VAL Chi-restraints excluded: chain c residue 58 SER Chi-restraints excluded: chain c residue 99 SER Chi-restraints excluded: chain b residue 34 VAL Chi-restraints excluded: chain b residue 58 SER Chi-restraints excluded: chain a residue 34 VAL Chi-restraints excluded: chain a residue 37 SER Chi-restraints excluded: chain a residue 58 SER Chi-restraints excluded: chain a residue 103 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 133 optimal weight: 5.9990 chunk 86 optimal weight: 6.9990 chunk 128 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 137 optimal weight: 3.9990 chunk 147 optimal weight: 2.9990 chunk 106 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 chunk 169 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** p 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 29 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.6107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 16912 Z= 0.276 Angle : 0.538 5.940 23056 Z= 0.280 Chirality : 0.044 0.143 2912 Planarity : 0.002 0.038 2928 Dihedral : 3.785 14.731 2384 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 2.71 % Allowed : 18.36 % Favored : 78.93 % 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: 0.19 (0.17), residues: 2256 helix: 1.49 (0.18), residues: 720 sheet: 0.08 (0.22), residues: 432 loop : -0.75 (0.18), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP h 132 PHE 0.004 0.001 PHE e 108 TYR 0.010 0.001 TYR f 30 ARG 0.001 0.000 ARG j 36 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 304 time to evaluate : 2.601 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: 0.7899 (OUTLIER) cc_final: 0.7424 (t80) REVERT: i 7 PHE cc_start: 0.7986 (OUTLIER) cc_final: 0.7282 (t80) REVERT: j 7 PHE cc_start: 0.7646 (OUTLIER) cc_final: 0.7099 (t80) REVERT: k 7 PHE cc_start: 0.7744 (OUTLIER) cc_final: 0.7084 (t80) REVERT: l 7 PHE cc_start: 0.7567 (OUTLIER) cc_final: 0.6865 (t80) REVERT: m 7 PHE cc_start: 0.7570 (OUTLIER) cc_final: 0.6947 (t80) REVERT: n 7 PHE cc_start: 0.7689 (OUTLIER) cc_final: 0.7204 (t80) REVERT: o 7 PHE cc_start: 0.7550 (OUTLIER) cc_final: 0.7278 (t80) REVERT: o 94 VAL cc_start: 0.8159 (OUTLIER) cc_final: 0.7938 (p) REVERT: p 7 PHE cc_start: 0.7420 (OUTLIER) cc_final: 0.7202 (t80) outliers start: 49 outliers final: 36 residues processed: 343 average time/residue: 0.5470 time to fit residues: 293.9596 Evaluate side-chains 345 residues out of total 1808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 299 time to evaluate : 2.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 58 SER Chi-restraints excluded: chain f residue 22 LEU Chi-restraints excluded: chain f residue 58 SER Chi-restraints excluded: chain f residue 98 ASP Chi-restraints excluded: chain f residue 149 ASN Chi-restraints excluded: chain g residue 57 LEU Chi-restraints excluded: chain g residue 148 ASP Chi-restraints excluded: chain g residue 149 ASN 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 i residue 56 SER Chi-restraints excluded: chain j residue 7 PHE Chi-restraints excluded: chain j residue 56 SER Chi-restraints excluded: chain j residue 94 VAL Chi-restraints excluded: chain k residue 7 PHE Chi-restraints excluded: chain k residue 56 SER Chi-restraints excluded: chain l residue 7 PHE Chi-restraints excluded: chain l residue 56 SER 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 m residue 56 SER Chi-restraints excluded: chain m residue 103 ASP 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 94 VAL 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 p residue 149 ASN Chi-restraints excluded: chain d residue 34 VAL Chi-restraints excluded: chain d residue 58 SER Chi-restraints excluded: chain d residue 148 ASP Chi-restraints excluded: chain d residue 149 ASN Chi-restraints excluded: chain c residue 22 LEU Chi-restraints excluded: chain c residue 34 VAL Chi-restraints excluded: chain c residue 58 SER Chi-restraints excluded: chain b residue 34 VAL Chi-restraints excluded: chain b residue 58 SER Chi-restraints excluded: chain a residue 34 VAL Chi-restraints excluded: chain a residue 37 SER Chi-restraints excluded: chain a residue 58 SER Chi-restraints excluded: chain a residue 103 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 196 optimal weight: 9.9990 chunk 206 optimal weight: 7.9990 chunk 188 optimal weight: 0.0170 chunk 201 optimal weight: 6.9990 chunk 121 optimal weight: 0.9980 chunk 87 optimal weight: 6.9990 chunk 157 optimal weight: 7.9990 chunk 61 optimal weight: 0.8980 chunk 181 optimal weight: 4.9990 chunk 190 optimal weight: 5.9990 chunk 200 optimal weight: 0.7980 overall best weight: 1.5420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** f 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.6116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 16912 Z= 0.160 Angle : 0.510 6.214 23056 Z= 0.258 Chirality : 0.044 0.147 2912 Planarity : 0.002 0.038 2928 Dihedral : 3.610 13.385 2384 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 2.27 % Allowed : 19.03 % Favored : 78.71 % 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: 0.51 (0.17), residues: 2256 helix: 1.90 (0.18), residues: 720 sheet: 0.28 (0.22), residues: 432 loop : -0.68 (0.18), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP i 132 PHE 0.003 0.000 PHE b 106 TYR 0.007 0.001 TYR g 79 ARG 0.001 0.000 ARG n 59 *********************** 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 371 residues out of total 1808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 330 time to evaluate : 2.593 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: g 7 PHE cc_start: 0.7571 (OUTLIER) cc_final: 0.7289 (t80) REVERT: h 7 PHE cc_start: 0.7869 (OUTLIER) cc_final: 0.7346 (t80) REVERT: i 7 PHE cc_start: 0.7992 (OUTLIER) cc_final: 0.7261 (t80) REVERT: j 7 PHE cc_start: 0.7616 (OUTLIER) cc_final: 0.7112 (t80) REVERT: k 7 PHE cc_start: 0.7790 (OUTLIER) cc_final: 0.7019 (t80) REVERT: l 7 PHE cc_start: 0.7565 (OUTLIER) cc_final: 0.6905 (t80) REVERT: m 7 PHE cc_start: 0.7507 (OUTLIER) cc_final: 0.6858 (t80) REVERT: n 7 PHE cc_start: 0.7667 (OUTLIER) cc_final: 0.7191 (t80) REVERT: o 7 PHE cc_start: 0.7522 (OUTLIER) cc_final: 0.7218 (t80) REVERT: o 94 VAL cc_start: 0.8129 (OUTLIER) cc_final: 0.7903 (p) REVERT: p 7 PHE cc_start: 0.7356 (OUTLIER) cc_final: 0.7151 (t80) outliers start: 41 outliers final: 25 residues processed: 362 average time/residue: 0.5553 time to fit residues: 315.6776 Evaluate side-chains 344 residues out of total 1808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 308 time to evaluate : 2.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 58 SER Chi-restraints excluded: chain f residue 22 LEU Chi-restraints excluded: chain g residue 7 PHE Chi-restraints excluded: chain g residue 57 LEU Chi-restraints excluded: chain g residue 148 ASP Chi-restraints excluded: chain g residue 149 ASN 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 i residue 56 SER Chi-restraints excluded: chain j residue 7 PHE Chi-restraints excluded: chain j residue 56 SER Chi-restraints excluded: chain k residue 7 PHE Chi-restraints excluded: chain l residue 7 PHE Chi-restraints excluded: chain l residue 56 SER Chi-restraints excluded: chain m residue 7 PHE Chi-restraints excluded: chain m residue 56 SER Chi-restraints excluded: chain m residue 103 ASP Chi-restraints excluded: chain n residue 7 PHE Chi-restraints excluded: chain o residue 7 PHE Chi-restraints excluded: chain o residue 94 VAL Chi-restraints excluded: chain p residue 7 PHE Chi-restraints excluded: chain p residue 34 VAL Chi-restraints excluded: chain p residue 43 LEU Chi-restraints excluded: chain p residue 94 VAL Chi-restraints excluded: chain d residue 34 VAL Chi-restraints excluded: chain d residue 58 SER Chi-restraints excluded: chain d residue 148 ASP Chi-restraints excluded: chain d residue 149 ASN Chi-restraints excluded: chain c residue 58 SER Chi-restraints excluded: chain c residue 68 ILE Chi-restraints excluded: chain b residue 34 VAL Chi-restraints excluded: chain b residue 58 SER Chi-restraints excluded: chain a residue 34 VAL Chi-restraints excluded: chain a residue 58 SER Chi-restraints excluded: chain a residue 103 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 132 optimal weight: 3.9990 chunk 212 optimal weight: 0.8980 chunk 129 optimal weight: 6.9990 chunk 100 optimal weight: 4.9990 chunk 147 optimal weight: 0.6980 chunk 223 optimal weight: 4.9990 chunk 205 optimal weight: 0.2980 chunk 177 optimal weight: 3.9990 chunk 18 optimal weight: 0.6980 chunk 137 optimal weight: 5.9990 chunk 108 optimal weight: 5.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** f 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.6170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 16912 Z= 0.157 Angle : 0.523 7.117 23056 Z= 0.264 Chirality : 0.044 0.145 2912 Planarity : 0.002 0.038 2928 Dihedral : 3.530 12.636 2384 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 2.05 % Allowed : 19.91 % Favored : 78.04 % 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: 0.67 (0.17), residues: 2256 helix: 2.06 (0.18), residues: 720 sheet: 0.47 (0.22), residues: 432 loop : -0.66 (0.18), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP i 132 PHE 0.003 0.000 PHE b 106 TYR 0.009 0.001 TYR a 79 ARG 0.001 0.000 ARG k 59 ********************** 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 361 residues out of total 1808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 324 time to evaluate : 2.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: g 7 PHE cc_start: 0.7504 (OUTLIER) cc_final: 0.7239 (t80) REVERT: h 7 PHE cc_start: 0.7862 (OUTLIER) cc_final: 0.7333 (t80) REVERT: i 7 PHE cc_start: 0.8022 (OUTLIER) cc_final: 0.7290 (t80) REVERT: j 7 PHE cc_start: 0.7583 (OUTLIER) cc_final: 0.7091 (t80) REVERT: k 7 PHE cc_start: 0.7773 (OUTLIER) cc_final: 0.7049 (t80) REVERT: l 7 PHE cc_start: 0.7561 (OUTLIER) cc_final: 0.6876 (t80) REVERT: m 7 PHE cc_start: 0.7472 (OUTLIER) cc_final: 0.6905 (t80) REVERT: n 7 PHE cc_start: 0.7659 (OUTLIER) cc_final: 0.7194 (t80) REVERT: o 7 PHE cc_start: 0.7515 (OUTLIER) cc_final: 0.7187 (t80) outliers start: 37 outliers final: 25 residues processed: 354 average time/residue: 0.5492 time to fit residues: 307.5555 Evaluate side-chains 352 residues out of total 1808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 318 time to evaluate : 2.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 58 SER Chi-restraints excluded: chain f residue 22 LEU Chi-restraints excluded: chain g residue 7 PHE Chi-restraints excluded: chain g residue 57 LEU Chi-restraints excluded: chain g residue 148 ASP Chi-restraints excluded: chain g residue 149 ASN 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 i residue 56 SER 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 56 SER Chi-restraints excluded: chain l residue 94 VAL Chi-restraints excluded: chain m residue 7 PHE Chi-restraints excluded: chain m residue 103 ASP Chi-restraints excluded: chain n residue 7 PHE Chi-restraints excluded: chain o residue 7 PHE Chi-restraints excluded: chain p residue 34 VAL Chi-restraints excluded: chain p residue 43 LEU Chi-restraints excluded: chain p residue 94 VAL Chi-restraints excluded: chain d residue 34 VAL Chi-restraints excluded: chain d residue 58 SER Chi-restraints excluded: chain d residue 148 ASP Chi-restraints excluded: chain d residue 149 ASN Chi-restraints excluded: chain c residue 34 VAL Chi-restraints excluded: chain c residue 58 SER 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 b residue 58 SER Chi-restraints excluded: chain a residue 34 VAL Chi-restraints excluded: chain a residue 103 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 141 optimal weight: 4.9990 chunk 189 optimal weight: 5.9990 chunk 54 optimal weight: 0.8980 chunk 163 optimal weight: 8.9990 chunk 26 optimal weight: 0.9980 chunk 49 optimal weight: 5.9990 chunk 177 optimal weight: 4.9990 chunk 74 optimal weight: 0.7980 chunk 182 optimal weight: 0.7980 chunk 22 optimal weight: 7.9990 chunk 32 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.3014 r_free = 0.3014 target = 0.059228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.048602 restraints weight = 170849.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.051214 restraints weight = 65596.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.052855 restraints weight = 32857.024| |-----------------------------------------------------------------------------| r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 moved from start: 0.6177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 16912 Z= 0.142 Angle : 0.517 6.827 23056 Z= 0.259 Chirality : 0.044 0.148 2912 Planarity : 0.002 0.038 2928 Dihedral : 3.420 12.490 2384 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.38 % Allowed : 20.69 % Favored : 77.93 % 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: 0.89 (0.17), residues: 2256 helix: 2.30 (0.19), residues: 720 sheet: 0.68 (0.22), residues: 432 loop : -0.60 (0.18), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP i 132 PHE 0.004 0.000 PHE p 7 TYR 0.008 0.000 TYR a 79 ARG 0.001 0.000 ARG n 59 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7256.85 seconds wall clock time: 127 minutes 16.18 seconds (7636.18 seconds total)