Starting phenix.real_space_refine on Wed Sep 17 18:55:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rnu_19395/09_2025/8rnu_19395.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rnu_19395/09_2025/8rnu_19395.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8rnu_19395/09_2025/8rnu_19395.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rnu_19395/09_2025/8rnu_19395.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8rnu_19395/09_2025/8rnu_19395.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rnu_19395/09_2025/8rnu_19395.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 48 5.16 5 C 7044 2.51 5 N 1692 2.21 5 O 2064 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 51 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10848 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 904 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 103} Chain breaks: 1 Chain: "K" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 904 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 103} Chain breaks: 1 Chain: "E" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 904 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 103} Chain breaks: 1 Chain: "I" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 904 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 103} Chain breaks: 1 Chain: "C" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 904 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 103} Chain breaks: 1 Chain: "G" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 904 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 103} Chain breaks: 1 Chain: "B" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 904 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 103} Chain breaks: 1 Chain: "H" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 904 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 103} Chain breaks: 1 Chain: "D" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 904 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 103} Chain breaks: 1 Chain: "J" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 904 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 103} Chain breaks: 1 Chain: "F" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 904 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 103} Chain breaks: 1 Chain: "L" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 904 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 103} Chain breaks: 1 Time building chain proxies: 2.90, per 1000 atoms: 0.27 Number of scatterers: 10848 At special positions: 0 Unit cell: (114.48, 110.24, 68.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 48 16.00 O 2064 8.00 N 1692 7.00 C 7044 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS B 111 " distance=2.04 Simple disulfide: pdb=" SG CYS E 52 " - pdb=" SG CYS F 111 " distance=2.03 Simple disulfide: pdb=" SG CYS E 111 " - pdb=" SG CYS F 52 " distance=2.03 Simple disulfide: pdb=" SG CYS C 111 " - pdb=" SG CYS D 52 " distance=2.03 Simple disulfide: pdb=" SG CYS G 52 " - pdb=" SG CYS H 111 " distance=2.03 Simple disulfide: pdb=" SG CYS G 111 " - pdb=" SG CYS H 52 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.93 Conformation dependent library (CDL) restraints added in 456.4 milliseconds Enol-peptide restraints added in 1.2 microseconds 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2592 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 16 sheets defined 18.9% alpha, 22.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 67 through 74 removed outlier: 3.982A pdb=" N ASN A 74 " --> pdb=" O GLU A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 111 Processing helix chain 'K' and resid 67 through 72 removed outlier: 4.230A pdb=" N LEU K 72 " --> pdb=" O LEU K 69 " (cutoff:3.500A) Processing helix chain 'K' and resid 100 through 103 Processing helix chain 'K' and resid 104 through 111 Processing helix chain 'E' and resid 67 through 72 Processing helix chain 'E' and resid 74 through 78 removed outlier: 3.524A pdb=" N ALA E 77 " --> pdb=" O ASN E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 111 Processing helix chain 'I' and resid 67 through 71 Processing helix chain 'I' and resid 74 through 78 Processing helix chain 'I' and resid 100 through 103 Processing helix chain 'I' and resid 104 through 111 Processing helix chain 'C' and resid 67 through 74 removed outlier: 3.756A pdb=" N ASN C 74 " --> pdb=" O GLU C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 78 Processing helix chain 'C' and resid 104 through 111 Processing helix chain 'G' and resid 37 through 39 No H-bonds generated for 'chain 'G' and resid 37 through 39' Processing helix chain 'G' and resid 67 through 72 removed outlier: 4.017A pdb=" N LEU G 72 " --> pdb=" O LEU G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 100 through 103 Processing helix chain 'G' and resid 104 through 111 Processing helix chain 'B' and resid 67 through 72 Processing helix chain 'B' and resid 74 through 78 removed outlier: 3.745A pdb=" N ALA B 77 " --> pdb=" O ASN B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 111 Processing helix chain 'H' and resid 67 through 71 Processing helix chain 'H' and resid 73 through 78 removed outlier: 4.539A pdb=" N ALA H 77 " --> pdb=" O ILE H 73 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 103 Processing helix chain 'H' and resid 104 through 111 Processing helix chain 'D' and resid 67 through 74 removed outlier: 3.888A pdb=" N ASN D 74 " --> pdb=" O GLU D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 78 Processing helix chain 'D' and resid 100 through 103 removed outlier: 4.028A pdb=" N LEU D 103 " --> pdb=" O ILE D 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 100 through 103' Processing helix chain 'D' and resid 104 through 111 Processing helix chain 'J' and resid 67 through 71 Processing helix chain 'J' and resid 73 through 78 removed outlier: 4.550A pdb=" N ALA J 77 " --> pdb=" O ILE J 73 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY J 78 " --> pdb=" O ASN J 74 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 73 through 78' Processing helix chain 'J' and resid 100 through 103 Processing helix chain 'J' and resid 104 through 111 Processing helix chain 'F' and resid 67 through 72 Processing helix chain 'F' and resid 74 through 78 Processing helix chain 'F' and resid 100 through 103 removed outlier: 3.504A pdb=" N LEU F 103 " --> pdb=" O ILE F 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 100 through 103' Processing helix chain 'F' and resid 104 through 112 Processing helix chain 'L' and resid 37 through 39 No H-bonds generated for 'chain 'L' and resid 37 through 39' Processing helix chain 'L' and resid 67 through 71 removed outlier: 3.602A pdb=" N GLU L 70 " --> pdb=" O ASN L 67 " (cutoff:3.500A) Processing helix chain 'L' and resid 100 through 103 Processing helix chain 'L' and resid 104 through 111 Processing sheet with id=AA1, first strand: chain 'A' and resid 6 through 10 removed outlier: 3.952A pdb=" N ASN A 6 " --> pdb=" O SER A 19 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL A 15 " --> pdb=" O PHE A 10 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N TYR A 44 " --> pdb=" O TYR A 53 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N TYR A 53 " --> pdb=" O TYR A 44 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N CYS A 52 " --> pdb=" O TYR B 117 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS B 118 " --> pdb=" O ASP B 95 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ASP B 95 " --> pdb=" O LYS B 118 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 95 through 96 removed outlier: 3.799A pdb=" N ASP A 95 " --> pdb=" O LYS A 118 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N GLU A 115 " --> pdb=" O CYS B 52 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N VAL B 54 " --> pdb=" O GLU A 115 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N TYR A 117 " --> pdb=" O VAL B 54 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASP B 46 " --> pdb=" O LYS B 51 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N VAL B 15 " --> pdb=" O PHE B 10 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE B 10 " --> pdb=" O VAL B 15 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'K' and resid 6 through 9 removed outlier: 3.529A pdb=" N LYS K 8 " --> pdb=" O PHE K 17 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL K 34 " --> pdb=" O ALA K 43 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA K 43 " --> pdb=" O VAL K 34 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ASP K 36 " --> pdb=" O LEU K 41 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LEU K 41 " --> pdb=" O ASP K 36 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'K' and resid 95 through 97 removed outlier: 3.740A pdb=" N THR K 116 " --> pdb=" O ILE K 97 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 6 through 10 removed outlier: 3.702A pdb=" N PHE E 10 " --> pdb=" O VAL E 15 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N VAL E 15 " --> pdb=" O PHE E 10 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 95 through 96 removed outlier: 4.377A pdb=" N ASP E 95 " --> pdb=" O LYS E 118 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS E 118 " --> pdb=" O ASP E 95 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N GLU E 115 " --> pdb=" O CYS F 52 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N VAL F 54 " --> pdb=" O GLU E 115 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N TYR E 117 " --> pdb=" O VAL F 54 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N VAL F 15 " --> pdb=" O PHE F 10 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE F 10 " --> pdb=" O VAL F 15 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'I' and resid 16 through 19 removed outlier: 3.525A pdb=" N ASN I 32 " --> pdb=" O LEU I 45 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU I 45 " --> pdb=" O ASN I 32 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N VAL I 34 " --> pdb=" O ALA I 43 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ALA I 43 " --> pdb=" O VAL I 34 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ASP I 36 " --> pdb=" O LEU I 41 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LEU I 41 " --> pdb=" O ASP I 36 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR I 42 " --> pdb=" O ILE I 55 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE I 55 " --> pdb=" O THR I 42 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N CYS I 52 " --> pdb=" O TYR J 117 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR J 116 " --> pdb=" O ILE J 97 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 95 through 96 removed outlier: 3.846A pdb=" N LEU J 41 " --> pdb=" O ASP J 36 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ASP J 36 " --> pdb=" O LEU J 41 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA J 43 " --> pdb=" O VAL J 34 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL J 34 " --> pdb=" O ALA J 43 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 8 through 10 removed outlier: 3.732A pdb=" N PHE C 10 " --> pdb=" O VAL C 15 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N VAL C 15 " --> pdb=" O PHE C 10 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N VAL C 34 " --> pdb=" O ALA C 43 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA C 43 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASP C 36 " --> pdb=" O LEU C 41 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU C 41 " --> pdb=" O ASP C 36 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL C 54 " --> pdb=" O TYR D 117 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ASP D 95 " --> pdb=" O LYS D 118 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 8 through 10 removed outlier: 3.732A pdb=" N PHE C 10 " --> pdb=" O VAL C 15 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N VAL C 15 " --> pdb=" O PHE C 10 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS C 51 " --> pdb=" O ASP C 46 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL C 54 " --> pdb=" O TYR D 117 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ASP D 95 " --> pdb=" O LYS D 118 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 95 through 96 removed outlier: 3.864A pdb=" N ASP C 95 " --> pdb=" O LYS C 118 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N TYR C 117 " --> pdb=" O VAL D 54 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N TYR D 44 " --> pdb=" O TYR D 53 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N VAL D 15 " --> pdb=" O PHE D 10 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ASN D 6 " --> pdb=" O SER D 19 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 8 through 9 removed outlier: 3.571A pdb=" N LYS G 8 " --> pdb=" O PHE G 17 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU G 45 " --> pdb=" O ASN G 32 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL G 34 " --> pdb=" O ALA G 43 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ALA G 43 " --> pdb=" O VAL G 34 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ASP G 36 " --> pdb=" O LEU G 41 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU G 41 " --> pdb=" O ASP G 36 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N CYS G 52 " --> pdb=" O TYR H 117 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASP H 95 " --> pdb=" O LYS H 118 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 95 through 97 removed outlier: 3.653A pdb=" N ASP G 95 " --> pdb=" O LYS G 118 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N THR G 116 " --> pdb=" O ILE G 97 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASP H 36 " --> pdb=" O LEU H 41 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA H 43 " --> pdb=" O VAL H 34 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS H 8 " --> pdb=" O PHE H 17 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 95 through 96 removed outlier: 4.406A pdb=" N ASP F 95 " --> pdb=" O LYS F 118 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 16 through 19 removed outlier: 3.504A pdb=" N ASN L 32 " --> pdb=" O LEU L 45 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU L 45 " --> pdb=" O ASN L 32 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL L 34 " --> pdb=" O ALA L 43 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ALA L 43 " --> pdb=" O VAL L 34 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ASP L 36 " --> pdb=" O LEU L 41 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU L 41 " --> pdb=" O ASP L 36 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR L 42 " --> pdb=" O ILE L 55 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE L 55 " --> pdb=" O THR L 42 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 95 through 97 removed outlier: 3.657A pdb=" N ASP L 95 " --> pdb=" O LYS L 118 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N THR L 116 " --> pdb=" O ILE L 97 " (cutoff:3.500A) 301 hydrogen bonds defined for protein. 711 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: 1.64 Time building geometry restraints manager: 1.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.89 - 1.07: 2 1.07 - 1.26: 1897 1.26 - 1.44: 2658 1.44 - 1.63: 6430 1.63 - 1.81: 77 Bond restraints: 11064 Sorted by residual: bond pdb=" CG PRO I 64 " pdb=" CD PRO I 64 " ideal model delta sigma weight residual 1.503 0.886 0.617 3.40e-02 8.65e+02 3.30e+02 bond pdb=" CG PRO L 30 " pdb=" CD PRO L 30 " ideal model delta sigma weight residual 1.503 0.983 0.520 3.40e-02 8.65e+02 2.34e+02 bond pdb=" CG PRO E 21 " pdb=" CD PRO E 21 " ideal model delta sigma weight residual 1.503 1.164 0.339 3.40e-02 8.65e+02 9.96e+01 bond pdb=" N PRO I 64 " pdb=" CD PRO I 64 " ideal model delta sigma weight residual 1.473 1.576 -0.103 1.40e-02 5.10e+03 5.45e+01 bond pdb=" N PRO L 30 " pdb=" CD PRO L 30 " ideal model delta sigma weight residual 1.473 1.570 -0.097 1.40e-02 5.10e+03 4.78e+01 ... (remaining 11059 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.38: 14962 5.38 - 10.77: 45 10.77 - 16.15: 8 16.15 - 21.53: 7 21.53 - 26.92: 2 Bond angle restraints: 15024 Sorted by residual: angle pdb=" N PRO L 30 " pdb=" CD PRO L 30 " pdb=" CG PRO L 30 " ideal model delta sigma weight residual 103.20 76.28 26.92 1.50e+00 4.44e-01 3.22e+02 angle pdb=" N PRO I 64 " pdb=" CD PRO I 64 " pdb=" CG PRO I 64 " ideal model delta sigma weight residual 103.20 76.91 26.29 1.50e+00 4.44e-01 3.07e+02 angle pdb=" CA PRO K 30 " pdb=" N PRO K 30 " pdb=" CD PRO K 30 " ideal model delta sigma weight residual 112.00 92.30 19.70 1.40e+00 5.10e-01 1.98e+02 angle pdb=" CA PRO E 21 " pdb=" N PRO E 21 " pdb=" CD PRO E 21 " ideal model delta sigma weight residual 112.00 94.08 17.92 1.40e+00 5.10e-01 1.64e+02 angle pdb=" N PRO E 21 " pdb=" CD PRO E 21 " pdb=" CG PRO E 21 " ideal model delta sigma weight residual 103.20 85.20 18.00 1.50e+00 4.44e-01 1.44e+02 ... (remaining 15019 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.61: 5730 17.61 - 35.23: 778 35.23 - 52.84: 220 52.84 - 70.45: 35 70.45 - 88.07: 11 Dihedral angle restraints: 6774 sinusoidal: 2826 harmonic: 3948 Sorted by residual: dihedral pdb=" CA PRO L 23 " pdb=" C PRO L 23 " pdb=" N GLU L 24 " pdb=" CA GLU L 24 " ideal model delta harmonic sigma weight residual -180.00 -146.86 -33.14 0 5.00e+00 4.00e-02 4.39e+01 dihedral pdb=" CA PRO I 23 " pdb=" C PRO I 23 " pdb=" N GLU I 24 " pdb=" CA GLU I 24 " ideal model delta harmonic sigma weight residual -180.00 -147.56 -32.44 0 5.00e+00 4.00e-02 4.21e+01 dihedral pdb=" CA ILE B 100 " pdb=" C ILE B 100 " pdb=" N ASP B 101 " pdb=" CA ASP B 101 " ideal model delta harmonic sigma weight residual -180.00 -148.28 -31.72 0 5.00e+00 4.00e-02 4.02e+01 ... (remaining 6771 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1410 0.060 - 0.119: 307 0.119 - 0.179: 45 0.179 - 0.238: 1 0.238 - 0.298: 1 Chirality restraints: 1764 Sorted by residual: chirality pdb=" CA PRO I 64 " pdb=" N PRO I 64 " pdb=" C PRO I 64 " pdb=" CB PRO I 64 " both_signs ideal model delta sigma weight residual False 2.72 2.42 0.30 2.00e-01 2.50e+01 2.22e+00 chirality pdb=" CG LEU I 72 " pdb=" CB LEU I 72 " pdb=" CD1 LEU I 72 " pdb=" CD2 LEU I 72 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 8.29e-01 chirality pdb=" CG LEU K 71 " pdb=" CB LEU K 71 " pdb=" CD1 LEU K 71 " pdb=" CD2 LEU K 71 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 7.69e-01 ... (remaining 1761 not shown) Planarity restraints: 1920 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP K 29 " -0.093 5.00e-02 4.00e+02 1.23e-01 2.44e+01 pdb=" N PRO K 30 " 0.212 5.00e-02 4.00e+02 pdb=" CA PRO K 30 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO K 30 " -0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL E 20 " 0.080 5.00e-02 4.00e+02 1.07e-01 1.82e+01 pdb=" N PRO E 21 " -0.184 5.00e-02 4.00e+02 pdb=" CA PRO E 21 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO E 21 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET D 63 " 0.070 5.00e-02 4.00e+02 1.06e-01 1.79e+01 pdb=" N PRO D 64 " -0.183 5.00e-02 4.00e+02 pdb=" CA PRO D 64 " 0.058 5.00e-02 4.00e+02 pdb=" CD PRO D 64 " 0.056 5.00e-02 4.00e+02 ... (remaining 1917 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 239 2.66 - 3.22: 10477 3.22 - 3.78: 17612 3.78 - 4.34: 23571 4.34 - 4.90: 36419 Nonbonded interactions: 88318 Sorted by model distance: nonbonded pdb=" NE2 GLN K 1 " pdb=" O VAL K 22 " model vdw 2.104 3.120 nonbonded pdb=" OG SER L 19 " pdb=" OD1 ASN L 32 " model vdw 2.136 3.040 nonbonded pdb=" ND2 ASN G 74 " pdb=" OG1 THR H 2 " model vdw 2.144 3.120 nonbonded pdb=" O ASP A 46 " pdb=" N ASP A 50 " model vdw 2.163 3.120 nonbonded pdb=" O ASN C 38 " pdb=" NH2 ARG G 66 " model vdw 2.170 3.120 ... (remaining 88313 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 0.260 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: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.760 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3017 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 : 0.010 0.617 11070 Z= 0.352 Angle : 1.036 26.917 15036 Z= 0.602 Chirality : 0.050 0.298 1764 Planarity : 0.009 0.123 1920 Dihedral : 17.191 88.067 4164 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 28.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.06 % Favored : 89.94 % Rotamer: Outliers : 0.32 % Allowed : 21.31 % Favored : 78.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.17 (0.22), residues: 1272 helix: -0.79 (0.46), residues: 124 sheet: -0.34 (0.27), residues: 358 loop : -2.20 (0.20), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 66 TYR 0.009 0.001 TYR K 117 PHE 0.029 0.002 PHE J 25 HIS 0.004 0.001 HIS F 102 Details of bonding type rmsd covalent geometry : bond 0.01036 (11064) covalent geometry : angle 1.03621 (15024) SS BOND : bond 0.00291 ( 6) SS BOND : angle 0.74806 ( 12) hydrogen bonds : bond 0.32038 ( 290) hydrogen bonds : angle 10.64478 ( 711) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 50 time to evaluate : 0.445 Fit side-chains REVERT: E 17 PHE cc_start: 0.4986 (t80) cc_final: 0.4681 (t80) REVERT: I 99 ASN cc_start: 0.7568 (t0) cc_final: 0.7287 (t0) REVERT: G 63 MET cc_start: 0.0841 (tmm) cc_final: 0.0368 (tmm) REVERT: B 17 PHE cc_start: 0.3153 (t80) cc_final: 0.2603 (t80) REVERT: F 63 MET cc_start: 0.2392 (tpt) cc_final: 0.0798 (tmm) REVERT: F 72 LEU cc_start: 0.6307 (mt) cc_final: 0.5652 (pp) outliers start: 4 outliers final: 1 residues processed: 53 average time/residue: 0.0781 time to fit residues: 7.1461 Evaluate side-chains 48 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 47 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 7 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 40.0000 chunk 10 optimal weight: 20.0000 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 30.0000 chunk 124 optimal weight: 40.0000 chunk 103 optimal weight: 20.0000 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 8.9990 chunk 91 optimal weight: 4.9990 chunk 55 optimal weight: 20.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 32 ASN A 112 HIS ** K 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 58 ASN K 112 HIS ** I 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 112 HIS ** C 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 58 ASN G 112 HIS ** B 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 112 HIS J 6 ASN J 112 HIS L 32 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4945 r_free = 0.4945 target = 0.166445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4873 r_free = 0.4873 target = 0.153890 restraints weight = 37422.485| |-----------------------------------------------------------------------------| r_work (start): 0.4903 rms_B_bonded: 4.57 r_work (final): 0.4903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3157 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 11070 Z= 0.200 Angle : 0.789 10.808 15036 Z= 0.415 Chirality : 0.052 0.172 1764 Planarity : 0.008 0.082 1920 Dihedral : 7.241 34.499 1406 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 25.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.22 % Favored : 89.78 % Rotamer: Outliers : 4.01 % Allowed : 20.43 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.15 (0.22), residues: 1272 helix: -1.38 (0.43), residues: 120 sheet: -0.13 (0.28), residues: 346 loop : -2.16 (0.21), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 66 TYR 0.012 0.001 TYR E 108 PHE 0.025 0.002 PHE H 17 HIS 0.007 0.002 HIS F 102 Details of bonding type rmsd covalent geometry : bond 0.00465 (11064) covalent geometry : angle 0.78860 (15024) SS BOND : bond 0.00852 ( 6) SS BOND : angle 0.87179 ( 12) hydrogen bonds : bond 0.04441 ( 290) hydrogen bonds : angle 9.03912 ( 711) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 49 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 ASP cc_start: 0.3151 (OUTLIER) cc_final: 0.1994 (m-30) REVERT: A 102 HIS cc_start: -0.3428 (OUTLIER) cc_final: -0.3973 (t-170) REVERT: E 21 PRO cc_start: 0.4528 (Cg_exo) cc_final: 0.3540 (Cg_endo) REVERT: E 50 ASP cc_start: 0.4352 (OUTLIER) cc_final: 0.1843 (m-30) REVERT: C 50 ASP cc_start: 0.5951 (OUTLIER) cc_final: 0.5556 (m-30) REVERT: C 102 HIS cc_start: -0.3617 (OUTLIER) cc_final: -0.4370 (t70) REVERT: G 63 MET cc_start: 0.1626 (tmm) cc_final: 0.1014 (tmm) REVERT: B 81 LEU cc_start: 0.7912 (OUTLIER) cc_final: 0.7545 (mm) REVERT: F 45 LEU cc_start: -0.2088 (OUTLIER) cc_final: -0.6038 (pt) REVERT: F 63 MET cc_start: 0.2714 (tpt) cc_final: 0.0776 (tmm) REVERT: F 72 LEU cc_start: 0.6910 (mt) cc_final: 0.6271 (pp) outliers start: 50 outliers final: 21 residues processed: 95 average time/residue: 0.0888 time to fit residues: 13.0738 Evaluate side-chains 74 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 46 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 PHE Chi-restraints excluded: chain A residue 50 ASP Chi-restraints excluded: chain A residue 102 HIS Chi-restraints excluded: chain K residue 22 VAL Chi-restraints excluded: chain E residue 27 ASP Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 114 LYS Chi-restraints excluded: chain I residue 22 VAL Chi-restraints excluded: chain I residue 25 PHE Chi-restraints excluded: chain C residue 25 PHE Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 50 ASP Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 102 HIS Chi-restraints excluded: chain G residue 7 ILE Chi-restraints excluded: chain G residue 66 ARG Chi-restraints excluded: chain B residue 25 PHE Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 102 HIS Chi-restraints excluded: chain B residue 109 ARG Chi-restraints excluded: chain H residue 22 VAL Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain L residue 22 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 106 optimal weight: 10.0000 chunk 64 optimal weight: 40.0000 chunk 26 optimal weight: 20.0000 chunk 38 optimal weight: 50.0000 chunk 107 optimal weight: 50.0000 chunk 4 optimal weight: 5.9990 chunk 81 optimal weight: 50.0000 chunk 46 optimal weight: 0.0870 chunk 102 optimal weight: 10.0000 chunk 76 optimal weight: 8.9990 chunk 9 optimal weight: 0.9980 overall best weight: 5.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 112 HIS ** K 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 102 HIS ** I 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 32 ASN J 74 ASN F 6 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5021 r_free = 0.5021 target = 0.170127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4847 r_free = 0.4847 target = 0.152681 restraints weight = 59594.278| |-----------------------------------------------------------------------------| r_work (start): 0.4815 rms_B_bonded: 8.32 r_work (final): 0.4815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3764 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 11070 Z= 0.157 Angle : 0.680 9.325 15036 Z= 0.359 Chirality : 0.050 0.161 1764 Planarity : 0.007 0.073 1920 Dihedral : 6.943 32.024 1406 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 22.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.67 % Favored : 90.33 % Rotamer: Outliers : 5.05 % Allowed : 19.71 % Favored : 75.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.15 (0.23), residues: 1272 helix: -1.72 (0.37), residues: 140 sheet: -0.09 (0.27), residues: 352 loop : -2.12 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 66 TYR 0.008 0.001 TYR E 108 PHE 0.026 0.002 PHE J 25 HIS 0.005 0.001 HIS F 102 Details of bonding type rmsd covalent geometry : bond 0.00372 (11064) covalent geometry : angle 0.67999 (15024) SS BOND : bond 0.00332 ( 6) SS BOND : angle 0.61796 ( 12) hydrogen bonds : bond 0.03743 ( 290) hydrogen bonds : angle 8.29630 ( 711) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 45 time to evaluate : 0.540 Fit side-chains revert: symmetry clash REVERT: A 50 ASP cc_start: 0.3271 (OUTLIER) cc_final: 0.2200 (m-30) REVERT: A 102 HIS cc_start: -0.3802 (OUTLIER) cc_final: -0.4159 (t-170) REVERT: K 30 PRO cc_start: 0.5974 (Cg_endo) cc_final: 0.5191 (Cg_endo) REVERT: K 91 MET cc_start: 0.0761 (pmm) cc_final: -0.0016 (mmp) REVERT: E 21 PRO cc_start: 0.4604 (Cg_exo) cc_final: 0.3970 (Cg_endo) REVERT: E 27 ASP cc_start: 0.1170 (OUTLIER) cc_final: -0.0601 (p0) REVERT: C 50 ASP cc_start: 0.6341 (OUTLIER) cc_final: 0.5808 (m-30) REVERT: C 102 HIS cc_start: -0.4548 (OUTLIER) cc_final: -0.4867 (t70) REVERT: G 63 MET cc_start: 0.1387 (tmm) cc_final: 0.0876 (tmm) REVERT: B 81 LEU cc_start: 0.7851 (OUTLIER) cc_final: 0.7441 (mm) REVERT: D 101 ASP cc_start: 0.4081 (OUTLIER) cc_final: 0.3785 (m-30) REVERT: J 102 HIS cc_start: -0.1610 (OUTLIER) cc_final: -0.4390 (t70) REVERT: F 45 LEU cc_start: -0.1972 (OUTLIER) cc_final: -0.5895 (pt) REVERT: F 63 MET cc_start: 0.2679 (tpt) cc_final: 0.1661 (tmm) REVERT: F 72 LEU cc_start: 0.6574 (mt) cc_final: 0.6164 (pp) REVERT: L 63 MET cc_start: 0.0728 (tmm) cc_final: 0.0128 (tpt) outliers start: 63 outliers final: 27 residues processed: 104 average time/residue: 0.0766 time to fit residues: 13.1333 Evaluate side-chains 81 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 45 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 PHE Chi-restraints excluded: chain A residue 50 ASP Chi-restraints excluded: chain A residue 102 HIS Chi-restraints excluded: chain K residue 7 ILE Chi-restraints excluded: chain K residue 25 PHE Chi-restraints excluded: chain E residue 27 ASP Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain I residue 22 VAL Chi-restraints excluded: chain I residue 25 PHE Chi-restraints excluded: chain C residue 25 PHE Chi-restraints excluded: chain C residue 50 ASP Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 102 HIS Chi-restraints excluded: chain G residue 7 ILE Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain B residue 25 PHE Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 102 HIS Chi-restraints excluded: chain B residue 109 ARG Chi-restraints excluded: chain H residue 91 MET Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain J residue 7 ILE Chi-restraints excluded: chain J residue 18 ILE Chi-restraints excluded: chain J residue 25 PHE Chi-restraints excluded: chain J residue 102 HIS Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 102 HIS Chi-restraints excluded: chain L residue 7 ILE Chi-restraints excluded: chain L residue 17 PHE Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 25 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 58 optimal weight: 10.0000 chunk 84 optimal weight: 0.0970 chunk 128 optimal weight: 10.0000 chunk 79 optimal weight: 2.9990 chunk 18 optimal weight: 8.9990 chunk 114 optimal weight: 9.9990 chunk 7 optimal weight: 0.0980 chunk 57 optimal weight: 0.0030 chunk 119 optimal weight: 9.9990 chunk 39 optimal weight: 1.9990 chunk 40 optimal weight: 30.0000 overall best weight: 1.0392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 1 GLN A 32 ASN A 112 HIS K 1 GLN K 38 ASN E 112 HIS ** I 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 ASN B 74 ASN ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4897 r_free = 0.4897 target = 0.160030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4856 r_free = 0.4856 target = 0.147692 restraints weight = 52698.104| |-----------------------------------------------------------------------------| r_work (start): 0.4840 rms_B_bonded: 6.81 r_work (final): 0.4840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3022 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 11070 Z= 0.117 Angle : 0.608 10.912 15036 Z= 0.320 Chirality : 0.048 0.165 1764 Planarity : 0.007 0.071 1920 Dihedral : 6.203 27.814 1406 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 3.12 % Allowed : 21.47 % Favored : 75.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.93 (0.23), residues: 1272 helix: -1.39 (0.39), residues: 140 sheet: -0.28 (0.26), residues: 394 loop : -1.89 (0.23), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 66 TYR 0.010 0.001 TYR B 80 PHE 0.031 0.001 PHE J 25 HIS 0.003 0.001 HIS H 112 Details of bonding type rmsd covalent geometry : bond 0.00298 (11064) covalent geometry : angle 0.60845 (15024) SS BOND : bond 0.00230 ( 6) SS BOND : angle 0.49993 ( 12) hydrogen bonds : bond 0.02950 ( 290) hydrogen bonds : angle 7.39730 ( 711) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 51 time to evaluate : 0.446 Fit side-chains revert: symmetry clash REVERT: A 1 GLN cc_start: 0.6114 (OUTLIER) cc_final: 0.5626 (pp30) REVERT: A 63 MET cc_start: 0.3839 (tpp) cc_final: 0.3547 (tpt) REVERT: K 91 MET cc_start: 0.0873 (pmm) cc_final: 0.0131 (mmp) REVERT: E 21 PRO cc_start: 0.5404 (Cg_exo) cc_final: 0.4568 (Cg_endo) REVERT: E 50 ASP cc_start: 0.4122 (OUTLIER) cc_final: 0.2772 (m-30) REVERT: I 99 ASN cc_start: 0.8375 (t0) cc_final: 0.8078 (t0) REVERT: G 63 MET cc_start: 0.0828 (tmm) cc_final: 0.0602 (tmm) REVERT: B 81 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7856 (mm) REVERT: D 50 ASP cc_start: 0.3021 (OUTLIER) cc_final: 0.1870 (m-30) REVERT: D 63 MET cc_start: 0.3642 (tpp) cc_final: 0.3339 (tpp) REVERT: J 18 ILE cc_start: 0.9060 (OUTLIER) cc_final: 0.8697 (tp) REVERT: J 63 MET cc_start: -0.0345 (ppp) cc_final: -0.0633 (ppp) REVERT: F 63 MET cc_start: 0.2356 (tpt) cc_final: 0.1184 (tmm) REVERT: L 63 MET cc_start: 0.0338 (tmm) cc_final: -0.0338 (tpt) outliers start: 39 outliers final: 21 residues processed: 88 average time/residue: 0.0772 time to fit residues: 11.1370 Evaluate side-chains 73 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 47 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 GLN Chi-restraints excluded: chain A residue 25 PHE Chi-restraints excluded: chain A residue 50 ASP Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain K residue 25 PHE Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 114 LYS Chi-restraints excluded: chain I residue 22 VAL Chi-restraints excluded: chain I residue 25 PHE Chi-restraints excluded: chain C residue 25 PHE Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain G residue 7 ILE Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain B residue 25 PHE Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 109 ARG Chi-restraints excluded: chain H residue 22 VAL Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain J residue 18 ILE Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain L residue 2 THR Chi-restraints excluded: chain L residue 17 PHE Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 25 PHE Chi-restraints excluded: chain L residue 79 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 115 optimal weight: 20.0000 chunk 117 optimal weight: 8.9990 chunk 19 optimal weight: 9.9990 chunk 54 optimal weight: 8.9990 chunk 25 optimal weight: 0.9990 chunk 36 optimal weight: 40.0000 chunk 89 optimal weight: 8.9990 chunk 93 optimal weight: 0.9980 chunk 118 optimal weight: 0.9980 chunk 126 optimal weight: 10.0000 chunk 107 optimal weight: 7.9990 overall best weight: 3.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 102 HIS ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4916 r_free = 0.4916 target = 0.162825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4859 r_free = 0.4859 target = 0.149617 restraints weight = 53315.562| |-----------------------------------------------------------------------------| r_work (start): 0.4868 rms_B_bonded: 7.34 r_work (final): 0.4868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3127 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 11070 Z= 0.137 Angle : 0.627 9.620 15036 Z= 0.329 Chirality : 0.048 0.232 1764 Planarity : 0.007 0.069 1920 Dihedral : 6.197 27.939 1406 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 19.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.88 % Favored : 91.12 % Rotamer: Outliers : 4.17 % Allowed : 21.39 % Favored : 74.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.90 (0.23), residues: 1272 helix: -1.41 (0.39), residues: 142 sheet: -0.13 (0.27), residues: 374 loop : -1.90 (0.23), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 66 TYR 0.007 0.001 TYR E 108 PHE 0.023 0.001 PHE J 25 HIS 0.005 0.001 HIS F 102 Details of bonding type rmsd covalent geometry : bond 0.00330 (11064) covalent geometry : angle 0.62708 (15024) SS BOND : bond 0.00209 ( 6) SS BOND : angle 0.60470 ( 12) hydrogen bonds : bond 0.02868 ( 290) hydrogen bonds : angle 7.35170 ( 711) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 50 time to evaluate : 0.432 Fit side-chains revert: symmetry clash REVERT: A 50 ASP cc_start: 0.3432 (OUTLIER) cc_final: 0.2550 (m-30) REVERT: A 102 HIS cc_start: -0.3213 (OUTLIER) cc_final: -0.3817 (t70) REVERT: K 91 MET cc_start: 0.1059 (pmm) cc_final: 0.0284 (mmp) REVERT: E 21 PRO cc_start: 0.5412 (Cg_exo) cc_final: 0.4545 (Cg_endo) REVERT: E 50 ASP cc_start: 0.4331 (OUTLIER) cc_final: 0.2775 (m-30) REVERT: I 99 ASN cc_start: 0.8372 (t0) cc_final: 0.8023 (t0) REVERT: C 102 HIS cc_start: -0.3795 (OUTLIER) cc_final: -0.4065 (t70) REVERT: G 63 MET cc_start: 0.1251 (tmm) cc_final: 0.0889 (tmm) REVERT: G 102 HIS cc_start: -0.3149 (OUTLIER) cc_final: -0.4481 (t70) REVERT: B 81 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7848 (mm) REVERT: J 63 MET cc_start: 0.0194 (ppp) cc_final: -0.0207 (ppp) REVERT: J 102 HIS cc_start: -0.0014 (OUTLIER) cc_final: -0.3709 (t70) REVERT: F 17 PHE cc_start: 0.2045 (m-80) cc_final: 0.1746 (m-80) REVERT: F 63 MET cc_start: 0.2115 (tpt) cc_final: 0.1115 (tmm) REVERT: L 102 HIS cc_start: 0.0864 (OUTLIER) cc_final: -0.0917 (t70) outliers start: 52 outliers final: 31 residues processed: 97 average time/residue: 0.0811 time to fit residues: 12.6942 Evaluate side-chains 90 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 51 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 PHE Chi-restraints excluded: chain A residue 50 ASP Chi-restraints excluded: chain A residue 102 HIS Chi-restraints excluded: chain K residue 22 VAL Chi-restraints excluded: chain K residue 25 PHE Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 114 LYS Chi-restraints excluded: chain I residue 22 VAL Chi-restraints excluded: chain I residue 25 PHE Chi-restraints excluded: chain I residue 72 LEU Chi-restraints excluded: chain C residue 25 PHE Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 102 HIS Chi-restraints excluded: chain G residue 7 ILE Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 102 HIS Chi-restraints excluded: chain B residue 25 PHE Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 109 ARG Chi-restraints excluded: chain H residue 7 ILE Chi-restraints excluded: chain H residue 22 VAL Chi-restraints excluded: chain H residue 91 MET Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 114 LYS Chi-restraints excluded: chain J residue 18 ILE Chi-restraints excluded: chain J residue 25 PHE Chi-restraints excluded: chain J residue 102 HIS Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 102 HIS Chi-restraints excluded: chain L residue 7 ILE Chi-restraints excluded: chain L residue 17 PHE Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 25 PHE Chi-restraints excluded: chain L residue 79 THR Chi-restraints excluded: chain L residue 102 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 60 optimal weight: 30.0000 chunk 110 optimal weight: 30.0000 chunk 98 optimal weight: 0.7980 chunk 86 optimal weight: 6.9990 chunk 61 optimal weight: 7.9990 chunk 79 optimal weight: 0.4980 chunk 47 optimal weight: 30.0000 chunk 113 optimal weight: 0.9990 chunk 123 optimal weight: 2.9990 chunk 78 optimal weight: 9.9990 chunk 117 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 1 GLN A 112 HIS ** K 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 6 ASN I 38 ASN C 1 GLN ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4963 r_free = 0.4963 target = 0.173779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4961 r_free = 0.4961 target = 0.173298 restraints weight = 36381.224| |-----------------------------------------------------------------------------| r_work (start): 0.5006 rms_B_bonded: 0.19 r_work: 0.5004 rms_B_bonded: 0.20 restraints_weight: 0.5000 r_work: 0.5004 rms_B_bonded: 0.20 restraints_weight: 0.2500 r_work: 0.5004 rms_B_bonded: 0.20 restraints_weight: 0.1250 r_work: 0.5004 rms_B_bonded: 0.20 restraints_weight: 0.0625 r_work: 0.5004 rms_B_bonded: 0.20 restraints_weight: 0.0312 r_work: 0.5004 rms_B_bonded: 0.20 restraints_weight: 0.0156 r_work: 0.5004 rms_B_bonded: 0.20 restraints_weight: 0.0078 r_work: 0.5004 rms_B_bonded: 0.20 restraints_weight: 0.0039 r_work: 0.5004 rms_B_bonded: 0.20 restraints_weight: 0.0020 r_work: 0.5004 rms_B_bonded: 0.20 restraints_weight: 0.0010 r_work: 0.5004 rms_B_bonded: 0.20 restraints_weight: 0.0005 r_work: 0.5004 rms_B_bonded: 0.20 restraints_weight: 0.0002 r_work: 0.5004 rms_B_bonded: 0.20 restraints_weight: 0.0001 r_work: 0.5004 rms_B_bonded: 0.20 restraints_weight: 0.0001 r_work: 0.5004 rms_B_bonded: 0.20 restraints_weight: 0.0000 r_work: 0.5004 rms_B_bonded: 0.20 restraints_weight: 0.0000 r_work: 0.5004 rms_B_bonded: 0.20 restraints_weight: 0.0000 r_work: 0.5004 rms_B_bonded: 0.20 restraints_weight: 0.0000 r_work: 0.5004 rms_B_bonded: 0.20 restraints_weight: 0.0000 r_work (final): 0.5004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2750 moved from start: 0.3259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 11070 Z= 0.110 Angle : 0.572 11.457 15036 Z= 0.301 Chirality : 0.047 0.192 1764 Planarity : 0.007 0.066 1920 Dihedral : 5.798 25.384 1406 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 4.25 % Allowed : 21.39 % Favored : 74.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.76 (0.23), residues: 1272 helix: -1.24 (0.40), residues: 142 sheet: -0.09 (0.27), residues: 390 loop : -1.82 (0.23), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 66 TYR 0.008 0.001 TYR I 117 PHE 0.026 0.001 PHE J 25 HIS 0.003 0.001 HIS H 112 Details of bonding type rmsd covalent geometry : bond 0.00278 (11064) covalent geometry : angle 0.57218 (15024) SS BOND : bond 0.00181 ( 6) SS BOND : angle 0.37649 ( 12) hydrogen bonds : bond 0.02729 ( 290) hydrogen bonds : angle 6.85667 ( 711) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 51 time to evaluate : 0.444 Fit side-chains revert: symmetry clash REVERT: A 1 GLN cc_start: 0.1834 (OUTLIER) cc_final: 0.1053 (pp30) REVERT: K 91 MET cc_start: 0.1771 (pmm) cc_final: 0.0309 (mmp) REVERT: E 21 PRO cc_start: 0.4711 (Cg_exo) cc_final: 0.4155 (Cg_endo) REVERT: E 50 ASP cc_start: 0.3868 (OUTLIER) cc_final: 0.1475 (m-30) REVERT: I 99 ASN cc_start: 0.7558 (t0) cc_final: 0.7170 (t0) REVERT: C 1 GLN cc_start: 0.3873 (OUTLIER) cc_final: 0.3062 (pp30) REVERT: C 102 HIS cc_start: -0.3102 (OUTLIER) cc_final: -0.3474 (t70) REVERT: G 102 HIS cc_start: -0.1937 (OUTLIER) cc_final: -0.3734 (t70) REVERT: B 81 LEU cc_start: 0.7954 (OUTLIER) cc_final: 0.7624 (mm) REVERT: D 50 ASP cc_start: 0.2998 (OUTLIER) cc_final: 0.1368 (m-30) REVERT: D 101 ASP cc_start: 0.3264 (OUTLIER) cc_final: 0.2448 (m-30) REVERT: J 63 MET cc_start: -0.0523 (ppp) cc_final: -0.0874 (ppp) REVERT: J 102 HIS cc_start: -0.0507 (OUTLIER) cc_final: -0.4031 (t70) REVERT: F 17 PHE cc_start: 0.2219 (m-80) cc_final: 0.1910 (m-80) REVERT: F 63 MET cc_start: 0.1710 (tpt) cc_final: 0.0776 (tmm) REVERT: L 10 PHE cc_start: 0.2261 (m-80) cc_final: 0.1933 (m-80) REVERT: L 63 MET cc_start: 0.0657 (tmm) cc_final: -0.0617 (tpt) REVERT: L 72 LEU cc_start: -0.1050 (tp) cc_final: -0.1337 (pt) REVERT: L 102 HIS cc_start: 0.0682 (OUTLIER) cc_final: -0.0973 (t70) outliers start: 53 outliers final: 30 residues processed: 100 average time/residue: 0.0806 time to fit residues: 13.1640 Evaluate side-chains 89 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 49 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 GLN Chi-restraints excluded: chain A residue 25 PHE Chi-restraints excluded: chain A residue 50 ASP Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain K residue 22 VAL Chi-restraints excluded: chain K residue 25 PHE Chi-restraints excluded: chain K residue 73 ILE Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain I residue 22 VAL Chi-restraints excluded: chain I residue 25 PHE Chi-restraints excluded: chain I residue 72 LEU Chi-restraints excluded: chain C residue 1 GLN Chi-restraints excluded: chain C residue 25 PHE Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 102 HIS Chi-restraints excluded: chain G residue 7 ILE Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 102 HIS Chi-restraints excluded: chain B residue 25 PHE Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain H residue 7 ILE Chi-restraints excluded: chain H residue 22 VAL Chi-restraints excluded: chain H residue 63 MET Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 117 TYR Chi-restraints excluded: chain J residue 18 ILE Chi-restraints excluded: chain J residue 25 PHE Chi-restraints excluded: chain J residue 102 HIS Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain L residue 2 THR Chi-restraints excluded: chain L residue 17 PHE Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 25 PHE Chi-restraints excluded: chain L residue 79 THR Chi-restraints excluded: chain L residue 102 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 15 optimal weight: 9.9990 chunk 94 optimal weight: 6.9990 chunk 99 optimal weight: 0.9990 chunk 113 optimal weight: 0.9980 chunk 122 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 chunk 118 optimal weight: 6.9990 chunk 30 optimal weight: 20.0000 chunk 9 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 112 HIS ** K 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 74 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4954 r_free = 0.4954 target = 0.173179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4951 r_free = 0.4951 target = 0.172532 restraints weight = 34853.040| |-----------------------------------------------------------------------------| r_work (start): 0.5030 rms_B_bonded: 0.29 r_work: 0.5019 rms_B_bonded: 0.39 restraints_weight: 0.5000 r_work: 0.5019 rms_B_bonded: 0.39 restraints_weight: 0.2500 r_work: 0.5016 rms_B_bonded: 0.49 restraints_weight: 0.1250 r_work: 0.5016 rms_B_bonded: 0.49 restraints_weight: 0.0625 r_work (final): 0.5016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2896 moved from start: 0.3414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 11070 Z= 0.123 Angle : 0.603 13.293 15036 Z= 0.313 Chirality : 0.047 0.186 1764 Planarity : 0.007 0.068 1920 Dihedral : 5.844 26.742 1406 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 17.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.96 % Favored : 91.04 % Rotamer: Outliers : 3.77 % Allowed : 21.39 % Favored : 74.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.80 (0.23), residues: 1272 helix: -1.21 (0.40), residues: 142 sheet: -0.13 (0.27), residues: 390 loop : -1.86 (0.23), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 66 TYR 0.009 0.001 TYR I 117 PHE 0.022 0.001 PHE J 25 HIS 0.005 0.001 HIS F 102 Details of bonding type rmsd covalent geometry : bond 0.00305 (11064) covalent geometry : angle 0.60353 (15024) SS BOND : bond 0.00164 ( 6) SS BOND : angle 0.49734 ( 12) hydrogen bonds : bond 0.02649 ( 290) hydrogen bonds : angle 6.83945 ( 711) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 49 time to evaluate : 0.538 Fit side-chains revert: symmetry clash REVERT: A 50 ASP cc_start: 0.3092 (OUTLIER) cc_final: 0.2326 (m-30) REVERT: K 91 MET cc_start: 0.1270 (pmm) cc_final: 0.0445 (mmp) REVERT: E 21 PRO cc_start: 0.4752 (Cg_exo) cc_final: 0.4211 (Cg_endo) REVERT: E 50 ASP cc_start: 0.4381 (OUTLIER) cc_final: 0.1837 (m-30) REVERT: I 99 ASN cc_start: 0.7630 (t0) cc_final: 0.7278 (t0) REVERT: C 102 HIS cc_start: -0.3367 (OUTLIER) cc_final: -0.3833 (t70) REVERT: G 102 HIS cc_start: -0.1840 (OUTLIER) cc_final: -0.3708 (t70) REVERT: B 17 PHE cc_start: 0.3046 (t80) cc_final: 0.2156 (t80) REVERT: B 81 LEU cc_start: 0.8006 (OUTLIER) cc_final: 0.7705 (mm) REVERT: D 101 ASP cc_start: 0.3456 (OUTLIER) cc_final: 0.2605 (m-30) REVERT: J 63 MET cc_start: -0.0331 (ppp) cc_final: -0.0796 (ppp) REVERT: J 102 HIS cc_start: -0.0686 (OUTLIER) cc_final: -0.3978 (t70) REVERT: F 17 PHE cc_start: 0.2326 (m-80) cc_final: 0.2060 (m-80) REVERT: F 63 MET cc_start: 0.1393 (tpt) cc_final: 0.0508 (tmm) REVERT: L 10 PHE cc_start: 0.2306 (m-80) cc_final: 0.1863 (m-80) REVERT: L 102 HIS cc_start: 0.0565 (OUTLIER) cc_final: -0.1071 (t70) outliers start: 47 outliers final: 31 residues processed: 93 average time/residue: 0.0803 time to fit residues: 12.1447 Evaluate side-chains 87 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 48 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 PHE Chi-restraints excluded: chain A residue 50 ASP Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain K residue 22 VAL Chi-restraints excluded: chain K residue 25 PHE Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 114 LYS Chi-restraints excluded: chain I residue 22 VAL Chi-restraints excluded: chain I residue 25 PHE Chi-restraints excluded: chain I residue 72 LEU Chi-restraints excluded: chain C residue 25 PHE Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 102 HIS Chi-restraints excluded: chain G residue 7 ILE Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 102 HIS Chi-restraints excluded: chain B residue 25 PHE Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 109 ARG Chi-restraints excluded: chain H residue 7 ILE Chi-restraints excluded: chain H residue 22 VAL Chi-restraints excluded: chain H residue 63 MET Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain J residue 7 ILE Chi-restraints excluded: chain J residue 18 ILE Chi-restraints excluded: chain J residue 25 PHE Chi-restraints excluded: chain J residue 102 HIS Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain L residue 2 THR Chi-restraints excluded: chain L residue 17 PHE Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 25 PHE Chi-restraints excluded: chain L residue 79 THR Chi-restraints excluded: chain L residue 102 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 21 optimal weight: 50.0000 chunk 84 optimal weight: 40.0000 chunk 89 optimal weight: 20.0000 chunk 57 optimal weight: 0.2980 chunk 13 optimal weight: 6.9990 chunk 44 optimal weight: 50.0000 chunk 95 optimal weight: 9.9990 chunk 96 optimal weight: 10.0000 chunk 10 optimal weight: 20.0000 chunk 104 optimal weight: 6.9990 chunk 74 optimal weight: 2.9990 overall best weight: 5.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 112 HIS ** K 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 1 GLN B 32 ASN ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 74 ASN L 6 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5007 r_free = 0.5007 target = 0.168560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4823 r_free = 0.4823 target = 0.149612 restraints weight = 58919.460| |-----------------------------------------------------------------------------| r_work (start): 0.4758 rms_B_bonded: 9.28 r_work (final): 0.4758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3828 moved from start: 0.3737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 11070 Z= 0.154 Angle : 0.684 16.357 15036 Z= 0.348 Chirality : 0.049 0.200 1764 Planarity : 0.007 0.066 1920 Dihedral : 6.238 28.063 1406 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 22.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.98 % Favored : 90.02 % Rotamer: Outliers : 4.17 % Allowed : 20.91 % Favored : 74.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.92 (0.23), residues: 1272 helix: -1.21 (0.41), residues: 128 sheet: -0.21 (0.27), residues: 390 loop : -1.95 (0.22), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG G 66 TYR 0.010 0.001 TYR F 80 PHE 0.024 0.002 PHE J 25 HIS 0.006 0.001 HIS F 102 Details of bonding type rmsd covalent geometry : bond 0.00363 (11064) covalent geometry : angle 0.68421 (15024) SS BOND : bond 0.00247 ( 6) SS BOND : angle 0.63693 ( 12) hydrogen bonds : bond 0.02919 ( 290) hydrogen bonds : angle 7.17583 ( 711) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 49 time to evaluate : 0.451 Fit side-chains revert: symmetry clash REVERT: A 50 ASP cc_start: 0.3182 (OUTLIER) cc_final: 0.1578 (m-30) REVERT: A 102 HIS cc_start: -0.2908 (OUTLIER) cc_final: -0.3817 (t70) REVERT: K 91 MET cc_start: 0.1063 (pmm) cc_final: 0.0727 (mmp) REVERT: E 21 PRO cc_start: 0.5060 (Cg_exo) cc_final: 0.4640 (Cg_endo) REVERT: I 99 ASN cc_start: 0.7781 (t0) cc_final: 0.7518 (t0) REVERT: C 102 HIS cc_start: -0.4264 (OUTLIER) cc_final: -0.4556 (t70) REVERT: G 102 HIS cc_start: -0.1582 (OUTLIER) cc_final: -0.3855 (t70) REVERT: B 17 PHE cc_start: 0.3387 (t80) cc_final: 0.2281 (t80) REVERT: B 81 LEU cc_start: 0.8097 (OUTLIER) cc_final: 0.7838 (mm) REVERT: H 63 MET cc_start: 0.0957 (OUTLIER) cc_final: 0.0071 (tmm) REVERT: D 101 ASP cc_start: 0.4434 (OUTLIER) cc_final: 0.3667 (m-30) REVERT: J 63 MET cc_start: -0.0966 (ppp) cc_final: -0.1489 (ppp) REVERT: J 102 HIS cc_start: -0.1476 (OUTLIER) cc_final: -0.4377 (t70) REVERT: F 63 MET cc_start: 0.2498 (tpt) cc_final: 0.1629 (tmm) REVERT: L 10 PHE cc_start: 0.2205 (m-80) cc_final: 0.1558 (m-80) REVERT: L 102 HIS cc_start: 0.1154 (OUTLIER) cc_final: -0.0610 (t70) outliers start: 52 outliers final: 32 residues processed: 96 average time/residue: 0.0824 time to fit residues: 12.7117 Evaluate side-chains 90 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 49 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 PHE Chi-restraints excluded: chain A residue 50 ASP Chi-restraints excluded: chain A residue 102 HIS Chi-restraints excluded: chain K residue 22 VAL Chi-restraints excluded: chain K residue 25 PHE Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 114 LYS Chi-restraints excluded: chain I residue 22 VAL Chi-restraints excluded: chain I residue 25 PHE Chi-restraints excluded: chain I residue 72 LEU Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain C residue 25 PHE Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 102 HIS Chi-restraints excluded: chain G residue 7 ILE Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 102 HIS Chi-restraints excluded: chain B residue 25 PHE Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 109 ARG Chi-restraints excluded: chain H residue 22 VAL Chi-restraints excluded: chain H residue 63 MET Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 114 LYS Chi-restraints excluded: chain J residue 7 ILE Chi-restraints excluded: chain J residue 18 ILE Chi-restraints excluded: chain J residue 25 PHE Chi-restraints excluded: chain J residue 102 HIS Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 102 HIS Chi-restraints excluded: chain L residue 2 THR Chi-restraints excluded: chain L residue 17 PHE Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 25 PHE Chi-restraints excluded: chain L residue 79 THR Chi-restraints excluded: chain L residue 102 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 75 optimal weight: 9.9990 chunk 27 optimal weight: 0.2980 chunk 93 optimal weight: 0.8980 chunk 101 optimal weight: 0.9990 chunk 18 optimal weight: 20.0000 chunk 76 optimal weight: 3.9990 chunk 34 optimal weight: 9.9990 chunk 118 optimal weight: 0.8980 chunk 17 optimal weight: 9.9990 chunk 98 optimal weight: 8.9990 chunk 23 optimal weight: 50.0000 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 112 HIS K 35 HIS B 32 ASN ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4962 r_free = 0.4962 target = 0.174148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4938 r_free = 0.4938 target = 0.169002 restraints weight = 34920.503| |-----------------------------------------------------------------------------| r_work (start): 0.5053 rms_B_bonded: 1.46 r_work: 0.4998 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.4969 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.4969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2991 moved from start: 0.3966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 11070 Z= 0.112 Angle : 0.607 14.058 15036 Z= 0.310 Chirality : 0.047 0.268 1764 Planarity : 0.007 0.069 1920 Dihedral : 5.774 25.030 1406 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 15.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 3.04 % Allowed : 21.88 % Favored : 75.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.83 (0.23), residues: 1272 helix: -1.21 (0.40), residues: 140 sheet: -0.15 (0.27), residues: 390 loop : -1.87 (0.23), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 66 TYR 0.009 0.001 TYR I 117 PHE 0.025 0.001 PHE J 25 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00284 (11064) covalent geometry : angle 0.60718 (15024) SS BOND : bond 0.00184 ( 6) SS BOND : angle 0.33238 ( 12) hydrogen bonds : bond 0.02677 ( 290) hydrogen bonds : angle 6.69294 ( 711) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 53 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 ASP cc_start: 0.2315 (OUTLIER) cc_final: 0.1387 (m-30) REVERT: K 91 MET cc_start: 0.1640 (pmm) cc_final: 0.0839 (mmp) REVERT: E 21 PRO cc_start: 0.5310 (Cg_exo) cc_final: 0.4680 (Cg_endo) REVERT: E 114 LYS cc_start: 0.1371 (OUTLIER) cc_final: 0.0377 (mppt) REVERT: G 102 HIS cc_start: -0.2246 (OUTLIER) cc_final: -0.3786 (t70) REVERT: B 17 PHE cc_start: 0.2881 (t80) cc_final: 0.2024 (t80) REVERT: B 81 LEU cc_start: 0.7959 (OUTLIER) cc_final: 0.7677 (mm) REVERT: D 101 ASP cc_start: 0.3595 (OUTLIER) cc_final: 0.3169 (m-30) REVERT: J 18 ILE cc_start: 0.8829 (OUTLIER) cc_final: 0.8574 (tp) REVERT: J 63 MET cc_start: -0.0558 (ppp) cc_final: -0.1010 (ppp) REVERT: J 99 ASN cc_start: 0.7482 (t0) cc_final: 0.7165 (t0) REVERT: J 102 HIS cc_start: -0.0739 (OUTLIER) cc_final: -0.4171 (t70) REVERT: F 63 MET cc_start: 0.1506 (tpt) cc_final: 0.0716 (tmm) REVERT: L 10 PHE cc_start: 0.2300 (m-80) cc_final: 0.1908 (m-80) REVERT: L 102 HIS cc_start: 0.0576 (OUTLIER) cc_final: -0.1109 (t70) outliers start: 38 outliers final: 26 residues processed: 88 average time/residue: 0.0825 time to fit residues: 11.7004 Evaluate side-chains 86 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 52 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 PHE Chi-restraints excluded: chain A residue 50 ASP Chi-restraints excluded: chain K residue 22 VAL Chi-restraints excluded: chain K residue 25 PHE Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 114 LYS Chi-restraints excluded: chain I residue 22 VAL Chi-restraints excluded: chain I residue 25 PHE Chi-restraints excluded: chain I residue 72 LEU Chi-restraints excluded: chain C residue 25 PHE Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain G residue 7 ILE Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 102 HIS Chi-restraints excluded: chain B residue 25 PHE Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 109 ARG Chi-restraints excluded: chain H residue 63 MET Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 117 TYR Chi-restraints excluded: chain J residue 7 ILE Chi-restraints excluded: chain J residue 18 ILE Chi-restraints excluded: chain J residue 25 PHE Chi-restraints excluded: chain J residue 102 HIS Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain L residue 2 THR Chi-restraints excluded: chain L residue 17 PHE Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 25 PHE Chi-restraints excluded: chain L residue 79 THR Chi-restraints excluded: chain L residue 102 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 50 optimal weight: 50.0000 chunk 111 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 98 optimal weight: 7.9990 chunk 30 optimal weight: 5.9990 chunk 128 optimal weight: 3.9990 chunk 34 optimal weight: 10.0000 chunk 33 optimal weight: 20.0000 chunk 88 optimal weight: 50.0000 chunk 10 optimal weight: 7.9990 chunk 5 optimal weight: 8.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 112 HIS ** K 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 ASN ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4912 r_free = 0.4912 target = 0.164795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4910 r_free = 0.4910 target = 0.164440 restraints weight = 53655.089| |-----------------------------------------------------------------------------| r_work (start): 0.5017 rms_B_bonded: 0.23 r_work: 0.5002 rms_B_bonded: 0.36 restraints_weight: 0.5000 r_work: 0.4999 rms_B_bonded: 0.45 restraints_weight: 0.2500 r_work: 0.4924 rms_B_bonded: 2.07 restraints_weight: 0.1250 r_work (final): 0.4924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3273 moved from start: 0.4122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 11070 Z= 0.142 Angle : 0.639 12.591 15036 Z= 0.331 Chirality : 0.048 0.198 1764 Planarity : 0.007 0.066 1920 Dihedral : 6.017 27.485 1406 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 20.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.67 % Favored : 90.33 % Rotamer: Outliers : 3.21 % Allowed : 21.63 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.81 (0.23), residues: 1272 helix: -1.10 (0.42), residues: 128 sheet: -0.17 (0.27), residues: 390 loop : -1.87 (0.23), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 66 TYR 0.011 0.001 TYR F 80 PHE 0.023 0.001 PHE J 25 HIS 0.005 0.001 HIS F 102 Details of bonding type rmsd covalent geometry : bond 0.00343 (11064) covalent geometry : angle 0.63921 (15024) SS BOND : bond 0.00204 ( 6) SS BOND : angle 0.64404 ( 12) hydrogen bonds : bond 0.02786 ( 290) hydrogen bonds : angle 6.95848 ( 711) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 52 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 ASP cc_start: 0.3524 (OUTLIER) cc_final: 0.2446 (m-30) REVERT: E 21 PRO cc_start: 0.5316 (Cg_exo) cc_final: 0.4724 (Cg_endo) REVERT: C 102 HIS cc_start: -0.3280 (OUTLIER) cc_final: -0.4061 (t70) REVERT: G 102 HIS cc_start: -0.1730 (OUTLIER) cc_final: -0.3910 (t70) REVERT: B 17 PHE cc_start: 0.3156 (t80) cc_final: 0.2210 (t80) REVERT: B 81 LEU cc_start: 0.8083 (OUTLIER) cc_final: 0.7761 (mm) REVERT: D 91 MET cc_start: 0.1001 (mpp) cc_final: 0.0410 (mpp) REVERT: J 63 MET cc_start: -0.0402 (ppp) cc_final: -0.0919 (ppp) REVERT: J 102 HIS cc_start: -0.0841 (OUTLIER) cc_final: -0.4125 (t70) REVERT: F 63 MET cc_start: 0.1488 (tpt) cc_final: 0.0638 (tmm) REVERT: L 10 PHE cc_start: 0.2347 (m-80) cc_final: 0.1841 (m-80) REVERT: L 102 HIS cc_start: 0.0655 (OUTLIER) cc_final: -0.1062 (t70) outliers start: 40 outliers final: 31 residues processed: 89 average time/residue: 0.0817 time to fit residues: 11.7544 Evaluate side-chains 89 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 52 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 PHE Chi-restraints excluded: chain A residue 50 ASP Chi-restraints excluded: chain K residue 22 VAL Chi-restraints excluded: chain K residue 25 PHE Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 114 LYS Chi-restraints excluded: chain I residue 22 VAL Chi-restraints excluded: chain I residue 25 PHE Chi-restraints excluded: chain I residue 72 LEU Chi-restraints excluded: chain C residue 25 PHE Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 102 HIS Chi-restraints excluded: chain G residue 7 ILE Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 102 HIS Chi-restraints excluded: chain B residue 25 PHE Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 109 ARG Chi-restraints excluded: chain H residue 63 MET Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 117 TYR Chi-restraints excluded: chain J residue 7 ILE Chi-restraints excluded: chain J residue 18 ILE Chi-restraints excluded: chain J residue 25 PHE Chi-restraints excluded: chain J residue 102 HIS Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 102 HIS Chi-restraints excluded: chain L residue 2 THR Chi-restraints excluded: chain L residue 17 PHE Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 25 PHE Chi-restraints excluded: chain L residue 79 THR Chi-restraints excluded: chain L residue 102 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 32 optimal weight: 3.9990 chunk 51 optimal weight: 50.0000 chunk 75 optimal weight: 9.9990 chunk 120 optimal weight: 8.9990 chunk 55 optimal weight: 5.9990 chunk 50 optimal weight: 10.0000 chunk 98 optimal weight: 7.9990 chunk 64 optimal weight: 30.0000 chunk 26 optimal weight: 9.9990 chunk 92 optimal weight: 4.9990 chunk 117 optimal weight: 30.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 112 HIS ** K 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 6 ASN J 1 GLN F 102 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5127 r_free = 0.5127 target = 0.172586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4875 r_free = 0.4875 target = 0.154764 restraints weight = 62636.096| |-----------------------------------------------------------------------------| r_work (start): 0.4743 rms_B_bonded: 9.25 r_work (final): 0.4743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3890 moved from start: 0.4699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 11070 Z= 0.170 Angle : 0.699 12.316 15036 Z= 0.365 Chirality : 0.050 0.208 1764 Planarity : 0.007 0.067 1920 Dihedral : 6.580 28.529 1406 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 25.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.14 % Favored : 89.86 % Rotamer: Outliers : 3.37 % Allowed : 21.23 % Favored : 75.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.03 (0.23), residues: 1272 helix: -1.22 (0.43), residues: 126 sheet: -0.45 (0.26), residues: 401 loop : -1.96 (0.22), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 66 TYR 0.012 0.001 TYR F 80 PHE 0.025 0.002 PHE J 25 HIS 0.006 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00393 (11064) covalent geometry : angle 0.69891 (15024) SS BOND : bond 0.00251 ( 6) SS BOND : angle 0.88369 ( 12) hydrogen bonds : bond 0.03137 ( 290) hydrogen bonds : angle 7.53394 ( 711) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2805.13 seconds wall clock time: 49 minutes 14.26 seconds (2954.26 seconds total)