Starting phenix.real_space_refine on Sun Oct 25 00:02:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9yga_72917/10_2026/9yga_72917.cif Found real_map, /net/cci-nas-00/data/ceres_data/9yga_72917/10_2026/9yga_72917.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9yga_72917/10_2026/9yga_72917.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9yga_72917/10_2026/9yga_72917.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9yga_72917/10_2026/9yga_72917.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9yga_72917/10_2026/9yga_72917.map" } resolution = 2.9 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= 0.030 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 12 5.16 5 C 9348 2.51 5 N 2472 2.21 5 O 2928 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14760 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1230 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 12, 'TRANS': 150} Chain: "J" Number of atoms: 1230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1230 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 12, 'TRANS': 150} Chain: "B" Number of atoms: 1230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1230 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 12, 'TRANS': 150} Chain: "G" Number of atoms: 1230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1230 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 12, 'TRANS': 150} Chain: "C" Number of atoms: 1230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1230 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 12, 'TRANS': 150} Chain: "H" Number of atoms: 1230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1230 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 12, 'TRANS': 150} Chain: "D" Number of atoms: 1230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1230 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 12, 'TRANS': 150} Chain: "I" Number of atoms: 1230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1230 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 12, 'TRANS': 150} Chain: "E" Number of atoms: 1230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1230 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 12, 'TRANS': 150} Chain: "K" Number of atoms: 1230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1230 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 12, 'TRANS': 150} Chain: "F" Number of atoms: 1230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1230 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 12, 'TRANS': 150} Chain: "L" Number of atoms: 1230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1230 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 12, 'TRANS': 150} Time building chain proxies: 3.01, per 1000 atoms: 0.20 Number of scatterers: 14760 At special positions: 0 Unit cell: (117.7, 115.5, 105.6, 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 12 16.00 O 2928 8.00 N 2472 7.00 C 9348 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.05 Conformation dependent library (CDL) restraints added in 612.6 milliseconds 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3528 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 48 sheets defined 7.7% alpha, 47.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'A' and resid 76 through 87 Processing helix chain 'J' and resid 76 through 88 Processing helix chain 'B' and resid 76 through 87 Processing helix chain 'G' and resid 76 through 88 Processing helix chain 'C' and resid 76 through 87 Processing helix chain 'H' and resid 76 through 88 removed outlier: 3.510A pdb=" N GLU H 87 " --> pdb=" O PHE H 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 87 Processing helix chain 'I' and resid 76 through 88 Processing helix chain 'E' and resid 76 through 87 Processing helix chain 'K' and resid 76 through 88 Processing helix chain 'F' and resid 76 through 87 Processing helix chain 'L' and resid 76 through 88 removed outlier: 3.512A pdb=" N GLU L 87 " --> pdb=" O PHE L 83 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 24 through 27 removed outlier: 4.252A pdb=" N LYS A 95 " --> pdb=" O LEU A 13 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 24 through 27 removed outlier: 4.252A pdb=" N LYS A 95 " --> pdb=" O LEU A 13 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N THR A 150 " --> pdb=" O SER A 133 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N GLN A 65 " --> pdb=" O PRO A 36 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N THR A 67 " --> pdb=" O PHE A 34 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N PHE A 34 " --> pdb=" O THR A 67 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N GLY A 69 " --> pdb=" O THR A 32 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N PHE B 137 " --> pdb=" O PRO A 36 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 41 through 45 removed outlier: 4.800A pdb=" N ASP A 42 " --> pdb=" O GLY A 59 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 109 through 110 Processing sheet with id=AA5, first strand: chain 'A' and resid 137 through 139 removed outlier: 7.274A pdb=" N PHE A 137 " --> pdb=" O PRO F 36 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N GLY F 69 " --> pdb=" O THR F 32 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N PHE F 34 " --> pdb=" O THR F 67 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N THR F 67 " --> pdb=" O PHE F 34 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N GLN F 65 " --> pdb=" O PRO F 36 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N THR F 150 " --> pdb=" O SER F 133 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LYS F 95 " --> pdb=" O LEU F 13 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 137 through 139 removed outlier: 7.274A pdb=" N PHE A 137 " --> pdb=" O PRO F 36 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N GLY F 69 " --> pdb=" O THR F 32 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N PHE F 34 " --> pdb=" O THR F 67 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N THR F 67 " --> pdb=" O PHE F 34 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N GLN F 65 " --> pdb=" O PRO F 36 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N THR F 150 " --> pdb=" O SER F 133 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'J' and resid 24 through 28 removed outlier: 4.833A pdb=" N ILE J 10 " --> pdb=" O ILE J 28 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N LYS J 95 " --> pdb=" O LEU J 13 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N THR J 150 " --> pdb=" O SER J 133 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N THR J 67 " --> pdb=" O PHE J 34 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N PHE J 34 " --> pdb=" O THR J 67 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N GLY J 69 " --> pdb=" O THR J 32 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'J' and resid 24 through 28 removed outlier: 4.833A pdb=" N ILE J 10 " --> pdb=" O ILE J 28 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N LYS J 95 " --> pdb=" O LEU J 13 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'J' and resid 41 through 45 removed outlier: 4.916A pdb=" N LEU J 60 " --> pdb=" O ASP J 42 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ILE J 44 " --> pdb=" O LYS J 58 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N LYS J 58 " --> pdb=" O ILE J 44 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 109 through 110 Processing sheet with id=AB2, first strand: chain 'B' and resid 24 through 27 removed outlier: 4.217A pdb=" N LYS B 95 " --> pdb=" O LEU B 13 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 24 through 27 removed outlier: 4.217A pdb=" N LYS B 95 " --> pdb=" O LEU B 13 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N THR B 150 " --> pdb=" O SER B 133 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N GLN B 65 " --> pdb=" O PRO B 36 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N THR B 67 " --> pdb=" O PHE B 34 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N PHE B 34 " --> pdb=" O THR B 67 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N GLY B 69 " --> pdb=" O THR B 32 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N PHE C 137 " --> pdb=" O PRO B 36 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 41 through 45 removed outlier: 4.783A pdb=" N ASP B 42 " --> pdb=" O GLY B 59 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 109 through 110 Processing sheet with id=AB6, first strand: chain 'G' and resid 24 through 28 removed outlier: 4.815A pdb=" N ILE G 10 " --> pdb=" O ILE G 28 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N LYS G 95 " --> pdb=" O LEU G 13 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N THR G 150 " --> pdb=" O SER G 133 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N THR G 67 " --> pdb=" O PHE G 34 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N PHE G 34 " --> pdb=" O THR G 67 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N GLY G 69 " --> pdb=" O THR G 32 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 24 through 28 removed outlier: 4.815A pdb=" N ILE G 10 " --> pdb=" O ILE G 28 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N LYS G 95 " --> pdb=" O LEU G 13 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 41 through 45 removed outlier: 4.903A pdb=" N LEU G 60 " --> pdb=" O ASP G 42 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ILE G 44 " --> pdb=" O LYS G 58 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N LYS G 58 " --> pdb=" O ILE G 44 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 109 through 110 Processing sheet with id=AC1, first strand: chain 'C' and resid 24 through 27 removed outlier: 4.262A pdb=" N LYS C 95 " --> pdb=" O LEU C 13 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 24 through 27 removed outlier: 4.262A pdb=" N LYS C 95 " --> pdb=" O LEU C 13 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N THR C 150 " --> pdb=" O SER C 133 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N GLN C 65 " --> pdb=" O PRO C 36 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N THR C 67 " --> pdb=" O PHE C 34 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N PHE C 34 " --> pdb=" O THR C 67 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N GLY C 69 " --> pdb=" O THR C 32 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N PHE D 137 " --> pdb=" O PRO C 36 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 41 through 45 removed outlier: 4.792A pdb=" N ASP C 42 " --> pdb=" O GLY C 59 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 109 through 110 Processing sheet with id=AC5, first strand: chain 'H' and resid 24 through 28 removed outlier: 4.836A pdb=" N ILE H 10 " --> pdb=" O ILE H 28 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N LYS H 95 " --> pdb=" O LEU H 13 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N THR H 150 " --> pdb=" O SER H 133 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N THR H 67 " --> pdb=" O PHE H 34 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N PHE H 34 " --> pdb=" O THR H 67 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N GLY H 69 " --> pdb=" O THR H 32 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 24 through 28 removed outlier: 4.836A pdb=" N ILE H 10 " --> pdb=" O ILE H 28 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N LYS H 95 " --> pdb=" O LEU H 13 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 41 through 45 removed outlier: 4.906A pdb=" N LEU H 60 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ILE H 44 " --> pdb=" O LYS H 58 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N LYS H 58 " --> pdb=" O ILE H 44 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 109 through 110 Processing sheet with id=AC9, first strand: chain 'D' and resid 24 through 27 removed outlier: 4.252A pdb=" N LYS D 95 " --> pdb=" O LEU D 13 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 24 through 27 removed outlier: 4.252A pdb=" N LYS D 95 " --> pdb=" O LEU D 13 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N THR D 150 " --> pdb=" O SER D 133 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N GLN D 65 " --> pdb=" O PRO D 36 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N THR D 67 " --> pdb=" O PHE D 34 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N PHE D 34 " --> pdb=" O THR D 67 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N GLY D 69 " --> pdb=" O THR D 32 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N PHE E 137 " --> pdb=" O PRO D 36 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 41 through 45 removed outlier: 4.795A pdb=" N ASP D 42 " --> pdb=" O GLY D 59 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 109 through 110 Processing sheet with id=AD4, first strand: chain 'I' and resid 24 through 28 removed outlier: 4.819A pdb=" N ILE I 10 " --> pdb=" O ILE I 28 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N LYS I 95 " --> pdb=" O LEU I 13 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N THR I 150 " --> pdb=" O SER I 133 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N THR I 67 " --> pdb=" O PHE I 34 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N PHE I 34 " --> pdb=" O THR I 67 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N GLY I 69 " --> pdb=" O THR I 32 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 24 through 28 removed outlier: 4.819A pdb=" N ILE I 10 " --> pdb=" O ILE I 28 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N LYS I 95 " --> pdb=" O LEU I 13 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 41 through 45 removed outlier: 4.900A pdb=" N LEU I 60 " --> pdb=" O ASP I 42 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ILE I 44 " --> pdb=" O LYS I 58 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N LYS I 58 " --> pdb=" O ILE I 44 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 109 through 110 Processing sheet with id=AD8, first strand: chain 'E' and resid 24 through 27 removed outlier: 4.216A pdb=" N LYS E 95 " --> pdb=" O LEU E 13 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 24 through 27 removed outlier: 4.216A pdb=" N LYS E 95 " --> pdb=" O LEU E 13 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N THR E 150 " --> pdb=" O SER E 133 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N GLN E 65 " --> pdb=" O PRO E 36 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N THR E 67 " --> pdb=" O PHE E 34 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N PHE E 34 " --> pdb=" O THR E 67 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N GLY E 69 " --> pdb=" O THR E 32 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N PHE F 137 " --> pdb=" O PRO E 36 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 41 through 45 removed outlier: 4.783A pdb=" N ASP E 42 " --> pdb=" O GLY E 59 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 109 through 110 Processing sheet with id=AE3, first strand: chain 'K' and resid 24 through 28 removed outlier: 4.815A pdb=" N ILE K 10 " --> pdb=" O ILE K 28 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N LYS K 95 " --> pdb=" O LEU K 13 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N THR K 150 " --> pdb=" O SER K 133 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N THR K 67 " --> pdb=" O PHE K 34 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N PHE K 34 " --> pdb=" O THR K 67 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N GLY K 69 " --> pdb=" O THR K 32 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'K' and resid 24 through 28 removed outlier: 4.815A pdb=" N ILE K 10 " --> pdb=" O ILE K 28 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N LYS K 95 " --> pdb=" O LEU K 13 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'K' and resid 41 through 45 removed outlier: 4.903A pdb=" N LEU K 60 " --> pdb=" O ASP K 42 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ILE K 44 " --> pdb=" O LYS K 58 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N LYS K 58 " --> pdb=" O ILE K 44 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 109 through 110 Processing sheet with id=AE7, first strand: chain 'F' and resid 41 through 45 removed outlier: 4.789A pdb=" N ASP F 42 " --> pdb=" O GLY F 59 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'F' and resid 109 through 110 Processing sheet with id=AE9, first strand: chain 'L' and resid 24 through 28 removed outlier: 4.835A pdb=" N ILE L 10 " --> pdb=" O ILE L 28 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N LYS L 95 " --> pdb=" O LEU L 13 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N THR L 150 " --> pdb=" O SER L 133 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N THR L 67 " --> pdb=" O PHE L 34 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N PHE L 34 " --> pdb=" O THR L 67 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N GLY L 69 " --> pdb=" O THR L 32 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'L' and resid 24 through 28 removed outlier: 4.835A pdb=" N ILE L 10 " --> pdb=" O ILE L 28 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N LYS L 95 " --> pdb=" O LEU L 13 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'L' and resid 41 through 45 removed outlier: 4.905A pdb=" N LEU L 60 " --> pdb=" O ASP L 42 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ILE L 44 " --> pdb=" O LYS L 58 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N LYS L 58 " --> pdb=" O ILE L 44 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'L' and resid 109 through 110 697 hydrogen bonds defined for protein. 1764 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: 2.36 Time building geometry restraints manager: 1.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4830 1.34 - 1.46: 3149 1.46 - 1.57: 7141 1.57 - 1.69: 0 1.69 - 1.81: 12 Bond restraints: 15132 Sorted by residual: bond pdb=" CA PRO J 120 " pdb=" C PRO J 120 " ideal model delta sigma weight residual 1.517 1.529 -0.012 6.70e-03 2.23e+04 3.19e+00 bond pdb=" C LEU G 68 " pdb=" N GLY G 69 " ideal model delta sigma weight residual 1.332 1.327 0.006 5.00e-03 4.00e+04 1.25e+00 bond pdb=" CB PRO G 136 " pdb=" CG PRO G 136 " ideal model delta sigma weight residual 1.492 1.534 -0.042 5.00e-02 4.00e+02 6.98e-01 bond pdb=" CB PRO L 136 " pdb=" CG PRO L 136 " ideal model delta sigma weight residual 1.492 1.533 -0.041 5.00e-02 4.00e+02 6.88e-01 bond pdb=" CB TRP A 125 " pdb=" CG TRP A 125 " ideal model delta sigma weight residual 1.498 1.472 0.026 3.10e-02 1.04e+03 6.80e-01 ... (remaining 15127 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.74: 18362 0.74 - 1.47: 1868 1.47 - 2.21: 257 2.21 - 2.94: 112 2.94 - 3.68: 65 Bond angle restraints: 20664 Sorted by residual: angle pdb=" C GLY G 38 " pdb=" N ASN G 39 " pdb=" CA ASN G 39 " ideal model delta sigma weight residual 122.37 124.26 -1.89 9.30e-01 1.16e+00 4.12e+00 angle pdb=" C GLY K 38 " pdb=" N ASN K 39 " pdb=" CA ASN K 39 " ideal model delta sigma weight residual 122.37 124.25 -1.88 9.30e-01 1.16e+00 4.07e+00 angle pdb=" CA SER I 101 " pdb=" C SER I 101 " pdb=" N ASP I 102 " ideal model delta sigma weight residual 118.27 121.46 -3.19 1.59e+00 3.96e-01 4.03e+00 angle pdb=" CA SER G 101 " pdb=" C SER G 101 " pdb=" N ASP G 102 " ideal model delta sigma weight residual 118.27 121.41 -3.14 1.59e+00 3.96e-01 3.91e+00 angle pdb=" CA SER J 101 " pdb=" C SER J 101 " pdb=" N ASP J 102 " ideal model delta sigma weight residual 118.27 121.40 -3.13 1.59e+00 3.96e-01 3.86e+00 ... (remaining 20659 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.30: 8378 17.30 - 34.61: 434 34.61 - 51.91: 66 51.91 - 69.22: 20 69.22 - 86.52: 6 Dihedral angle restraints: 8904 sinusoidal: 3396 harmonic: 5508 Sorted by residual: dihedral pdb=" CA TYR F 56 " pdb=" C TYR F 56 " pdb=" N LYS F 57 " pdb=" CA LYS F 57 " ideal model delta harmonic sigma weight residual 180.00 163.95 16.05 0 5.00e+00 4.00e-02 1.03e+01 dihedral pdb=" CA TYR C 56 " pdb=" C TYR C 56 " pdb=" N LYS C 57 " pdb=" CA LYS C 57 " ideal model delta harmonic sigma weight residual 180.00 163.99 16.01 0 5.00e+00 4.00e-02 1.03e+01 dihedral pdb=" CA TYR E 56 " pdb=" C TYR E 56 " pdb=" N LYS E 57 " pdb=" CA LYS E 57 " ideal model delta harmonic sigma weight residual 180.00 164.12 15.88 0 5.00e+00 4.00e-02 1.01e+01 ... (remaining 8901 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1409 0.026 - 0.053: 534 0.053 - 0.079: 179 0.079 - 0.106: 130 0.106 - 0.132: 76 Chirality restraints: 2328 Sorted by residual: chirality pdb=" CA ILE E 151 " pdb=" N ILE E 151 " pdb=" C ILE E 151 " pdb=" CB ILE E 151 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.37e-01 chirality pdb=" CA ILE D 151 " pdb=" N ILE D 151 " pdb=" C ILE D 151 " pdb=" CB ILE D 151 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.29e-01 chirality pdb=" CA ILE F 151 " pdb=" N ILE F 151 " pdb=" C ILE F 151 " pdb=" CB ILE F 151 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.27e-01 ... (remaining 2325 not shown) Planarity restraints: 2700 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 107 " -0.017 5.00e-02 4.00e+02 2.54e-02 1.03e+00 pdb=" N PRO B 108 " 0.044 5.00e-02 4.00e+02 pdb=" CA PRO B 108 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO B 108 " -0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS E 107 " 0.017 5.00e-02 4.00e+02 2.54e-02 1.03e+00 pdb=" N PRO E 108 " -0.044 5.00e-02 4.00e+02 pdb=" CA PRO E 108 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO E 108 " 0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS D 107 " -0.017 5.00e-02 4.00e+02 2.53e-02 1.02e+00 pdb=" N PRO D 108 " 0.044 5.00e-02 4.00e+02 pdb=" CA PRO D 108 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO D 108 " -0.014 5.00e-02 4.00e+02 ... (remaining 2697 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 2403 2.77 - 3.30: 12371 3.30 - 3.83: 21994 3.83 - 4.37: 27041 4.37 - 4.90: 49979 Nonbonded interactions: 113788 Sorted by model distance: nonbonded pdb=" OD2 ASP K 102 " pdb=" OG1 THR K 124 " model vdw 2.234 3.040 nonbonded pdb=" OD2 ASP G 102 " pdb=" OG1 THR G 124 " model vdw 2.234 3.040 nonbonded pdb=" OD2 ASP I 102 " pdb=" OG1 THR I 124 " model vdw 2.242 3.040 nonbonded pdb=" OD2 ASP J 102 " pdb=" OG1 THR J 124 " model vdw 2.255 3.040 nonbonded pdb=" OD2 ASP L 102 " pdb=" OG1 THR L 124 " model vdw 2.270 3.040 ... (remaining 113783 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: 1.080 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: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 13.600 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 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 : 0.003 0.042 15132 Z= 0.133 Angle : 0.529 3.675 20664 Z= 0.291 Chirality : 0.041 0.132 2328 Planarity : 0.004 0.038 2700 Dihedral : 10.865 86.521 5376 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 0.75 % Allowed : 1.38 % Favored : 97.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.12 (0.15), residues: 1932 helix: -3.74 (0.14), residues: 144 sheet: -1.22 (0.19), residues: 672 loop : -2.46 (0.13), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 81 TYR 0.010 0.001 TYR A 131 PHE 0.012 0.002 PHE B 117 TRP 0.007 0.001 TRP A 96 HIS 0.001 0.001 HIS J 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (15132) covalent geometry : angle 0.52880 / 0.29 (20664) hydrogen bonds : bond 0.22620 / 15.49 ( 514) hydrogen bonds : angle 9.42891 / 6.57 ( 1764) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 434 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 142 ASN cc_start: 0.8736 (t0) cc_final: 0.8486 (t0) REVERT: K 142 ASN cc_start: 0.8726 (t0) cc_final: 0.8478 (t0) outliers start: 12 outliers final: 0 residues processed: 444 average time/residue: 0.6360 time to fit residues: 306.8003 Evaluate side-chains 336 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 336 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 149] chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 9.9990 chunk 149 optimal weight: 10.0000 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 43 GLN J 142 ASN J 148 GLN B 43 GLN B 65 GLN G 43 GLN H 43 GLN I 43 GLN I 148 GLN E 43 GLN E 65 GLN K 43 GLN L 43 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.073389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2596 r_free = 0.2596 target = 0.054959 restraints weight = 29301.213| |-----------------------------------------------------------------------------| r_work (start): 0.2597 rms_B_bonded: 3.47 r_work: 0.2458 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 15132 Z= 0.220 Angle : 0.618 5.706 20664 Z= 0.320 Chirality : 0.045 0.147 2328 Planarity : 0.005 0.031 2700 Dihedral : 4.403 16.123 2052 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.88 % Allowed : 11.40 % Favored : 86.72 % 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 are not related in a simple way. whole: -2.22 (0.17), residues: 1932 helix: 0.13 (0.39), residues: 156 sheet: -1.18 (0.17), residues: 840 loop : -1.99 (0.16), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 75 TYR 0.015 0.002 TYR A 131 PHE 0.014 0.002 PHE K 128 TRP 0.009 0.001 TRP C 100 HIS 0.002 0.001 HIS J 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00523 / 0.22 (15132) covalent geometry : angle 0.61753 / 0.32 (20664) hydrogen bonds : bond 0.05087 / 3.47 ( 514) hydrogen bonds : angle 5.61346 / 3.97 ( 1764) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 333 time to evaluate : 0.565 Fit side-chains revert: symmetry clash REVERT: A 29 GLU cc_start: 0.8587 (mt-10) cc_final: 0.7922 (mp0) REVERT: A 134 ASP cc_start: 0.8500 (t0) cc_final: 0.8225 (t0) REVERT: J 27 GLU cc_start: 0.8387 (tt0) cc_final: 0.8047 (tt0) REVERT: J 29 GLU cc_start: 0.8346 (mp0) cc_final: 0.7647 (pm20) REVERT: B 29 GLU cc_start: 0.8585 (mt-10) cc_final: 0.8239 (mp0) REVERT: B 54 ARG cc_start: 0.7103 (mmt90) cc_final: 0.6713 (mtt90) REVERT: B 88 LYS cc_start: 0.8743 (tppp) cc_final: 0.8516 (tppp) REVERT: B 92 THR cc_start: 0.9013 (OUTLIER) cc_final: 0.8802 (p) REVERT: B 102 ASP cc_start: 0.9447 (m-30) cc_final: 0.9064 (m-30) REVERT: B 134 ASP cc_start: 0.8519 (t0) cc_final: 0.8232 (t0) REVERT: G 29 GLU cc_start: 0.8360 (mp0) cc_final: 0.7537 (pm20) REVERT: G 65 GLN cc_start: 0.8652 (mp10) cc_final: 0.8430 (mp10) REVERT: G 116 ASP cc_start: 0.9031 (t0) cc_final: 0.8634 (m-30) REVERT: C 29 GLU cc_start: 0.8510 (mp0) cc_final: 0.7941 (mp0) REVERT: C 102 ASP cc_start: 0.9335 (m-30) cc_final: 0.9083 (m-30) REVERT: C 134 ASP cc_start: 0.8612 (t0) cc_final: 0.8331 (t0) REVERT: H 29 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.7625 (pm20) REVERT: H 65 GLN cc_start: 0.8735 (mp10) cc_final: 0.8534 (mp10) REVERT: H 116 ASP cc_start: 0.9098 (t0) cc_final: 0.8820 (m-30) REVERT: D 29 GLU cc_start: 0.8637 (mt-10) cc_final: 0.7922 (mp0) REVERT: D 88 LYS cc_start: 0.8571 (tptt) cc_final: 0.8334 (tppp) REVERT: D 134 ASP cc_start: 0.8480 (t0) cc_final: 0.8223 (t0) REVERT: I 3 ILE cc_start: 0.8343 (tp) cc_final: 0.8115 (tp) REVERT: I 27 GLU cc_start: 0.8495 (tt0) cc_final: 0.8016 (tt0) REVERT: I 29 GLU cc_start: 0.8346 (mp0) cc_final: 0.7674 (pm20) REVERT: I 65 GLN cc_start: 0.8663 (mp10) cc_final: 0.8459 (mp10) REVERT: I 95 LYS cc_start: 0.8363 (mttp) cc_final: 0.8142 (mttt) REVERT: E 29 GLU cc_start: 0.8598 (mt-10) cc_final: 0.8255 (mp0) REVERT: E 88 LYS cc_start: 0.8732 (tppp) cc_final: 0.8525 (tppp) REVERT: E 92 THR cc_start: 0.9007 (OUTLIER) cc_final: 0.8786 (p) REVERT: E 102 ASP cc_start: 0.9419 (m-30) cc_final: 0.9058 (m-30) REVERT: E 134 ASP cc_start: 0.8520 (t0) cc_final: 0.8231 (t0) REVERT: K 29 GLU cc_start: 0.8361 (mp0) cc_final: 0.7542 (pm20) REVERT: K 65 GLN cc_start: 0.8646 (mp10) cc_final: 0.8423 (mp10) REVERT: K 116 ASP cc_start: 0.9027 (t0) cc_final: 0.8632 (m-30) REVERT: F 29 GLU cc_start: 0.8624 (mp0) cc_final: 0.7881 (mp0) REVERT: F 102 ASP cc_start: 0.9326 (m-30) cc_final: 0.9080 (m-30) REVERT: F 134 ASP cc_start: 0.8612 (t0) cc_final: 0.8333 (t0) REVERT: L 29 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.7617 (pm20) outliers start: 30 outliers final: 8 residues processed: 351 average time/residue: 0.6549 time to fit residues: 249.4936 Evaluate side-chains 348 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 336 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2 SER Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 162 LYS Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain I residue 89 ASP Chi-restraints excluded: chain E residue 2 SER Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain K residue 89 ASP Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 162 LYS Chi-restraints excluded: chain L residue 29 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: [145, 170, 112, 97, 0, 37, 93, 142, 156, 71, 25] chunk 145 optimal weight: 7.9990 chunk 170 optimal weight: 2.9990 chunk 112 optimal weight: 6.9990 chunk 97 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 37 optimal weight: 9.9990 chunk 93 optimal weight: 3.9990 chunk 142 optimal weight: 5.9990 chunk 156 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 25 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 65 GLN J 43 GLN B 43 GLN G 43 GLN H 43 GLN D 65 GLN I 43 GLN I 148 GLN E 43 GLN K 43 GLN L 43 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.071773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2574 r_free = 0.2574 target = 0.053657 restraints weight = 29733.140| |-----------------------------------------------------------------------------| r_work (start): 0.2576 rms_B_bonded: 3.46 r_work: 0.2440 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 15132 Z= 0.259 Angle : 0.589 5.006 20664 Z= 0.306 Chirality : 0.044 0.145 2328 Planarity : 0.004 0.036 2700 Dihedral : 4.363 16.192 2052 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.13 % Allowed : 13.41 % Favored : 84.46 % 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 are not related in a simple way. whole: -1.96 (0.17), residues: 1932 helix: 1.91 (0.45), residues: 156 sheet: -1.33 (0.16), residues: 900 loop : -1.77 (0.17), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 75 TYR 0.014 0.002 TYR K 131 PHE 0.011 0.002 PHE G 128 TRP 0.010 0.001 TRP F 100 HIS 0.002 0.001 HIS I 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00632 / 0.26 (15132) covalent geometry : angle 0.58873 / 0.31 (20664) hydrogen bonds : bond 0.04804 / 3.28 ( 514) hydrogen bonds : angle 5.19400 / 3.68 ( 1764) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 338 time to evaluate : 0.473 Fit side-chains revert: symmetry clash REVERT: A 29 GLU cc_start: 0.8727 (mt-10) cc_final: 0.8522 (mt-10) REVERT: J 3 ILE cc_start: 0.8251 (tp) cc_final: 0.8012 (tp) REVERT: B 29 GLU cc_start: 0.8740 (mt-10) cc_final: 0.8368 (mp0) REVERT: B 54 ARG cc_start: 0.7697 (mmt90) cc_final: 0.7362 (mtt90) REVERT: B 55 LYS cc_start: 0.8857 (mtmt) cc_final: 0.8636 (mtmm) REVERT: B 88 LYS cc_start: 0.8758 (tppp) cc_final: 0.8543 (tppp) REVERT: B 134 ASP cc_start: 0.8568 (t0) cc_final: 0.8264 (t0) REVERT: G 29 GLU cc_start: 0.8368 (mp0) cc_final: 0.7692 (pm20) REVERT: G 65 GLN cc_start: 0.8735 (mp10) cc_final: 0.8493 (mp10) REVERT: G 116 ASP cc_start: 0.9134 (t0) cc_final: 0.8804 (m-30) REVERT: G 129 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.7495 (tm-30) REVERT: C 29 GLU cc_start: 0.8624 (mp0) cc_final: 0.8142 (mp0) REVERT: C 42 ASP cc_start: 0.8398 (m-30) cc_final: 0.7685 (p0) REVERT: C 102 ASP cc_start: 0.9428 (m-30) cc_final: 0.9110 (m-30) REVERT: C 134 ASP cc_start: 0.8639 (t0) cc_final: 0.8268 (t0) REVERT: H 29 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7562 (pm20) REVERT: H 65 GLN cc_start: 0.8786 (mp10) cc_final: 0.8583 (mp10) REVERT: H 116 ASP cc_start: 0.9098 (t0) cc_final: 0.8824 (m-30) REVERT: D 29 GLU cc_start: 0.8762 (mt-10) cc_final: 0.8550 (mt-10) REVERT: D 88 LYS cc_start: 0.8628 (tptt) cc_final: 0.8355 (tppp) REVERT: D 134 ASP cc_start: 0.8509 (t0) cc_final: 0.8132 (t0) REVERT: I 3 ILE cc_start: 0.8352 (tp) cc_final: 0.8115 (tp) REVERT: I 65 GLN cc_start: 0.8843 (mp10) cc_final: 0.8585 (mp10) REVERT: I 89 ASP cc_start: 0.9021 (OUTLIER) cc_final: 0.8811 (m-30) REVERT: I 134 ASP cc_start: 0.8728 (t0) cc_final: 0.8518 (t0) REVERT: E 29 GLU cc_start: 0.8746 (mt-10) cc_final: 0.8391 (mp0) REVERT: E 55 LYS cc_start: 0.8858 (mtmt) cc_final: 0.8639 (mtmm) REVERT: E 88 LYS cc_start: 0.8780 (tppp) cc_final: 0.8561 (tppp) REVERT: E 134 ASP cc_start: 0.8555 (t0) cc_final: 0.8251 (t0) REVERT: K 29 GLU cc_start: 0.8373 (mp0) cc_final: 0.7695 (pm20) REVERT: K 65 GLN cc_start: 0.8736 (mp10) cc_final: 0.8492 (mp10) REVERT: K 116 ASP cc_start: 0.9119 (t0) cc_final: 0.8800 (m-30) REVERT: F 29 GLU cc_start: 0.8772 (mp0) cc_final: 0.8086 (mp0) REVERT: F 42 ASP cc_start: 0.8394 (m-30) cc_final: 0.7673 (p0) REVERT: F 102 ASP cc_start: 0.9425 (m-30) cc_final: 0.9118 (m-30) REVERT: F 134 ASP cc_start: 0.8639 (t0) cc_final: 0.8269 (t0) REVERT: L 27 GLU cc_start: 0.8405 (tt0) cc_final: 0.8037 (tt0) REVERT: L 29 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7558 (pm20) REVERT: L 116 ASP cc_start: 0.9117 (t0) cc_final: 0.8846 (m-30) outliers start: 34 outliers final: 11 residues processed: 354 average time/residue: 0.6833 time to fit residues: 262.1164 Evaluate side-chains 344 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 329 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 129 GLU Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 162 LYS Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain I residue 89 ASP Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 162 LYS Chi-restraints excluded: chain L residue 29 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: [60, 66, 191, 16, 1, 101, 179, 19, 155, 48, 39] chunk 60 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 191 optimal weight: 6.9990 chunk 16 optimal weight: 6.9990 chunk 1 optimal weight: 0.1980 chunk 101 optimal weight: 10.0000 chunk 179 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 155 optimal weight: 0.0060 chunk 48 optimal weight: 6.9990 chunk 39 optimal weight: 0.8980 overall best weight: 1.6200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 43 GLN J 84 GLN G 43 GLN H 43 GLN D 84 GLN I 43 GLN I 148 GLN K 43 GLN L 43 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.072928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2599 r_free = 0.2599 target = 0.054835 restraints weight = 29521.039| |-----------------------------------------------------------------------------| r_work (start): 0.2602 rms_B_bonded: 3.46 r_work: 0.2463 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.2774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 15132 Z= 0.154 Angle : 0.545 5.235 20664 Z= 0.279 Chirality : 0.043 0.142 2328 Planarity : 0.004 0.035 2700 Dihedral : 4.141 15.496 2052 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 1.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.26 % Allowed : 13.97 % Favored : 83.77 % 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 are not related in a simple way. whole: -1.66 (0.18), residues: 1932 helix: 2.34 (0.46), residues: 156 sheet: -1.06 (0.17), residues: 888 loop : -1.71 (0.17), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 75 TYR 0.009 0.001 TYR K 131 PHE 0.009 0.001 PHE D 128 TRP 0.009 0.001 TRP I 96 HIS 0.002 0.001 HIS I 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.15 (15132) covalent geometry : angle 0.54525 / 0.28 (20664) hydrogen bonds : bond 0.03814 / 2.60 ( 514) hydrogen bonds : angle 4.81303 / 3.41 ( 1764) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 346 time to evaluate : 0.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 GLU cc_start: 0.8766 (mt-10) cc_final: 0.7971 (mp0) REVERT: A 134 ASP cc_start: 0.8522 (t0) cc_final: 0.8141 (t0) REVERT: J 3 ILE cc_start: 0.8235 (tp) cc_final: 0.7988 (tp) REVERT: J 29 GLU cc_start: 0.8382 (mp0) cc_final: 0.7767 (pm20) REVERT: B 29 GLU cc_start: 0.8758 (mt-10) cc_final: 0.8460 (mp0) REVERT: B 54 ARG cc_start: 0.7809 (mmt90) cc_final: 0.7400 (mtt90) REVERT: B 55 LYS cc_start: 0.8840 (mtmt) cc_final: 0.8638 (mtmm) REVERT: G 29 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.7711 (pm20) REVERT: G 65 GLN cc_start: 0.8848 (mp10) cc_final: 0.8566 (mp10) REVERT: C 29 GLU cc_start: 0.8699 (mp0) cc_final: 0.8172 (mp0) REVERT: C 42 ASP cc_start: 0.8424 (m-30) cc_final: 0.7731 (p0) REVERT: C 55 LYS cc_start: 0.8720 (mtpt) cc_final: 0.8486 (mtmm) REVERT: C 102 ASP cc_start: 0.9446 (m-30) cc_final: 0.9126 (m-30) REVERT: C 134 ASP cc_start: 0.8718 (t0) cc_final: 0.8295 (t0) REVERT: H 27 GLU cc_start: 0.8379 (tt0) cc_final: 0.8021 (tt0) REVERT: H 29 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7758 (pm20) REVERT: H 65 GLN cc_start: 0.8800 (mp10) cc_final: 0.8556 (mp10) REVERT: H 116 ASP cc_start: 0.9145 (t0) cc_final: 0.8860 (m-30) REVERT: D 29 GLU cc_start: 0.8762 (mt-10) cc_final: 0.7991 (mp0) REVERT: D 88 LYS cc_start: 0.8703 (tptt) cc_final: 0.8477 (tppp) REVERT: D 134 ASP cc_start: 0.8497 (t0) cc_final: 0.8060 (t0) REVERT: D 148 GLN cc_start: 0.8876 (mm-40) cc_final: 0.8620 (mm-40) REVERT: I 3 ILE cc_start: 0.8341 (tp) cc_final: 0.8104 (tp) REVERT: I 29 GLU cc_start: 0.8331 (mp0) cc_final: 0.7775 (pm20) REVERT: I 65 GLN cc_start: 0.8854 (mp10) cc_final: 0.8530 (mp10) REVERT: I 107 LYS cc_start: 0.9088 (mtpp) cc_final: 0.8792 (mtmp) REVERT: I 134 ASP cc_start: 0.8634 (t0) cc_final: 0.8416 (t0) REVERT: E 29 GLU cc_start: 0.8764 (mt-10) cc_final: 0.8469 (mp0) REVERT: E 55 LYS cc_start: 0.8851 (mtmt) cc_final: 0.8647 (mtmm) REVERT: E 115 ASP cc_start: 0.9294 (p0) cc_final: 0.9007 (p0) REVERT: K 29 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.7714 (pm20) REVERT: K 65 GLN cc_start: 0.8841 (mp10) cc_final: 0.8557 (mp10) REVERT: F 29 GLU cc_start: 0.8818 (mp0) cc_final: 0.8171 (mp0) REVERT: F 42 ASP cc_start: 0.8473 (m-30) cc_final: 0.7769 (p0) REVERT: F 102 ASP cc_start: 0.9439 (m-30) cc_final: 0.9132 (m-30) REVERT: F 134 ASP cc_start: 0.8686 (t0) cc_final: 0.8254 (t0) REVERT: L 27 GLU cc_start: 0.8370 (tt0) cc_final: 0.8012 (tt0) REVERT: L 29 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.7756 (pm20) REVERT: L 116 ASP cc_start: 0.9142 (t0) cc_final: 0.8887 (m-30) outliers start: 36 outliers final: 18 residues processed: 366 average time/residue: 0.6392 time to fit residues: 254.2557 Evaluate side-chains 354 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 332 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 70 ILE Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 29 GLU Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain I residue 17 VAL Chi-restraints excluded: chain I residue 70 ILE Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain K residue 29 GLU Chi-restraints excluded: chain F residue 43 GLN Chi-restraints excluded: chain L residue 17 VAL Chi-restraints excluded: chain L residue 29 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: [87, 136, 109, 12, 112, 131, 179, 47, 147, 94, 176] chunk 87 optimal weight: 0.8980 chunk 136 optimal weight: 5.9990 chunk 109 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 112 optimal weight: 6.9990 chunk 131 optimal weight: 0.9980 chunk 179 optimal weight: 4.9990 chunk 47 optimal weight: 8.9990 chunk 147 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 176 optimal weight: 4.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 43 GLN J 84 GLN J 148 GLN G 43 GLN G 148 GLN H 43 GLN H 148 GLN I 43 GLN I 148 GLN K 43 GLN K 148 GLN L 43 GLN L 148 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.073653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2617 r_free = 0.2617 target = 0.055518 restraints weight = 29462.646| |-----------------------------------------------------------------------------| r_work (start): 0.2610 rms_B_bonded: 3.45 r_work: 0.2472 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.2921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15132 Z= 0.137 Angle : 0.539 4.914 20664 Z= 0.277 Chirality : 0.042 0.138 2328 Planarity : 0.003 0.036 2700 Dihedral : 4.013 14.942 2052 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.75 % Allowed : 14.79 % Favored : 83.46 % 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 are not related in a simple way. whole: -1.47 (0.18), residues: 1932 helix: 2.44 (0.47), residues: 156 sheet: -0.91 (0.17), residues: 888 loop : -1.61 (0.17), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 75 TYR 0.010 0.001 TYR J 131 PHE 0.008 0.001 PHE I 128 TRP 0.006 0.001 TRP J 96 HIS 0.002 0.001 HIS J 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.14 (15132) covalent geometry : angle 0.53901 / 0.28 (20664) hydrogen bonds : bond 0.03540 / 2.41 ( 514) hydrogen bonds : angle 4.60191 / 3.26 ( 1764) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 341 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 GLU cc_start: 0.8808 (mt-10) cc_final: 0.7899 (mp0) REVERT: A 134 ASP cc_start: 0.8458 (t0) cc_final: 0.7998 (t0) REVERT: A 148 GLN cc_start: 0.8857 (mm-40) cc_final: 0.8649 (mm-40) REVERT: J 3 ILE cc_start: 0.8245 (tp) cc_final: 0.7989 (tp) REVERT: J 29 GLU cc_start: 0.8287 (mp0) cc_final: 0.7736 (pm20) REVERT: B 29 GLU cc_start: 0.8728 (mt-10) cc_final: 0.8353 (mp0) REVERT: B 88 LYS cc_start: 0.8829 (tppp) cc_final: 0.8626 (tppp) REVERT: B 102 ASP cc_start: 0.9459 (m-30) cc_final: 0.9097 (m-30) REVERT: B 134 ASP cc_start: 0.8592 (t70) cc_final: 0.7997 (t0) REVERT: G 29 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.7688 (pm20) REVERT: G 65 GLN cc_start: 0.8867 (mp10) cc_final: 0.8554 (mp10) REVERT: G 148 GLN cc_start: 0.8802 (tp40) cc_final: 0.8548 (mm110) REVERT: C 29 GLU cc_start: 0.8705 (mp0) cc_final: 0.8241 (mp0) REVERT: C 42 ASP cc_start: 0.8432 (m-30) cc_final: 0.7764 (p0) REVERT: C 55 LYS cc_start: 0.8707 (OUTLIER) cc_final: 0.8490 (mtmm) REVERT: C 102 ASP cc_start: 0.9437 (m-30) cc_final: 0.9125 (m-30) REVERT: C 134 ASP cc_start: 0.8728 (t0) cc_final: 0.8266 (t0) REVERT: H 27 GLU cc_start: 0.8378 (tt0) cc_final: 0.8027 (tt0) REVERT: H 29 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.7821 (pm20) REVERT: H 65 GLN cc_start: 0.8794 (mp10) cc_final: 0.8531 (mp10) REVERT: H 116 ASP cc_start: 0.9137 (t0) cc_final: 0.8879 (m-30) REVERT: D 29 GLU cc_start: 0.8800 (mt-10) cc_final: 0.7953 (mp0) REVERT: D 88 LYS cc_start: 0.8682 (tptt) cc_final: 0.8418 (tppp) REVERT: D 134 ASP cc_start: 0.8510 (t0) cc_final: 0.8033 (t0) REVERT: D 148 GLN cc_start: 0.8869 (mm-40) cc_final: 0.8601 (mm-40) REVERT: I 3 ILE cc_start: 0.8344 (tp) cc_final: 0.8109 (tp) REVERT: I 29 GLU cc_start: 0.8302 (mp0) cc_final: 0.7699 (pm20) REVERT: I 65 GLN cc_start: 0.8915 (mp10) cc_final: 0.8579 (mp10) REVERT: I 134 ASP cc_start: 0.8610 (t0) cc_final: 0.8386 (t0) REVERT: E 29 GLU cc_start: 0.8731 (mt-10) cc_final: 0.8357 (mp0) REVERT: E 88 LYS cc_start: 0.8821 (tppp) cc_final: 0.8619 (tppp) REVERT: E 102 ASP cc_start: 0.9457 (m-30) cc_final: 0.9100 (m-30) REVERT: E 134 ASP cc_start: 0.8583 (t70) cc_final: 0.7984 (t0) REVERT: K 29 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.7671 (pm20) REVERT: K 65 GLN cc_start: 0.8861 (mp10) cc_final: 0.8544 (mp10) REVERT: K 148 GLN cc_start: 0.8806 (tp40) cc_final: 0.8550 (mm110) REVERT: F 29 GLU cc_start: 0.8813 (mp0) cc_final: 0.8192 (mp0) REVERT: F 42 ASP cc_start: 0.8509 (m-30) cc_final: 0.7849 (p0) REVERT: F 102 ASP cc_start: 0.9435 (m-30) cc_final: 0.9116 (m-30) REVERT: F 134 ASP cc_start: 0.8699 (t0) cc_final: 0.8270 (t0) REVERT: L 29 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.7818 (pm20) REVERT: L 116 ASP cc_start: 0.9130 (t0) cc_final: 0.8879 (m-30) outliers start: 28 outliers final: 16 residues processed: 357 average time/residue: 0.6519 time to fit residues: 252.6613 Evaluate side-chains 356 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 335 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 70 ILE Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 29 GLU Chi-restraints excluded: chain C residue 55 LYS Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain I residue 17 VAL Chi-restraints excluded: chain I residue 70 ILE Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain K residue 29 GLU Chi-restraints excluded: chain F residue 60 LEU Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain L residue 17 VAL Chi-restraints excluded: chain L residue 29 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: [129, 119, 116, 78, 52, 177, 131, 109, 151, 169, 61] chunk 129 optimal weight: 7.9990 chunk 119 optimal weight: 5.9990 chunk 116 optimal weight: 0.8980 chunk 78 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 177 optimal weight: 6.9990 chunk 131 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 151 optimal weight: 3.9990 chunk 169 optimal weight: 7.9990 chunk 61 optimal weight: 0.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 43 GLN J 148 GLN B 43 GLN G 43 GLN H 43 GLN I 43 GLN I 148 GLN E 43 GLN K 43 GLN L 43 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.072052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2574 r_free = 0.2574 target = 0.053758 restraints weight = 29743.862| |-----------------------------------------------------------------------------| r_work (start): 0.2566 rms_B_bonded: 3.50 r_work: 0.2427 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.3017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 15132 Z= 0.213 Angle : 0.573 5.745 20664 Z= 0.294 Chirality : 0.043 0.134 2328 Planarity : 0.004 0.041 2700 Dihedral : 4.121 15.627 2052 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.19 % Allowed : 14.79 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.49 (0.18), residues: 1932 helix: 2.50 (0.47), residues: 156 sheet: -1.01 (0.17), residues: 900 loop : -1.52 (0.17), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 75 TYR 0.013 0.002 TYR J 131 PHE 0.011 0.002 PHE D 128 TRP 0.009 0.001 TRP F 100 HIS 0.001 0.000 HIS J 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00521 / 0.21 (15132) covalent geometry : angle 0.57268 / 0.29 (20664) hydrogen bonds : bond 0.03974 / 2.71 ( 514) hydrogen bonds : angle 4.66233 / 3.31 ( 1764) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 337 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 GLU cc_start: 0.8852 (OUTLIER) cc_final: 0.8029 (mp0) REVERT: A 134 ASP cc_start: 0.8541 (t0) cc_final: 0.8079 (t0) REVERT: J 3 ILE cc_start: 0.8326 (tp) cc_final: 0.8073 (tp) REVERT: J 29 GLU cc_start: 0.8368 (mp0) cc_final: 0.7747 (pm20) REVERT: B 29 GLU cc_start: 0.8785 (mt-10) cc_final: 0.8421 (mp0) REVERT: B 88 LYS cc_start: 0.8918 (tppp) cc_final: 0.8703 (tppp) REVERT: G 29 GLU cc_start: 0.8400 (mt-10) cc_final: 0.7718 (pm20) REVERT: G 65 GLN cc_start: 0.8935 (mp10) cc_final: 0.8651 (mp10) REVERT: C 29 GLU cc_start: 0.8722 (mp0) cc_final: 0.8212 (mp0) REVERT: C 42 ASP cc_start: 0.8479 (m-30) cc_final: 0.7821 (p0) REVERT: C 43 GLN cc_start: 0.8816 (mt0) cc_final: 0.8430 (mt0) REVERT: C 102 ASP cc_start: 0.9443 (m-30) cc_final: 0.9127 (m-30) REVERT: C 134 ASP cc_start: 0.8770 (t0) cc_final: 0.8295 (t0) REVERT: H 27 GLU cc_start: 0.8410 (tt0) cc_final: 0.8013 (tt0) REVERT: H 29 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.7831 (pm20) REVERT: H 65 GLN cc_start: 0.8857 (mp10) cc_final: 0.8576 (mp10) REVERT: H 116 ASP cc_start: 0.9131 (t0) cc_final: 0.8888 (m-30) REVERT: D 29 GLU cc_start: 0.8851 (OUTLIER) cc_final: 0.8017 (mp0) REVERT: D 134 ASP cc_start: 0.8599 (t0) cc_final: 0.8093 (t0) REVERT: I 3 ILE cc_start: 0.8398 (tp) cc_final: 0.8159 (tp) REVERT: I 29 GLU cc_start: 0.8380 (mp0) cc_final: 0.7727 (pm20) REVERT: I 65 GLN cc_start: 0.8893 (mp10) cc_final: 0.8544 (mp10) REVERT: I 107 LYS cc_start: 0.9111 (mtpp) cc_final: 0.8891 (mtmp) REVERT: I 134 ASP cc_start: 0.8666 (t0) cc_final: 0.8452 (t0) REVERT: E 29 GLU cc_start: 0.8806 (mt-10) cc_final: 0.8443 (mp0) REVERT: E 88 LYS cc_start: 0.8921 (tppp) cc_final: 0.8706 (tppp) REVERT: K 29 GLU cc_start: 0.8397 (mt-10) cc_final: 0.7723 (pm20) REVERT: K 65 GLN cc_start: 0.8925 (mp10) cc_final: 0.8638 (mp10) REVERT: F 29 GLU cc_start: 0.8855 (mp0) cc_final: 0.8259 (mp0) REVERT: F 42 ASP cc_start: 0.8512 (m-30) cc_final: 0.7889 (p0) REVERT: F 102 ASP cc_start: 0.9409 (m-30) cc_final: 0.9101 (m-30) REVERT: F 134 ASP cc_start: 0.8789 (t0) cc_final: 0.8305 (t0) REVERT: L 29 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.7855 (pm20) REVERT: L 116 ASP cc_start: 0.9124 (t0) cc_final: 0.8867 (m-30) outliers start: 35 outliers final: 21 residues processed: 358 average time/residue: 0.6723 time to fit residues: 261.0592 Evaluate side-chains 352 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 327 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 162 LYS Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain H residue 58 LYS Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain I residue 17 VAL Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain F residue 60 LEU Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 162 LYS Chi-restraints excluded: chain L residue 17 VAL Chi-restraints excluded: chain L residue 29 GLU Chi-restraints excluded: chain L residue 58 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: [55, 60, 99, 126, 90, 158, 18, 20, 106, 33, 98] chunk 55 optimal weight: 4.9990 chunk 60 optimal weight: 0.7980 chunk 99 optimal weight: 0.9990 chunk 126 optimal weight: 4.9990 chunk 90 optimal weight: 5.9990 chunk 158 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 98 optimal weight: 3.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 43 GLN J 148 GLN G 43 GLN G 148 GLN H 43 GLN H 84 GLN I 43 GLN I 148 GLN K 43 GLN K 148 GLN L 43 GLN L 84 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.073315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.2610 r_free = 0.2610 target = 0.055163 restraints weight = 29307.877| |-----------------------------------------------------------------------------| r_work (start): 0.2597 rms_B_bonded: 3.46 r_work: 0.2459 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.3096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15132 Z= 0.140 Angle : 0.566 6.644 20664 Z= 0.290 Chirality : 0.042 0.137 2328 Planarity : 0.003 0.040 2700 Dihedral : 4.005 16.573 2052 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 2.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.63 % Allowed : 15.66 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.18), residues: 1932 helix: 2.47 (0.47), residues: 156 sheet: -0.54 (0.17), residues: 828 loop : -1.63 (0.16), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 75 TYR 0.009 0.001 TYR J 131 PHE 0.008 0.001 PHE D 128 TRP 0.007 0.001 TRP J 96 HIS 0.002 0.001 HIS K 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.14 (15132) covalent geometry : angle 0.56638 / 0.29 (20664) hydrogen bonds : bond 0.03481 / 2.37 ( 514) hydrogen bonds : angle 4.52531 / 3.20 ( 1764) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 337 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 GLU cc_start: 0.8819 (OUTLIER) cc_final: 0.7933 (mp0) REVERT: A 134 ASP cc_start: 0.8481 (t0) cc_final: 0.7974 (t0) REVERT: J 3 ILE cc_start: 0.8276 (tp) cc_final: 0.8021 (tp) REVERT: J 29 GLU cc_start: 0.8291 (mp0) cc_final: 0.7751 (pm20) REVERT: B 29 GLU cc_start: 0.8735 (mt-10) cc_final: 0.8386 (mp0) REVERT: B 55 LYS cc_start: 0.8881 (mtmt) cc_final: 0.8661 (mtmm) REVERT: G 29 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.7759 (pm20) REVERT: G 65 GLN cc_start: 0.8883 (mp10) cc_final: 0.8591 (mp10) REVERT: C 29 GLU cc_start: 0.8739 (mp0) cc_final: 0.8250 (mp0) REVERT: C 42 ASP cc_start: 0.8457 (m-30) cc_final: 0.7765 (p0) REVERT: C 43 GLN cc_start: 0.8815 (OUTLIER) cc_final: 0.8405 (mt0) REVERT: C 102 ASP cc_start: 0.9387 (m-30) cc_final: 0.9061 (m-30) REVERT: C 134 ASP cc_start: 0.8805 (t0) cc_final: 0.8262 (t0) REVERT: H 29 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.7836 (pm20) REVERT: H 65 GLN cc_start: 0.8818 (mp10) cc_final: 0.8521 (mp10) REVERT: H 89 ASP cc_start: 0.9037 (m-30) cc_final: 0.8819 (m-30) REVERT: H 116 ASP cc_start: 0.9124 (t0) cc_final: 0.8869 (m-30) REVERT: D 29 GLU cc_start: 0.8827 (OUTLIER) cc_final: 0.7952 (mp0) REVERT: D 134 ASP cc_start: 0.8555 (t0) cc_final: 0.8219 (t0) REVERT: I 3 ILE cc_start: 0.8301 (tp) cc_final: 0.8063 (tp) REVERT: I 29 GLU cc_start: 0.8311 (mp0) cc_final: 0.7685 (pm20) REVERT: I 65 GLN cc_start: 0.8898 (mp10) cc_final: 0.8521 (mp10) REVERT: I 107 LYS cc_start: 0.9094 (mtpp) cc_final: 0.8847 (mtmp) REVERT: I 134 ASP cc_start: 0.8596 (t0) cc_final: 0.8353 (t0) REVERT: E 29 GLU cc_start: 0.8759 (mt-10) cc_final: 0.8418 (mp0) REVERT: E 55 LYS cc_start: 0.8821 (mtmt) cc_final: 0.8570 (mtmm) REVERT: E 113 GLU cc_start: 0.7584 (pm20) cc_final: 0.7373 (pm20) REVERT: E 115 ASP cc_start: 0.9256 (p0) cc_final: 0.9014 (p0) REVERT: K 29 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.7651 (pm20) REVERT: K 65 GLN cc_start: 0.8879 (mp10) cc_final: 0.8596 (mp10) REVERT: F 29 GLU cc_start: 0.8798 (mp0) cc_final: 0.8201 (mp0) REVERT: F 42 ASP cc_start: 0.8519 (m-30) cc_final: 0.7853 (p0) REVERT: F 43 GLN cc_start: 0.8814 (mt0) cc_final: 0.8436 (mt0) REVERT: F 134 ASP cc_start: 0.8744 (t0) cc_final: 0.8261 (t0) REVERT: L 29 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.7842 (pm20) REVERT: L 116 ASP cc_start: 0.9130 (t0) cc_final: 0.8879 (m-30) outliers start: 26 outliers final: 15 residues processed: 351 average time/residue: 0.6608 time to fit residues: 251.6007 Evaluate side-chains 350 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 328 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain G residue 29 GLU Chi-restraints excluded: chain C residue 43 GLN Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 162 LYS Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain I residue 17 VAL Chi-restraints excluded: chain K residue 29 GLU Chi-restraints excluded: chain F residue 60 LEU Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 162 LYS Chi-restraints excluded: chain L residue 17 VAL Chi-restraints excluded: chain L residue 29 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: [112, 29, 180, 64, 49, 136, 179, 149, 145, 19, 36] chunk 112 optimal weight: 7.9990 chunk 29 optimal weight: 2.9990 chunk 180 optimal weight: 0.9990 chunk 64 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 179 optimal weight: 0.9980 chunk 149 optimal weight: 1.9990 chunk 145 optimal weight: 0.2980 chunk 19 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 43 GLN J 84 GLN J 148 GLN G 35 ASN G 43 GLN G 148 GLN H 43 GLN I 43 GLN I 84 GLN K 35 ASN K 43 GLN K 148 GLN F 35 ASN L 43 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.072987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2604 r_free = 0.2604 target = 0.055195 restraints weight = 29687.385| |-----------------------------------------------------------------------------| r_work (start): 0.2603 rms_B_bonded: 3.40 r_work: 0.2468 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.3190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15132 Z= 0.136 Angle : 0.569 5.907 20664 Z= 0.291 Chirality : 0.042 0.136 2328 Planarity : 0.003 0.040 2700 Dihedral : 3.911 16.011 2052 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.63 % Allowed : 16.17 % Favored : 82.21 % 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 are not related in a simple way. whole: -1.19 (0.18), residues: 1932 helix: 2.48 (0.47), residues: 156 sheet: -0.25 (0.18), residues: 756 loop : -1.79 (0.16), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 75 TYR 0.009 0.001 TYR J 131 PHE 0.008 0.001 PHE D 128 TRP 0.007 0.001 TRP J 96 HIS 0.002 0.001 HIS J 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.14 (15132) covalent geometry : angle 0.56855 / 0.29 (20664) hydrogen bonds : bond 0.03411 / 2.33 ( 514) hydrogen bonds : angle 4.43625 / 3.14 ( 1764) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 335 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 GLU cc_start: 0.8836 (OUTLIER) cc_final: 0.7924 (mp0) REVERT: A 134 ASP cc_start: 0.8455 (t0) cc_final: 0.7929 (t0) REVERT: J 3 ILE cc_start: 0.8286 (tp) cc_final: 0.8027 (tp) REVERT: J 29 GLU cc_start: 0.8250 (mp0) cc_final: 0.7780 (pm20) REVERT: J 105 ASP cc_start: 0.8969 (m-30) cc_final: 0.8757 (m-30) REVERT: B 29 GLU cc_start: 0.8761 (mt-10) cc_final: 0.8403 (mp0) REVERT: B 115 ASP cc_start: 0.9370 (p0) cc_final: 0.9140 (p0) REVERT: B 158 LYS cc_start: 0.7535 (ttmm) cc_final: 0.7313 (ttpt) REVERT: G 29 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.7768 (pm20) REVERT: G 65 GLN cc_start: 0.8911 (mp10) cc_final: 0.8600 (mp10) REVERT: G 87 GLU cc_start: 0.8354 (mm-30) cc_final: 0.8037 (mt-10) REVERT: G 148 GLN cc_start: 0.8739 (tp40) cc_final: 0.8470 (mm110) REVERT: C 29 GLU cc_start: 0.8748 (mp0) cc_final: 0.8276 (mp0) REVERT: C 42 ASP cc_start: 0.8444 (m-30) cc_final: 0.7764 (p0) REVERT: C 43 GLN cc_start: 0.8818 (OUTLIER) cc_final: 0.8420 (mt0) REVERT: C 102 ASP cc_start: 0.9406 (m-30) cc_final: 0.9109 (m-30) REVERT: C 134 ASP cc_start: 0.8821 (t0) cc_final: 0.8287 (t0) REVERT: H 29 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.7828 (pm20) REVERT: H 65 GLN cc_start: 0.8819 (mp10) cc_final: 0.8520 (mp10) REVERT: H 116 ASP cc_start: 0.9102 (t0) cc_final: 0.8852 (m-30) REVERT: D 29 GLU cc_start: 0.8841 (OUTLIER) cc_final: 0.7946 (mp0) REVERT: D 134 ASP cc_start: 0.8534 (t0) cc_final: 0.8183 (t0) REVERT: I 3 ILE cc_start: 0.8312 (tp) cc_final: 0.8065 (tp) REVERT: I 29 GLU cc_start: 0.8279 (mp0) cc_final: 0.7700 (pm20) REVERT: I 65 GLN cc_start: 0.8877 (mp10) cc_final: 0.8503 (mp10) REVERT: I 107 LYS cc_start: 0.9054 (mtpp) cc_final: 0.8814 (mtmp) REVERT: I 134 ASP cc_start: 0.8586 (t0) cc_final: 0.8349 (t0) REVERT: E 29 GLU cc_start: 0.8780 (mt-10) cc_final: 0.8427 (mp0) REVERT: E 158 LYS cc_start: 0.7539 (ttmm) cc_final: 0.7316 (ttpt) REVERT: K 29 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.7677 (pm20) REVERT: K 65 GLN cc_start: 0.8894 (mp10) cc_final: 0.8582 (mp10) REVERT: K 148 GLN cc_start: 0.8709 (tp40) cc_final: 0.8441 (mm110) REVERT: F 29 GLU cc_start: 0.8829 (mp0) cc_final: 0.8259 (mp0) REVERT: F 42 ASP cc_start: 0.8491 (m-30) cc_final: 0.7838 (p0) REVERT: F 43 GLN cc_start: 0.8803 (mt0) cc_final: 0.8425 (mt0) REVERT: F 55 LYS cc_start: 0.8728 (OUTLIER) cc_final: 0.8503 (mtmm) REVERT: F 134 ASP cc_start: 0.8846 (t0) cc_final: 0.8313 (t0) REVERT: L 27 GLU cc_start: 0.8304 (tt0) cc_final: 0.7830 (tt0) REVERT: L 29 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.7822 (pm20) REVERT: L 116 ASP cc_start: 0.9112 (t0) cc_final: 0.8864 (m-30) outliers start: 26 outliers final: 17 residues processed: 347 average time/residue: 0.6640 time to fit residues: 249.8783 Evaluate side-chains 349 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 324 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 70 ILE Chi-restraints excluded: chain J residue 89 ASP Chi-restraints excluded: chain G residue 29 GLU Chi-restraints excluded: chain C residue 43 GLN Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 162 LYS Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain I residue 17 VAL Chi-restraints excluded: chain K residue 29 GLU Chi-restraints excluded: chain F residue 55 LYS Chi-restraints excluded: chain F residue 60 LEU Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 162 LYS Chi-restraints excluded: chain L residue 17 VAL Chi-restraints excluded: chain L residue 29 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: [135, 184, 55, 28, 165, 83, 147, 142, 78, 152, 88] chunk 135 optimal weight: 0.8980 chunk 184 optimal weight: 5.9990 chunk 55 optimal weight: 10.0000 chunk 28 optimal weight: 4.9990 chunk 165 optimal weight: 7.9990 chunk 83 optimal weight: 4.9990 chunk 147 optimal weight: 0.9980 chunk 142 optimal weight: 0.7980 chunk 78 optimal weight: 2.9990 chunk 152 optimal weight: 5.9990 chunk 88 optimal weight: 5.9990 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 43 GLN B 43 GLN G 43 GLN H 43 GLN I 43 GLN I 148 GLN E 43 GLN K 43 GLN L 43 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.072106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2590 r_free = 0.2590 target = 0.054387 restraints weight = 30053.620| |-----------------------------------------------------------------------------| r_work (start): 0.2574 rms_B_bonded: 3.42 r_work: 0.2435 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 15132 Z= 0.190 Angle : 0.609 6.724 20664 Z= 0.311 Chirality : 0.043 0.134 2328 Planarity : 0.004 0.043 2700 Dihedral : 3.995 17.370 2052 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.75 % Allowed : 16.48 % Favored : 81.77 % 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 are not related in a simple way. whole: -1.14 (0.18), residues: 1932 helix: 2.57 (0.47), residues: 156 sheet: -0.49 (0.18), residues: 828 loop : -1.57 (0.16), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 75 TYR 0.011 0.001 TYR I 131 PHE 0.010 0.001 PHE D 128 TRP 0.007 0.001 TRP F 100 HIS 0.001 0.000 HIS J 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.19 (15132) covalent geometry : angle 0.60909 / 0.31 (20664) hydrogen bonds : bond 0.03705 / 2.52 ( 514) hydrogen bonds : angle 4.49710 / 3.18 ( 1764) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 324 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 ILE cc_start: 0.9005 (OUTLIER) cc_final: 0.8690 (mm) REVERT: A 29 GLU cc_start: 0.8884 (OUTLIER) cc_final: 0.7990 (mp0) REVERT: A 134 ASP cc_start: 0.8517 (t0) cc_final: 0.7980 (t0) REVERT: J 3 ILE cc_start: 0.8366 (tp) cc_final: 0.8110 (tp) REVERT: J 29 GLU cc_start: 0.8333 (mp0) cc_final: 0.7717 (pm20) REVERT: J 105 ASP cc_start: 0.8945 (m-30) cc_final: 0.8745 (m-30) REVERT: B 29 GLU cc_start: 0.8803 (mt-10) cc_final: 0.8452 (mp0) REVERT: B 113 GLU cc_start: 0.7498 (pm20) cc_final: 0.7209 (pm20) REVERT: B 158 LYS cc_start: 0.7659 (ttmm) cc_final: 0.7450 (ttpt) REVERT: G 29 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.7696 (pm20) REVERT: G 65 GLN cc_start: 0.8939 (mp10) cc_final: 0.8631 (mp10) REVERT: C 29 GLU cc_start: 0.8775 (mp0) cc_final: 0.8270 (mp0) REVERT: C 43 GLN cc_start: 0.8820 (OUTLIER) cc_final: 0.8494 (mt0) REVERT: C 134 ASP cc_start: 0.8863 (t0) cc_final: 0.8329 (t0) REVERT: H 29 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.7857 (pm20) REVERT: H 65 GLN cc_start: 0.8846 (mp10) cc_final: 0.8543 (mp10) REVERT: H 116 ASP cc_start: 0.9108 (t0) cc_final: 0.8850 (m-30) REVERT: D 29 GLU cc_start: 0.8867 (OUTLIER) cc_final: 0.8028 (mp0) REVERT: D 134 ASP cc_start: 0.8601 (t0) cc_final: 0.8246 (t0) REVERT: I 3 ILE cc_start: 0.8360 (tp) cc_final: 0.8105 (tp) REVERT: I 29 GLU cc_start: 0.8356 (mp0) cc_final: 0.7737 (pm20) REVERT: I 65 GLN cc_start: 0.8915 (mp10) cc_final: 0.8593 (mp10) REVERT: I 88 LYS cc_start: 0.9061 (ttmm) cc_final: 0.8723 (ttmm) REVERT: I 107 LYS cc_start: 0.9104 (mtpp) cc_final: 0.8875 (mtmp) REVERT: E 29 GLU cc_start: 0.8821 (mt-10) cc_final: 0.8475 (mp0) REVERT: E 158 LYS cc_start: 0.7659 (ttmm) cc_final: 0.7447 (ttpt) REVERT: K 29 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.7688 (pm20) REVERT: K 65 GLN cc_start: 0.8926 (mp10) cc_final: 0.8619 (mp10) REVERT: F 29 GLU cc_start: 0.8844 (mp0) cc_final: 0.8282 (mp0) REVERT: F 42 ASP cc_start: 0.8497 (m-30) cc_final: 0.7861 (p0) REVERT: F 43 GLN cc_start: 0.8818 (mt0) cc_final: 0.8427 (mt0) REVERT: F 55 LYS cc_start: 0.8732 (OUTLIER) cc_final: 0.8496 (mtmm) REVERT: F 134 ASP cc_start: 0.8890 (t0) cc_final: 0.8341 (t0) REVERT: L 29 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.7861 (pm20) REVERT: L 116 ASP cc_start: 0.9118 (t0) cc_final: 0.8868 (m-30) outliers start: 28 outliers final: 18 residues processed: 339 average time/residue: 0.6964 time to fit residues: 255.1587 Evaluate side-chains 350 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 323 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 89 ASP Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain G residue 29 GLU Chi-restraints excluded: chain C residue 43 GLN Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 162 LYS Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain I residue 17 VAL Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain K residue 29 GLU Chi-restraints excluded: chain F residue 55 LYS Chi-restraints excluded: chain F residue 60 LEU Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 162 LYS Chi-restraints excluded: chain L residue 17 VAL Chi-restraints excluded: chain L residue 29 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: [93, 186, 79, 55, 157, 190, 152, 90, 27, 48, 164] chunk 93 optimal weight: 5.9990 chunk 186 optimal weight: 10.0000 chunk 79 optimal weight: 3.9990 chunk 55 optimal weight: 8.9990 chunk 157 optimal weight: 2.9990 chunk 190 optimal weight: 6.9990 chunk 152 optimal weight: 4.9990 chunk 90 optimal weight: 0.3980 chunk 27 optimal weight: 5.9990 chunk 48 optimal weight: 6.9990 chunk 164 optimal weight: 4.9990 overall best weight: 3.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 43 GLN J 43 GLN J 65 GLN B 43 GLN G 43 GLN G 148 GLN H 43 GLN D 43 GLN I 43 GLN I 148 GLN E 43 GLN K 43 GLN K 148 GLN L 43 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.071432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2566 r_free = 0.2566 target = 0.053182 restraints weight = 29519.456| |-----------------------------------------------------------------------------| r_work (start): 0.2571 rms_B_bonded: 3.43 r_work: 0.2436 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.3194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.079 15132 Z= 0.284 Angle : 0.665 6.711 20664 Z= 0.342 Chirality : 0.045 0.134 2328 Planarity : 0.004 0.045 2700 Dihedral : 4.235 21.887 2052 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.63 % Allowed : 16.79 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.18), residues: 1932 helix: 2.64 (0.48), residues: 156 sheet: -0.65 (0.18), residues: 840 loop : -1.65 (0.16), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG J 75 TYR 0.015 0.002 TYR F 131 PHE 0.011 0.002 PHE K 128 TRP 0.012 0.001 TRP F 100 HIS 0.001 0.001 HIS G 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00696 / 0.28 (15132) covalent geometry : angle 0.66512 / 0.34 (20664) hydrogen bonds : bond 0.04315 / 2.94 ( 514) hydrogen bonds : angle 4.70720 / 3.33 ( 1764) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 315 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 ILE cc_start: 0.9020 (OUTLIER) cc_final: 0.8702 (mm) REVERT: A 29 GLU cc_start: 0.8836 (OUTLIER) cc_final: 0.8592 (mp0) REVERT: A 134 ASP cc_start: 0.8619 (t0) cc_final: 0.8007 (t0) REVERT: J 3 ILE cc_start: 0.8314 (tp) cc_final: 0.8042 (tp) REVERT: J 29 GLU cc_start: 0.8326 (mp0) cc_final: 0.7627 (pm20) REVERT: J 116 ASP cc_start: 0.9152 (t0) cc_final: 0.8735 (m-30) REVERT: B 29 GLU cc_start: 0.8787 (mt-10) cc_final: 0.8423 (mp0) REVERT: G 29 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.7629 (pm20) REVERT: G 65 GLN cc_start: 0.8925 (mp10) cc_final: 0.8650 (mp10) REVERT: C 29 GLU cc_start: 0.8745 (mp0) cc_final: 0.8197 (mp0) REVERT: C 43 GLN cc_start: 0.8848 (OUTLIER) cc_final: 0.8596 (mt0) REVERT: C 134 ASP cc_start: 0.8840 (t0) cc_final: 0.8313 (t0) REVERT: H 29 GLU cc_start: 0.8348 (mp0) cc_final: 0.7783 (pm20) REVERT: H 65 GLN cc_start: 0.8855 (mp10) cc_final: 0.8515 (mp10) REVERT: H 116 ASP cc_start: 0.9138 (t0) cc_final: 0.8863 (m-30) REVERT: D 29 GLU cc_start: 0.8850 (OUTLIER) cc_final: 0.8070 (mp0) REVERT: D 134 ASP cc_start: 0.8658 (t0) cc_final: 0.8293 (t0) REVERT: I 3 ILE cc_start: 0.8298 (tp) cc_final: 0.8048 (tp) REVERT: I 29 GLU cc_start: 0.8369 (mp0) cc_final: 0.8169 (mp0) REVERT: I 65 GLN cc_start: 0.8946 (mp10) cc_final: 0.8615 (mp10) REVERT: I 107 LYS cc_start: 0.9114 (mtpp) cc_final: 0.8854 (mtmp) REVERT: E 29 GLU cc_start: 0.8774 (mt-10) cc_final: 0.8413 (mp0) REVERT: K 29 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.7646 (pm20) REVERT: K 65 GLN cc_start: 0.8919 (mp10) cc_final: 0.8646 (mp10) REVERT: F 29 GLU cc_start: 0.8838 (mp0) cc_final: 0.8274 (mp0) REVERT: F 42 ASP cc_start: 0.8488 (m-30) cc_final: 0.7851 (p0) REVERT: F 43 GLN cc_start: 0.8813 (mt0) cc_final: 0.8402 (mt0) REVERT: F 55 LYS cc_start: 0.8731 (OUTLIER) cc_final: 0.8498 (mtmm) REVERT: F 134 ASP cc_start: 0.8854 (t0) cc_final: 0.8317 (t0) REVERT: L 29 GLU cc_start: 0.8347 (mp0) cc_final: 0.7806 (pm20) REVERT: L 116 ASP cc_start: 0.9129 (t0) cc_final: 0.8846 (m-30) outliers start: 26 outliers final: 18 residues processed: 333 average time/residue: 0.7085 time to fit residues: 254.5445 Evaluate side-chains 337 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 312 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain G residue 29 GLU Chi-restraints excluded: chain C residue 43 GLN Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 162 LYS Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain I residue 17 VAL Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain K residue 29 GLU Chi-restraints excluded: chain K residue 86 SER Chi-restraints excluded: chain F residue 55 LYS Chi-restraints excluded: chain F residue 60 LEU Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 162 LYS Chi-restraints excluded: chain L residue 17 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: [99, 91, 11, 83, 87, 69, 140, 177, 84, 26, 96] chunk 99 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 69 optimal weight: 10.0000 chunk 140 optimal weight: 0.9980 chunk 177 optimal weight: 0.9990 chunk 84 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 43 GLN J 43 GLN J 65 GLN G 43 GLN G 148 GLN H 43 GLN H 84 GLN I 43 GLN K 43 GLN K 148 GLN L 43 GLN L 84 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.073621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2618 r_free = 0.2618 target = 0.055442 restraints weight = 29216.560| |-----------------------------------------------------------------------------| r_work (start): 0.2603 rms_B_bonded: 3.45 r_work: 0.2466 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.3267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 15132 Z= 0.142 Angle : 0.623 7.548 20664 Z= 0.319 Chirality : 0.043 0.137 2328 Planarity : 0.003 0.042 2700 Dihedral : 4.019 19.910 2052 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.57 % Allowed : 16.92 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.18), residues: 1932 helix: 2.66 (0.47), residues: 156 sheet: 0.18 (0.19), residues: 696 loop : -1.94 (0.15), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 75 TYR 0.008 0.001 TYR F 131 PHE 0.009 0.001 PHE I 128 TRP 0.007 0.001 TRP I 96 HIS 0.002 0.001 HIS I 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.14 (15132) covalent geometry : angle 0.62290 / 0.32 (20664) hydrogen bonds : bond 0.03436 / 2.34 ( 514) hydrogen bonds : angle 4.51297 / 3.19 ( 1764) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4871.85 seconds wall clock time: 83 minutes 39.67 seconds (5019.67 seconds total)