Starting phenix.real_space_refine on Sun Aug 24 06:58:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k37_36846/08_2025/8k37_36846.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k37_36846/08_2025/8k37_36846.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8k37_36846/08_2025/8k37_36846.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k37_36846/08_2025/8k37_36846.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8k37_36846/08_2025/8k37_36846.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k37_36846/08_2025/8k37_36846.map" } resolution = 3.5 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 ------------------------------------------------------------------------------- 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= -0.006 sd= 1.080 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 60 5.16 5 C 11598 2.51 5 N 3138 2.21 5 O 3732 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 63 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18528 Number of models: 1 Model: "" Number of chains: 18 Chain: "G" Number of atoms: 1181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1181 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 9, 'TRANS': 144} Chain: "H" Number of atoms: 1181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1181 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 9, 'TRANS': 144} Chain: "I" Number of atoms: 1181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1181 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 9, 'TRANS': 144} Chain: "J" Number of atoms: 1181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1181 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 9, 'TRANS': 144} Chain: "K" Number of atoms: 1181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1181 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 9, 'TRANS': 144} Chain: "L" Number of atoms: 1181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1181 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 9, 'TRANS': 144} Chain: "A" Number of atoms: 1031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1031 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 6, 'TRANS': 124} Chain: "B" Number of atoms: 1031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1031 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 6, 'TRANS': 124} Chain: "C" Number of atoms: 1031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1031 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 6, 'TRANS': 124} Chain: "D" Number of atoms: 1031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1031 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 6, 'TRANS': 124} Chain: "E" Number of atoms: 1031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1031 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 6, 'TRANS': 124} Chain: "F" Number of atoms: 1031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1031 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 6, 'TRANS': 124} Chain: "M" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 876 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "N" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 876 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "O" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 876 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "P" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 876 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "Q" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 876 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "R" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 876 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 5, 'TRANS': 108} Time building chain proxies: 3.92, per 1000 atoms: 0.21 Number of scatterers: 18528 At special positions: 0 Unit cell: (110.16, 107.44, 137.36, 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 60 16.00 O 3732 8.00 N 3138 7.00 C 11598 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: 1.56 Conformation dependent library (CDL) restraints added in 762.7 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4368 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 34 sheets defined 18.8% alpha, 38.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'G' and resid 90 through 102 removed outlier: 3.557A pdb=" N GLN G 94 " --> pdb=" O GLU G 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 151 through 155 removed outlier: 3.768A pdb=" N ASP G 154 " --> pdb=" O MET G 151 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ARG G 155 " --> pdb=" O ALA G 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 151 through 155' Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 151 through 155 removed outlier: 3.647A pdb=" N ASP H 154 " --> pdb=" O MET H 151 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ARG H 155 " --> pdb=" O ALA H 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 151 through 155' Processing helix chain 'I' and resid 90 through 102 removed outlier: 3.601A pdb=" N GLN I 94 " --> pdb=" O GLU I 90 " (cutoff:3.500A) Processing helix chain 'I' and resid 151 through 155 removed outlier: 3.775A pdb=" N ASP I 154 " --> pdb=" O MET I 151 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ARG I 155 " --> pdb=" O ALA I 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 151 through 155' Processing helix chain 'J' and resid 90 through 102 removed outlier: 3.567A pdb=" N GLN J 94 " --> pdb=" O GLU J 90 " (cutoff:3.500A) Processing helix chain 'J' and resid 151 through 155 removed outlier: 3.768A pdb=" N ASP J 154 " --> pdb=" O MET J 151 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ARG J 155 " --> pdb=" O ALA J 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 151 through 155' Processing helix chain 'K' and resid 90 through 102 Processing helix chain 'K' and resid 151 through 155 removed outlier: 3.723A pdb=" N ASP K 154 " --> pdb=" O MET K 151 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ARG K 155 " --> pdb=" O ALA K 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 151 through 155' Processing helix chain 'L' and resid 90 through 102 Processing helix chain 'L' and resid 151 through 155 removed outlier: 3.542A pdb=" N ASP L 154 " --> pdb=" O MET L 151 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ARG L 155 " --> pdb=" O ALA L 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 151 through 155' Processing helix chain 'A' and resid 2 through 16 removed outlier: 3.511A pdb=" N LEU A 6 " --> pdb=" O LYS A 2 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS A 16 " --> pdb=" O ASP A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 84 removed outlier: 3.982A pdb=" N LEU A 77 " --> pdb=" O PRO A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 91 removed outlier: 3.881A pdb=" N VAL A 88 " --> pdb=" O ARG A 84 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N MET A 89 " --> pdb=" O ILE A 85 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ASP A 91 " --> pdb=" O PRO A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 98 removed outlier: 4.279A pdb=" N LEU A 98 " --> pdb=" O ALA A 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 94 through 98' Processing helix chain 'B' and resid 2 through 16 removed outlier: 3.752A pdb=" N LEU B 6 " --> pdb=" O LYS B 2 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS B 16 " --> pdb=" O ASP B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 91 removed outlier: 3.688A pdb=" N LEU B 77 " --> pdb=" O PRO B 73 " (cutoff:3.500A) Proline residue: B 87 - end of helix removed outlier: 4.306A pdb=" N ASP B 91 " --> pdb=" O PRO B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 99 removed outlier: 4.345A pdb=" N LEU B 98 " --> pdb=" O ALA B 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 16 removed outlier: 3.695A pdb=" N ALA C 13 " --> pdb=" O ALA C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 82 removed outlier: 3.723A pdb=" N LEU C 77 " --> pdb=" O PRO C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 91 removed outlier: 4.180A pdb=" N VAL C 88 " --> pdb=" O ARG C 84 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ASP C 91 " --> pdb=" O PRO C 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 16 removed outlier: 3.516A pdb=" N LEU D 6 " --> pdb=" O LYS D 2 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS D 16 " --> pdb=" O ASP D 12 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 84 removed outlier: 3.674A pdb=" N LEU D 77 " --> pdb=" O PRO D 73 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TRP D 80 " --> pdb=" O GLU D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 91 removed outlier: 4.077A pdb=" N VAL D 88 " --> pdb=" O ARG D 84 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ASP D 91 " --> pdb=" O PRO D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 98 removed outlier: 4.299A pdb=" N LEU D 98 " --> pdb=" O ALA D 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 94 through 98' Processing helix chain 'E' and resid 2 through 16 removed outlier: 3.743A pdb=" N LEU E 6 " --> pdb=" O LYS E 2 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS E 16 " --> pdb=" O ASP E 12 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 82 removed outlier: 3.742A pdb=" N LEU E 77 " --> pdb=" O PRO E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 84 through 91 removed outlier: 3.934A pdb=" N VAL E 88 " --> pdb=" O ARG E 84 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ASP E 91 " --> pdb=" O PRO E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 94 through 99 removed outlier: 4.365A pdb=" N LEU E 98 " --> pdb=" O ALA E 94 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 16 removed outlier: 3.710A pdb=" N ALA F 13 " --> pdb=" O ALA F 9 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS F 16 " --> pdb=" O ASP F 12 " (cutoff:3.500A) Processing helix chain 'F' and resid 73 through 83 removed outlier: 3.907A pdb=" N LEU F 77 " --> pdb=" O PRO F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 84 through 91 removed outlier: 4.105A pdb=" N VAL F 88 " --> pdb=" O ARG F 84 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ASP F 91 " --> pdb=" O PRO F 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 94 through 99 removed outlier: 4.173A pdb=" N LEU F 98 " --> pdb=" O ALA F 94 " (cutoff:3.500A) Processing helix chain 'M' and resid 6 through 23 removed outlier: 3.694A pdb=" N ALA M 10 " --> pdb=" O ASN M 6 " (cutoff:3.500A) Processing helix chain 'N' and resid 6 through 24 removed outlier: 3.632A pdb=" N ALA N 10 " --> pdb=" O ASN N 6 " (cutoff:3.500A) Processing helix chain 'O' and resid 6 through 23 removed outlier: 3.728A pdb=" N ALA O 10 " --> pdb=" O ASN O 6 " (cutoff:3.500A) Processing helix chain 'P' and resid 6 through 23 removed outlier: 3.703A pdb=" N ALA P 10 " --> pdb=" O ASN P 6 " (cutoff:3.500A) Processing helix chain 'Q' and resid 6 through 24 removed outlier: 3.667A pdb=" N ALA Q 10 " --> pdb=" O ASN Q 6 " (cutoff:3.500A) Processing helix chain 'R' and resid 6 through 23 removed outlier: 3.730A pdb=" N ALA R 10 " --> pdb=" O ASN R 6 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 36 through 39 removed outlier: 4.829A pdb=" N LEU G 17 " --> pdb=" O LEU G 39 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N ALA G 107 " --> pdb=" O TYR G 20 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N VAL G 124 " --> pdb=" O THR G 144 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N THR G 144 " --> pdb=" O VAL G 124 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ALA G 85 " --> pdb=" O VAL G 42 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N VAL G 42 " --> pdb=" O ALA G 85 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 36 through 39 removed outlier: 4.829A pdb=" N LEU G 17 " --> pdb=" O LEU G 39 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N ALA G 107 " --> pdb=" O TYR G 20 " (cutoff:3.500A) removed outlier: 17.875A pdb=" N ARG G 121 " --> pdb=" O ASP L 56 " (cutoff:3.500A) removed outlier: 14.392A pdb=" N ASP L 56 " --> pdb=" O ARG G 121 " (cutoff:3.500A) removed outlier: 12.184A pdb=" N TRP G 123 " --> pdb=" O SER L 54 " (cutoff:3.500A) removed outlier: 9.476A pdb=" N SER L 54 " --> pdb=" O TRP G 123 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N SER G 125 " --> pdb=" O ALA L 52 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N THR L 51 " --> pdb=" O LYS L 75 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N LYS L 75 " --> pdb=" O THR L 51 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N GLU L 53 " --> pdb=" O GLY L 73 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 50 through 51 removed outlier: 5.060A pdb=" N ALA H 107 " --> pdb=" O TYR H 20 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N LEU H 17 " --> pdb=" O LEU H 39 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 50 through 51 removed outlier: 5.104A pdb=" N VAL H 124 " --> pdb=" O THR H 144 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N THR H 144 " --> pdb=" O VAL H 124 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ALA H 85 " --> pdb=" O VAL H 42 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N VAL H 42 " --> pdb=" O ALA H 85 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 54 through 56 Processing sheet with id=AA6, first strand: chain 'H' and resid 50 through 51 removed outlier: 4.975A pdb=" N ALA I 107 " --> pdb=" O TYR I 20 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N LEU I 17 " --> pdb=" O LEU I 39 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 50 through 51 removed outlier: 6.655A pdb=" N LYS I 142 " --> pdb=" O SER I 125 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ILE I 127 " --> pdb=" O THR I 140 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N THR I 140 " --> pdb=" O ILE I 127 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N LYS I 129 " --> pdb=" O THR I 138 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N THR I 138 " --> pdb=" O LYS I 129 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ALA I 85 " --> pdb=" O VAL I 42 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N VAL I 42 " --> pdb=" O ALA I 85 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 54 through 56 Processing sheet with id=AA9, first strand: chain 'I' and resid 70 through 76 removed outlier: 5.912A pdb=" N GLU I 53 " --> pdb=" O GLY I 73 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N LYS I 75 " --> pdb=" O THR I 51 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N THR I 51 " --> pdb=" O LYS I 75 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N SER J 125 " --> pdb=" O ALA I 52 " (cutoff:3.500A) removed outlier: 9.426A pdb=" N SER I 54 " --> pdb=" O TRP J 123 " (cutoff:3.500A) removed outlier: 12.176A pdb=" N TRP J 123 " --> pdb=" O SER I 54 " (cutoff:3.500A) removed outlier: 14.353A pdb=" N ASP I 56 " --> pdb=" O ARG J 121 " (cutoff:3.500A) removed outlier: 17.822A pdb=" N ARG J 121 " --> pdb=" O ASP I 56 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N ALA J 107 " --> pdb=" O TYR J 20 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N LEU J 17 " --> pdb=" O LEU J 39 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 70 through 76 removed outlier: 5.912A pdb=" N GLU I 53 " --> pdb=" O GLY I 73 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N LYS I 75 " --> pdb=" O THR I 51 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N THR I 51 " --> pdb=" O LYS I 75 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N SER J 125 " --> pdb=" O ALA I 52 " (cutoff:3.500A) removed outlier: 9.426A pdb=" N SER I 54 " --> pdb=" O TRP J 123 " (cutoff:3.500A) removed outlier: 12.176A pdb=" N TRP J 123 " --> pdb=" O SER I 54 " (cutoff:3.500A) removed outlier: 14.353A pdb=" N ASP I 56 " --> pdb=" O ARG J 121 " (cutoff:3.500A) removed outlier: 17.822A pdb=" N ARG J 121 " --> pdb=" O ASP I 56 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N VAL J 124 " --> pdb=" O THR J 144 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N THR J 144 " --> pdb=" O VAL J 124 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ALA J 85 " --> pdb=" O VAL J 42 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N VAL J 42 " --> pdb=" O ALA J 85 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'J' and resid 50 through 51 removed outlier: 5.069A pdb=" N ALA K 107 " --> pdb=" O TYR K 20 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'J' and resid 50 through 51 removed outlier: 5.105A pdb=" N VAL K 124 " --> pdb=" O THR K 144 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N THR K 144 " --> pdb=" O VAL K 124 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ALA K 85 " --> pdb=" O VAL K 42 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N VAL K 42 " --> pdb=" O ALA K 85 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'J' and resid 54 through 56 Processing sheet with id=AB5, first strand: chain 'K' and resid 50 through 51 removed outlier: 5.129A pdb=" N ALA L 107 " --> pdb=" O TYR L 20 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'K' and resid 50 through 51 removed outlier: 6.648A pdb=" N LYS L 142 " --> pdb=" O SER L 125 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ILE L 127 " --> pdb=" O THR L 140 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N THR L 140 " --> pdb=" O ILE L 127 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N LYS L 129 " --> pdb=" O THR L 138 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N THR L 138 " --> pdb=" O LYS L 129 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER L 81 " --> pdb=" O THR L 46 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ALA L 85 " --> pdb=" O VAL L 42 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N VAL L 42 " --> pdb=" O ALA L 85 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'K' and resid 54 through 56 Processing sheet with id=AB8, first strand: chain 'A' and resid 23 through 25 removed outlier: 4.213A pdb=" N ALA A 46 " --> pdb=" O GLN A 59 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N GLN A 59 " --> pdb=" O ALA A 46 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N SER A 120 " --> pdb=" O TYR A 109 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N TYR A 109 " --> pdb=" O SER A 120 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ASP A 122 " --> pdb=" O TYR A 107 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N TYR A 107 " --> pdb=" O ASP A 122 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N THR A 124 " --> pdb=" O SER A 105 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 29 through 31 removed outlier: 6.816A pdb=" N ALA A 29 " --> pdb=" O ARG O 57 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N GLU O 59 " --> pdb=" O ALA A 29 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N PHE A 31 " --> pdb=" O GLU O 59 " (cutoff:3.500A) removed outlier: 9.171A pdb=" N SER O 61 " --> pdb=" O PHE A 31 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 30 through 31 removed outlier: 6.736A pdb=" N PHE B 31 " --> pdb=" O GLU P 59 " (cutoff:3.500A) removed outlier: 9.114A pdb=" N SER P 61 " --> pdb=" O PHE B 31 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 40 through 48 removed outlier: 4.262A pdb=" N ALA B 46 " --> pdb=" O GLN B 59 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N GLN B 59 " --> pdb=" O ALA B 46 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N SER B 120 " --> pdb=" O TYR B 109 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N TYR B 109 " --> pdb=" O SER B 120 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ASP B 122 " --> pdb=" O TYR B 107 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N TYR B 107 " --> pdb=" O ASP B 122 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N THR B 124 " --> pdb=" O SER B 105 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 22 through 25 removed outlier: 3.571A pdb=" N ALA C 38 " --> pdb=" O PHE C 67 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ALA C 46 " --> pdb=" O GLN C 59 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N GLN C 59 " --> pdb=" O ALA C 46 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N SER C 120 " --> pdb=" O TYR C 109 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N TYR C 109 " --> pdb=" O SER C 120 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ASP C 122 " --> pdb=" O TYR C 107 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N TYR C 107 " --> pdb=" O ASP C 122 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N THR C 124 " --> pdb=" O SER C 105 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 30 through 31 removed outlier: 6.752A pdb=" N PHE C 31 " --> pdb=" O GLU Q 59 " (cutoff:3.500A) removed outlier: 9.132A pdb=" N SER Q 61 " --> pdb=" O PHE C 31 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 22 through 25 removed outlier: 3.674A pdb=" N ALA D 38 " --> pdb=" O PHE D 67 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ALA D 46 " --> pdb=" O GLN D 59 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N GLN D 59 " --> pdb=" O ALA D 46 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N SER D 120 " --> pdb=" O TYR D 109 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N TYR D 109 " --> pdb=" O SER D 120 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ASP D 122 " --> pdb=" O TYR D 107 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N TYR D 107 " --> pdb=" O ASP D 122 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N THR D 124 " --> pdb=" O SER D 105 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 30 through 31 removed outlier: 3.616A pdb=" N GLU R 59 " --> pdb=" O PHE D 31 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 23 through 25 removed outlier: 4.239A pdb=" N ALA E 46 " --> pdb=" O GLN E 59 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N GLN E 59 " --> pdb=" O ALA E 46 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N SER E 120 " --> pdb=" O TYR E 109 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N TYR E 109 " --> pdb=" O SER E 120 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ASP E 122 " --> pdb=" O TYR E 107 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N TYR E 107 " --> pdb=" O ASP E 122 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N THR E 124 " --> pdb=" O SER E 105 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 30 through 31 removed outlier: 6.686A pdb=" N PHE E 31 " --> pdb=" O GLU M 59 " (cutoff:3.500A) removed outlier: 9.116A pdb=" N SER M 61 " --> pdb=" O PHE E 31 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 22 through 25 removed outlier: 3.724A pdb=" N ALA F 38 " --> pdb=" O PHE F 67 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ALA F 46 " --> pdb=" O GLN F 59 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N GLN F 59 " --> pdb=" O ALA F 46 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N SER F 120 " --> pdb=" O TYR F 109 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N TYR F 109 " --> pdb=" O SER F 120 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ASP F 122 " --> pdb=" O TYR F 107 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N TYR F 107 " --> pdb=" O ASP F 122 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N THR F 124 " --> pdb=" O SER F 105 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 29 through 32 removed outlier: 7.129A pdb=" N ALA F 29 " --> pdb=" O ARG N 57 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N GLU N 59 " --> pdb=" O ALA F 29 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N PHE F 31 " --> pdb=" O GLU N 59 " (cutoff:3.500A) removed outlier: 9.204A pdb=" N SER N 61 " --> pdb=" O PHE F 31 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'M' and resid 25 through 31 removed outlier: 8.074A pdb=" N ARG M 40 " --> pdb=" O ARG M 68 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N ARG M 68 " --> pdb=" O ARG M 40 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N HIS M 102 " --> pdb=" O VAL M 93 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N VAL M 93 " --> pdb=" O HIS M 102 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N TRP M 104 " --> pdb=" O ASP M 91 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR M 80 " --> pdb=" O THR M 30 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'N' and resid 25 through 31 removed outlier: 8.145A pdb=" N ARG N 40 " --> pdb=" O ARG N 68 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N ARG N 68 " --> pdb=" O ARG N 40 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N HIS N 102 " --> pdb=" O VAL N 93 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N VAL N 93 " --> pdb=" O HIS N 102 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N TRP N 104 " --> pdb=" O ASP N 91 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N THR N 80 " --> pdb=" O THR N 30 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'O' and resid 25 through 31 removed outlier: 8.120A pdb=" N ARG O 40 " --> pdb=" O ARG O 68 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N ARG O 68 " --> pdb=" O ARG O 40 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N HIS O 102 " --> pdb=" O VAL O 93 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N VAL O 93 " --> pdb=" O HIS O 102 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N TRP O 104 " --> pdb=" O ASP O 91 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N THR O 80 " --> pdb=" O THR O 30 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'P' and resid 25 through 31 removed outlier: 8.178A pdb=" N ARG P 40 " --> pdb=" O ARG P 68 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N ARG P 68 " --> pdb=" O ARG P 40 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N HIS P 102 " --> pdb=" O VAL P 93 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N VAL P 93 " --> pdb=" O HIS P 102 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N TRP P 104 " --> pdb=" O ASP P 91 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N THR P 80 " --> pdb=" O THR P 30 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'Q' and resid 38 through 41 removed outlier: 6.907A pdb=" N THR Q 80 " --> pdb=" O THR Q 30 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N TRP Q 104 " --> pdb=" O ASP Q 91 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N VAL Q 93 " --> pdb=" O HIS Q 102 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N HIS Q 102 " --> pdb=" O VAL Q 93 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'R' and resid 25 through 31 removed outlier: 8.155A pdb=" N ARG R 40 " --> pdb=" O ARG R 68 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N ARG R 68 " --> pdb=" O ARG R 40 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N HIS R 102 " --> pdb=" O VAL R 93 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N VAL R 93 " --> pdb=" O HIS R 102 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N TRP R 104 " --> pdb=" O ASP R 91 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU R 86 " --> pdb=" O ILE R 83 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N THR R 80 " --> pdb=" O THR R 30 " (cutoff:3.500A) 766 hydrogen bonds defined for protein. 2121 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: 2.37 Time building geometry restraints manager: 2.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6238 1.34 - 1.46: 3561 1.46 - 1.58: 9041 1.58 - 1.69: 0 1.69 - 1.81: 114 Bond restraints: 18954 Sorted by residual: bond pdb=" CA ASP B 35 " pdb=" C ASP B 35 " ideal model delta sigma weight residual 1.530 1.499 0.031 1.14e-02 7.69e+03 7.42e+00 bond pdb=" N ALA B 38 " pdb=" CA ALA B 38 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.29e-02 6.01e+03 5.97e+00 bond pdb=" CA ALA D 38 " pdb=" C ALA D 38 " ideal model delta sigma weight residual 1.520 1.492 0.029 1.20e-02 6.94e+03 5.66e+00 bond pdb=" C PHE B 36 " pdb=" O PHE B 36 " ideal model delta sigma weight residual 1.244 1.221 0.023 1.00e-02 1.00e+04 5.12e+00 bond pdb=" CA PRO B 37 " pdb=" C PRO B 37 " ideal model delta sigma weight residual 1.517 1.548 -0.031 1.46e-02 4.69e+03 4.53e+00 ... (remaining 18949 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.56: 25492 2.56 - 5.12: 288 5.12 - 7.68: 19 7.68 - 10.24: 10 10.24 - 12.80: 3 Bond angle restraints: 25812 Sorted by residual: angle pdb=" N PHE B 36 " pdb=" CA PHE B 36 " pdb=" C PHE B 36 " ideal model delta sigma weight residual 112.35 121.93 -9.58 1.34e+00 5.57e-01 5.11e+01 angle pdb=" C PHE D 36 " pdb=" N PRO D 37 " pdb=" CA PRO D 37 " ideal model delta sigma weight residual 120.23 111.71 8.52 1.23e+00 6.61e-01 4.80e+01 angle pdb=" N GLU A 82 " pdb=" CA GLU A 82 " pdb=" C GLU A 82 " ideal model delta sigma weight residual 111.36 118.22 -6.86 1.09e+00 8.42e-01 3.96e+01 angle pdb=" N ALA B 38 " pdb=" CA ALA B 38 " pdb=" C ALA B 38 " ideal model delta sigma weight residual 110.80 123.21 -12.41 2.13e+00 2.20e-01 3.40e+01 angle pdb=" N PHE E 36 " pdb=" CA PHE E 36 " pdb=" C PHE E 36 " ideal model delta sigma weight residual 109.81 122.61 -12.80 2.21e+00 2.05e-01 3.36e+01 ... (remaining 25807 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 10189 17.96 - 35.92: 785 35.92 - 53.88: 144 53.88 - 71.83: 18 71.83 - 89.79: 12 Dihedral angle restraints: 11148 sinusoidal: 4320 harmonic: 6828 Sorted by residual: dihedral pdb=" N PHE E 36 " pdb=" C PHE E 36 " pdb=" CA PHE E 36 " pdb=" CB PHE E 36 " ideal model delta harmonic sigma weight residual 122.80 139.99 -17.19 0 2.50e+00 1.60e-01 4.73e+01 dihedral pdb=" C PHE E 36 " pdb=" N PHE E 36 " pdb=" CA PHE E 36 " pdb=" CB PHE E 36 " ideal model delta harmonic sigma weight residual -122.60 -138.78 16.18 0 2.50e+00 1.60e-01 4.19e+01 dihedral pdb=" N PHE B 36 " pdb=" C PHE B 36 " pdb=" CA PHE B 36 " pdb=" CB PHE B 36 " ideal model delta harmonic sigma weight residual 122.80 137.52 -14.72 0 2.50e+00 1.60e-01 3.47e+01 ... (remaining 11145 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.161: 2791 0.161 - 0.322: 10 0.322 - 0.483: 3 0.483 - 0.644: 2 0.644 - 0.805: 2 Chirality restraints: 2808 Sorted by residual: chirality pdb=" CA PHE E 36 " pdb=" N PHE E 36 " pdb=" C PHE E 36 " pdb=" CB PHE E 36 " both_signs ideal model delta sigma weight residual False 2.51 1.71 0.80 2.00e-01 2.50e+01 1.62e+01 chirality pdb=" CA PHE B 36 " pdb=" N PHE B 36 " pdb=" C PHE B 36 " pdb=" CB PHE B 36 " both_signs ideal model delta sigma weight residual False 2.51 1.81 0.70 2.00e-01 2.50e+01 1.23e+01 chirality pdb=" CA PHE D 36 " pdb=" N PHE D 36 " pdb=" C PHE D 36 " pdb=" CB PHE D 36 " both_signs ideal model delta sigma weight residual False 2.51 1.91 0.60 2.00e-01 2.50e+01 9.05e+00 ... (remaining 2805 not shown) Planarity restraints: 3408 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU C 82 " -0.013 2.00e-02 2.50e+03 2.51e-02 6.32e+00 pdb=" C GLU C 82 " 0.043 2.00e-02 2.50e+03 pdb=" O GLU C 82 " -0.016 2.00e-02 2.50e+03 pdb=" N SER C 83 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA D 34 " -0.012 2.00e-02 2.50e+03 2.49e-02 6.22e+00 pdb=" C ALA D 34 " 0.043 2.00e-02 2.50e+03 pdb=" O ALA D 34 " -0.016 2.00e-02 2.50e+03 pdb=" N ASP D 35 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 38 " 0.012 2.00e-02 2.50e+03 2.43e-02 5.90e+00 pdb=" C ALA B 38 " -0.042 2.00e-02 2.50e+03 pdb=" O ALA B 38 " 0.015 2.00e-02 2.50e+03 pdb=" N VAL B 39 " 0.014 2.00e-02 2.50e+03 ... (remaining 3405 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2917 2.76 - 3.29: 16565 3.29 - 3.83: 28558 3.83 - 4.36: 32315 4.36 - 4.90: 60650 Nonbonded interactions: 141005 Sorted by model distance: nonbonded pdb=" NH1 ARG H 148 " pdb=" O PRO H 149 " model vdw 2.224 3.120 nonbonded pdb=" OD2 ASP A 35 " pdb=" NH2 ARG P 115 " model vdw 2.250 3.120 nonbonded pdb=" OD1 ASP K 44 " pdb=" N LEU K 45 " model vdw 2.254 3.120 nonbonded pdb=" OD1 ASP H 44 " pdb=" N LEU H 45 " model vdw 2.255 3.120 nonbonded pdb=" OD2 ASP F 35 " pdb=" NH2 ARG O 115 " model vdw 2.263 3.120 ... (remaining 141000 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 15.860 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 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 : 0.006 0.051 18954 Z= 0.268 Angle : 0.693 12.803 25812 Z= 0.377 Chirality : 0.055 0.805 2808 Planarity : 0.004 0.044 3408 Dihedral : 13.201 89.792 6780 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.41 % Allowed : 0.31 % Favored : 99.28 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.80 (0.16), residues: 2358 helix: 1.35 (0.30), residues: 306 sheet: 0.07 (0.18), residues: 822 loop : -1.48 (0.14), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG M 73 TYR 0.013 0.002 TYR B 129 PHE 0.039 0.002 PHE A 36 TRP 0.010 0.001 TRP L 99 HIS 0.005 0.001 HIS E 17 Details of bonding type rmsd covalent geometry : bond 0.00600 (18954) covalent geometry : angle 0.69274 (25812) hydrogen bonds : bond 0.21360 ( 738) hydrogen bonds : angle 9.45386 ( 2121) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 504 time to evaluate : 0.733 Fit side-chains revert: symmetry clash REVERT: G 142 LYS cc_start: 0.8702 (ttmm) cc_final: 0.8421 (ttpp) REVERT: I 59 TYR cc_start: 0.7949 (m-80) cc_final: 0.7662 (m-10) REVERT: I 142 LYS cc_start: 0.8712 (ttmm) cc_final: 0.8480 (ttpp) REVERT: J 139 ARG cc_start: 0.9178 (tpp-160) cc_final: 0.8913 (ttm-80) REVERT: L 21 LYS cc_start: 0.8282 (mtpt) cc_final: 0.7896 (pttm) REVERT: L 59 TYR cc_start: 0.7870 (m-80) cc_final: 0.7640 (m-10) REVERT: L 87 MET cc_start: 0.7541 (mtp) cc_final: 0.6920 (mtm) REVERT: L 151 MET cc_start: 0.8621 (mmm) cc_final: 0.8319 (mmp) REVERT: A 4 THR cc_start: 0.8523 (m) cc_final: 0.7953 (p) REVERT: C 76 GLU cc_start: 0.7575 (tm-30) cc_final: 0.7346 (tm-30) REVERT: D 4 THR cc_start: 0.8616 (m) cc_final: 0.8065 (p) REVERT: D 35 ASP cc_start: 0.7459 (OUTLIER) cc_final: 0.6799 (p0) REVERT: E 19 THR cc_start: 0.5995 (m) cc_final: 0.5675 (m) REVERT: E 80 TRP cc_start: 0.8607 (OUTLIER) cc_final: 0.6517 (t60) REVERT: F 18 ASP cc_start: 0.5926 (t70) cc_final: 0.5706 (m-30) REVERT: M 70 ASP cc_start: 0.8295 (m-30) cc_final: 0.8091 (m-30) REVERT: O 79 ASP cc_start: 0.7988 (m-30) cc_final: 0.7655 (m-30) REVERT: Q 25 THR cc_start: 0.8121 (t) cc_final: 0.7916 (t) REVERT: Q 39 ILE cc_start: 0.9122 (mt) cc_final: 0.8839 (mt) REVERT: R 79 ASP cc_start: 0.7986 (m-30) cc_final: 0.7665 (m-30) REVERT: R 91 ASP cc_start: 0.8872 (t0) cc_final: 0.8148 (t0) outliers start: 8 outliers final: 0 residues processed: 512 average time/residue: 0.1685 time to fit residues: 124.2797 Evaluate side-chains 351 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 349 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 35 ASP Chi-restraints excluded: chain E residue 80 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 216 optimal weight: 8.9990 chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 5.9990 chunk 227 optimal weight: 7.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.6980 chunk 200 optimal weight: 5.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 91 GLN I 101 ASN ** K 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 101 ASN A 17 HIS C 17 HIS F 59 GLN N 6 ASN P 34 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.101512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.092055 restraints weight = 35505.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.094035 restraints weight = 19999.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.095387 restraints weight = 12996.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.096303 restraints weight = 9353.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.096951 restraints weight = 7222.834| |-----------------------------------------------------------------------------| r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 18954 Z= 0.233 Angle : 0.655 8.663 25812 Z= 0.345 Chirality : 0.048 0.269 2808 Planarity : 0.005 0.042 3408 Dihedral : 5.174 55.134 2614 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.45 % Allowed : 10.28 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.84 (0.16), residues: 2358 helix: 0.71 (0.27), residues: 348 sheet: -0.08 (0.17), residues: 894 loop : -1.36 (0.15), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG Q 73 TYR 0.016 0.001 TYR L 55 PHE 0.039 0.002 PHE C 36 TRP 0.020 0.002 TRP F 80 HIS 0.004 0.001 HIS F 63 Details of bonding type rmsd covalent geometry : bond 0.00555 (18954) covalent geometry : angle 0.65492 (25812) hydrogen bonds : bond 0.04772 ( 738) hydrogen bonds : angle 6.78795 ( 2121) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 360 time to evaluate : 0.746 Fit side-chains REVERT: G 142 LYS cc_start: 0.8580 (ttmm) cc_final: 0.8292 (ttpp) REVERT: I 102 GLU cc_start: 0.7522 (pp20) cc_final: 0.7220 (pp20) REVERT: K 102 GLU cc_start: 0.7225 (pp20) cc_final: 0.6837 (pp20) REVERT: B 51 GLU cc_start: 0.7673 (pp20) cc_final: 0.7447 (pt0) REVERT: C 18 ASP cc_start: 0.5781 (t70) cc_final: 0.5577 (m-30) REVERT: E 80 TRP cc_start: 0.8872 (OUTLIER) cc_final: 0.6648 (t60) REVERT: P 34 GLN cc_start: 0.8472 (mt0) cc_final: 0.8178 (mt0) outliers start: 48 outliers final: 38 residues processed: 388 average time/residue: 0.1446 time to fit residues: 83.8503 Evaluate side-chains 365 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 326 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain H residue 51 THR Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain I residue 17 LEU Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain I residue 81 SER Chi-restraints excluded: chain I residue 87 MET Chi-restraints excluded: chain I residue 116 THR Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 81 SER Chi-restraints excluded: chain L residue 17 LEU Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain A residue 17 HIS Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 102 MET Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 80 TRP Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 102 MET Chi-restraints excluded: chain F residue 120 SER Chi-restraints excluded: chain M residue 44 ASP Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain N residue 35 SER Chi-restraints excluded: chain N residue 47 GLU Chi-restraints excluded: chain N residue 94 SER Chi-restraints excluded: chain O residue 5 ASP Chi-restraints excluded: chain O residue 44 ASP Chi-restraints excluded: chain O residue 94 SER Chi-restraints excluded: chain O residue 109 VAL Chi-restraints excluded: chain P residue 44 ASP Chi-restraints excluded: chain P residue 109 VAL Chi-restraints excluded: chain R residue 5 ASP Chi-restraints excluded: chain R residue 44 ASP Chi-restraints excluded: chain R residue 94 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 27 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 119 optimal weight: 4.9990 chunk 48 optimal weight: 6.9990 chunk 33 optimal weight: 10.0000 chunk 118 optimal weight: 1.9990 chunk 120 optimal weight: 7.9990 chunk 204 optimal weight: 10.0000 chunk 136 optimal weight: 0.9990 chunk 226 optimal weight: 7.9990 chunk 225 optimal weight: 0.0980 overall best weight: 2.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 101 ASN ** H 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 101 ASN ** K 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 6 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.103419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.093905 restraints weight = 35523.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.095917 restraints weight = 19833.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.097306 restraints weight = 12843.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.098225 restraints weight = 9176.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.098905 restraints weight = 7085.376| |-----------------------------------------------------------------------------| r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18954 Z= 0.139 Angle : 0.562 7.328 25812 Z= 0.295 Chirality : 0.046 0.221 2808 Planarity : 0.004 0.045 3408 Dihedral : 4.846 54.364 2612 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.04 % Favored : 97.92 % Rotamer: Outliers : 2.97 % Allowed : 13.04 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.57 (0.16), residues: 2358 helix: 0.78 (0.27), residues: 348 sheet: 0.09 (0.16), residues: 1002 loop : -1.24 (0.16), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 121 TYR 0.009 0.001 TYR L 108 PHE 0.030 0.002 PHE C 36 TRP 0.007 0.001 TRP F 80 HIS 0.008 0.001 HIS A 17 Details of bonding type rmsd covalent geometry : bond 0.00323 (18954) covalent geometry : angle 0.56206 (25812) hydrogen bonds : bond 0.03828 ( 738) hydrogen bonds : angle 6.23879 ( 2121) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 367 time to evaluate : 0.768 Fit side-chains REVERT: G 142 LYS cc_start: 0.8633 (ttmm) cc_final: 0.8416 (ttpp) REVERT: I 102 GLU cc_start: 0.7559 (pp20) cc_final: 0.7220 (pp20) REVERT: K 7 THR cc_start: 0.8912 (OUTLIER) cc_final: 0.8572 (t) REVERT: K 102 GLU cc_start: 0.7385 (pp20) cc_final: 0.6919 (pp20) REVERT: C 18 ASP cc_start: 0.5700 (t70) cc_final: 0.5436 (m-30) REVERT: E 19 THR cc_start: 0.6280 (OUTLIER) cc_final: 0.5956 (m) REVERT: E 80 TRP cc_start: 0.8799 (OUTLIER) cc_final: 0.6465 (t60) REVERT: P 39 ILE cc_start: 0.9067 (mt) cc_final: 0.8704 (mm) REVERT: R 86 GLU cc_start: 0.7269 (mt-10) cc_final: 0.7044 (mt-10) REVERT: R 103 LEU cc_start: 0.8875 (mp) cc_final: 0.8568 (mp) outliers start: 58 outliers final: 48 residues processed: 394 average time/residue: 0.1457 time to fit residues: 86.1388 Evaluate side-chains 374 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 323 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain G residue 90 GLU Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain I residue 17 LEU Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain I residue 81 SER Chi-restraints excluded: chain I residue 87 MET Chi-restraints excluded: chain I residue 116 THR Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 42 VAL Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain J residue 90 GLU Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 81 SER Chi-restraints excluded: chain K residue 151 MET Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 51 GLU Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 102 MET Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain D residue 5 GLU Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 80 TRP Chi-restraints excluded: chain F residue 18 ASP Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 102 MET Chi-restraints excluded: chain F residue 120 SER Chi-restraints excluded: chain M residue 44 ASP Chi-restraints excluded: chain N residue 17 GLU Chi-restraints excluded: chain N residue 35 SER Chi-restraints excluded: chain N residue 44 ASP Chi-restraints excluded: chain N residue 47 GLU Chi-restraints excluded: chain O residue 5 ASP Chi-restraints excluded: chain O residue 44 ASP Chi-restraints excluded: chain O residue 94 SER Chi-restraints excluded: chain O residue 109 VAL Chi-restraints excluded: chain P residue 44 ASP Chi-restraints excluded: chain Q residue 35 SER Chi-restraints excluded: chain Q residue 44 ASP Chi-restraints excluded: chain R residue 5 ASP Chi-restraints excluded: chain R residue 44 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 53 optimal weight: 6.9990 chunk 84 optimal weight: 8.9990 chunk 128 optimal weight: 1.9990 chunk 36 optimal weight: 6.9990 chunk 13 optimal weight: 10.0000 chunk 58 optimal weight: 6.9990 chunk 224 optimal weight: 0.8980 chunk 203 optimal weight: 6.9990 chunk 109 optimal weight: 4.9990 chunk 227 optimal weight: 4.9990 chunk 138 optimal weight: 6.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 101 ASN ** H 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 101 ASN ** K 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 17 HIS B 63 HIS M 6 ASN P 6 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.100930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.091545 restraints weight = 35721.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.093509 restraints weight = 20056.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.094855 restraints weight = 13060.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.095778 restraints weight = 9371.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.096431 restraints weight = 7225.526| |-----------------------------------------------------------------------------| r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 18954 Z= 0.228 Angle : 0.621 7.917 25812 Z= 0.327 Chirality : 0.048 0.258 2808 Planarity : 0.005 0.042 3408 Dihedral : 5.151 57.961 2612 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.04 % Favored : 97.92 % Rotamer: Outliers : 4.14 % Allowed : 14.67 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.72 (0.16), residues: 2358 helix: 0.59 (0.27), residues: 348 sheet: -0.02 (0.16), residues: 984 loop : -1.26 (0.16), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 121 TYR 0.013 0.002 TYR E 129 PHE 0.036 0.002 PHE C 36 TRP 0.012 0.002 TRP D 80 HIS 0.003 0.001 HIS E 17 Details of bonding type rmsd covalent geometry : bond 0.00546 (18954) covalent geometry : angle 0.62100 (25812) hydrogen bonds : bond 0.04171 ( 738) hydrogen bonds : angle 6.12211 ( 2121) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 319 time to evaluate : 0.494 Fit side-chains REVERT: G 142 LYS cc_start: 0.8637 (ttmm) cc_final: 0.8407 (ttpp) REVERT: H 8 MET cc_start: 0.7767 (mtm) cc_final: 0.7500 (mtt) REVERT: I 102 GLU cc_start: 0.7483 (pp20) cc_final: 0.7269 (pp20) REVERT: K 102 GLU cc_start: 0.7525 (pp20) cc_final: 0.7025 (pp20) REVERT: E 19 THR cc_start: 0.6407 (OUTLIER) cc_final: 0.6143 (m) REVERT: E 80 TRP cc_start: 0.8980 (OUTLIER) cc_final: 0.6860 (t60) REVERT: O 91 ASP cc_start: 0.8919 (t0) cc_final: 0.8122 (t0) REVERT: Q 71 GLU cc_start: 0.7191 (pt0) cc_final: 0.6961 (pt0) REVERT: R 91 ASP cc_start: 0.8875 (t0) cc_final: 0.8245 (t0) outliers start: 81 outliers final: 65 residues processed: 370 average time/residue: 0.1382 time to fit residues: 76.3503 Evaluate side-chains 369 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 302 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain G residue 90 GLU Chi-restraints excluded: chain H residue 51 THR Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain I residue 17 LEU Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain I residue 81 SER Chi-restraints excluded: chain I residue 87 MET Chi-restraints excluded: chain I residue 116 THR Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 42 VAL Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain J residue 90 GLU Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 81 SER Chi-restraints excluded: chain K residue 143 VAL Chi-restraints excluded: chain K residue 151 MET Chi-restraints excluded: chain L residue 11 LYS Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 81 SER Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 5 GLU Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain C residue 4 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 51 GLU Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 102 MET Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 5 GLU Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 51 GLU Chi-restraints excluded: chain E residue 80 TRP Chi-restraints excluded: chain E residue 120 SER Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 102 MET Chi-restraints excluded: chain F residue 120 SER Chi-restraints excluded: chain M residue 35 SER Chi-restraints excluded: chain M residue 44 ASP Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain N residue 17 GLU Chi-restraints excluded: chain N residue 35 SER Chi-restraints excluded: chain N residue 47 GLU Chi-restraints excluded: chain O residue 5 ASP Chi-restraints excluded: chain O residue 34 GLN Chi-restraints excluded: chain O residue 44 ASP Chi-restraints excluded: chain O residue 109 VAL Chi-restraints excluded: chain P residue 44 ASP Chi-restraints excluded: chain P residue 71 GLU Chi-restraints excluded: chain P residue 109 VAL Chi-restraints excluded: chain Q residue 35 SER Chi-restraints excluded: chain Q residue 44 ASP Chi-restraints excluded: chain R residue 5 ASP Chi-restraints excluded: chain R residue 44 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 108 optimal weight: 9.9990 chunk 53 optimal weight: 0.6980 chunk 35 optimal weight: 4.9990 chunk 164 optimal weight: 7.9990 chunk 229 optimal weight: 0.9980 chunk 166 optimal weight: 3.9990 chunk 153 optimal weight: 7.9990 chunk 37 optimal weight: 9.9990 chunk 143 optimal weight: 3.9990 chunk 46 optimal weight: 10.0000 chunk 44 optimal weight: 9.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 6 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.101769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.092435 restraints weight = 35338.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.094409 restraints weight = 19761.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.095753 restraints weight = 12815.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.096682 restraints weight = 9150.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.097270 restraints weight = 7049.112| |-----------------------------------------------------------------------------| r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 18954 Z= 0.176 Angle : 0.573 7.252 25812 Z= 0.302 Chirality : 0.046 0.230 2808 Planarity : 0.005 0.043 3408 Dihedral : 4.995 58.104 2612 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.82 % Favored : 98.13 % Rotamer: Outliers : 4.29 % Allowed : 15.54 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.60 (0.16), residues: 2358 helix: 0.66 (0.27), residues: 348 sheet: 0.08 (0.16), residues: 1014 loop : -1.22 (0.17), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 121 TYR 0.012 0.001 TYR L 55 PHE 0.031 0.002 PHE C 36 TRP 0.008 0.001 TRP B 80 HIS 0.002 0.001 HIS B 17 Details of bonding type rmsd covalent geometry : bond 0.00420 (18954) covalent geometry : angle 0.57334 (25812) hydrogen bonds : bond 0.03694 ( 738) hydrogen bonds : angle 5.90141 ( 2121) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 326 time to evaluate : 0.610 Fit side-chains REVERT: G 142 LYS cc_start: 0.8643 (ttmm) cc_final: 0.8418 (ttpp) REVERT: H 8 MET cc_start: 0.7818 (mtm) cc_final: 0.7564 (mtt) REVERT: I 102 GLU cc_start: 0.7564 (pp20) cc_final: 0.7325 (pp20) REVERT: J 87 MET cc_start: 0.7710 (mtp) cc_final: 0.7477 (mtp) REVERT: K 7 THR cc_start: 0.8898 (OUTLIER) cc_final: 0.8543 (t) REVERT: K 102 GLU cc_start: 0.7495 (pp20) cc_final: 0.7042 (pp20) REVERT: E 19 THR cc_start: 0.5796 (OUTLIER) cc_final: 0.5349 (m) REVERT: E 80 TRP cc_start: 0.8939 (OUTLIER) cc_final: 0.6907 (t60) REVERT: F 6 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8319 (tt) REVERT: O 91 ASP cc_start: 0.8928 (t0) cc_final: 0.8177 (t0) REVERT: Q 54 GLN cc_start: 0.8271 (OUTLIER) cc_final: 0.7024 (mp10) REVERT: R 91 ASP cc_start: 0.8861 (t0) cc_final: 0.7912 (t0) outliers start: 84 outliers final: 62 residues processed: 377 average time/residue: 0.1530 time to fit residues: 86.4247 Evaluate side-chains 382 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 315 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain G residue 90 GLU Chi-restraints excluded: chain H residue 51 THR Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain I residue 17 LEU Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain I residue 81 SER Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 87 MET Chi-restraints excluded: chain I residue 116 THR Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 42 VAL Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 81 SER Chi-restraints excluded: chain K residue 143 VAL Chi-restraints excluded: chain K residue 151 MET Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 81 SER Chi-restraints excluded: chain A residue 5 GLU Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain C residue 4 THR Chi-restraints excluded: chain C residue 18 ASP Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 51 GLU Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 102 MET Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain D residue 5 GLU Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 51 GLU Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 80 TRP Chi-restraints excluded: chain F residue 6 LEU Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 51 GLU Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 102 MET Chi-restraints excluded: chain F residue 120 SER Chi-restraints excluded: chain M residue 35 SER Chi-restraints excluded: chain M residue 44 ASP Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain N residue 17 GLU Chi-restraints excluded: chain N residue 35 SER Chi-restraints excluded: chain N residue 47 GLU Chi-restraints excluded: chain O residue 5 ASP Chi-restraints excluded: chain O residue 109 VAL Chi-restraints excluded: chain P residue 44 ASP Chi-restraints excluded: chain P residue 96 ASP Chi-restraints excluded: chain P residue 109 VAL Chi-restraints excluded: chain Q residue 35 SER Chi-restraints excluded: chain Q residue 44 ASP Chi-restraints excluded: chain Q residue 54 GLN Chi-restraints excluded: chain R residue 5 ASP Chi-restraints excluded: chain R residue 44 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 202 optimal weight: 2.9990 chunk 218 optimal weight: 4.9990 chunk 187 optimal weight: 6.9990 chunk 71 optimal weight: 8.9990 chunk 114 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 192 optimal weight: 10.0000 chunk 220 optimal weight: 5.9990 chunk 143 optimal weight: 0.5980 chunk 158 optimal weight: 2.9990 chunk 205 optimal weight: 5.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 6 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.101870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.092258 restraints weight = 35064.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.094309 restraints weight = 19413.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.095683 restraints weight = 12524.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.096632 restraints weight = 8952.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.097301 restraints weight = 6881.783| |-----------------------------------------------------------------------------| r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.2753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 18954 Z= 0.158 Angle : 0.561 7.330 25812 Z= 0.294 Chirality : 0.046 0.217 2808 Planarity : 0.004 0.043 3408 Dihedral : 4.912 58.657 2612 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.87 % Favored : 98.09 % Rotamer: Outliers : 4.29 % Allowed : 16.51 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.66 (0.16), residues: 2358 helix: 0.72 (0.27), residues: 348 sheet: 0.16 (0.17), residues: 876 loop : -1.29 (0.16), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 121 TYR 0.012 0.001 TYR I 55 PHE 0.028 0.002 PHE C 36 TRP 0.013 0.001 TRP J 86 HIS 0.002 0.001 HIS N 102 Details of bonding type rmsd covalent geometry : bond 0.00376 (18954) covalent geometry : angle 0.56097 (25812) hydrogen bonds : bond 0.03540 ( 738) hydrogen bonds : angle 5.77879 ( 2121) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 333 time to evaluate : 0.527 Fit side-chains REVERT: G 118 ASP cc_start: 0.8412 (t0) cc_final: 0.8116 (t0) REVERT: G 142 LYS cc_start: 0.8683 (ttmm) cc_final: 0.8447 (ttpp) REVERT: H 8 MET cc_start: 0.7820 (mtm) cc_final: 0.7580 (mtt) REVERT: I 102 GLU cc_start: 0.7589 (pp20) cc_final: 0.7359 (pp20) REVERT: J 84 LEU cc_start: 0.9244 (OUTLIER) cc_final: 0.9010 (pp) REVERT: K 7 THR cc_start: 0.8912 (OUTLIER) cc_final: 0.8549 (t) REVERT: K 102 GLU cc_start: 0.7558 (pp20) cc_final: 0.7113 (pp20) REVERT: L 151 MET cc_start: 0.8790 (mmm) cc_final: 0.8540 (mmp) REVERT: D 117 LEU cc_start: 0.9368 (OUTLIER) cc_final: 0.9116 (tp) REVERT: E 80 TRP cc_start: 0.8941 (OUTLIER) cc_final: 0.6953 (t60) REVERT: N 73 ARG cc_start: 0.7742 (ttm110) cc_final: 0.7329 (ttm-80) REVERT: O 91 ASP cc_start: 0.8804 (t0) cc_final: 0.8039 (t0) REVERT: P 34 GLN cc_start: 0.8322 (mt0) cc_final: 0.7847 (mt0) REVERT: Q 47 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7794 (tt0) outliers start: 84 outliers final: 68 residues processed: 385 average time/residue: 0.1437 time to fit residues: 83.3089 Evaluate side-chains 397 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 324 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain G residue 90 GLU Chi-restraints excluded: chain H residue 51 THR Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain I residue 17 LEU Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain I residue 81 SER Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 87 MET Chi-restraints excluded: chain I residue 116 THR Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 42 VAL Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain J residue 84 LEU Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 81 SER Chi-restraints excluded: chain K residue 143 VAL Chi-restraints excluded: chain K residue 151 MET Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 81 SER Chi-restraints excluded: chain L residue 148 ARG Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 5 GLU Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain C residue 4 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 51 GLU Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 102 MET Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 5 GLU Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 51 GLU Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 80 TRP Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 102 MET Chi-restraints excluded: chain F residue 120 SER Chi-restraints excluded: chain M residue 35 SER Chi-restraints excluded: chain M residue 44 ASP Chi-restraints excluded: chain M residue 96 ASP Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain N residue 17 GLU Chi-restraints excluded: chain N residue 35 SER Chi-restraints excluded: chain N residue 47 GLU Chi-restraints excluded: chain O residue 5 ASP Chi-restraints excluded: chain O residue 34 GLN Chi-restraints excluded: chain O residue 44 ASP Chi-restraints excluded: chain O residue 109 VAL Chi-restraints excluded: chain P residue 44 ASP Chi-restraints excluded: chain P residue 71 GLU Chi-restraints excluded: chain P residue 109 VAL Chi-restraints excluded: chain Q residue 35 SER Chi-restraints excluded: chain Q residue 44 ASP Chi-restraints excluded: chain Q residue 47 GLU Chi-restraints excluded: chain R residue 5 ASP Chi-restraints excluded: chain R residue 44 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 146 optimal weight: 7.9990 chunk 66 optimal weight: 1.9990 chunk 4 optimal weight: 8.9990 chunk 94 optimal weight: 4.9990 chunk 145 optimal weight: 0.9990 chunk 34 optimal weight: 10.0000 chunk 46 optimal weight: 9.9990 chunk 50 optimal weight: 9.9990 chunk 140 optimal weight: 9.9990 chunk 232 optimal weight: 8.9990 chunk 226 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 6 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.100444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.090823 restraints weight = 35590.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.092859 restraints weight = 19980.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.094236 restraints weight = 12980.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.095173 restraints weight = 9305.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.095842 restraints weight = 7173.007| |-----------------------------------------------------------------------------| r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 18954 Z= 0.218 Angle : 0.605 8.799 25812 Z= 0.318 Chirality : 0.047 0.247 2808 Planarity : 0.005 0.042 3408 Dihedral : 5.067 59.350 2612 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.12 % Favored : 97.84 % Rotamer: Outliers : 4.60 % Allowed : 16.82 % Favored : 78.58 % 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 aren not related in a simple way. whole: -0.62 (0.16), residues: 2358 helix: 0.61 (0.27), residues: 348 sheet: 0.07 (0.16), residues: 1020 loop : -1.24 (0.17), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 121 TYR 0.013 0.002 TYR I 55 PHE 0.033 0.002 PHE C 36 TRP 0.011 0.001 TRP B 80 HIS 0.003 0.001 HIS N 102 Details of bonding type rmsd covalent geometry : bond 0.00524 (18954) covalent geometry : angle 0.60505 (25812) hydrogen bonds : bond 0.03862 ( 738) hydrogen bonds : angle 5.82257 ( 2121) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 320 time to evaluate : 0.748 Fit side-chains REVERT: G 102 GLU cc_start: 0.7856 (pp20) cc_final: 0.7592 (pp20) REVERT: G 118 ASP cc_start: 0.8455 (t0) cc_final: 0.8169 (t0) REVERT: G 142 LYS cc_start: 0.8672 (ttmm) cc_final: 0.8431 (ttpp) REVERT: H 8 MET cc_start: 0.7855 (mtm) cc_final: 0.7616 (mtt) REVERT: I 102 GLU cc_start: 0.7626 (pp20) cc_final: 0.7368 (pp20) REVERT: K 7 THR cc_start: 0.8918 (OUTLIER) cc_final: 0.8553 (t) REVERT: K 102 GLU cc_start: 0.7616 (pp20) cc_final: 0.7151 (pp20) REVERT: A 6 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8248 (tt) REVERT: D 6 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8187 (tt) REVERT: D 117 LEU cc_start: 0.9386 (OUTLIER) cc_final: 0.9155 (tp) REVERT: E 80 TRP cc_start: 0.8994 (OUTLIER) cc_final: 0.6954 (t60) REVERT: F 6 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8323 (tt) REVERT: N 73 ARG cc_start: 0.7718 (ttm110) cc_final: 0.7317 (ttm-80) REVERT: O 91 ASP cc_start: 0.8816 (t0) cc_final: 0.7885 (t0) REVERT: P 34 GLN cc_start: 0.8344 (mt0) cc_final: 0.7981 (mt0) REVERT: Q 47 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7907 (tt0) outliers start: 90 outliers final: 75 residues processed: 377 average time/residue: 0.1419 time to fit residues: 80.2238 Evaluate side-chains 400 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 318 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain G residue 90 GLU Chi-restraints excluded: chain H residue 51 THR Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain I residue 17 LEU Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain I residue 81 SER Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 87 MET Chi-restraints excluded: chain I residue 116 THR Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 42 VAL Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 81 SER Chi-restraints excluded: chain K residue 143 VAL Chi-restraints excluded: chain K residue 151 MET Chi-restraints excluded: chain L residue 11 LYS Chi-restraints excluded: chain L residue 17 LEU Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 81 SER Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 5 GLU Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain C residue 4 THR Chi-restraints excluded: chain C residue 18 ASP Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 51 GLU Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 102 MET Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 5 GLU Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 51 GLU Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 80 TRP Chi-restraints excluded: chain E residue 120 SER Chi-restraints excluded: chain F residue 6 LEU Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 51 GLU Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 102 MET Chi-restraints excluded: chain F residue 120 SER Chi-restraints excluded: chain M residue 35 SER Chi-restraints excluded: chain M residue 44 ASP Chi-restraints excluded: chain M residue 96 ASP Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain N residue 17 GLU Chi-restraints excluded: chain N residue 35 SER Chi-restraints excluded: chain N residue 47 GLU Chi-restraints excluded: chain O residue 5 ASP Chi-restraints excluded: chain O residue 34 GLN Chi-restraints excluded: chain O residue 44 ASP Chi-restraints excluded: chain O residue 109 VAL Chi-restraints excluded: chain P residue 44 ASP Chi-restraints excluded: chain P residue 71 GLU Chi-restraints excluded: chain P residue 96 ASP Chi-restraints excluded: chain P residue 109 VAL Chi-restraints excluded: chain Q residue 35 SER Chi-restraints excluded: chain Q residue 44 ASP Chi-restraints excluded: chain Q residue 47 GLU Chi-restraints excluded: chain R residue 5 ASP Chi-restraints excluded: chain R residue 44 ASP Chi-restraints excluded: chain R residue 96 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 125 optimal weight: 10.0000 chunk 164 optimal weight: 6.9990 chunk 222 optimal weight: 0.5980 chunk 100 optimal weight: 2.9990 chunk 65 optimal weight: 10.0000 chunk 17 optimal weight: 9.9990 chunk 184 optimal weight: 9.9990 chunk 194 optimal weight: 7.9990 chunk 201 optimal weight: 6.9990 chunk 145 optimal weight: 1.9990 chunk 233 optimal weight: 0.0980 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 6 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.101767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.092369 restraints weight = 35159.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.094383 restraints weight = 19568.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.095718 restraints weight = 12654.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.096658 restraints weight = 9043.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.097293 restraints weight = 6950.003| |-----------------------------------------------------------------------------| r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 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 : 0.004 0.041 18954 Z= 0.157 Angle : 0.565 7.643 25812 Z= 0.296 Chirality : 0.046 0.216 2808 Planarity : 0.005 0.042 3408 Dihedral : 4.909 59.772 2612 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.95 % Favored : 98.01 % Rotamer: Outliers : 4.75 % Allowed : 16.87 % Favored : 78.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.56 (0.16), residues: 2358 helix: 0.70 (0.27), residues: 348 sheet: 0.11 (0.16), residues: 1020 loop : -1.22 (0.17), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 121 TYR 0.011 0.001 TYR I 55 PHE 0.033 0.002 PHE C 36 TRP 0.007 0.001 TRP E 80 HIS 0.002 0.001 HIS O 102 Details of bonding type rmsd covalent geometry : bond 0.00373 (18954) covalent geometry : angle 0.56516 (25812) hydrogen bonds : bond 0.03494 ( 738) hydrogen bonds : angle 5.67582 ( 2121) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 334 time to evaluate : 0.767 Fit side-chains REVERT: G 84 LEU cc_start: 0.9288 (OUTLIER) cc_final: 0.9069 (pp) REVERT: G 102 GLU cc_start: 0.7736 (pp20) cc_final: 0.7519 (pp20) REVERT: G 118 ASP cc_start: 0.8418 (t0) cc_final: 0.7971 (t0) REVERT: G 142 LYS cc_start: 0.8669 (ttmm) cc_final: 0.8408 (ttpp) REVERT: H 8 MET cc_start: 0.7843 (mtm) cc_final: 0.7596 (mtt) REVERT: I 102 GLU cc_start: 0.7594 (pp20) cc_final: 0.7329 (pp20) REVERT: J 102 GLU cc_start: 0.7544 (pp20) cc_final: 0.7241 (pp20) REVERT: K 7 THR cc_start: 0.8903 (OUTLIER) cc_final: 0.8551 (t) REVERT: K 102 GLU cc_start: 0.7710 (pp20) cc_final: 0.7260 (pp20) REVERT: L 151 MET cc_start: 0.8727 (mmm) cc_final: 0.8386 (mmp) REVERT: A 6 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8222 (tt) REVERT: C 6 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8234 (tt) REVERT: D 6 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8231 (tt) REVERT: D 117 LEU cc_start: 0.9390 (OUTLIER) cc_final: 0.9139 (tp) REVERT: E 80 TRP cc_start: 0.8996 (OUTLIER) cc_final: 0.7018 (t60) REVERT: E 102 MET cc_start: 0.8493 (ttm) cc_final: 0.8084 (ttp) REVERT: F 6 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8349 (tt) REVERT: N 73 ARG cc_start: 0.7668 (ttm110) cc_final: 0.7450 (ttm-80) REVERT: P 34 GLN cc_start: 0.8295 (mt0) cc_final: 0.7775 (mt0) REVERT: Q 47 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.7923 (tt0) outliers start: 93 outliers final: 75 residues processed: 392 average time/residue: 0.1430 time to fit residues: 84.0929 Evaluate side-chains 402 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 318 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 90 GLU Chi-restraints excluded: chain H residue 51 THR Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain I residue 17 LEU Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain I residue 81 SER Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 87 MET Chi-restraints excluded: chain I residue 116 THR Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 42 VAL Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 81 SER Chi-restraints excluded: chain K residue 143 VAL Chi-restraints excluded: chain K residue 151 MET Chi-restraints excluded: chain L residue 11 LYS Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 81 SER Chi-restraints excluded: chain L residue 124 VAL Chi-restraints excluded: chain L residue 148 ARG Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 5 GLU Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain C residue 4 THR Chi-restraints excluded: chain C residue 6 LEU Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 51 GLU Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 102 MET Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 5 GLU Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 51 GLU Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 80 TRP Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 120 SER Chi-restraints excluded: chain F residue 6 LEU Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 51 GLU Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 102 MET Chi-restraints excluded: chain F residue 120 SER Chi-restraints excluded: chain M residue 35 SER Chi-restraints excluded: chain M residue 44 ASP Chi-restraints excluded: chain M residue 96 ASP Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain N residue 17 GLU Chi-restraints excluded: chain N residue 35 SER Chi-restraints excluded: chain N residue 47 GLU Chi-restraints excluded: chain O residue 5 ASP Chi-restraints excluded: chain O residue 34 GLN Chi-restraints excluded: chain O residue 44 ASP Chi-restraints excluded: chain O residue 109 VAL Chi-restraints excluded: chain P residue 44 ASP Chi-restraints excluded: chain P residue 71 GLU Chi-restraints excluded: chain P residue 96 ASP Chi-restraints excluded: chain P residue 109 VAL Chi-restraints excluded: chain Q residue 35 SER Chi-restraints excluded: chain Q residue 44 ASP Chi-restraints excluded: chain Q residue 47 GLU Chi-restraints excluded: chain R residue 5 ASP Chi-restraints excluded: chain R residue 44 ASP Chi-restraints excluded: chain R residue 96 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 198 optimal weight: 6.9990 chunk 164 optimal weight: 0.0030 chunk 46 optimal weight: 9.9990 chunk 143 optimal weight: 0.8980 chunk 180 optimal weight: 2.9990 chunk 204 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 13 optimal weight: 6.9990 chunk 222 optimal weight: 0.9980 chunk 233 optimal weight: 0.0270 chunk 133 optimal weight: 10.0000 overall best weight: 0.9850 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 102 HIS R 102 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.104511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.095212 restraints weight = 34852.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.097245 restraints weight = 19395.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.098608 restraints weight = 12481.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.099531 restraints weight = 8876.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.100125 restraints weight = 6814.435| |-----------------------------------------------------------------------------| r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 18954 Z= 0.102 Angle : 0.525 6.625 25812 Z= 0.274 Chirality : 0.044 0.164 2808 Planarity : 0.004 0.044 3408 Dihedral : 4.547 58.396 2612 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.70 % Favored : 98.26 % Rotamer: Outliers : 3.78 % Allowed : 18.25 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.59 (0.16), residues: 2358 helix: 0.91 (0.28), residues: 348 sheet: 0.30 (0.18), residues: 786 loop : -1.26 (0.15), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG J 121 TYR 0.015 0.001 TYR I 20 PHE 0.024 0.001 PHE F 36 TRP 0.007 0.001 TRP M 89 HIS 0.001 0.000 HIS C 3 Details of bonding type rmsd covalent geometry : bond 0.00232 (18954) covalent geometry : angle 0.52463 (25812) hydrogen bonds : bond 0.02987 ( 738) hydrogen bonds : angle 5.41212 ( 2121) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 366 time to evaluate : 0.792 Fit side-chains REVERT: G 84 LEU cc_start: 0.9241 (OUTLIER) cc_final: 0.8987 (pp) REVERT: G 102 GLU cc_start: 0.7741 (pp20) cc_final: 0.7528 (pp20) REVERT: G 118 ASP cc_start: 0.8336 (t0) cc_final: 0.7891 (t0) REVERT: G 142 LYS cc_start: 0.8632 (ttmm) cc_final: 0.8400 (ttpp) REVERT: H 8 MET cc_start: 0.7793 (mtm) cc_final: 0.7523 (mtt) REVERT: H 84 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8814 (pp) REVERT: I 102 GLU cc_start: 0.7585 (pp20) cc_final: 0.7335 (pp20) REVERT: J 102 GLU cc_start: 0.7566 (pp20) cc_final: 0.7260 (pp20) REVERT: K 7 THR cc_start: 0.8861 (OUTLIER) cc_final: 0.8541 (t) REVERT: K 102 GLU cc_start: 0.7730 (pp20) cc_final: 0.7328 (pp20) REVERT: L 151 MET cc_start: 0.8726 (mmm) cc_final: 0.8408 (mmp) REVERT: A 6 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.8133 (tt) REVERT: C 6 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8193 (tt) REVERT: D 6 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.8087 (tt) REVERT: E 80 TRP cc_start: 0.8915 (OUTLIER) cc_final: 0.6929 (t60) REVERT: F 6 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8249 (tt) REVERT: N 73 ARG cc_start: 0.7658 (ttm110) cc_final: 0.7287 (ttm-80) REVERT: N 91 ASP cc_start: 0.8792 (t0) cc_final: 0.8570 (t0) REVERT: P 33 GLU cc_start: 0.6947 (tm-30) cc_final: 0.6671 (tt0) REVERT: Q 47 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.7836 (tp30) REVERT: Q 103 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8676 (mp) outliers start: 74 outliers final: 54 residues processed: 406 average time/residue: 0.1365 time to fit residues: 83.9485 Evaluate side-chains 401 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 337 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 90 GLU Chi-restraints excluded: chain H residue 51 THR Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain I residue 81 SER Chi-restraints excluded: chain I residue 87 MET Chi-restraints excluded: chain I residue 116 THR Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 42 VAL Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 81 SER Chi-restraints excluded: chain K residue 143 VAL Chi-restraints excluded: chain K residue 151 MET Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 81 SER Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain C residue 6 LEU Chi-restraints excluded: chain C residue 51 GLU Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 102 MET Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 80 TRP Chi-restraints excluded: chain E residue 120 SER Chi-restraints excluded: chain F residue 6 LEU Chi-restraints excluded: chain F residue 51 GLU Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 102 MET Chi-restraints excluded: chain F residue 120 SER Chi-restraints excluded: chain M residue 35 SER Chi-restraints excluded: chain M residue 44 ASP Chi-restraints excluded: chain M residue 96 ASP Chi-restraints excluded: chain N residue 17 GLU Chi-restraints excluded: chain N residue 35 SER Chi-restraints excluded: chain N residue 47 GLU Chi-restraints excluded: chain O residue 5 ASP Chi-restraints excluded: chain O residue 34 GLN Chi-restraints excluded: chain O residue 109 VAL Chi-restraints excluded: chain P residue 44 ASP Chi-restraints excluded: chain P residue 71 GLU Chi-restraints excluded: chain P residue 96 ASP Chi-restraints excluded: chain Q residue 35 SER Chi-restraints excluded: chain Q residue 44 ASP Chi-restraints excluded: chain Q residue 47 GLU Chi-restraints excluded: chain Q residue 103 LEU Chi-restraints excluded: chain R residue 5 ASP Chi-restraints excluded: chain R residue 44 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 106 optimal weight: 6.9990 chunk 160 optimal weight: 9.9990 chunk 166 optimal weight: 7.9990 chunk 133 optimal weight: 4.9990 chunk 199 optimal weight: 3.9990 chunk 65 optimal weight: 0.1980 chunk 36 optimal weight: 10.0000 chunk 190 optimal weight: 7.9990 chunk 9 optimal weight: 10.0000 chunk 211 optimal weight: 2.9990 chunk 62 optimal weight: 0.0030 overall best weight: 2.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.102188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.092564 restraints weight = 35115.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.094653 restraints weight = 19312.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.096041 restraints weight = 12376.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.096958 restraints weight = 8807.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.097642 restraints weight = 6773.592| |-----------------------------------------------------------------------------| r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.3101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 18954 Z= 0.152 Angle : 0.563 6.974 25812 Z= 0.295 Chirality : 0.046 0.194 2808 Planarity : 0.005 0.044 3408 Dihedral : 4.675 59.200 2612 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.70 % Favored : 98.26 % Rotamer: Outliers : 3.58 % Allowed : 18.51 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.44 (0.16), residues: 2358 helix: 0.89 (0.27), residues: 354 sheet: 0.23 (0.16), residues: 1020 loop : -1.27 (0.17), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 148 TYR 0.012 0.001 TYR I 20 PHE 0.027 0.002 PHE C 36 TRP 0.007 0.001 TRP E 80 HIS 0.002 0.001 HIS B 17 Details of bonding type rmsd covalent geometry : bond 0.00364 (18954) covalent geometry : angle 0.56334 (25812) hydrogen bonds : bond 0.03332 ( 738) hydrogen bonds : angle 5.45311 ( 2121) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 333 time to evaluate : 0.465 Fit side-chains REVERT: G 84 LEU cc_start: 0.9262 (OUTLIER) cc_final: 0.9011 (pp) REVERT: G 102 GLU cc_start: 0.7873 (pp20) cc_final: 0.7637 (pp20) REVERT: G 118 ASP cc_start: 0.8380 (t0) cc_final: 0.7960 (t0) REVERT: G 142 LYS cc_start: 0.8648 (ttmm) cc_final: 0.8420 (ttpp) REVERT: H 8 MET cc_start: 0.7827 (mtm) cc_final: 0.7576 (mtt) REVERT: I 102 GLU cc_start: 0.7788 (pp20) cc_final: 0.7514 (pp20) REVERT: J 102 GLU cc_start: 0.7613 (pp20) cc_final: 0.7292 (pp20) REVERT: K 7 THR cc_start: 0.8771 (OUTLIER) cc_final: 0.8359 (t) REVERT: K 102 GLU cc_start: 0.7795 (pp20) cc_final: 0.7362 (pp20) REVERT: L 151 MET cc_start: 0.8768 (mmm) cc_final: 0.8481 (mmp) REVERT: A 6 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8205 (tt) REVERT: B 16 LYS cc_start: 0.7833 (mmtp) cc_final: 0.7615 (mmtp) REVERT: C 6 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8116 (tt) REVERT: D 6 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.8148 (tt) REVERT: E 80 TRP cc_start: 0.9006 (OUTLIER) cc_final: 0.7007 (t60) REVERT: F 6 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8343 (tt) REVERT: M 70 ASP cc_start: 0.8107 (m-30) cc_final: 0.7846 (m-30) REVERT: N 73 ARG cc_start: 0.7646 (ttm110) cc_final: 0.7422 (ttm-80) REVERT: Q 47 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7859 (tp30) outliers start: 70 outliers final: 58 residues processed: 374 average time/residue: 0.1296 time to fit residues: 72.9323 Evaluate side-chains 401 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 335 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 90 GLU Chi-restraints excluded: chain H residue 51 THR Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain I residue 31 LEU Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain I residue 81 SER Chi-restraints excluded: chain I residue 87 MET Chi-restraints excluded: chain I residue 116 THR Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 42 VAL Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 81 SER Chi-restraints excluded: chain K residue 143 VAL Chi-restraints excluded: chain K residue 151 MET Chi-restraints excluded: chain L residue 11 LYS Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 81 SER Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain C residue 6 LEU Chi-restraints excluded: chain C residue 51 GLU Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 102 MET Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 80 TRP Chi-restraints excluded: chain E residue 120 SER Chi-restraints excluded: chain F residue 6 LEU Chi-restraints excluded: chain F residue 51 GLU Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 102 MET Chi-restraints excluded: chain F residue 120 SER Chi-restraints excluded: chain M residue 35 SER Chi-restraints excluded: chain M residue 44 ASP Chi-restraints excluded: chain M residue 96 ASP Chi-restraints excluded: chain N residue 17 GLU Chi-restraints excluded: chain N residue 35 SER Chi-restraints excluded: chain N residue 47 GLU Chi-restraints excluded: chain O residue 5 ASP Chi-restraints excluded: chain O residue 34 GLN Chi-restraints excluded: chain O residue 109 VAL Chi-restraints excluded: chain P residue 44 ASP Chi-restraints excluded: chain P residue 71 GLU Chi-restraints excluded: chain P residue 96 ASP Chi-restraints excluded: chain Q residue 35 SER Chi-restraints excluded: chain Q residue 44 ASP Chi-restraints excluded: chain Q residue 47 GLU Chi-restraints excluded: chain R residue 5 ASP Chi-restraints excluded: chain R residue 44 ASP Chi-restraints excluded: chain R residue 96 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 215 optimal weight: 2.9990 chunk 72 optimal weight: 7.9990 chunk 157 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 46 optimal weight: 7.9990 chunk 225 optimal weight: 9.9990 chunk 19 optimal weight: 9.9990 chunk 121 optimal weight: 9.9990 chunk 83 optimal weight: 0.8980 chunk 30 optimal weight: 8.9990 chunk 75 optimal weight: 0.0770 overall best weight: 1.3942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 74 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.104370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.094983 restraints weight = 35123.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.097036 restraints weight = 19530.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.098382 restraints weight = 12569.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.099319 restraints weight = 8962.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.099929 restraints weight = 6885.587| |-----------------------------------------------------------------------------| r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.3201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 18954 Z= 0.112 Angle : 0.531 6.625 25812 Z= 0.277 Chirality : 0.044 0.165 2808 Planarity : 0.004 0.053 3408 Dihedral : 4.519 59.868 2612 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.74 % Favored : 98.22 % Rotamer: Outliers : 3.73 % Allowed : 18.20 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.54 (0.16), residues: 2358 helix: 1.01 (0.28), residues: 354 sheet: 0.36 (0.18), residues: 786 loop : -1.29 (0.15), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG J 121 TYR 0.015 0.001 TYR L 55 PHE 0.025 0.001 PHE F 36 TRP 0.008 0.001 TRP I 18 HIS 0.001 0.000 HIS R 102 Details of bonding type rmsd covalent geometry : bond 0.00260 (18954) covalent geometry : angle 0.53085 (25812) hydrogen bonds : bond 0.03017 ( 738) hydrogen bonds : angle 5.28723 ( 2121) =============================================================================== Job complete usr+sys time: 2691.94 seconds wall clock time: 47 minutes 25.75 seconds (2845.75 seconds total)