Starting phenix.real_space_refine on Sun Jun 15 22:30:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k37_36846/06_2025/8k37_36846.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k37_36846/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8k37_36846/06_2025/8k37_36846.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k37_36846/06_2025/8k37_36846.map" model { file = "/net/cci-nas-00/data/ceres_data/8k37_36846/06_2025/8k37_36846.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k37_36846/06_2025/8k37_36846.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 12.78, per 1000 atoms: 0.69 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: 4.97 Conformation dependent library (CDL) restraints added in 2.5 seconds 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: 3.10 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: 6.46 Time building geometry restraints manager: 5.87 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: 0.010 Normalize map: mean=0, sd=1: 2.890 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: 0.040 Extract box with map and model: 0.890 Check model and map are aligned: 0.160 Set scattering table: 0.210 Process input model: 47.700 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.170 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: 0.020 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.060 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (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 TRP 0.010 0.001 TRP L 99 HIS 0.005 0.001 HIS E 17 PHE 0.039 0.002 PHE A 36 TYR 0.013 0.002 TYR B 129 ARG 0.008 0.001 ARG M 73 Details of bonding type rmsd hydrogen bonds : bond 0.21360 ( 738) hydrogen bonds : angle 9.45386 ( 2121) covalent geometry : bond 0.00600 (18954) covalent geometry : angle 0.69274 (25812) *********************** 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 : 2.364 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: 0.6797 (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: 0.8090 (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: 0.8147 (t0) outliers start: 8 outliers final: 0 residues processed: 512 average time/residue: 0.3470 time to fit residues: 254.5658 Evaluate side-chains 355 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 353 time to evaluate : 2.034 ------------------------------------------------------------------------------- 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 197 optimal weight: 0.8980 chunk 177 optimal weight: 10.0000 chunk 98 optimal weight: 5.9990 chunk 60 optimal weight: 8.9990 chunk 119 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 chunk 183 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 111 optimal weight: 7.9990 chunk 136 optimal weight: 10.0000 chunk 212 optimal weight: 0.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3247 r_free = 0.3247 target = 0.103294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.093957 restraints weight = 35218.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.095917 restraints weight = 19812.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.097271 restraints weight = 12940.549| |-----------------------------------------------------------------------------| r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 18954 Z= 0.182 Angle : 0.614 7.938 25812 Z= 0.323 Chirality : 0.047 0.233 2808 Planarity : 0.004 0.042 3408 Dihedral : 4.989 53.413 2614 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.45 % Allowed : 9.92 % Favored : 87.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.16), residues: 2358 helix: 0.85 (0.27), residues: 348 sheet: 0.01 (0.17), residues: 894 loop : -1.31 (0.15), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP F 80 HIS 0.004 0.001 HIS F 63 PHE 0.034 0.002 PHE C 36 TYR 0.017 0.001 TYR L 55 ARG 0.005 0.000 ARG G 121 Details of bonding type rmsd hydrogen bonds : bond 0.04400 ( 738) hydrogen bonds : angle 6.69283 ( 2121) covalent geometry : bond 0.00422 (18954) covalent geometry : angle 0.61425 (25812) *********************** 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 430 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 382 time to evaluate : 2.298 Fit side-chains REVERT: G 142 LYS cc_start: 0.8621 (ttmm) cc_final: 0.8395 (ttpp) REVERT: K 102 GLU cc_start: 0.7195 (pp20) cc_final: 0.6860 (pp20) REVERT: L 59 TYR cc_start: 0.8036 (m-80) cc_final: 0.7721 (m-10) REVERT: C 18 ASP cc_start: 0.5846 (t70) cc_final: 0.5623 (m-30) REVERT: E 80 TRP cc_start: 0.8807 (OUTLIER) cc_final: 0.6630 (t60) REVERT: O 73 ARG cc_start: 0.7798 (ttm110) cc_final: 0.7375 (tpp-160) REVERT: O 86 GLU cc_start: 0.7287 (mt-10) cc_final: 0.7050 (mt-10) REVERT: P 34 GLN cc_start: 0.8479 (mt0) cc_final: 0.8185 (mt0) REVERT: P 94 SER cc_start: 0.9152 (t) cc_final: 0.8949 (p) REVERT: R 86 GLU cc_start: 0.7408 (mt-10) cc_final: 0.7137 (mt-10) REVERT: R 103 LEU cc_start: 0.8879 (mp) cc_final: 0.8557 (mp) outliers start: 48 outliers final: 38 residues processed: 406 average time/residue: 0.3287 time to fit residues: 198.2282 Evaluate side-chains 372 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 333 time to evaluate : 1.927 ------------------------------------------------------------------------------- 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 34 VAL 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 51 THR Chi-restraints excluded: chain A residue 17 HIS 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 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 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 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 53 optimal weight: 5.9990 chunk 225 optimal weight: 9.9990 chunk 68 optimal weight: 0.7980 chunk 224 optimal weight: 1.9990 chunk 166 optimal weight: 0.0570 chunk 192 optimal weight: 5.9990 chunk 230 optimal weight: 4.9990 chunk 128 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 80 optimal weight: 10.0000 chunk 72 optimal weight: 8.9990 overall best weight: 2.1704 ------------------------------------------------------------------------------- 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** B 63 HIS P 6 ASN P 74 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.103334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.093973 restraints weight = 35012.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.095937 restraints weight = 19653.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.097286 restraints weight = 12776.263| |-----------------------------------------------------------------------------| r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18954 Z= 0.146 Angle : 0.561 7.331 25812 Z= 0.294 Chirality : 0.046 0.216 2808 Planarity : 0.004 0.044 3408 Dihedral : 4.780 53.928 2612 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.91 % Favored : 98.05 % Rotamer: Outliers : 3.07 % Allowed : 12.58 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.16), residues: 2358 helix: 0.85 (0.27), residues: 348 sheet: 0.14 (0.16), residues: 1002 loop : -1.23 (0.16), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 80 HIS 0.009 0.001 HIS A 17 PHE 0.029 0.002 PHE C 36 TYR 0.010 0.001 TYR I 55 ARG 0.006 0.000 ARG J 148 Details of bonding type rmsd hydrogen bonds : bond 0.03847 ( 738) hydrogen bonds : angle 6.18462 ( 2121) covalent geometry : bond 0.00340 (18954) covalent geometry : angle 0.56080 (25812) *********************** 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 409 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 349 time to evaluate : 2.089 Fit side-chains REVERT: G 142 LYS cc_start: 0.8627 (ttmm) cc_final: 0.8419 (ttpp) REVERT: K 7 THR cc_start: 0.8936 (OUTLIER) cc_final: 0.8582 (t) REVERT: K 102 GLU cc_start: 0.7373 (pp20) cc_final: 0.6882 (pp20) REVERT: L 59 TYR cc_start: 0.8062 (m-80) cc_final: 0.7827 (m-80) REVERT: E 80 TRP cc_start: 0.8821 (OUTLIER) cc_final: 0.6487 (t60) REVERT: P 39 ILE cc_start: 0.9077 (mt) cc_final: 0.8693 (mm) REVERT: P 94 SER cc_start: 0.9137 (t) cc_final: 0.8935 (p) REVERT: R 86 GLU cc_start: 0.7356 (mt-10) cc_final: 0.7072 (mt-10) REVERT: R 91 ASP cc_start: 0.8905 (t0) cc_final: 0.8218 (t0) outliers start: 60 outliers final: 50 residues processed: 382 average time/residue: 0.3133 time to fit residues: 179.1809 Evaluate side-chains 379 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 327 time to evaluate : 2.231 ------------------------------------------------------------------------------- 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 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 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 4 THR 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 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 75 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 35 SER Chi-restraints excluded: chain M residue 44 ASP 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 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 220 optimal weight: 10.0000 chunk 88 optimal weight: 8.9990 chunk 1 optimal weight: 10.0000 chunk 208 optimal weight: 10.0000 chunk 222 optimal weight: 3.9990 chunk 83 optimal weight: 0.7980 chunk 75 optimal weight: 5.9990 chunk 29 optimal weight: 9.9990 chunk 104 optimal weight: 8.9990 chunk 119 optimal weight: 0.6980 chunk 48 optimal weight: 9.9990 overall best weight: 4.0986 ------------------------------------------------------------------------------- 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** H 101 ASN ** K 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 72 GLN A 17 HIS M 6 ASN Q 6 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.100727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.091060 restraints weight = 35467.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.093096 restraints weight = 19695.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.094475 restraints weight = 12701.497| |-----------------------------------------------------------------------------| r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 18954 Z= 0.235 Angle : 0.629 7.909 25812 Z= 0.331 Chirality : 0.048 0.255 2808 Planarity : 0.005 0.043 3408 Dihedral : 5.159 58.292 2612 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.04 % Favored : 97.92 % Rotamer: Outliers : 4.14 % Allowed : 14.47 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.16), residues: 2358 helix: 0.61 (0.27), residues: 348 sheet: -0.00 (0.16), residues: 984 loop : -1.26 (0.16), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 80 HIS 0.003 0.001 HIS N 102 PHE 0.037 0.002 PHE C 36 TYR 0.014 0.002 TYR E 129 ARG 0.006 0.001 ARG J 121 Details of bonding type rmsd hydrogen bonds : bond 0.04192 ( 738) hydrogen bonds : angle 6.11052 ( 2121) covalent geometry : bond 0.00564 (18954) covalent geometry : angle 0.62853 (25812) *********************** 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 : 2.254 Fit side-chains REVERT: G 142 LYS cc_start: 0.8646 (ttmm) cc_final: 0.8418 (ttpp) REVERT: H 8 MET cc_start: 0.7800 (mtm) cc_final: 0.7527 (mtt) REVERT: I 102 GLU cc_start: 0.7632 (pp20) cc_final: 0.7295 (pp20) REVERT: K 7 THR cc_start: 0.8963 (OUTLIER) cc_final: 0.8584 (t) REVERT: K 102 GLU cc_start: 0.7534 (pp20) cc_final: 0.7011 (pp20) REVERT: L 59 TYR cc_start: 0.8121 (m-80) cc_final: 0.7851 (m-80) REVERT: E 80 TRP cc_start: 0.8995 (OUTLIER) cc_final: 0.6897 (t60) REVERT: O 91 ASP cc_start: 0.8929 (t0) cc_final: 0.8137 (t0) REVERT: R 103 LEU cc_start: 0.8993 (mp) cc_final: 0.8644 (mp) outliers start: 81 outliers final: 63 residues processed: 370 average time/residue: 0.3143 time to fit residues: 172.8383 Evaluate side-chains 372 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 307 time to evaluate : 2.091 ------------------------------------------------------------------------------- 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 I residue 148 ARG 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 49 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 17 LEU 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 98 LEU 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 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 44 ASP 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 Q residue 35 SER 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 65 optimal weight: 0.0020 chunk 134 optimal weight: 10.0000 chunk 80 optimal weight: 5.9990 chunk 214 optimal weight: 3.9990 chunk 189 optimal weight: 3.9990 chunk 215 optimal weight: 2.9990 chunk 173 optimal weight: 7.9990 chunk 64 optimal weight: 7.9990 chunk 115 optimal weight: 5.9990 chunk 151 optimal weight: 5.9990 chunk 196 optimal weight: 0.9980 overall best weight: 2.3994 ------------------------------------------------------------------------------- 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 = 0.3233 r_free = 0.3233 target = 0.102408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.092774 restraints weight = 35396.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.094838 restraints weight = 19509.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.096228 restraints weight = 12520.622| |-----------------------------------------------------------------------------| r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 18954 Z= 0.151 Angle : 0.551 7.072 25812 Z= 0.289 Chirality : 0.045 0.211 2808 Planarity : 0.004 0.044 3408 Dihedral : 4.830 57.365 2612 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.91 % Favored : 98.05 % Rotamer: Outliers : 3.99 % Allowed : 15.44 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.16), residues: 2358 helix: 0.76 (0.27), residues: 348 sheet: 0.14 (0.16), residues: 1014 loop : -1.22 (0.17), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 80 HIS 0.002 0.001 HIS E 17 PHE 0.029 0.002 PHE C 36 TYR 0.011 0.001 TYR L 55 ARG 0.007 0.000 ARG J 121 Details of bonding type rmsd hydrogen bonds : bond 0.03482 ( 738) hydrogen bonds : angle 5.77468 ( 2121) covalent geometry : bond 0.00356 (18954) covalent geometry : angle 0.55089 (25812) *********************** 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 417 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 339 time to evaluate : 2.262 Fit side-chains REVERT: G 118 ASP cc_start: 0.8391 (t0) cc_final: 0.8093 (t0) REVERT: G 142 LYS cc_start: 0.8665 (ttmm) cc_final: 0.8452 (ttpp) REVERT: H 8 MET cc_start: 0.7839 (mtm) cc_final: 0.7598 (mtt) REVERT: J 87 MET cc_start: 0.7729 (mtp) cc_final: 0.7487 (mtp) REVERT: K 7 THR cc_start: 0.8936 (OUTLIER) cc_final: 0.8572 (t) REVERT: K 102 GLU cc_start: 0.7512 (pp20) cc_final: 0.7045 (pp20) REVERT: L 59 TYR cc_start: 0.8109 (m-80) cc_final: 0.7829 (m-80) REVERT: E 80 TRP cc_start: 0.8914 (OUTLIER) cc_final: 0.6698 (t60) REVERT: O 91 ASP cc_start: 0.8866 (t0) cc_final: 0.8081 (t0) REVERT: R 103 LEU cc_start: 0.8963 (mp) cc_final: 0.8632 (mp) outliers start: 78 outliers final: 62 residues processed: 390 average time/residue: 0.3160 time to fit residues: 184.3622 Evaluate side-chains 386 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 322 time to evaluate : 2.018 ------------------------------------------------------------------------------- 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 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 I residue 148 ARG Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 42 VAL 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 148 ARG Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 61 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 72 VAL Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B 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 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 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 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 109 VAL Chi-restraints excluded: chain P residue 44 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 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 86 optimal weight: 0.9980 chunk 220 optimal weight: 10.0000 chunk 193 optimal weight: 8.9990 chunk 151 optimal weight: 4.9990 chunk 205 optimal weight: 3.9990 chunk 68 optimal weight: 7.9990 chunk 34 optimal weight: 6.9990 chunk 179 optimal weight: 0.1980 chunk 120 optimal weight: 5.9990 chunk 96 optimal weight: 8.9990 chunk 75 optimal weight: 0.5980 overall best weight: 2.1584 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.102795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.093140 restraints weight = 35362.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.095227 restraints weight = 19475.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.096603 restraints weight = 12477.940| |-----------------------------------------------------------------------------| r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.2742 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= 0.143 Angle : 0.550 7.218 25812 Z= 0.288 Chirality : 0.045 0.208 2808 Planarity : 0.004 0.043 3408 Dihedral : 4.797 57.741 2612 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.82 % Favored : 98.13 % Rotamer: Outliers : 4.24 % Allowed : 16.00 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.16), residues: 2358 helix: 0.82 (0.27), residues: 348 sheet: 0.26 (0.17), residues: 834 loop : -1.25 (0.15), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 86 HIS 0.002 0.001 HIS O 102 PHE 0.028 0.002 PHE C 36 TYR 0.012 0.001 TYR I 55 ARG 0.007 0.000 ARG G 121 Details of bonding type rmsd hydrogen bonds : bond 0.03391 ( 738) hydrogen bonds : angle 5.62474 ( 2121) covalent geometry : bond 0.00339 (18954) covalent geometry : angle 0.55034 (25812) *********************** 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 415 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 332 time to evaluate : 2.093 Fit side-chains REVERT: G 102 GLU cc_start: 0.7782 (pp20) cc_final: 0.7487 (pp20) REVERT: G 118 ASP cc_start: 0.8393 (t0) cc_final: 0.7952 (t0) REVERT: G 142 LYS cc_start: 0.8671 (ttmm) cc_final: 0.8462 (ttpp) REVERT: H 8 MET cc_start: 0.7835 (mtm) cc_final: 0.7603 (mtt) REVERT: K 7 THR cc_start: 0.8934 (OUTLIER) cc_final: 0.8555 (t) REVERT: K 102 GLU cc_start: 0.7559 (pp20) cc_final: 0.7095 (pp20) REVERT: L 59 TYR cc_start: 0.8104 (m-80) cc_final: 0.7818 (m-80) REVERT: L 87 MET cc_start: 0.7886 (OUTLIER) cc_final: 0.7670 (mtm) REVERT: E 80 TRP cc_start: 0.8931 (OUTLIER) cc_final: 0.6774 (t60) REVERT: E 102 MET cc_start: 0.8386 (ttm) cc_final: 0.7964 (ttp) REVERT: F 6 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8256 (tt) REVERT: N 73 ARG cc_start: 0.7714 (ttm110) cc_final: 0.7288 (ttm-80) REVERT: Q 103 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8690 (mp) outliers start: 83 outliers final: 70 residues processed: 383 average time/residue: 0.3113 time to fit residues: 178.8447 Evaluate side-chains 394 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 319 time to evaluate : 2.704 ------------------------------------------------------------------------------- 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 I residue 148 ARG 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 49 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 L residue 87 MET Chi-restraints excluded: chain L residue 148 ARG Chi-restraints excluded: chain A residue 4 THR 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 4 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B 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 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 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 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 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 44 ASP 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 129 optimal weight: 10.0000 chunk 70 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 5.9990 chunk 111 optimal weight: 7.9990 chunk 196 optimal weight: 0.9980 chunk 103 optimal weight: 8.9990 chunk 3 optimal weight: 9.9990 chunk 107 optimal weight: 7.9990 chunk 38 optimal weight: 3.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 101 ASN ** H 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.100995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.091248 restraints weight = 35266.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.093311 restraints weight = 19531.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.094713 restraints weight = 12608.818| |-----------------------------------------------------------------------------| r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.2828 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= 0.215 Angle : 0.602 7.692 25812 Z= 0.316 Chirality : 0.047 0.241 2808 Planarity : 0.005 0.040 3408 Dihedral : 5.017 59.523 2612 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.12 % Favored : 97.84 % Rotamer: Outliers : 5.16 % Allowed : 15.54 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.16), residues: 2358 helix: 0.68 (0.27), residues: 348 sheet: 0.12 (0.17), residues: 876 loop : -1.29 (0.16), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 80 HIS 0.003 0.001 HIS O 102 PHE 0.032 0.002 PHE F 36 TYR 0.014 0.002 TYR L 55 ARG 0.007 0.001 ARG J 121 Details of bonding type rmsd hydrogen bonds : bond 0.03839 ( 738) hydrogen bonds : angle 5.73156 ( 2121) covalent geometry : bond 0.00517 (18954) covalent geometry : angle 0.60195 (25812) *********************** 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 411 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 310 time to evaluate : 2.307 Fit side-chains REVERT: G 102 GLU cc_start: 0.7751 (pp20) cc_final: 0.7503 (pp20) REVERT: G 118 ASP cc_start: 0.8472 (t0) cc_final: 0.8171 (t0) REVERT: G 142 LYS cc_start: 0.8672 (ttmm) cc_final: 0.8423 (ttpp) REVERT: H 8 MET cc_start: 0.7866 (mtm) cc_final: 0.7637 (mtt) REVERT: J 84 LEU cc_start: 0.9300 (OUTLIER) cc_final: 0.9076 (pp) REVERT: K 7 THR cc_start: 0.8958 (OUTLIER) cc_final: 0.8564 (t) REVERT: K 102 GLU cc_start: 0.7653 (pp20) cc_final: 0.7152 (pp20) REVERT: L 59 TYR cc_start: 0.8108 (m-80) cc_final: 0.7901 (m-80) REVERT: L 87 MET cc_start: 0.7943 (OUTLIER) cc_final: 0.7721 (mtm) REVERT: A 6 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.8144 (tt) REVERT: D 6 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8191 (tt) REVERT: D 117 LEU cc_start: 0.9401 (OUTLIER) cc_final: 0.9185 (tp) REVERT: E 80 TRP cc_start: 0.9023 (OUTLIER) cc_final: 0.7031 (t60) REVERT: F 6 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8313 (tt) REVERT: N 73 ARG cc_start: 0.7756 (ttm110) cc_final: 0.7395 (ttm-80) outliers start: 101 outliers final: 79 residues processed: 377 average time/residue: 0.3293 time to fit residues: 188.0629 Evaluate side-chains 394 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 307 time to evaluate : 2.153 ------------------------------------------------------------------------------- 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 142 LYS 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 I residue 148 ARG 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 49 GLU Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 81 SER Chi-restraints excluded: chain K residue 142 LYS 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 31 LEU Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 81 SER Chi-restraints excluded: chain L residue 87 MET Chi-restraints excluded: chain A residue 4 THR 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 A residue 120 SER Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 98 LEU 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 6 LEU Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 120 SER 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 44 ASP 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 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 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 154 optimal weight: 1.9990 chunk 170 optimal weight: 5.9990 chunk 194 optimal weight: 2.9990 chunk 13 optimal weight: 7.9990 chunk 17 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 87 optimal weight: 9.9990 chunk 106 optimal weight: 5.9990 chunk 79 optimal weight: 4.9990 chunk 56 optimal weight: 7.9990 chunk 50 optimal weight: 9.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.101392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.091711 restraints weight = 35250.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.093800 restraints weight = 19477.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.095191 restraints weight = 12516.602| |-----------------------------------------------------------------------------| r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.2908 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= 0.170 Angle : 0.575 7.835 25812 Z= 0.302 Chirality : 0.046 0.218 2808 Planarity : 0.005 0.041 3408 Dihedral : 4.936 59.413 2612 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.04 % Favored : 97.92 % Rotamer: Outliers : 4.75 % Allowed : 16.16 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.16), residues: 2358 helix: 0.72 (0.27), residues: 348 sheet: 0.16 (0.17), residues: 876 loop : -1.26 (0.16), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 80 HIS 0.002 0.001 HIS O 102 PHE 0.034 0.002 PHE C 36 TYR 0.011 0.001 TYR G 55 ARG 0.009 0.000 ARG J 121 Details of bonding type rmsd hydrogen bonds : bond 0.03556 ( 738) hydrogen bonds : angle 5.63964 ( 2121) covalent geometry : bond 0.00405 (18954) covalent geometry : angle 0.57489 (25812) *********************** 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 415 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 322 time to evaluate : 2.062 Fit side-chains REVERT: G 102 GLU cc_start: 0.7758 (pp20) cc_final: 0.7495 (pp20) REVERT: G 118 ASP cc_start: 0.8440 (t0) cc_final: 0.7990 (t0) REVERT: G 142 LYS cc_start: 0.8632 (ttmm) cc_final: 0.8400 (ttpp) REVERT: H 8 MET cc_start: 0.7870 (mtm) cc_final: 0.7644 (mtt) REVERT: H 84 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.8953 (pp) REVERT: J 84 LEU cc_start: 0.9285 (OUTLIER) cc_final: 0.9050 (pp) REVERT: K 7 THR cc_start: 0.8941 (OUTLIER) cc_final: 0.8557 (t) REVERT: K 102 GLU cc_start: 0.7712 (pp20) cc_final: 0.7243 (pp20) REVERT: L 87 MET cc_start: 0.7937 (OUTLIER) cc_final: 0.7703 (mtm) REVERT: A 6 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.8198 (tt) REVERT: D 117 LEU cc_start: 0.9402 (OUTLIER) cc_final: 0.9156 (tp) REVERT: E 80 TRP cc_start: 0.9008 (OUTLIER) cc_final: 0.7032 (t60) REVERT: F 6 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8289 (tt) REVERT: N 73 ARG cc_start: 0.7696 (ttm110) cc_final: 0.7469 (ttm-80) REVERT: N 79 ASP cc_start: 0.8247 (m-30) cc_final: 0.7999 (m-30) REVERT: Q 103 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8753 (mp) outliers start: 93 outliers final: 79 residues processed: 380 average time/residue: 0.3087 time to fit residues: 176.3457 Evaluate side-chains 404 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 316 time to evaluate : 2.103 ------------------------------------------------------------------------------- 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 84 LEU 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 I residue 148 ARG 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 10 VAL Chi-restraints excluded: chain K residue 49 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 31 LEU Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 81 SER Chi-restraints excluded: chain L residue 87 MET 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 B residue 98 LEU 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 5 GLU Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 131 MET 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 109 VAL Chi-restraints excluded: chain O residue 113 VAL Chi-restraints excluded: chain P residue 44 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 103 LEU 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 121 optimal weight: 7.9990 chunk 10 optimal weight: 9.9990 chunk 138 optimal weight: 9.9990 chunk 228 optimal weight: 10.0000 chunk 65 optimal weight: 9.9990 chunk 29 optimal weight: 10.0000 chunk 55 optimal weight: 10.0000 chunk 212 optimal weight: 0.2980 chunk 53 optimal weight: 6.9990 chunk 216 optimal weight: 6.9990 chunk 157 optimal weight: 10.0000 overall best weight: 6.4588 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.098046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.088292 restraints weight = 35899.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.090346 restraints weight = 20376.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.091747 restraints weight = 13317.522| |-----------------------------------------------------------------------------| r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.3029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.099 18954 Z= 0.348 Angle : 0.721 10.188 25812 Z= 0.381 Chirality : 0.052 0.302 2808 Planarity : 0.006 0.046 3408 Dihedral : 5.557 54.731 2612 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.80 % Favored : 97.16 % Rotamer: Outliers : 5.01 % Allowed : 16.41 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.16), residues: 2358 helix: 0.27 (0.27), residues: 348 sheet: -0.12 (0.16), residues: 1020 loop : -1.35 (0.17), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 80 HIS 0.006 0.002 HIS E 17 PHE 0.046 0.003 PHE C 36 TYR 0.018 0.002 TYR B 129 ARG 0.009 0.001 ARG G 121 Details of bonding type rmsd hydrogen bonds : bond 0.04660 ( 738) hydrogen bonds : angle 6.04528 ( 2121) covalent geometry : bond 0.00839 (18954) covalent geometry : angle 0.72111 (25812) *********************** 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 401 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 303 time to evaluate : 2.042 Fit side-chains REVERT: G 84 LEU cc_start: 0.9379 (OUTLIER) cc_final: 0.9160 (pp) REVERT: G 102 GLU cc_start: 0.7867 (pp20) cc_final: 0.7595 (pp20) REVERT: G 142 LYS cc_start: 0.8661 (ttmm) cc_final: 0.8347 (ttpp) REVERT: H 142 LYS cc_start: 0.8887 (OUTLIER) cc_final: 0.8613 (ttpp) REVERT: I 102 GLU cc_start: 0.7685 (pp20) cc_final: 0.7379 (pp20) REVERT: K 102 GLU cc_start: 0.7821 (pp20) cc_final: 0.7274 (pp20) REVERT: L 87 MET cc_start: 0.7993 (OUTLIER) cc_final: 0.7756 (mtm) REVERT: L 102 GLU cc_start: 0.7755 (pp20) cc_final: 0.7437 (pp20) REVERT: A 6 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8279 (tt) REVERT: C 6 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8246 (tt) REVERT: D 6 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8372 (tt) REVERT: D 117 LEU cc_start: 0.9453 (OUTLIER) cc_final: 0.9234 (tp) REVERT: F 6 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8411 (tt) REVERT: M 71 GLU cc_start: 0.7346 (pt0) cc_final: 0.7034 (pt0) REVERT: N 73 ARG cc_start: 0.7759 (ttm110) cc_final: 0.7379 (ttm-80) REVERT: N 79 ASP cc_start: 0.8391 (m-30) cc_final: 0.8185 (m-30) outliers start: 98 outliers final: 80 residues processed: 368 average time/residue: 0.3152 time to fit residues: 173.7536 Evaluate side-chains 379 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 291 time to evaluate : 1.953 ------------------------------------------------------------------------------- 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 142 LYS Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain I residue 17 LEU 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 83 THR Chi-restraints excluded: chain I residue 87 MET Chi-restraints excluded: chain I residue 116 THR Chi-restraints excluded: chain I residue 124 VAL 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 10 VAL Chi-restraints excluded: chain K residue 49 GLU Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 81 SER Chi-restraints excluded: chain K residue 142 LYS 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 31 LEU Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 81 SER Chi-restraints excluded: chain L residue 87 MET 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 74 ASP 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 B residue 98 LEU 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 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 51 GLU Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 100 THR 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 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 67 VAL Chi-restraints excluded: chain O residue 109 VAL Chi-restraints excluded: chain O residue 113 VAL Chi-restraints excluded: chain P residue 44 ASP Chi-restraints excluded: chain P residue 109 VAL Chi-restraints excluded: chain Q residue 35 SER 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 48 optimal weight: 5.9990 chunk 212 optimal weight: 0.7980 chunk 86 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 39 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 224 optimal weight: 5.9990 chunk 206 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 104 optimal weight: 0.9980 chunk 12 optimal weight: 7.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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** N 54 GLN O 102 HIS R 102 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.103291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.093886 restraints weight = 35020.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.095961 restraints weight = 19217.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.097338 restraints weight = 12254.021| |-----------------------------------------------------------------------------| r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 18954 Z= 0.106 Angle : 0.549 6.789 25812 Z= 0.288 Chirality : 0.045 0.174 2808 Planarity : 0.004 0.042 3408 Dihedral : 4.705 25.657 2610 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.57 % Favored : 98.39 % Rotamer: Outliers : 2.86 % Allowed : 18.92 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.16), residues: 2358 helix: 0.69 (0.28), residues: 348 sheet: 0.16 (0.17), residues: 876 loop : -1.29 (0.16), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 118 HIS 0.002 0.000 HIS B 63 PHE 0.029 0.001 PHE C 36 TYR 0.013 0.001 TYR I 20 ARG 0.010 0.000 ARG J 121 Details of bonding type rmsd hydrogen bonds : bond 0.03191 ( 738) hydrogen bonds : angle 5.54675 ( 2121) covalent geometry : bond 0.00238 (18954) covalent geometry : angle 0.54927 (25812) ********************** 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 395 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 339 time to evaluate : 2.325 Fit side-chains REVERT: G 84 LEU cc_start: 0.9272 (OUTLIER) cc_final: 0.9029 (pp) REVERT: G 102 GLU cc_start: 0.7799 (pp20) cc_final: 0.7587 (pp20) REVERT: G 118 ASP cc_start: 0.8382 (t0) cc_final: 0.7935 (t0) REVERT: G 142 LYS cc_start: 0.8643 (ttmm) cc_final: 0.8411 (ttpp) REVERT: H 8 MET cc_start: 0.7839 (mtm) cc_final: 0.7634 (mtt) REVERT: I 102 GLU cc_start: 0.7701 (pp20) cc_final: 0.7449 (pp20) REVERT: J 102 GLU cc_start: 0.7571 (pp20) cc_final: 0.7325 (pp20) REVERT: K 102 GLU cc_start: 0.7725 (pp20) cc_final: 0.7272 (pp20) REVERT: L 59 TYR cc_start: 0.7864 (m-80) cc_final: 0.7635 (m-80) REVERT: L 87 MET cc_start: 0.7863 (OUTLIER) cc_final: 0.7618 (mtm) REVERT: L 102 GLU cc_start: 0.7700 (pp20) cc_final: 0.7401 (pp20) REVERT: D 117 LEU cc_start: 0.9410 (OUTLIER) cc_final: 0.9161 (tp) REVERT: F 6 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8282 (tt) REVERT: N 73 ARG cc_start: 0.7682 (ttm110) cc_final: 0.7449 (ttm-80) REVERT: N 79 ASP cc_start: 0.8386 (m-30) cc_final: 0.8160 (m-30) outliers start: 56 outliers final: 47 residues processed: 373 average time/residue: 0.3217 time to fit residues: 179.4507 Evaluate side-chains 372 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 321 time to evaluate : 2.193 ------------------------------------------------------------------------------- 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 84 LEU Chi-restraints excluded: chain G residue 90 GLU 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 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 81 SER Chi-restraints excluded: chain L residue 87 MET 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 72 VAL Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain B residue 98 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 75 SER Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain F residue 6 LEU 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 109 VAL Chi-restraints excluded: chain P residue 44 ASP Chi-restraints excluded: chain Q residue 35 SER 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 221 optimal weight: 7.9990 chunk 12 optimal weight: 9.9990 chunk 65 optimal weight: 0.0670 chunk 22 optimal weight: 10.0000 chunk 134 optimal weight: 0.0980 chunk 118 optimal weight: 6.9990 chunk 179 optimal weight: 0.9980 chunk 183 optimal weight: 0.0980 chunk 217 optimal weight: 7.9990 chunk 210 optimal weight: 0.0770 chunk 173 optimal weight: 10.0000 overall best weight: 0.2676 ------------------------------------------------------------------------------- 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** L 72 GLN N 102 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.105598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.096182 restraints weight = 34725.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.098255 restraints weight = 19165.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.099635 restraints weight = 12321.112| |-----------------------------------------------------------------------------| r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 18954 Z= 0.093 Angle : 0.519 6.749 25812 Z= 0.271 Chirality : 0.044 0.194 2808 Planarity : 0.004 0.044 3408 Dihedral : 4.304 21.175 2610 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.61 % Favored : 98.35 % Rotamer: Outliers : 2.66 % Allowed : 19.02 % Favored : 78.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.16), residues: 2358 helix: 0.91 (0.28), residues: 348 sheet: 0.20 (0.17), residues: 816 loop : -1.27 (0.15), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 104 HIS 0.002 0.000 HIS N 102 PHE 0.024 0.001 PHE F 36 TYR 0.012 0.001 TYR G 20 ARG 0.007 0.000 ARG J 148 Details of bonding type rmsd hydrogen bonds : bond 0.02857 ( 738) hydrogen bonds : angle 5.29381 ( 2121) covalent geometry : bond 0.00202 (18954) covalent geometry : angle 0.51858 (25812) =============================================================================== Job complete usr+sys time: 5615.12 seconds wall clock time: 98 minutes 0.81 seconds (5880.81 seconds total)