Starting phenix.real_space_refine on Fri Sep 19 02:10:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nvc_49832/09_2025/9nvc_49832.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nvc_49832/09_2025/9nvc_49832.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9nvc_49832/09_2025/9nvc_49832.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nvc_49832/09_2025/9nvc_49832.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9nvc_49832/09_2025/9nvc_49832.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nvc_49832/09_2025/9nvc_49832.map" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 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 72 5.16 5 C 14304 2.51 5 N 3696 2.21 5 O 4416 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22488 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 937 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 6, 'TRANS': 114} Chain: "B" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 937 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 6, 'TRANS': 114} Chain: "D" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 937 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 6, 'TRANS': 114} Chain: "C" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 937 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 6, 'TRANS': 114} Chain: "E" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 937 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 6, 'TRANS': 114} Chain: "F" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 937 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 6, 'TRANS': 114} Chain: "G" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 937 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 6, 'TRANS': 114} Chain: "H" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 937 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 6, 'TRANS': 114} Chain: "I" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 937 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 6, 'TRANS': 114} Chain: "J" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 937 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 6, 'TRANS': 114} Chain: "K" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 937 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 6, 'TRANS': 114} Chain: "L" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 937 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 6, 'TRANS': 114} Chain: "M" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 937 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 6, 'TRANS': 114} Chain: "N" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 937 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 6, 'TRANS': 114} Chain: "O" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 937 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 6, 'TRANS': 114} Chain: "P" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 937 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 6, 'TRANS': 114} Chain: "Q" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 937 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 6, 'TRANS': 114} Chain: "R" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 937 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 6, 'TRANS': 114} Chain: "S" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 937 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 6, 'TRANS': 114} Chain: "T" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 937 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 6, 'TRANS': 114} Chain: "V" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 937 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 6, 'TRANS': 114} Chain: "W" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 937 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 6, 'TRANS': 114} Chain: "X" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 937 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 6, 'TRANS': 114} Chain: "Y" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 937 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 6, 'TRANS': 114} Time building chain proxies: 4.96, per 1000 atoms: 0.22 Number of scatterers: 22488 At special positions: 0 Unit cell: (132.5, 123.75, 127.5, 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 72 16.00 O 4416 8.00 N 3696 7.00 C 14304 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.74 Conformation dependent library (CDL) restraints added in 885.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5424 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 48 sheets defined 6.6% alpha, 39.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.22 Creating SS restraints... Processing helix chain 'A' and resid 64 through 66 No H-bonds generated for 'chain 'A' and resid 64 through 66' Processing helix chain 'A' and resid 116 through 120 removed outlier: 3.532A pdb=" N ALA A 120 " --> pdb=" O GLU A 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 66 No H-bonds generated for 'chain 'B' and resid 64 through 66' Processing helix chain 'B' and resid 116 through 120 removed outlier: 3.596A pdb=" N ALA B 120 " --> pdb=" O GLU B 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 66 No H-bonds generated for 'chain 'D' and resid 64 through 66' Processing helix chain 'D' and resid 116 through 120 removed outlier: 3.570A pdb=" N ALA D 120 " --> pdb=" O GLU D 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 66 No H-bonds generated for 'chain 'C' and resid 64 through 66' Processing helix chain 'C' and resid 116 through 120 removed outlier: 3.616A pdb=" N ALA C 120 " --> pdb=" O GLU C 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 66 No H-bonds generated for 'chain 'E' and resid 64 through 66' Processing helix chain 'E' and resid 116 through 120 removed outlier: 3.604A pdb=" N ALA E 120 " --> pdb=" O GLU E 117 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 66 No H-bonds generated for 'chain 'F' and resid 64 through 66' Processing helix chain 'F' and resid 116 through 120 removed outlier: 3.573A pdb=" N ALA F 120 " --> pdb=" O GLU F 117 " (cutoff:3.500A) Processing helix chain 'G' and resid 64 through 66 No H-bonds generated for 'chain 'G' and resid 64 through 66' Processing helix chain 'G' and resid 116 through 120 removed outlier: 3.609A pdb=" N ALA G 120 " --> pdb=" O GLU G 117 " (cutoff:3.500A) Processing helix chain 'H' and resid 64 through 66 No H-bonds generated for 'chain 'H' and resid 64 through 66' Processing helix chain 'H' and resid 116 through 120 removed outlier: 3.592A pdb=" N ALA H 120 " --> pdb=" O GLU H 117 " (cutoff:3.500A) Processing helix chain 'I' and resid 64 through 66 No H-bonds generated for 'chain 'I' and resid 64 through 66' Processing helix chain 'I' and resid 116 through 120 removed outlier: 3.606A pdb=" N ALA I 120 " --> pdb=" O GLU I 117 " (cutoff:3.500A) Processing helix chain 'J' and resid 64 through 66 No H-bonds generated for 'chain 'J' and resid 64 through 66' Processing helix chain 'J' and resid 116 through 120 removed outlier: 3.605A pdb=" N ALA J 120 " --> pdb=" O GLU J 117 " (cutoff:3.500A) Processing helix chain 'K' and resid 64 through 66 No H-bonds generated for 'chain 'K' and resid 64 through 66' Processing helix chain 'K' and resid 116 through 120 removed outlier: 3.582A pdb=" N ALA K 120 " --> pdb=" O GLU K 117 " (cutoff:3.500A) Processing helix chain 'L' and resid 64 through 66 No H-bonds generated for 'chain 'L' and resid 64 through 66' Processing helix chain 'L' and resid 116 through 120 removed outlier: 3.609A pdb=" N ALA L 120 " --> pdb=" O GLU L 117 " (cutoff:3.500A) Processing helix chain 'M' and resid 64 through 66 No H-bonds generated for 'chain 'M' and resid 64 through 66' Processing helix chain 'M' and resid 116 through 120 removed outlier: 3.589A pdb=" N ALA M 120 " --> pdb=" O GLU M 117 " (cutoff:3.500A) Processing helix chain 'N' and resid 64 through 66 No H-bonds generated for 'chain 'N' and resid 64 through 66' Processing helix chain 'N' and resid 116 through 120 removed outlier: 3.595A pdb=" N ALA N 120 " --> pdb=" O GLU N 117 " (cutoff:3.500A) Processing helix chain 'O' and resid 64 through 66 No H-bonds generated for 'chain 'O' and resid 64 through 66' Processing helix chain 'O' and resid 116 through 120 removed outlier: 3.601A pdb=" N ALA O 120 " --> pdb=" O GLU O 117 " (cutoff:3.500A) Processing helix chain 'P' and resid 64 through 66 No H-bonds generated for 'chain 'P' and resid 64 through 66' Processing helix chain 'P' and resid 116 through 120 removed outlier: 3.638A pdb=" N ALA P 120 " --> pdb=" O GLU P 117 " (cutoff:3.500A) Processing helix chain 'Q' and resid 64 through 66 No H-bonds generated for 'chain 'Q' and resid 64 through 66' Processing helix chain 'Q' and resid 116 through 120 removed outlier: 3.640A pdb=" N ALA Q 120 " --> pdb=" O GLU Q 117 " (cutoff:3.500A) Processing helix chain 'R' and resid 64 through 66 No H-bonds generated for 'chain 'R' and resid 64 through 66' Processing helix chain 'R' and resid 116 through 120 removed outlier: 3.575A pdb=" N ALA R 120 " --> pdb=" O GLU R 117 " (cutoff:3.500A) Processing helix chain 'S' and resid 64 through 66 No H-bonds generated for 'chain 'S' and resid 64 through 66' Processing helix chain 'S' and resid 116 through 120 removed outlier: 3.585A pdb=" N ALA S 120 " --> pdb=" O GLU S 117 " (cutoff:3.500A) Processing helix chain 'T' and resid 64 through 66 No H-bonds generated for 'chain 'T' and resid 64 through 66' Processing helix chain 'T' and resid 116 through 120 removed outlier: 3.582A pdb=" N ALA T 120 " --> pdb=" O GLU T 117 " (cutoff:3.500A) Processing helix chain 'V' and resid 64 through 66 No H-bonds generated for 'chain 'V' and resid 64 through 66' Processing helix chain 'V' and resid 116 through 120 removed outlier: 3.577A pdb=" N ALA V 120 " --> pdb=" O GLU V 117 " (cutoff:3.500A) Processing helix chain 'W' and resid 64 through 66 No H-bonds generated for 'chain 'W' and resid 64 through 66' Processing helix chain 'W' and resid 116 through 120 removed outlier: 3.592A pdb=" N ALA W 120 " --> pdb=" O GLU W 117 " (cutoff:3.500A) Processing helix chain 'X' and resid 64 through 66 No H-bonds generated for 'chain 'X' and resid 64 through 66' Processing helix chain 'X' and resid 116 through 120 removed outlier: 3.574A pdb=" N ALA X 120 " --> pdb=" O GLU X 117 " (cutoff:3.500A) Processing helix chain 'Y' and resid 64 through 66 No H-bonds generated for 'chain 'Y' and resid 64 through 66' Processing helix chain 'Y' and resid 116 through 120 removed outlier: 3.620A pdb=" N ALA Y 120 " --> pdb=" O GLU Y 117 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 40 Processing sheet with id=AA2, first strand: chain 'E' and resid 146 through 147 removed outlier: 6.834A pdb=" N ALA A 122 " --> pdb=" O GLU E 147 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N GLU A 49 " --> pdb=" O ILE W 94 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N ILE W 94 " --> pdb=" O GLU A 49 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 93 through 97 removed outlier: 5.644A pdb=" N ILE A 94 " --> pdb=" O GLU W 49 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N GLU W 49 " --> pdb=" O ILE A 94 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N PHE W 124 " --> pdb=" O GLU O 147 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 142 through 143 Processing sheet with id=AA5, first strand: chain 'A' and resid 146 through 147 removed outlier: 4.400A pdb=" N PHE T 124 " --> pdb=" O GLU A 147 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N GLU T 49 " --> pdb=" O ILE N 94 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N ILE N 94 " --> pdb=" O GLU T 49 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 31 through 32 removed outlier: 3.787A pdb=" N SER B 31 " --> pdb=" O ILE B 37 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN B 36 " --> pdb=" O LYS B 110 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 93 through 97 removed outlier: 5.653A pdb=" N ILE C 94 " --> pdb=" O GLU B 49 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N GLU B 49 " --> pdb=" O ILE C 94 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TYR C 96 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ALA B 122 " --> pdb=" O GLU X 147 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 93 through 97 removed outlier: 5.664A pdb=" N ILE B 94 " --> pdb=" O GLU C 49 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N GLU C 49 " --> pdb=" O ILE B 94 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ALA C 122 " --> pdb=" O GLU W 147 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 142 through 143 removed outlier: 3.676A pdb=" N SER R 31 " --> pdb=" O ILE R 37 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 146 through 147 removed outlier: 4.111A pdb=" N PHE R 124 " --> pdb=" O GLU B 147 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLU R 49 " --> pdb=" O ILE E 94 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N ILE E 94 " --> pdb=" O GLU R 49 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 31 through 32 removed outlier: 3.626A pdb=" N SER D 31 " --> pdb=" O ILE D 37 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'M' and resid 93 through 97 removed outlier: 5.756A pdb=" N ILE M 94 " --> pdb=" O GLU D 49 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLU D 49 " --> pdb=" O ILE M 94 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR M 96 " --> pdb=" O ILE D 47 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ALA D 122 " --> pdb=" O GLU R 147 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 93 through 97 removed outlier: 5.636A pdb=" N ILE D 94 " --> pdb=" O GLU M 49 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N GLU M 49 " --> pdb=" O ILE D 94 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ALA M 122 " --> pdb=" O GLU S 147 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 142 through 143 removed outlier: 3.614A pdb=" N GLN X 36 " --> pdb=" O LYS X 110 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER X 31 " --> pdb=" O ILE X 37 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 146 through 147 removed outlier: 4.317A pdb=" N PHE X 124 " --> pdb=" O GLU D 147 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N GLU X 49 " --> pdb=" O ILE H 94 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N ILE H 94 " --> pdb=" O GLU X 49 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 36 through 40 removed outlier: 3.604A pdb=" N GLN C 36 " --> pdb=" O LYS C 110 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 142 through 143 removed outlier: 3.524A pdb=" N GLN I 36 " --> pdb=" O LYS I 110 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER I 31 " --> pdb=" O ILE I 37 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 146 through 147 removed outlier: 4.250A pdb=" N PHE I 124 " --> pdb=" O GLU C 147 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N GLU I 49 " --> pdb=" O ILE P 94 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N ILE P 94 " --> pdb=" O GLU I 49 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 31 through 32 Processing sheet with id=AC2, first strand: chain 'Q' and resid 146 through 147 removed outlier: 6.770A pdb=" N ALA E 122 " --> pdb=" O GLU Q 147 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N GLU E 49 " --> pdb=" O ILE R 94 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N ILE R 94 " --> pdb=" O GLU E 49 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 31 through 32 Processing sheet with id=AC4, first strand: chain 'F' and resid 121 through 125 removed outlier: 6.686A pdb=" N GLU F 49 " --> pdb=" O ILE S 94 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N ILE S 94 " --> pdb=" O GLU F 49 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 93 through 97 removed outlier: 5.459A pdb=" N ILE F 94 " --> pdb=" O GLU S 49 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N GLU S 49 " --> pdb=" O ILE F 94 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ALA S 122 " --> pdb=" O GLU Y 147 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 142 through 143 removed outlier: 3.565A pdb=" N SER K 31 " --> pdb=" O ILE K 37 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 146 through 147 removed outlier: 4.232A pdb=" N PHE K 124 " --> pdb=" O GLU F 147 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N GLU K 49 " --> pdb=" O ILE G 94 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N ILE G 94 " --> pdb=" O GLU K 49 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 31 through 32 removed outlier: 3.564A pdb=" N GLN G 36 " --> pdb=" O LYS G 110 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 121 through 125 removed outlier: 3.569A pdb=" N TYR K 96 " --> pdb=" O ILE G 47 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N GLU G 49 " --> pdb=" O ILE K 94 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N ILE K 94 " --> pdb=" O GLU G 49 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 142 through 143 removed outlier: 3.507A pdb=" N GLN V 36 " --> pdb=" O LYS V 110 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 146 through 147 removed outlier: 4.193A pdb=" N PHE V 124 " --> pdb=" O GLU G 147 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TYR Y 96 " --> pdb=" O ILE V 47 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N GLU V 49 " --> pdb=" O ILE Y 94 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N ILE Y 94 " --> pdb=" O GLU V 49 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 31 through 32 Processing sheet with id=AD4, first strand: chain 'P' and resid 146 through 147 removed outlier: 6.598A pdb=" N ALA H 122 " --> pdb=" O GLU P 147 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR X 96 " --> pdb=" O ILE H 47 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N GLU H 49 " --> pdb=" O ILE X 94 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N ILE X 94 " --> pdb=" O GLU H 49 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 93 through 97 removed outlier: 5.566A pdb=" N ILE I 94 " --> pdb=" O GLU P 49 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N GLU P 49 " --> pdb=" O ILE I 94 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N PHE P 124 " --> pdb=" O GLU K 147 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 142 through 143 Processing sheet with id=AD7, first strand: chain 'I' and resid 146 through 147 removed outlier: 4.300A pdb=" N PHE O 124 " --> pdb=" O GLU I 147 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N GLU O 49 " --> pdb=" O ILE L 94 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N ILE L 94 " --> pdb=" O GLU O 49 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 31 through 32 Processing sheet with id=AD9, first strand: chain 'M' and resid 146 through 147 removed outlier: 6.711A pdb=" N ALA J 122 " --> pdb=" O GLU M 147 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N GLU J 49 " --> pdb=" O ILE Q 94 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N ILE Q 94 " --> pdb=" O GLU J 49 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 93 through 97 removed outlier: 5.584A pdb=" N ILE J 94 " --> pdb=" O GLU Q 49 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N GLU Q 49 " --> pdb=" O ILE J 94 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ALA Q 122 " --> pdb=" O GLU T 147 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 142 through 143 removed outlier: 3.708A pdb=" N SER Y 31 " --> pdb=" O ILE Y 37 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 146 through 147 removed outlier: 4.246A pdb=" N PHE Y 124 " --> pdb=" O GLU J 147 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N GLU Y 49 " --> pdb=" O ILE V 94 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N ILE V 94 " --> pdb=" O GLU Y 49 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'K' and resid 142 through 143 Processing sheet with id=AE5, first strand: chain 'L' and resid 31 through 32 removed outlier: 3.536A pdb=" N GLN L 36 " --> pdb=" O LYS L 110 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'N' and resid 146 through 147 removed outlier: 6.780A pdb=" N ALA L 122 " --> pdb=" O GLU N 147 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N GLU L 49 " --> pdb=" O ILE O 94 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N ILE O 94 " --> pdb=" O GLU L 49 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'M' and resid 31 through 32 removed outlier: 3.531A pdb=" N SER M 31 " --> pdb=" O ILE M 37 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'N' and resid 31 through 32 removed outlier: 3.549A pdb=" N SER N 31 " --> pdb=" O ILE N 37 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN N 36 " --> pdb=" O LYS N 110 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'T' and resid 93 through 97 removed outlier: 5.710A pdb=" N ILE T 94 " --> pdb=" O GLU N 49 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N GLU N 49 " --> pdb=" O ILE T 94 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ALA N 122 " --> pdb=" O GLU V 147 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'O' and resid 142 through 143 removed outlier: 3.513A pdb=" N GLN W 36 " --> pdb=" O LYS W 110 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'Q' and resid 31 through 32 removed outlier: 3.542A pdb=" N SER Q 31 " --> pdb=" O ILE Q 37 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN Q 36 " --> pdb=" O LYS Q 110 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'S' and resid 31 through 32 removed outlier: 3.623A pdb=" N SER S 31 " --> pdb=" O ILE S 37 " (cutoff:3.500A) 962 hydrogen bonds defined for protein. 2454 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: 4.52 Time building geometry restraints manager: 2.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 7368 1.34 - 1.46: 3366 1.46 - 1.57: 11898 1.57 - 1.69: 0 1.69 - 1.80: 144 Bond restraints: 22776 Sorted by residual: bond pdb=" CG1 ILE V 37 " pdb=" CD1 ILE V 37 " ideal model delta sigma weight residual 1.513 1.465 0.048 3.90e-02 6.57e+02 1.54e+00 bond pdb=" CG1 ILE E 37 " pdb=" CD1 ILE E 37 " ideal model delta sigma weight residual 1.513 1.467 0.046 3.90e-02 6.57e+02 1.42e+00 bond pdb=" CG1 ILE G 37 " pdb=" CD1 ILE G 37 " ideal model delta sigma weight residual 1.513 1.468 0.045 3.90e-02 6.57e+02 1.35e+00 bond pdb=" CG1 ILE L 37 " pdb=" CD1 ILE L 37 " ideal model delta sigma weight residual 1.513 1.468 0.045 3.90e-02 6.57e+02 1.32e+00 bond pdb=" CG1 ILE Y 37 " pdb=" CD1 ILE Y 37 " ideal model delta sigma weight residual 1.513 1.469 0.044 3.90e-02 6.57e+02 1.25e+00 ... (remaining 22771 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.93: 27614 0.93 - 1.86: 2397 1.86 - 2.79: 478 2.79 - 3.73: 184 3.73 - 4.66: 47 Bond angle restraints: 30720 Sorted by residual: angle pdb=" C ILE G 35 " pdb=" CA ILE G 35 " pdb=" CB ILE G 35 " ideal model delta sigma weight residual 110.50 114.11 -3.61 1.54e+00 4.22e-01 5.48e+00 angle pdb=" C ILE J 35 " pdb=" CA ILE J 35 " pdb=" CB ILE J 35 " ideal model delta sigma weight residual 110.50 114.05 -3.55 1.54e+00 4.22e-01 5.32e+00 angle pdb=" C ILE E 35 " pdb=" CA ILE E 35 " pdb=" CB ILE E 35 " ideal model delta sigma weight residual 110.50 114.03 -3.53 1.54e+00 4.22e-01 5.25e+00 angle pdb=" C MET L 28 " pdb=" N ILE L 29 " pdb=" CA ILE L 29 " ideal model delta sigma weight residual 121.97 126.09 -4.12 1.80e+00 3.09e-01 5.23e+00 angle pdb=" C MET Q 28 " pdb=" N ILE Q 29 " pdb=" CA ILE Q 29 " ideal model delta sigma weight residual 121.97 126.01 -4.04 1.80e+00 3.09e-01 5.05e+00 ... (remaining 30715 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 9.16: 11474 9.16 - 18.32: 1679 18.32 - 27.47: 599 27.47 - 36.63: 264 36.63 - 45.79: 288 Dihedral angle restraints: 14304 sinusoidal: 5952 harmonic: 8352 Sorted by residual: dihedral pdb=" CA SER I 97 " pdb=" C SER I 97 " pdb=" N GLU I 98 " pdb=" CA GLU I 98 " ideal model delta harmonic sigma weight residual 180.00 165.47 14.53 0 5.00e+00 4.00e-02 8.45e+00 dihedral pdb=" CA SER W 97 " pdb=" C SER W 97 " pdb=" N GLU W 98 " pdb=" CA GLU W 98 " ideal model delta harmonic sigma weight residual 180.00 165.48 14.52 0 5.00e+00 4.00e-02 8.43e+00 dihedral pdb=" CA SER M 97 " pdb=" C SER M 97 " pdb=" N GLU M 98 " pdb=" CA GLU M 98 " ideal model delta harmonic sigma weight residual 180.00 165.50 14.50 0 5.00e+00 4.00e-02 8.41e+00 ... (remaining 14301 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 2073 0.033 - 0.067: 861 0.067 - 0.100: 359 0.100 - 0.134: 320 0.134 - 0.167: 59 Chirality restraints: 3672 Sorted by residual: chirality pdb=" CA ILE E 146 " pdb=" N ILE E 146 " pdb=" C ILE E 146 " pdb=" CB ILE E 146 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.99e-01 chirality pdb=" CA ILE B 146 " pdb=" N ILE B 146 " pdb=" C ILE B 146 " pdb=" CB ILE B 146 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.98e-01 chirality pdb=" CA ILE R 146 " pdb=" N ILE R 146 " pdb=" C ILE R 146 " pdb=" CB ILE R 146 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.87e-01 ... (remaining 3669 not shown) Planarity restraints: 3888 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU M 133 " 0.019 5.00e-02 4.00e+02 2.88e-02 1.33e+00 pdb=" N PRO M 134 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO M 134 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO M 134 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU T 133 " -0.019 5.00e-02 4.00e+02 2.87e-02 1.32e+00 pdb=" N PRO T 134 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO T 134 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO T 134 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU N 133 " 0.019 5.00e-02 4.00e+02 2.87e-02 1.32e+00 pdb=" N PRO N 134 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO N 134 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO N 134 " 0.016 5.00e-02 4.00e+02 ... (remaining 3885 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 2795 2.77 - 3.30: 18752 3.30 - 3.83: 35255 3.83 - 4.37: 42121 4.37 - 4.90: 76345 Nonbonded interactions: 175268 Sorted by model distance: nonbonded pdb=" O ILE M 140 " pdb=" NZ LYS M 142 " model vdw 2.235 3.120 nonbonded pdb=" O ILE W 140 " pdb=" NZ LYS W 142 " model vdw 2.247 3.120 nonbonded pdb=" O ILE C 140 " pdb=" NZ LYS C 142 " model vdw 2.247 3.120 nonbonded pdb=" O ILE A 140 " pdb=" NZ LYS A 142 " model vdw 2.252 3.120 nonbonded pdb=" O ILE B 140 " pdb=" NZ LYS B 142 " model vdw 2.252 3.120 ... (remaining 175263 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.070 Set scattering table: 0.030 Process input model: 20.010 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 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 : 0.004 0.048 22776 Z= 0.164 Angle : 0.638 4.657 30720 Z= 0.352 Chirality : 0.054 0.167 3672 Planarity : 0.003 0.029 3888 Dihedral : 12.808 45.791 8880 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 0.00 % Allowed : 14.43 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.03 (0.15), residues: 2856 helix: None (None), residues: 0 sheet: 2.31 (0.14), residues: 1104 loop : -0.46 (0.14), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG Q 80 TYR 0.017 0.002 TYR E 106 PHE 0.016 0.001 PHE L 124 TRP 0.012 0.001 TRP L 59 HIS 0.005 0.001 HIS N 53 Details of bonding type rmsd covalent geometry : bond 0.00418 (22776) covalent geometry : angle 0.63779 (30720) hydrogen bonds : bond 0.22427 ( 962) hydrogen bonds : angle 5.80643 ( 2454) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 828 residues out of total 2544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 828 time to evaluate : 0.980 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 LYS cc_start: 0.8537 (ptmm) cc_final: 0.8328 (pttm) REVERT: B 43 MET cc_start: 0.8330 (ttm) cc_final: 0.8123 (ttp) REVERT: D 28 MET cc_start: 0.4197 (mmt) cc_final: 0.3733 (tpp) REVERT: D 40 LYS cc_start: 0.8348 (ptmm) cc_final: 0.8099 (pttt) REVERT: C 28 MET cc_start: 0.2886 (mmt) cc_final: 0.1956 (mpp) REVERT: E 43 MET cc_start: 0.8334 (ttm) cc_final: 0.7962 (ttm) REVERT: E 93 ARG cc_start: 0.7999 (ptp90) cc_final: 0.7671 (ptp90) REVERT: F 104 GLU cc_start: 0.7193 (tp30) cc_final: 0.6915 (tp30) REVERT: F 116 LYS cc_start: 0.8763 (mtmt) cc_final: 0.8361 (mtmt) REVERT: G 28 MET cc_start: 0.4488 (mmt) cc_final: 0.4118 (tpp) REVERT: H 28 MET cc_start: 0.5229 (mmt) cc_final: 0.4551 (tpp) REVERT: H 93 ARG cc_start: 0.7769 (ptp90) cc_final: 0.7279 (ptp90) REVERT: I 52 GLN cc_start: 0.7371 (mm-40) cc_final: 0.7124 (tp-100) REVERT: I 115 VAL cc_start: 0.8625 (m) cc_final: 0.8400 (m) REVERT: J 28 MET cc_start: 0.3064 (mmt) cc_final: 0.2781 (tpp) REVERT: J 49 GLU cc_start: 0.7708 (tt0) cc_final: 0.7467 (tt0) REVERT: J 75 ASP cc_start: 0.8517 (p0) cc_final: 0.8189 (p0) REVERT: M 43 MET cc_start: 0.8861 (ttm) cc_final: 0.8617 (ttp) REVERT: O 93 ARG cc_start: 0.8350 (ptp90) cc_final: 0.7901 (pmt170) REVERT: P 67 ASP cc_start: 0.8135 (m-30) cc_final: 0.7883 (t0) REVERT: Q 52 GLN cc_start: 0.7889 (mm-40) cc_final: 0.7662 (mm-40) REVERT: Q 133 LEU cc_start: 0.8426 (mt) cc_final: 0.8215 (mt) REVERT: R 49 GLU cc_start: 0.7333 (tt0) cc_final: 0.7097 (tt0) REVERT: R 75 ASP cc_start: 0.7290 (p0) cc_final: 0.6200 (p0) REVERT: R 93 ARG cc_start: 0.8068 (ptp90) cc_final: 0.7782 (pmt170) REVERT: S 80 ARG cc_start: 0.7978 (mtm180) cc_final: 0.7627 (mtm180) REVERT: S 111 LEU cc_start: 0.8759 (mt) cc_final: 0.8502 (mt) REVERT: T 28 MET cc_start: 0.5740 (mmt) cc_final: 0.5454 (tpp) REVERT: V 28 MET cc_start: 0.5890 (mmt) cc_final: 0.4535 (mpt) REVERT: W 40 LYS cc_start: 0.8358 (ptmm) cc_final: 0.7924 (ptmm) REVERT: W 60 LEU cc_start: 0.8567 (mt) cc_final: 0.8366 (mt) REVERT: W 75 ASP cc_start: 0.8137 (p0) cc_final: 0.7725 (p0) REVERT: W 93 ARG cc_start: 0.8115 (ptp90) cc_final: 0.7672 (pmt170) REVERT: W 96 TYR cc_start: 0.8710 (t80) cc_final: 0.8187 (t80) REVERT: X 28 MET cc_start: 0.3489 (mmt) cc_final: 0.2198 (mpm) REVERT: Y 75 ASP cc_start: 0.8119 (p0) cc_final: 0.7748 (p0) outliers start: 0 outliers final: 1 residues processed: 828 average time/residue: 0.7044 time to fit residues: 650.8819 Evaluate side-chains 581 residues out of total 2544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 580 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 45 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 5.9990 chunk 111 optimal weight: 6.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 GLN D 53 HIS D 145 ASN C 30 GLN E 36 GLN F 30 GLN F 52 GLN G 145 ASN H 30 GLN I 71 ASN J 36 GLN J 119 ASN K 36 GLN K 52 GLN L 52 GLN N 30 GLN N 119 ASN O 71 ASN O 119 ASN P 30 GLN Q 36 GLN R 30 GLN R 119 ASN ** S 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 52 GLN X 119 ASN Y 36 GLN Y 52 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.120289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.093793 restraints weight = 33197.952| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 2.63 r_work: 0.3197 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.4229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.058 22776 Z= 0.352 Angle : 0.744 9.585 30720 Z= 0.390 Chirality : 0.058 0.206 3672 Planarity : 0.005 0.054 3888 Dihedral : 5.288 25.488 3026 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Rotamer: Outliers : 5.50 % Allowed : 23.82 % Favored : 70.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.55 (0.16), residues: 2856 helix: None (None), residues: 0 sheet: 2.94 (0.15), residues: 1104 loop : -0.31 (0.15), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 107 TYR 0.013 0.002 TYR T 106 PHE 0.015 0.003 PHE T 124 TRP 0.006 0.002 TRP F 59 HIS 0.010 0.002 HIS N 53 Details of bonding type rmsd covalent geometry : bond 0.00873 (22776) covalent geometry : angle 0.74444 (30720) hydrogen bonds : bond 0.05345 ( 962) hydrogen bonds : angle 5.05482 ( 2454) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 736 residues out of total 2544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 596 time to evaluate : 0.614 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 LYS cc_start: 0.8432 (ptmm) cc_final: 0.7861 (pttm) REVERT: A 49 GLU cc_start: 0.8380 (tt0) cc_final: 0.8082 (tt0) REVERT: A 102 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7593 (pm20) REVERT: B 52 GLN cc_start: 0.8182 (mt0) cc_final: 0.6722 (tm130) REVERT: B 55 LYS cc_start: 0.8730 (tttt) cc_final: 0.8525 (tttm) REVERT: B 87 MET cc_start: 0.6997 (ppp) cc_final: 0.6560 (pmm) REVERT: B 94 ILE cc_start: 0.9215 (mt) cc_final: 0.9007 (mp) REVERT: D 28 MET cc_start: 0.4608 (mmt) cc_final: 0.3566 (tpp) REVERT: D 40 LYS cc_start: 0.8318 (ptmm) cc_final: 0.7801 (pttt) REVERT: D 52 GLN cc_start: 0.8750 (OUTLIER) cc_final: 0.8327 (mp10) REVERT: D 80 ARG cc_start: 0.8909 (OUTLIER) cc_final: 0.8224 (mtp85) REVERT: D 84 SER cc_start: 0.9178 (m) cc_final: 0.8690 (t) REVERT: D 93 ARG cc_start: 0.7915 (ptp90) cc_final: 0.6962 (pmt170) REVERT: D 110 LYS cc_start: 0.8676 (tttt) cc_final: 0.8364 (ttpp) REVERT: D 137 GLU cc_start: 0.7786 (mm-30) cc_final: 0.7543 (tp30) REVERT: D 142 LYS cc_start: 0.8413 (mmtm) cc_final: 0.8123 (mmtm) REVERT: C 28 MET cc_start: 0.2968 (mmt) cc_final: 0.2629 (mpp) REVERT: C 42 PHE cc_start: 0.8602 (t80) cc_final: 0.8233 (t80) REVERT: C 48 ILE cc_start: 0.8237 (OUTLIER) cc_final: 0.7961 (mp) REVERT: C 67 ASP cc_start: 0.8687 (m-30) cc_final: 0.8329 (m-30) REVERT: C 96 TYR cc_start: 0.8933 (t80) cc_final: 0.8663 (t80) REVERT: C 116 LYS cc_start: 0.7633 (mtmt) cc_final: 0.7422 (mtpt) REVERT: C 123 LYS cc_start: 0.7719 (mmpt) cc_final: 0.7382 (mppt) REVERT: C 142 LYS cc_start: 0.7703 (mmtm) cc_final: 0.7456 (mmmm) REVERT: E 28 MET cc_start: 0.4395 (mmp) cc_final: 0.3323 (mmt) REVERT: E 36 GLN cc_start: 0.8437 (mt0) cc_final: 0.8214 (mt0) REVERT: E 43 MET cc_start: 0.8786 (ttm) cc_final: 0.8480 (ttm) REVERT: E 64 ASN cc_start: 0.8727 (m-40) cc_final: 0.8376 (m-40) REVERT: E 123 LYS cc_start: 0.8373 (mttm) cc_final: 0.8083 (mmtp) REVERT: G 28 MET cc_start: 0.4077 (mmt) cc_final: 0.3547 (tpp) REVERT: G 43 MET cc_start: 0.9106 (ttm) cc_final: 0.8794 (ttm) REVERT: G 51 ASP cc_start: 0.8946 (OUTLIER) cc_final: 0.8623 (t0) REVERT: G 55 LYS cc_start: 0.8753 (tttt) cc_final: 0.8546 (tttp) REVERT: G 67 ASP cc_start: 0.8960 (m-30) cc_final: 0.8718 (m-30) REVERT: G 78 GLU cc_start: 0.8755 (tt0) cc_final: 0.8292 (tm-30) REVERT: G 84 SER cc_start: 0.9046 (OUTLIER) cc_final: 0.8837 (p) REVERT: G 96 TYR cc_start: 0.9121 (t80) cc_final: 0.8898 (t80) REVERT: G 116 LYS cc_start: 0.8520 (mtmt) cc_final: 0.8274 (mtpt) REVERT: H 28 MET cc_start: 0.4430 (mmt) cc_final: 0.3874 (tpp) REVERT: H 104 GLU cc_start: 0.8846 (OUTLIER) cc_final: 0.8194 (mt-10) REVERT: I 45 ILE cc_start: 0.8743 (mt) cc_final: 0.8489 (mm) REVERT: I 51 ASP cc_start: 0.8433 (m-30) cc_final: 0.7977 (m-30) REVERT: I 52 GLN cc_start: 0.7736 (mm-40) cc_final: 0.7164 (tm-30) REVERT: J 28 MET cc_start: 0.3806 (mmt) cc_final: 0.2929 (tpp) REVERT: J 36 GLN cc_start: 0.8582 (mt0) cc_final: 0.8068 (mt0) REVERT: J 110 LYS cc_start: 0.9020 (tptt) cc_final: 0.8481 (tptt) REVERT: J 123 LYS cc_start: 0.8928 (OUTLIER) cc_final: 0.8658 (mttm) REVERT: J 141 LYS cc_start: 0.8527 (OUTLIER) cc_final: 0.8320 (mttt) REVERT: K 75 ASP cc_start: 0.8901 (p0) cc_final: 0.8629 (p0) REVERT: L 65 LYS cc_start: 0.8890 (OUTLIER) cc_final: 0.8543 (tttm) REVERT: L 80 ARG cc_start: 0.8768 (mtp180) cc_final: 0.8340 (mtm-85) REVERT: L 110 LYS cc_start: 0.8926 (tppt) cc_final: 0.8318 (tppt) REVERT: L 116 LYS cc_start: 0.8056 (mtmt) cc_final: 0.7804 (mtmm) REVERT: L 142 LYS cc_start: 0.8450 (mmtt) cc_final: 0.8112 (mmtt) REVERT: M 43 MET cc_start: 0.9136 (ttm) cc_final: 0.8897 (ttp) REVERT: M 76 THR cc_start: 0.9171 (m) cc_final: 0.8847 (p) REVERT: M 78 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.8109 (tt0) REVERT: M 110 LYS cc_start: 0.8640 (OUTLIER) cc_final: 0.8324 (tmmt) REVERT: N 145 ASN cc_start: 0.8416 (OUTLIER) cc_final: 0.7941 (t0) REVERT: O 52 GLN cc_start: 0.8456 (mm110) cc_final: 0.8160 (mm-40) REVERT: O 78 GLU cc_start: 0.7999 (tt0) cc_final: 0.7450 (pp20) REVERT: O 80 ARG cc_start: 0.8011 (mtp85) cc_final: 0.7725 (mtm-85) REVERT: O 106 TYR cc_start: 0.8132 (p90) cc_final: 0.7907 (p90) REVERT: O 110 LYS cc_start: 0.8401 (tmmm) cc_final: 0.8040 (tmmm) REVERT: O 123 LYS cc_start: 0.8516 (mmtp) cc_final: 0.8241 (mtpp) REVERT: P 55 LYS cc_start: 0.8355 (tttt) cc_final: 0.8096 (mtpm) REVERT: P 67 ASP cc_start: 0.8647 (m-30) cc_final: 0.7650 (t0) REVERT: P 78 GLU cc_start: 0.8492 (tt0) cc_final: 0.7386 (tm-30) REVERT: P 106 TYR cc_start: 0.8426 (p90) cc_final: 0.8134 (p90) REVERT: P 130 SER cc_start: 0.9210 (m) cc_final: 0.8926 (p) REVERT: Q 55 LYS cc_start: 0.8851 (tttt) cc_final: 0.8631 (tttt) REVERT: Q 106 TYR cc_start: 0.8574 (p90) cc_final: 0.7735 (p90) REVERT: R 51 ASP cc_start: 0.8578 (m-30) cc_final: 0.8294 (m-30) REVERT: R 55 LYS cc_start: 0.8254 (tttt) cc_final: 0.7942 (mtpp) REVERT: R 75 ASP cc_start: 0.8333 (p0) cc_final: 0.7658 (p0) REVERT: R 80 ARG cc_start: 0.7907 (mtm180) cc_final: 0.7533 (mtm110) REVERT: S 40 LYS cc_start: 0.8346 (ptmm) cc_final: 0.8100 (ptmm) REVERT: S 75 ASP cc_start: 0.8683 (p0) cc_final: 0.8150 (p0) REVERT: T 28 MET cc_start: 0.5790 (mmt) cc_final: 0.5118 (mpp) REVERT: T 43 MET cc_start: 0.9054 (ttm) cc_final: 0.8667 (ttm) REVERT: T 75 ASP cc_start: 0.8947 (p0) cc_final: 0.8723 (p0) REVERT: T 101 GLU cc_start: 0.8260 (tp30) cc_final: 0.7914 (tm-30) REVERT: T 142 LYS cc_start: 0.8751 (mttp) cc_final: 0.8506 (mptt) REVERT: V 28 MET cc_start: 0.5367 (mmt) cc_final: 0.3999 (mpt) REVERT: V 75 ASP cc_start: 0.8287 (p0) cc_final: 0.7982 (p0) REVERT: W 28 MET cc_start: 0.4629 (tpp) cc_final: 0.3908 (tpp) REVERT: W 75 ASP cc_start: 0.8891 (p0) cc_final: 0.8546 (p0) REVERT: W 80 ARG cc_start: 0.8540 (mtm180) cc_final: 0.8285 (mtp180) REVERT: W 123 LYS cc_start: 0.8788 (OUTLIER) cc_final: 0.8399 (mttm) REVERT: X 49 GLU cc_start: 0.7871 (tt0) cc_final: 0.7527 (tt0) REVERT: X 82 LYS cc_start: 0.8379 (ptpp) cc_final: 0.7752 (pttp) REVERT: X 104 GLU cc_start: 0.7871 (tp30) cc_final: 0.7639 (tp30) REVERT: X 130 SER cc_start: 0.8806 (m) cc_final: 0.8444 (t) REVERT: X 135 LYS cc_start: 0.8125 (OUTLIER) cc_final: 0.7607 (mttm) REVERT: Y 75 ASP cc_start: 0.8648 (p0) cc_final: 0.8106 (p0) REVERT: Y 78 GLU cc_start: 0.8701 (tt0) cc_final: 0.8433 (tt0) REVERT: Y 110 LYS cc_start: 0.8853 (OUTLIER) cc_final: 0.8596 (ttmm) REVERT: Y 142 LYS cc_start: 0.8636 (mmtt) cc_final: 0.8412 (mmtt) outliers start: 140 outliers final: 46 residues processed: 675 average time/residue: 0.7421 time to fit residues: 555.9626 Evaluate side-chains 604 residues out of total 2544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 542 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain D residue 52 GLN Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 80 ARG Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain F residue 46 SER Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain F residue 138 SER Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 51 ASP Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain H residue 104 GLU Chi-restraints excluded: chain I residue 46 SER Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain I residue 121 SER Chi-restraints excluded: chain J residue 97 SER Chi-restraints excluded: chain J residue 123 LYS Chi-restraints excluded: chain J residue 141 LYS Chi-restraints excluded: chain K residue 37 ILE Chi-restraints excluded: chain K residue 133 LEU Chi-restraints excluded: chain L residue 65 LYS Chi-restraints excluded: chain M residue 51 ASP Chi-restraints excluded: chain M residue 78 GLU Chi-restraints excluded: chain M residue 110 LYS Chi-restraints excluded: chain M residue 139 SER Chi-restraints excluded: chain N residue 54 ILE Chi-restraints excluded: chain N residue 133 LEU Chi-restraints excluded: chain N residue 145 ASN Chi-restraints excluded: chain O residue 28 MET Chi-restraints excluded: chain O residue 38 SER Chi-restraints excluded: chain O residue 73 VAL Chi-restraints excluded: chain P residue 28 MET Chi-restraints excluded: chain Q residue 45 ILE Chi-restraints excluded: chain Q residue 46 SER Chi-restraints excluded: chain Q residue 82 LYS Chi-restraints excluded: chain Q residue 108 THR Chi-restraints excluded: chain Q residue 110 LYS Chi-restraints excluded: chain Q residue 121 SER Chi-restraints excluded: chain R residue 84 SER Chi-restraints excluded: chain R residue 145 ASN Chi-restraints excluded: chain T residue 38 SER Chi-restraints excluded: chain T residue 52 GLN Chi-restraints excluded: chain T residue 102 GLU Chi-restraints excluded: chain T residue 105 ILE Chi-restraints excluded: chain V residue 114 THR Chi-restraints excluded: chain V residue 131 VAL Chi-restraints excluded: chain W residue 45 ILE Chi-restraints excluded: chain W residue 123 LYS Chi-restraints excluded: chain X residue 86 LEU Chi-restraints excluded: chain X residue 102 GLU Chi-restraints excluded: chain X residue 135 LYS Chi-restraints excluded: chain Y residue 46 SER Chi-restraints excluded: chain Y residue 110 LYS Chi-restraints excluded: chain Y residue 138 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 71 optimal weight: 0.9990 chunk 24 optimal weight: 10.0000 chunk 69 optimal weight: 0.6980 chunk 173 optimal weight: 3.9990 chunk 180 optimal weight: 9.9990 chunk 10 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 260 optimal weight: 0.9980 chunk 256 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 145 ASN F 52 GLN G 36 GLN I 119 ASN K 36 GLN K 52 GLN L 52 GLN M 52 GLN O 119 ASN P 119 ASN R 119 ASN S 119 ASN T 30 GLN T 36 GLN W 52 GLN Y 36 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.123090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.096423 restraints weight = 32963.259| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.67 r_work: 0.3237 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.4363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 22776 Z= 0.126 Angle : 0.557 8.892 30720 Z= 0.290 Chirality : 0.053 0.165 3672 Planarity : 0.003 0.032 3888 Dihedral : 4.467 15.827 3024 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 4.21 % Allowed : 25.90 % Favored : 69.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.87 (0.17), residues: 2856 helix: None (None), residues: 0 sheet: 3.04 (0.15), residues: 1104 loop : -0.00 (0.16), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG T 93 TYR 0.016 0.001 TYR Y 106 PHE 0.007 0.001 PHE C 42 TRP 0.002 0.000 TRP X 59 HIS 0.003 0.001 HIS N 53 Details of bonding type rmsd covalent geometry : bond 0.00300 (22776) covalent geometry : angle 0.55700 (30720) hydrogen bonds : bond 0.03852 ( 962) hydrogen bonds : angle 4.76132 ( 2454) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 706 residues out of total 2544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 599 time to evaluate : 0.725 Fit side-chains revert: symmetry clash REVERT: A 40 LYS cc_start: 0.8371 (ptmm) cc_final: 0.7806 (pttm) REVERT: A 49 GLU cc_start: 0.8191 (tt0) cc_final: 0.7978 (tt0) REVERT: A 78 GLU cc_start: 0.8734 (tt0) cc_final: 0.8278 (tm-30) REVERT: A 102 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7496 (pm20) REVERT: B 52 GLN cc_start: 0.8181 (mt0) cc_final: 0.6734 (tm130) REVERT: B 87 MET cc_start: 0.7069 (ppp) cc_final: 0.6783 (pmm) REVERT: B 116 LYS cc_start: 0.7900 (mtmt) cc_final: 0.7610 (mtpp) REVERT: D 28 MET cc_start: 0.4519 (mmt) cc_final: 0.3599 (tpp) REVERT: D 45 ILE cc_start: 0.9127 (mt) cc_final: 0.8881 (mm) REVERT: D 52 GLN cc_start: 0.8717 (OUTLIER) cc_final: 0.8407 (mp10) REVERT: D 84 SER cc_start: 0.9100 (m) cc_final: 0.8629 (t) REVERT: D 87 MET cc_start: 0.8279 (pmm) cc_final: 0.7976 (ppp) REVERT: D 93 ARG cc_start: 0.7778 (ptp90) cc_final: 0.6439 (pmt170) REVERT: D 110 LYS cc_start: 0.8658 (tttt) cc_final: 0.8316 (ttpp) REVERT: D 116 LYS cc_start: 0.8318 (mtmt) cc_final: 0.8114 (mtmm) REVERT: D 142 LYS cc_start: 0.8418 (mmtm) cc_final: 0.7921 (mmtm) REVERT: C 28 MET cc_start: 0.3092 (mmt) cc_final: 0.2669 (mpp) REVERT: C 42 PHE cc_start: 0.8455 (t80) cc_final: 0.8147 (t80) REVERT: C 67 ASP cc_start: 0.8560 (m-30) cc_final: 0.8190 (m-30) REVERT: C 93 ARG cc_start: 0.7722 (ptt-90) cc_final: 0.6911 (pmt170) REVERT: C 96 TYR cc_start: 0.8922 (t80) cc_final: 0.8645 (t80) REVERT: C 116 LYS cc_start: 0.7568 (mtmt) cc_final: 0.7320 (mtpt) REVERT: C 123 LYS cc_start: 0.7528 (mmpt) cc_final: 0.7213 (mppt) REVERT: C 142 LYS cc_start: 0.7669 (mmtm) cc_final: 0.7369 (mmmm) REVERT: E 36 GLN cc_start: 0.8296 (mt0) cc_final: 0.8085 (mt0) REVERT: E 43 MET cc_start: 0.8757 (ttm) cc_final: 0.8423 (ttm) REVERT: E 64 ASN cc_start: 0.8691 (m-40) cc_final: 0.8342 (m-40) REVERT: E 78 GLU cc_start: 0.8847 (OUTLIER) cc_final: 0.8476 (pp20) REVERT: E 80 ARG cc_start: 0.8555 (mtm-85) cc_final: 0.8229 (mtm-85) REVERT: E 123 LYS cc_start: 0.8374 (mttm) cc_final: 0.8157 (mmtp) REVERT: G 28 MET cc_start: 0.3852 (mmt) cc_final: 0.3434 (tpp) REVERT: G 43 MET cc_start: 0.9147 (ttm) cc_final: 0.8661 (ttm) REVERT: G 45 ILE cc_start: 0.9187 (OUTLIER) cc_final: 0.8956 (mm) REVERT: G 55 LYS cc_start: 0.8754 (tttt) cc_final: 0.8442 (tttp) REVERT: G 78 GLU cc_start: 0.8750 (tt0) cc_final: 0.8346 (tm-30) REVERT: G 96 TYR cc_start: 0.8965 (t80) cc_final: 0.8748 (t80) REVERT: G 116 LYS cc_start: 0.8449 (mtmt) cc_final: 0.8192 (mtpt) REVERT: H 28 MET cc_start: 0.4649 (mmt) cc_final: 0.4109 (tpp) REVERT: H 142 LYS cc_start: 0.8453 (mmtm) cc_final: 0.8214 (mptt) REVERT: I 45 ILE cc_start: 0.8730 (mt) cc_final: 0.8479 (mm) REVERT: I 51 ASP cc_start: 0.8350 (m-30) cc_final: 0.7996 (m-30) REVERT: I 52 GLN cc_start: 0.7878 (mm-40) cc_final: 0.7392 (tm-30) REVERT: J 28 MET cc_start: 0.3775 (mmt) cc_final: 0.3314 (tpp) REVERT: J 36 GLN cc_start: 0.8427 (mt0) cc_final: 0.7900 (mm-40) REVERT: J 55 LYS cc_start: 0.8589 (tttp) cc_final: 0.8300 (mtpp) REVERT: J 110 LYS cc_start: 0.9125 (tptt) cc_final: 0.8896 (tptt) REVERT: J 123 LYS cc_start: 0.8912 (OUTLIER) cc_final: 0.8648 (mttm) REVERT: J 141 LYS cc_start: 0.8380 (OUTLIER) cc_final: 0.8094 (mttt) REVERT: K 55 LYS cc_start: 0.8249 (ttpt) cc_final: 0.7907 (tppp) REVERT: K 75 ASP cc_start: 0.8972 (p0) cc_final: 0.8612 (p0) REVERT: L 65 LYS cc_start: 0.8869 (tttp) cc_final: 0.8591 (tttm) REVERT: L 80 ARG cc_start: 0.8691 (mtp180) cc_final: 0.8361 (mtm-85) REVERT: L 110 LYS cc_start: 0.8885 (tppt) cc_final: 0.8292 (tptt) REVERT: L 116 LYS cc_start: 0.8082 (mtmt) cc_final: 0.7711 (mtmm) REVERT: M 36 GLN cc_start: 0.8059 (mt0) cc_final: 0.7786 (mt0) REVERT: M 40 LYS cc_start: 0.8413 (ptmt) cc_final: 0.7599 (pttp) REVERT: M 43 MET cc_start: 0.9100 (ttm) cc_final: 0.8885 (ttp) REVERT: M 76 THR cc_start: 0.9157 (m) cc_final: 0.8778 (p) REVERT: M 78 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.8147 (tm-30) REVERT: M 80 ARG cc_start: 0.8639 (mtm180) cc_final: 0.8384 (mtm180) REVERT: M 96 TYR cc_start: 0.9280 (t80) cc_final: 0.8932 (t80) REVERT: M 110 LYS cc_start: 0.8624 (OUTLIER) cc_final: 0.8247 (ttpp) REVERT: M 123 LYS cc_start: 0.8625 (mtmt) cc_final: 0.8229 (mtmp) REVERT: N 145 ASN cc_start: 0.8402 (OUTLIER) cc_final: 0.7891 (t0) REVERT: O 52 GLN cc_start: 0.8470 (mm110) cc_final: 0.8133 (mm-40) REVERT: O 55 LYS cc_start: 0.8494 (mtpp) cc_final: 0.8166 (tttt) REVERT: O 106 TYR cc_start: 0.7945 (p90) cc_final: 0.7694 (p90) REVERT: O 110 LYS cc_start: 0.8511 (tmmm) cc_final: 0.8134 (tmmm) REVERT: O 123 LYS cc_start: 0.8383 (mmtp) cc_final: 0.8158 (mtpp) REVERT: P 67 ASP cc_start: 0.8584 (m-30) cc_final: 0.7638 (t0) REVERT: P 78 GLU cc_start: 0.8359 (tt0) cc_final: 0.7354 (tm-30) REVERT: P 119 ASN cc_start: 0.8925 (m-40) cc_final: 0.8354 (m110) REVERT: P 121 SER cc_start: 0.8257 (p) cc_final: 0.7978 (t) REVERT: Q 55 LYS cc_start: 0.8824 (tttt) cc_final: 0.8624 (tttt) REVERT: Q 75 ASP cc_start: 0.9071 (p0) cc_final: 0.8627 (p0) REVERT: Q 102 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.7940 (pm20) REVERT: R 123 LYS cc_start: 0.8092 (mtpt) cc_final: 0.7360 (mtpp) REVERT: S 36 GLN cc_start: 0.8345 (mt0) cc_final: 0.8117 (mt0) REVERT: S 78 GLU cc_start: 0.8273 (tm-30) cc_final: 0.7954 (tm-30) REVERT: T 28 MET cc_start: 0.5701 (mmt) cc_final: 0.4959 (mpp) REVERT: T 43 MET cc_start: 0.8990 (ttm) cc_final: 0.8645 (ttm) REVERT: T 75 ASP cc_start: 0.8957 (p0) cc_final: 0.8734 (p0) REVERT: T 101 GLU cc_start: 0.8262 (tp30) cc_final: 0.7956 (tm-30) REVERT: V 28 MET cc_start: 0.5357 (mmt) cc_final: 0.4021 (mpt) REVERT: V 35 ILE cc_start: 0.7376 (OUTLIER) cc_final: 0.7173 (pp) REVERT: V 43 MET cc_start: 0.8958 (ttm) cc_final: 0.8518 (ttp) REVERT: V 75 ASP cc_start: 0.8309 (p0) cc_final: 0.7900 (p0) REVERT: V 80 ARG cc_start: 0.8659 (mtp85) cc_final: 0.8410 (mpp80) REVERT: W 28 MET cc_start: 0.4828 (tpp) cc_final: 0.3799 (tpp) REVERT: W 51 ASP cc_start: 0.8111 (m-30) cc_final: 0.7846 (m-30) REVERT: W 65 LYS cc_start: 0.8432 (ttpt) cc_final: 0.8163 (tttt) REVERT: W 75 ASP cc_start: 0.8885 (p0) cc_final: 0.8472 (p0) REVERT: W 80 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.8157 (mtp180) REVERT: W 93 ARG cc_start: 0.7868 (ptt-90) cc_final: 0.7629 (ptp90) REVERT: W 110 LYS cc_start: 0.8953 (OUTLIER) cc_final: 0.8681 (tptp) REVERT: W 123 LYS cc_start: 0.8820 (mppt) cc_final: 0.8112 (mtmm) REVERT: W 142 LYS cc_start: 0.7646 (mmpt) cc_final: 0.6950 (mmmt) REVERT: X 49 GLU cc_start: 0.7713 (tt0) cc_final: 0.7417 (tt0) REVERT: X 82 LYS cc_start: 0.8324 (ptpp) cc_final: 0.7795 (pttp) REVERT: X 96 TYR cc_start: 0.9262 (t80) cc_final: 0.8807 (t80) REVERT: X 130 SER cc_start: 0.8743 (m) cc_final: 0.8425 (t) REVERT: X 135 LYS cc_start: 0.8017 (OUTLIER) cc_final: 0.7449 (mttm) REVERT: Y 28 MET cc_start: 0.5181 (mmp) cc_final: 0.4431 (mpp) REVERT: Y 75 ASP cc_start: 0.8646 (p0) cc_final: 0.8009 (p0) REVERT: Y 78 GLU cc_start: 0.8799 (tt0) cc_final: 0.8569 (tt0) REVERT: Y 82 LYS cc_start: 0.8539 (ptmt) cc_final: 0.8283 (ptmm) REVERT: Y 102 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.7773 (pm20) REVERT: Y 110 LYS cc_start: 0.8789 (OUTLIER) cc_final: 0.8463 (ttmm) outliers start: 107 outliers final: 39 residues processed: 656 average time/residue: 0.7400 time to fit residues: 538.7952 Evaluate side-chains 602 residues out of total 2544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 547 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 147 GLU Chi-restraints excluded: chain D residue 52 GLN Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain E residue 78 GLU Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain I residue 46 SER Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 121 SER Chi-restraints excluded: chain J residue 97 SER Chi-restraints excluded: chain J residue 123 LYS Chi-restraints excluded: chain J residue 141 LYS Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain L residue 88 ILE Chi-restraints excluded: chain M residue 78 GLU Chi-restraints excluded: chain M residue 110 LYS Chi-restraints excluded: chain M residue 139 SER Chi-restraints excluded: chain M residue 147 GLU Chi-restraints excluded: chain N residue 121 SER Chi-restraints excluded: chain N residue 145 ASN Chi-restraints excluded: chain O residue 38 SER Chi-restraints excluded: chain O residue 46 SER Chi-restraints excluded: chain O residue 73 VAL Chi-restraints excluded: chain O residue 76 THR Chi-restraints excluded: chain P residue 38 SER Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain P residue 131 VAL Chi-restraints excluded: chain Q residue 45 ILE Chi-restraints excluded: chain Q residue 46 SER Chi-restraints excluded: chain Q residue 102 GLU Chi-restraints excluded: chain Q residue 110 LYS Chi-restraints excluded: chain Q residue 121 SER Chi-restraints excluded: chain R residue 145 ASN Chi-restraints excluded: chain S residue 45 ILE Chi-restraints excluded: chain T residue 52 GLN Chi-restraints excluded: chain V residue 35 ILE Chi-restraints excluded: chain V residue 131 VAL Chi-restraints excluded: chain V residue 147 GLU Chi-restraints excluded: chain W residue 80 ARG Chi-restraints excluded: chain W residue 110 LYS Chi-restraints excluded: chain X residue 45 ILE Chi-restraints excluded: chain X residue 84 SER Chi-restraints excluded: chain X residue 102 GLU Chi-restraints excluded: chain X residue 131 VAL Chi-restraints excluded: chain X residue 135 LYS Chi-restraints excluded: chain Y residue 102 GLU Chi-restraints excluded: chain Y residue 110 LYS Chi-restraints excluded: chain Y residue 116 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 182 optimal weight: 8.9990 chunk 74 optimal weight: 5.9990 chunk 134 optimal weight: 5.9990 chunk 262 optimal weight: 1.9990 chunk 241 optimal weight: 0.9980 chunk 77 optimal weight: 4.9990 chunk 277 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 154 optimal weight: 4.9990 chunk 202 optimal weight: 2.9990 chunk 261 optimal weight: 0.7980 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 145 ASN F 52 GLN G 36 GLN G 126 ASN I 119 ASN K 36 GLN K 52 GLN K 126 ASN M 52 GLN T 36 GLN V 52 GLN W 52 GLN Y 36 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.121374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.094216 restraints weight = 33395.182| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 2.69 r_work: 0.3213 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.4646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 22776 Z= 0.219 Angle : 0.614 9.405 30720 Z= 0.318 Chirality : 0.054 0.175 3672 Planarity : 0.003 0.033 3888 Dihedral : 4.636 15.782 3024 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 4.83 % Allowed : 26.81 % Favored : 68.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.75 (0.17), residues: 2856 helix: None (None), residues: 0 sheet: 3.02 (0.16), residues: 1104 loop : -0.12 (0.15), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG T 93 TYR 0.026 0.002 TYR Q 106 PHE 0.010 0.002 PHE T 124 TRP 0.004 0.001 TRP F 59 HIS 0.006 0.001 HIS N 53 Details of bonding type rmsd covalent geometry : bond 0.00535 (22776) covalent geometry : angle 0.61404 (30720) hydrogen bonds : bond 0.04254 ( 962) hydrogen bonds : angle 4.79743 ( 2454) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 669 residues out of total 2544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 546 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 GLU cc_start: 0.8310 (tt0) cc_final: 0.8038 (tt0) REVERT: A 78 GLU cc_start: 0.8756 (tt0) cc_final: 0.8321 (tm-30) REVERT: B 52 GLN cc_start: 0.8176 (mt0) cc_final: 0.6764 (tm130) REVERT: B 116 LYS cc_start: 0.7937 (mtmt) cc_final: 0.7678 (mtpp) REVERT: D 28 MET cc_start: 0.4548 (mmt) cc_final: 0.3645 (tpp) REVERT: D 52 GLN cc_start: 0.8737 (OUTLIER) cc_final: 0.8413 (mp10) REVERT: D 87 MET cc_start: 0.8402 (pmm) cc_final: 0.8039 (ppp) REVERT: D 110 LYS cc_start: 0.8714 (tttt) cc_final: 0.8419 (ttpp) REVERT: D 142 LYS cc_start: 0.8352 (mmtm) cc_final: 0.7940 (mmtm) REVERT: C 28 MET cc_start: 0.3233 (mmt) cc_final: 0.2701 (mpp) REVERT: C 67 ASP cc_start: 0.8545 (m-30) cc_final: 0.8164 (m-30) REVERT: C 93 ARG cc_start: 0.7677 (ptt-90) cc_final: 0.6816 (pmt170) REVERT: C 96 TYR cc_start: 0.9018 (t80) cc_final: 0.8716 (t80) REVERT: C 116 LYS cc_start: 0.7729 (mtmt) cc_final: 0.7386 (mtpp) REVERT: C 123 LYS cc_start: 0.7738 (mmpt) cc_final: 0.7386 (mppt) REVERT: C 142 LYS cc_start: 0.7733 (mmtm) cc_final: 0.7418 (mmmm) REVERT: E 43 MET cc_start: 0.8811 (ttm) cc_final: 0.8537 (ttm) REVERT: E 78 GLU cc_start: 0.8994 (OUTLIER) cc_final: 0.8577 (pp20) REVERT: E 93 ARG cc_start: 0.8063 (ptt-90) cc_final: 0.7818 (ptp90) REVERT: E 123 LYS cc_start: 0.8305 (mttm) cc_final: 0.7970 (mmtp) REVERT: G 28 MET cc_start: 0.4322 (mmt) cc_final: 0.3664 (tpp) REVERT: G 51 ASP cc_start: 0.8874 (OUTLIER) cc_final: 0.8525 (t0) REVERT: G 67 ASP cc_start: 0.8948 (m-30) cc_final: 0.8719 (m-30) REVERT: G 78 GLU cc_start: 0.8718 (tt0) cc_final: 0.8234 (tm-30) REVERT: G 96 TYR cc_start: 0.8964 (t80) cc_final: 0.8710 (t80) REVERT: G 116 LYS cc_start: 0.8520 (mtmt) cc_final: 0.8276 (mtpt) REVERT: H 28 MET cc_start: 0.4535 (mmt) cc_final: 0.3775 (tpp) REVERT: H 40 LYS cc_start: 0.7660 (ptmm) cc_final: 0.7266 (ptmt) REVERT: I 45 ILE cc_start: 0.8737 (mt) cc_final: 0.8441 (mm) REVERT: I 52 GLN cc_start: 0.7888 (mm-40) cc_final: 0.7360 (tm-30) REVERT: I 78 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.7294 (pp20) REVERT: I 147 GLU cc_start: 0.7384 (OUTLIER) cc_final: 0.7176 (pp20) REVERT: J 28 MET cc_start: 0.3729 (mmt) cc_final: 0.3281 (tpp) REVERT: J 36 GLN cc_start: 0.8482 (mt0) cc_final: 0.7939 (mm-40) REVERT: J 93 ARG cc_start: 0.8350 (OUTLIER) cc_final: 0.7118 (ptp-170) REVERT: J 110 LYS cc_start: 0.9118 (tptt) cc_final: 0.8633 (tptt) REVERT: J 123 LYS cc_start: 0.8915 (OUTLIER) cc_final: 0.8619 (mttm) REVERT: J 141 LYS cc_start: 0.8449 (OUTLIER) cc_final: 0.8195 (mttt) REVERT: K 55 LYS cc_start: 0.8319 (ttpt) cc_final: 0.7919 (tppp) REVERT: K 75 ASP cc_start: 0.8965 (p0) cc_final: 0.8569 (p0) REVERT: L 65 LYS cc_start: 0.8827 (OUTLIER) cc_final: 0.8522 (tttm) REVERT: L 80 ARG cc_start: 0.8782 (OUTLIER) cc_final: 0.8396 (mtm-85) REVERT: L 110 LYS cc_start: 0.8920 (tppt) cc_final: 0.8285 (tptt) REVERT: L 116 LYS cc_start: 0.8098 (mtmt) cc_final: 0.7807 (mtmm) REVERT: M 36 GLN cc_start: 0.8118 (mt0) cc_final: 0.7717 (mt0) REVERT: M 40 LYS cc_start: 0.8444 (ptmt) cc_final: 0.7571 (pttm) REVERT: M 43 MET cc_start: 0.9098 (ttm) cc_final: 0.8859 (ttp) REVERT: M 76 THR cc_start: 0.9150 (m) cc_final: 0.8794 (p) REVERT: M 78 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.7941 (tm-30) REVERT: M 80 ARG cc_start: 0.8552 (mtm180) cc_final: 0.7879 (mtm-85) REVERT: M 96 TYR cc_start: 0.9279 (t80) cc_final: 0.8945 (t80) REVERT: M 110 LYS cc_start: 0.8736 (OUTLIER) cc_final: 0.8301 (ttpp) REVERT: N 77 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8785 (tp) REVERT: N 145 ASN cc_start: 0.8433 (OUTLIER) cc_final: 0.7923 (t0) REVERT: O 52 GLN cc_start: 0.8468 (mm110) cc_final: 0.8127 (mm-40) REVERT: O 55 LYS cc_start: 0.8530 (mtpp) cc_final: 0.8120 (tttt) REVERT: O 65 LYS cc_start: 0.9339 (OUTLIER) cc_final: 0.9001 (ttmm) REVERT: O 106 TYR cc_start: 0.8002 (p90) cc_final: 0.7791 (p90) REVERT: O 123 LYS cc_start: 0.8434 (mmtp) cc_final: 0.8208 (mtpp) REVERT: P 67 ASP cc_start: 0.8606 (m-30) cc_final: 0.7631 (t0) REVERT: P 78 GLU cc_start: 0.8322 (tt0) cc_final: 0.7347 (tm-30) REVERT: Q 55 LYS cc_start: 0.8849 (tttt) cc_final: 0.8637 (tttt) REVERT: Q 75 ASP cc_start: 0.9056 (p0) cc_final: 0.8648 (p0) REVERT: Q 102 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.7907 (pm20) REVERT: R 43 MET cc_start: 0.9063 (ttm) cc_final: 0.8523 (ttm) REVERT: R 55 LYS cc_start: 0.8207 (tttt) cc_final: 0.7817 (mtpp) REVERT: R 103 GLU cc_start: 0.8129 (tt0) cc_final: 0.7818 (tt0) REVERT: S 36 GLN cc_start: 0.8420 (mt0) cc_final: 0.8166 (mt0) REVERT: S 78 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7857 (tm-30) REVERT: T 28 MET cc_start: 0.5688 (mmt) cc_final: 0.4803 (mpp) REVERT: T 43 MET cc_start: 0.9104 (ttm) cc_final: 0.8699 (ttm) REVERT: T 75 ASP cc_start: 0.8996 (p0) cc_final: 0.8783 (p0) REVERT: T 101 GLU cc_start: 0.8289 (tp30) cc_final: 0.7792 (tm-30) REVERT: T 142 LYS cc_start: 0.8796 (mptt) cc_final: 0.8516 (mptt) REVERT: V 28 MET cc_start: 0.4893 (mmt) cc_final: 0.3681 (mpp) REVERT: V 35 ILE cc_start: 0.7545 (OUTLIER) cc_final: 0.7313 (pp) REVERT: V 75 ASP cc_start: 0.8402 (p0) cc_final: 0.7922 (p0) REVERT: V 80 ARG cc_start: 0.8701 (OUTLIER) cc_final: 0.8414 (mpp80) REVERT: W 28 MET cc_start: 0.5107 (tpp) cc_final: 0.3956 (tpp) REVERT: W 51 ASP cc_start: 0.8105 (m-30) cc_final: 0.7848 (m-30) REVERT: W 65 LYS cc_start: 0.8479 (ttpt) cc_final: 0.8191 (tttt) REVERT: W 75 ASP cc_start: 0.8868 (p0) cc_final: 0.8493 (p0) REVERT: W 80 ARG cc_start: 0.8537 (OUTLIER) cc_final: 0.8198 (mtp180) REVERT: W 93 ARG cc_start: 0.7936 (ptt-90) cc_final: 0.7621 (ptp90) REVERT: W 123 LYS cc_start: 0.8819 (mppt) cc_final: 0.8114 (mtmm) REVERT: W 142 LYS cc_start: 0.7644 (mmpt) cc_final: 0.6936 (mmmt) REVERT: X 49 GLU cc_start: 0.7837 (tt0) cc_final: 0.7552 (tt0) REVERT: X 52 GLN cc_start: 0.8523 (mm-40) cc_final: 0.8320 (mm-40) REVERT: X 82 LYS cc_start: 0.8244 (ptpp) cc_final: 0.7707 (ptpp) REVERT: X 86 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.7882 (tt) REVERT: X 96 TYR cc_start: 0.9267 (t80) cc_final: 0.8720 (t80) REVERT: X 130 SER cc_start: 0.8757 (m) cc_final: 0.8375 (t) REVERT: X 135 LYS cc_start: 0.8123 (OUTLIER) cc_final: 0.7512 (mttm) REVERT: Y 28 MET cc_start: 0.5324 (mmp) cc_final: 0.5085 (mpm) REVERT: Y 75 ASP cc_start: 0.8591 (p0) cc_final: 0.8080 (p0) REVERT: Y 77 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8632 (tp) REVERT: Y 78 GLU cc_start: 0.8677 (tt0) cc_final: 0.8461 (tt0) REVERT: Y 82 LYS cc_start: 0.8564 (ptmt) cc_final: 0.8311 (ptmm) REVERT: Y 102 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.7852 (pm20) REVERT: Y 110 LYS cc_start: 0.8781 (OUTLIER) cc_final: 0.8544 (ttmm) outliers start: 123 outliers final: 61 residues processed: 622 average time/residue: 0.7594 time to fit residues: 522.7824 Evaluate side-chains 617 residues out of total 2544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 531 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain D residue 46 SER Chi-restraints excluded: chain D residue 52 GLN Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 130 SER Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain E residue 78 GLU Chi-restraints excluded: chain F residue 46 SER Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 51 ASP Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain I residue 38 SER Chi-restraints excluded: chain I residue 40 LYS Chi-restraints excluded: chain I residue 46 SER Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 78 GLU Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain I residue 121 SER Chi-restraints excluded: chain I residue 147 GLU Chi-restraints excluded: chain J residue 73 VAL Chi-restraints excluded: chain J residue 93 ARG Chi-restraints excluded: chain J residue 97 SER Chi-restraints excluded: chain J residue 123 LYS Chi-restraints excluded: chain J residue 141 LYS Chi-restraints excluded: chain K residue 116 LYS Chi-restraints excluded: chain K residue 133 LEU Chi-restraints excluded: chain L residue 65 LYS Chi-restraints excluded: chain L residue 80 ARG Chi-restraints excluded: chain L residue 88 ILE Chi-restraints excluded: chain M residue 51 ASP Chi-restraints excluded: chain M residue 78 GLU Chi-restraints excluded: chain M residue 110 LYS Chi-restraints excluded: chain M residue 147 GLU Chi-restraints excluded: chain N residue 77 LEU Chi-restraints excluded: chain N residue 121 SER Chi-restraints excluded: chain N residue 133 LEU Chi-restraints excluded: chain N residue 145 ASN Chi-restraints excluded: chain O residue 28 MET Chi-restraints excluded: chain O residue 38 SER Chi-restraints excluded: chain O residue 46 SER Chi-restraints excluded: chain O residue 65 LYS Chi-restraints excluded: chain O residue 73 VAL Chi-restraints excluded: chain O residue 76 THR Chi-restraints excluded: chain P residue 38 SER Chi-restraints excluded: chain P residue 51 ASP Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain P residue 131 VAL Chi-restraints excluded: chain Q residue 45 ILE Chi-restraints excluded: chain Q residue 46 SER Chi-restraints excluded: chain Q residue 77 LEU Chi-restraints excluded: chain Q residue 102 GLU Chi-restraints excluded: chain Q residue 108 THR Chi-restraints excluded: chain Q residue 110 LYS Chi-restraints excluded: chain Q residue 121 SER Chi-restraints excluded: chain Q residue 130 SER Chi-restraints excluded: chain R residue 73 VAL Chi-restraints excluded: chain R residue 145 ASN Chi-restraints excluded: chain S residue 45 ILE Chi-restraints excluded: chain S residue 78 GLU Chi-restraints excluded: chain S residue 131 VAL Chi-restraints excluded: chain T residue 38 SER Chi-restraints excluded: chain T residue 52 GLN Chi-restraints excluded: chain T residue 102 GLU Chi-restraints excluded: chain V residue 35 ILE Chi-restraints excluded: chain V residue 80 ARG Chi-restraints excluded: chain V residue 131 VAL Chi-restraints excluded: chain W residue 80 ARG Chi-restraints excluded: chain X residue 45 ILE Chi-restraints excluded: chain X residue 84 SER Chi-restraints excluded: chain X residue 86 LEU Chi-restraints excluded: chain X residue 102 GLU Chi-restraints excluded: chain X residue 135 LYS Chi-restraints excluded: chain Y residue 46 SER Chi-restraints excluded: chain Y residue 77 LEU Chi-restraints excluded: chain Y residue 102 GLU Chi-restraints excluded: chain Y residue 110 LYS Chi-restraints excluded: chain Y residue 138 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 134 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 30 optimal weight: 0.0870 chunk 254 optimal weight: 6.9990 chunk 245 optimal weight: 5.9990 chunk 287 optimal weight: 0.0470 chunk 137 optimal weight: 5.9990 chunk 207 optimal weight: 0.8980 chunk 209 optimal weight: 0.8980 chunk 139 optimal weight: 0.9980 chunk 115 optimal weight: 0.5980 overall best weight: 0.5056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 145 ASN C 52 GLN F 52 GLN G 36 GLN G 52 GLN K 36 GLN K 52 GLN L 36 GLN M 52 GLN N 52 GLN P 30 GLN W 52 GLN X 145 ASN Y 36 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.124435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.097375 restraints weight = 32732.314| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 2.70 r_work: 0.3268 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.4729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 22776 Z= 0.092 Angle : 0.539 9.196 30720 Z= 0.276 Chirality : 0.052 0.173 3672 Planarity : 0.002 0.023 3888 Dihedral : 4.064 15.262 3024 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 3.58 % Allowed : 28.73 % Favored : 67.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.02 (0.17), residues: 2856 helix: None (None), residues: 0 sheet: 3.31 (0.15), residues: 1080 loop : 0.03 (0.16), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG P 107 TYR 0.021 0.001 TYR P 106 PHE 0.005 0.001 PHE C 42 TRP 0.001 0.000 TRP S 59 HIS 0.002 0.001 HIS N 53 Details of bonding type rmsd covalent geometry : bond 0.00207 (22776) covalent geometry : angle 0.53949 (30720) hydrogen bonds : bond 0.03310 ( 962) hydrogen bonds : angle 4.60000 ( 2454) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 667 residues out of total 2544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 576 time to evaluate : 0.928 Fit side-chains revert: symmetry clash REVERT: A 40 LYS cc_start: 0.8552 (ptmt) cc_final: 0.8094 (pttm) REVERT: A 78 GLU cc_start: 0.8712 (tt0) cc_final: 0.8301 (tm-30) REVERT: A 87 MET cc_start: 0.7955 (pmm) cc_final: 0.7721 (ppp) REVERT: B 52 GLN cc_start: 0.8242 (mt0) cc_final: 0.6892 (tm130) REVERT: B 116 LYS cc_start: 0.7896 (mtmt) cc_final: 0.7622 (mtpp) REVERT: D 28 MET cc_start: 0.4179 (mmt) cc_final: 0.3473 (tpp) REVERT: D 45 ILE cc_start: 0.9115 (mt) cc_final: 0.8893 (mm) REVERT: D 49 GLU cc_start: 0.8500 (tt0) cc_final: 0.8295 (tt0) REVERT: D 52 GLN cc_start: 0.8700 (OUTLIER) cc_final: 0.8411 (mp10) REVERT: D 84 SER cc_start: 0.9208 (OUTLIER) cc_final: 0.8987 (p) REVERT: D 87 MET cc_start: 0.8421 (pmm) cc_final: 0.8046 (ppp) REVERT: D 110 LYS cc_start: 0.8607 (tttt) cc_final: 0.8274 (ttpp) REVERT: D 142 LYS cc_start: 0.8366 (mmtm) cc_final: 0.7959 (mmtm) REVERT: C 28 MET cc_start: 0.3207 (mmt) cc_final: 0.2672 (mpp) REVERT: C 67 ASP cc_start: 0.8482 (m-30) cc_final: 0.8161 (m-30) REVERT: C 96 TYR cc_start: 0.8928 (t80) cc_final: 0.8611 (t80) REVERT: C 116 LYS cc_start: 0.7663 (mtmt) cc_final: 0.7373 (mtpp) REVERT: C 123 LYS cc_start: 0.7548 (mmpt) cc_final: 0.7124 (mppt) REVERT: C 142 LYS cc_start: 0.7694 (mmtm) cc_final: 0.7386 (mmmm) REVERT: E 78 GLU cc_start: 0.8620 (OUTLIER) cc_final: 0.8262 (pp20) REVERT: E 80 ARG cc_start: 0.8537 (mtm-85) cc_final: 0.7827 (mtm-85) REVERT: E 93 ARG cc_start: 0.8048 (ptt-90) cc_final: 0.7812 (ptp90) REVERT: E 123 LYS cc_start: 0.8245 (mttm) cc_final: 0.7771 (tmtm) REVERT: F 40 LYS cc_start: 0.8113 (ptmt) cc_final: 0.7882 (pttt) REVERT: G 28 MET cc_start: 0.4335 (mmt) cc_final: 0.3903 (tpp) REVERT: G 55 LYS cc_start: 0.8597 (tttp) cc_final: 0.8369 (tttt) REVERT: G 75 ASP cc_start: 0.8706 (p0) cc_final: 0.8499 (p0) REVERT: G 78 GLU cc_start: 0.8601 (tt0) cc_final: 0.8234 (tm-30) REVERT: G 96 TYR cc_start: 0.8942 (t80) cc_final: 0.8732 (t80) REVERT: G 116 LYS cc_start: 0.8452 (mtmt) cc_final: 0.8214 (mtpt) REVERT: H 28 MET cc_start: 0.4650 (mmt) cc_final: 0.3908 (tpp) REVERT: H 40 LYS cc_start: 0.7546 (ptmm) cc_final: 0.7205 (ptmt) REVERT: H 78 GLU cc_start: 0.8541 (tt0) cc_final: 0.8046 (tm-30) REVERT: I 45 ILE cc_start: 0.8757 (mt) cc_final: 0.8437 (mm) REVERT: I 52 GLN cc_start: 0.7880 (mm-40) cc_final: 0.7306 (tm-30) REVERT: I 55 LYS cc_start: 0.8829 (mtpp) cc_final: 0.8504 (mmtt) REVERT: I 78 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.7190 (pp20) REVERT: I 80 ARG cc_start: 0.7947 (mtm-85) cc_final: 0.7246 (mtm-85) REVERT: I 101 GLU cc_start: 0.7858 (tp30) cc_final: 0.7430 (tp30) REVERT: I 147 GLU cc_start: 0.7528 (OUTLIER) cc_final: 0.7288 (pp20) REVERT: J 28 MET cc_start: 0.3707 (mmt) cc_final: 0.3246 (tpt) REVERT: J 36 GLN cc_start: 0.8331 (mt0) cc_final: 0.7824 (mm-40) REVERT: J 55 LYS cc_start: 0.8614 (tttp) cc_final: 0.8329 (mtpp) REVERT: J 93 ARG cc_start: 0.8423 (OUTLIER) cc_final: 0.7089 (ptp-170) REVERT: J 110 LYS cc_start: 0.9131 (tptt) cc_final: 0.8857 (tptt) REVERT: J 123 LYS cc_start: 0.8888 (OUTLIER) cc_final: 0.8613 (mttm) REVERT: K 36 GLN cc_start: 0.8249 (mt0) cc_final: 0.7971 (mt0) REVERT: K 55 LYS cc_start: 0.8126 (ttpt) cc_final: 0.7822 (tppp) REVERT: K 75 ASP cc_start: 0.8892 (p0) cc_final: 0.8515 (p0) REVERT: L 65 LYS cc_start: 0.8845 (OUTLIER) cc_final: 0.8517 (tttm) REVERT: L 75 ASP cc_start: 0.8768 (p0) cc_final: 0.8518 (p0) REVERT: L 80 ARG cc_start: 0.8734 (mtp180) cc_final: 0.8205 (mtt90) REVERT: L 110 LYS cc_start: 0.8938 (tppt) cc_final: 0.8247 (tptt) REVERT: M 36 GLN cc_start: 0.8068 (mt0) cc_final: 0.7184 (tt0) REVERT: M 40 LYS cc_start: 0.8367 (OUTLIER) cc_final: 0.7498 (pttm) REVERT: M 43 MET cc_start: 0.9125 (ttm) cc_final: 0.8815 (ttp) REVERT: M 76 THR cc_start: 0.9120 (m) cc_final: 0.8704 (p) REVERT: M 78 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.8160 (tm-30) REVERT: M 96 TYR cc_start: 0.9247 (t80) cc_final: 0.8859 (t80) REVERT: M 110 LYS cc_start: 0.8734 (OUTLIER) cc_final: 0.8263 (ttpp) REVERT: M 123 LYS cc_start: 0.8720 (mtmt) cc_final: 0.8369 (mtmp) REVERT: N 78 GLU cc_start: 0.8773 (OUTLIER) cc_final: 0.8442 (tm-30) REVERT: N 145 ASN cc_start: 0.8400 (OUTLIER) cc_final: 0.7921 (t0) REVERT: O 52 GLN cc_start: 0.8440 (mm110) cc_final: 0.8136 (mm-40) REVERT: O 55 LYS cc_start: 0.8452 (mtpp) cc_final: 0.8030 (tttt) REVERT: O 106 TYR cc_start: 0.7843 (p90) cc_final: 0.7602 (p90) REVERT: O 110 LYS cc_start: 0.8564 (tmmm) cc_final: 0.8124 (tmmm) REVERT: P 67 ASP cc_start: 0.8539 (m-30) cc_final: 0.7708 (t0) REVERT: P 78 GLU cc_start: 0.8292 (tt0) cc_final: 0.8023 (tt0) REVERT: P 106 TYR cc_start: 0.8464 (p90) cc_final: 0.8212 (p90) REVERT: P 119 ASN cc_start: 0.8796 (m-40) cc_final: 0.8298 (m110) REVERT: R 43 MET cc_start: 0.9092 (ttm) cc_final: 0.8546 (ttm) REVERT: R 90 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7830 (tp30) REVERT: R 103 GLU cc_start: 0.8072 (tt0) cc_final: 0.7777 (tt0) REVERT: R 123 LYS cc_start: 0.8090 (mtpt) cc_final: 0.7323 (mtpp) REVERT: R 147 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.7198 (pp20) REVERT: S 78 GLU cc_start: 0.8276 (tm-30) cc_final: 0.7971 (tm-30) REVERT: S 123 LYS cc_start: 0.8818 (mttt) cc_final: 0.8489 (mttm) REVERT: T 28 MET cc_start: 0.5633 (mmt) cc_final: 0.4853 (mpp) REVERT: T 43 MET cc_start: 0.9112 (ttm) cc_final: 0.8774 (ttm) REVERT: T 75 ASP cc_start: 0.8956 (p0) cc_final: 0.8713 (p0) REVERT: T 101 GLU cc_start: 0.8240 (tp30) cc_final: 0.7918 (tm-30) REVERT: V 28 MET cc_start: 0.4968 (mmt) cc_final: 0.3766 (mpp) REVERT: V 35 ILE cc_start: 0.7629 (OUTLIER) cc_final: 0.7417 (pp) REVERT: V 75 ASP cc_start: 0.8357 (p0) cc_final: 0.7968 (p0) REVERT: V 80 ARG cc_start: 0.8660 (mtp85) cc_final: 0.8421 (mtm180) REVERT: W 28 MET cc_start: 0.4879 (tpp) cc_final: 0.3632 (tpp) REVERT: W 65 LYS cc_start: 0.8410 (ttpt) cc_final: 0.8120 (tttt) REVERT: W 75 ASP cc_start: 0.8855 (p0) cc_final: 0.8424 (p0) REVERT: W 80 ARG cc_start: 0.8425 (OUTLIER) cc_final: 0.8213 (mtp180) REVERT: W 110 LYS cc_start: 0.8953 (OUTLIER) cc_final: 0.8670 (tptp) REVERT: W 123 LYS cc_start: 0.8860 (mppt) cc_final: 0.8143 (mtmm) REVERT: W 142 LYS cc_start: 0.7680 (mmpt) cc_final: 0.6998 (mmmt) REVERT: X 49 GLU cc_start: 0.7729 (tt0) cc_final: 0.7469 (tt0) REVERT: X 52 GLN cc_start: 0.8408 (mm-40) cc_final: 0.8160 (mm-40) REVERT: X 82 LYS cc_start: 0.8063 (ptpp) cc_final: 0.7514 (pttp) REVERT: X 86 LEU cc_start: 0.8263 (OUTLIER) cc_final: 0.7835 (tt) REVERT: X 96 TYR cc_start: 0.9220 (t80) cc_final: 0.8688 (t80) REVERT: X 130 SER cc_start: 0.8697 (m) cc_final: 0.8389 (t) REVERT: X 135 LYS cc_start: 0.8038 (OUTLIER) cc_final: 0.7412 (mttm) REVERT: X 145 ASN cc_start: 0.8234 (p0) cc_final: 0.7786 (p0) REVERT: Y 75 ASP cc_start: 0.8585 (p0) cc_final: 0.8121 (p0) REVERT: Y 82 LYS cc_start: 0.8580 (ptmt) cc_final: 0.8307 (ptmm) outliers start: 91 outliers final: 33 residues processed: 625 average time/residue: 0.7567 time to fit residues: 523.4672 Evaluate side-chains 599 residues out of total 2544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 546 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain B residue 123 LYS Chi-restraints excluded: chain D residue 52 GLN Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 130 SER Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain E residue 78 GLU Chi-restraints excluded: chain F residue 46 SER Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain I residue 46 SER Chi-restraints excluded: chain I residue 78 GLU Chi-restraints excluded: chain I residue 102 GLU Chi-restraints excluded: chain I residue 147 GLU Chi-restraints excluded: chain J residue 93 ARG Chi-restraints excluded: chain J residue 123 LYS Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain L residue 65 LYS Chi-restraints excluded: chain L residue 88 ILE Chi-restraints excluded: chain M residue 40 LYS Chi-restraints excluded: chain M residue 78 GLU Chi-restraints excluded: chain M residue 110 LYS Chi-restraints excluded: chain M residue 139 SER Chi-restraints excluded: chain M residue 147 GLU Chi-restraints excluded: chain N residue 78 GLU Chi-restraints excluded: chain N residue 121 SER Chi-restraints excluded: chain N residue 145 ASN Chi-restraints excluded: chain O residue 46 SER Chi-restraints excluded: chain O residue 73 VAL Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain P residue 131 VAL Chi-restraints excluded: chain Q residue 46 SER Chi-restraints excluded: chain Q residue 121 SER Chi-restraints excluded: chain R residue 90 GLU Chi-restraints excluded: chain R residue 147 GLU Chi-restraints excluded: chain T residue 52 GLN Chi-restraints excluded: chain T residue 102 GLU Chi-restraints excluded: chain V residue 35 ILE Chi-restraints excluded: chain V residue 131 VAL Chi-restraints excluded: chain W residue 80 ARG Chi-restraints excluded: chain W residue 110 LYS Chi-restraints excluded: chain X residue 84 SER Chi-restraints excluded: chain X residue 86 LEU Chi-restraints excluded: chain X residue 102 GLU Chi-restraints excluded: chain X residue 131 VAL Chi-restraints excluded: chain X residue 135 LYS Chi-restraints excluded: chain X residue 138 SER Chi-restraints excluded: chain Y residue 46 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 115 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 190 optimal weight: 0.5980 chunk 154 optimal weight: 5.9990 chunk 185 optimal weight: 2.9990 chunk 109 optimal weight: 6.9990 chunk 281 optimal weight: 6.9990 chunk 243 optimal weight: 1.9990 chunk 238 optimal weight: 4.9990 chunk 122 optimal weight: 5.9990 chunk 5 optimal weight: 7.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN D 145 ASN G 36 GLN G 52 GLN H 126 ASN J 30 GLN J 36 GLN K 52 GLN M 52 GLN O 126 ASN R 126 ASN W 52 GLN Y 36 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.119481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.092505 restraints weight = 33137.427| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.67 r_work: 0.3200 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.4878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 22776 Z= 0.263 Angle : 0.639 10.104 30720 Z= 0.329 Chirality : 0.055 0.172 3672 Planarity : 0.003 0.040 3888 Dihedral : 4.648 16.341 3024 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 5.23 % Allowed : 28.42 % Favored : 66.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.76 (0.16), residues: 2856 helix: None (None), residues: 0 sheet: 3.23 (0.15), residues: 1080 loop : -0.23 (0.15), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG T 93 TYR 0.027 0.002 TYR Q 106 PHE 0.011 0.002 PHE N 124 TRP 0.005 0.001 TRP N 59 HIS 0.007 0.001 HIS N 53 Details of bonding type rmsd covalent geometry : bond 0.00646 (22776) covalent geometry : angle 0.63946 (30720) hydrogen bonds : bond 0.04373 ( 962) hydrogen bonds : angle 4.79667 ( 2454) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 667 residues out of total 2544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 534 time to evaluate : 0.825 Fit side-chains REVERT: A 40 LYS cc_start: 0.8614 (ptmt) cc_final: 0.8049 (pttm) REVERT: A 78 GLU cc_start: 0.8724 (tt0) cc_final: 0.8295 (tm-30) REVERT: B 52 GLN cc_start: 0.8186 (mt0) cc_final: 0.6565 (tm130) REVERT: B 116 LYS cc_start: 0.7942 (mtmt) cc_final: 0.7696 (mtpp) REVERT: D 28 MET cc_start: 0.4351 (mmt) cc_final: 0.3597 (tpp) REVERT: D 52 GLN cc_start: 0.8784 (OUTLIER) cc_final: 0.8427 (mp10) REVERT: D 77 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8767 (tp) REVERT: D 87 MET cc_start: 0.8487 (pmm) cc_final: 0.8093 (ppp) REVERT: D 110 LYS cc_start: 0.8705 (tttt) cc_final: 0.8416 (ttpp) REVERT: D 142 LYS cc_start: 0.8379 (mmtm) cc_final: 0.7962 (mmtm) REVERT: C 28 MET cc_start: 0.3253 (mmt) cc_final: 0.2891 (mpp) REVERT: C 67 ASP cc_start: 0.8529 (m-30) cc_final: 0.8143 (m-30) REVERT: C 96 TYR cc_start: 0.9014 (t80) cc_final: 0.8714 (t80) REVERT: C 123 LYS cc_start: 0.7791 (mmpt) cc_final: 0.7422 (mppt) REVERT: C 142 LYS cc_start: 0.7640 (mmtm) cc_final: 0.7357 (mmmm) REVERT: E 78 GLU cc_start: 0.9001 (OUTLIER) cc_final: 0.8625 (pp20) REVERT: E 123 LYS cc_start: 0.8352 (mttm) cc_final: 0.8002 (mtpt) REVERT: E 142 LYS cc_start: 0.8544 (mppt) cc_final: 0.8275 (mmtm) REVERT: G 28 MET cc_start: 0.4611 (mmt) cc_final: 0.3997 (tpp) REVERT: G 55 LYS cc_start: 0.8704 (tttp) cc_final: 0.8493 (tttt) REVERT: G 78 GLU cc_start: 0.8720 (tt0) cc_final: 0.8232 (tm-30) REVERT: G 96 TYR cc_start: 0.8963 (t80) cc_final: 0.8752 (t80) REVERT: G 116 LYS cc_start: 0.8527 (mtmt) cc_final: 0.8288 (mtpt) REVERT: H 28 MET cc_start: 0.4754 (mmt) cc_final: 0.4182 (tpp) REVERT: I 45 ILE cc_start: 0.8702 (mt) cc_final: 0.8404 (mm) REVERT: I 52 GLN cc_start: 0.7720 (mm-40) cc_final: 0.6906 (tm-30) REVERT: I 78 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.7290 (pp20) REVERT: I 147 GLU cc_start: 0.7537 (OUTLIER) cc_final: 0.7088 (pp20) REVERT: J 28 MET cc_start: 0.3735 (mmt) cc_final: 0.3218 (tpp) REVERT: J 36 GLN cc_start: 0.8522 (mt0) cc_final: 0.7992 (mm-40) REVERT: J 93 ARG cc_start: 0.8365 (OUTLIER) cc_final: 0.7145 (ptp-170) REVERT: J 110 LYS cc_start: 0.9051 (tptt) cc_final: 0.8607 (tptt) REVERT: J 123 LYS cc_start: 0.8917 (OUTLIER) cc_final: 0.8615 (mttm) REVERT: J 141 LYS cc_start: 0.8435 (OUTLIER) cc_final: 0.8189 (mttt) REVERT: K 55 LYS cc_start: 0.8373 (ttpt) cc_final: 0.7885 (tppp) REVERT: K 75 ASP cc_start: 0.8954 (p0) cc_final: 0.8488 (p0) REVERT: L 65 LYS cc_start: 0.8894 (OUTLIER) cc_final: 0.8581 (tttm) REVERT: L 80 ARG cc_start: 0.8773 (OUTLIER) cc_final: 0.8440 (mtm-85) REVERT: L 110 LYS cc_start: 0.8925 (tppt) cc_final: 0.8295 (tptt) REVERT: M 36 GLN cc_start: 0.8148 (mt0) cc_final: 0.7187 (tt0) REVERT: M 40 LYS cc_start: 0.8467 (ptmt) cc_final: 0.7651 (pttm) REVERT: M 43 MET cc_start: 0.9092 (ttm) cc_final: 0.8809 (ttp) REVERT: M 75 ASP cc_start: 0.8843 (p0) cc_final: 0.8520 (p0) REVERT: M 76 THR cc_start: 0.8973 (m) cc_final: 0.8691 (p) REVERT: M 78 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.8222 (tm-30) REVERT: M 96 TYR cc_start: 0.9266 (t80) cc_final: 0.9003 (t80) REVERT: M 110 LYS cc_start: 0.8742 (OUTLIER) cc_final: 0.8234 (ttpp) REVERT: N 77 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8802 (tp) REVERT: N 145 ASN cc_start: 0.8467 (OUTLIER) cc_final: 0.7961 (t0) REVERT: O 52 GLN cc_start: 0.8436 (mm110) cc_final: 0.8126 (mm-40) REVERT: O 106 TYR cc_start: 0.8016 (p90) cc_final: 0.7656 (p90) REVERT: P 40 LYS cc_start: 0.7975 (mtmt) cc_final: 0.7769 (mtmt) REVERT: P 67 ASP cc_start: 0.8598 (m-30) cc_final: 0.7646 (t0) REVERT: P 78 GLU cc_start: 0.8255 (tt0) cc_final: 0.7310 (tm-30) REVERT: Q 102 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.7978 (pm20) REVERT: R 55 LYS cc_start: 0.8217 (tttt) cc_final: 0.7826 (mtpp) REVERT: R 78 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7788 (tm-30) REVERT: R 80 ARG cc_start: 0.7934 (mtm180) cc_final: 0.7544 (mtm110) REVERT: R 103 GLU cc_start: 0.8220 (tt0) cc_final: 0.7880 (tt0) REVERT: S 78 GLU cc_start: 0.8239 (tm-30) cc_final: 0.7844 (tm-30) REVERT: S 110 LYS cc_start: 0.8891 (tmtp) cc_final: 0.8557 (tptp) REVERT: S 123 LYS cc_start: 0.8848 (mttt) cc_final: 0.8493 (mttm) REVERT: T 28 MET cc_start: 0.5810 (mmt) cc_final: 0.5167 (mpp) REVERT: T 43 MET cc_start: 0.9117 (ttm) cc_final: 0.8819 (ttm) REVERT: T 101 GLU cc_start: 0.8240 (tp30) cc_final: 0.7770 (tm-30) REVERT: T 142 LYS cc_start: 0.8715 (mptt) cc_final: 0.8450 (mptt) REVERT: T 147 GLU cc_start: 0.6656 (OUTLIER) cc_final: 0.6445 (pm20) REVERT: V 28 MET cc_start: 0.4792 (mmt) cc_final: 0.3633 (mpm) REVERT: V 75 ASP cc_start: 0.8512 (p0) cc_final: 0.8049 (p0) REVERT: V 80 ARG cc_start: 0.8793 (OUTLIER) cc_final: 0.8520 (mpp80) REVERT: W 28 MET cc_start: 0.5436 (tpp) cc_final: 0.4454 (tpp) REVERT: W 43 MET cc_start: 0.9235 (ttm) cc_final: 0.8740 (ttm) REVERT: W 75 ASP cc_start: 0.8910 (p0) cc_final: 0.8529 (p0) REVERT: W 80 ARG cc_start: 0.8543 (mtm180) cc_final: 0.8280 (mtp180) REVERT: W 123 LYS cc_start: 0.8806 (mppt) cc_final: 0.8075 (mtmm) REVERT: W 142 LYS cc_start: 0.7652 (mmpt) cc_final: 0.6988 (mmmt) REVERT: X 82 LYS cc_start: 0.8295 (ptpp) cc_final: 0.7826 (ptpp) REVERT: X 96 TYR cc_start: 0.9280 (t80) cc_final: 0.8839 (t80) REVERT: X 130 SER cc_start: 0.8770 (m) cc_final: 0.8394 (t) REVERT: X 135 LYS cc_start: 0.8209 (OUTLIER) cc_final: 0.7616 (mttm) REVERT: X 145 ASN cc_start: 0.8176 (p0) cc_final: 0.7705 (p0) REVERT: Y 75 ASP cc_start: 0.8638 (p0) cc_final: 0.8097 (p0) REVERT: Y 77 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8613 (tp) REVERT: Y 78 GLU cc_start: 0.8666 (tt0) cc_final: 0.8456 (pt0) REVERT: Y 82 LYS cc_start: 0.8560 (ptmt) cc_final: 0.8304 (ptmm) outliers start: 133 outliers final: 74 residues processed: 626 average time/residue: 0.7354 time to fit residues: 511.4038 Evaluate side-chains 619 residues out of total 2544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 525 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 123 LYS Chi-restraints excluded: chain B residue 147 GLU Chi-restraints excluded: chain D residue 46 SER Chi-restraints excluded: chain D residue 52 GLN Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 130 SER Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 78 GLU Chi-restraints excluded: chain E residue 110 LYS Chi-restraints excluded: chain F residue 40 LYS Chi-restraints excluded: chain F residue 46 SER Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain G residue 147 GLU Chi-restraints excluded: chain I residue 40 LYS Chi-restraints excluded: chain I residue 46 SER Chi-restraints excluded: chain I residue 78 GLU Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain I residue 102 GLU Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain I residue 121 SER Chi-restraints excluded: chain I residue 147 GLU Chi-restraints excluded: chain J residue 73 VAL Chi-restraints excluded: chain J residue 93 ARG Chi-restraints excluded: chain J residue 97 SER Chi-restraints excluded: chain J residue 123 LYS Chi-restraints excluded: chain J residue 141 LYS Chi-restraints excluded: chain K residue 37 ILE Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 116 LYS Chi-restraints excluded: chain K residue 133 LEU Chi-restraints excluded: chain L residue 65 LYS Chi-restraints excluded: chain L residue 70 LEU Chi-restraints excluded: chain L residue 73 VAL Chi-restraints excluded: chain L residue 80 ARG Chi-restraints excluded: chain L residue 88 ILE Chi-restraints excluded: chain M residue 78 GLU Chi-restraints excluded: chain M residue 110 LYS Chi-restraints excluded: chain M residue 139 SER Chi-restraints excluded: chain M residue 147 GLU Chi-restraints excluded: chain N residue 77 LEU Chi-restraints excluded: chain N residue 121 SER Chi-restraints excluded: chain N residue 125 GLU Chi-restraints excluded: chain N residue 133 LEU Chi-restraints excluded: chain N residue 145 ASN Chi-restraints excluded: chain O residue 46 SER Chi-restraints excluded: chain O residue 73 VAL Chi-restraints excluded: chain O residue 76 THR Chi-restraints excluded: chain P residue 38 SER Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain P residue 97 SER Chi-restraints excluded: chain P residue 131 VAL Chi-restraints excluded: chain Q residue 46 SER Chi-restraints excluded: chain Q residue 84 SER Chi-restraints excluded: chain Q residue 102 GLU Chi-restraints excluded: chain Q residue 108 THR Chi-restraints excluded: chain Q residue 110 LYS Chi-restraints excluded: chain Q residue 121 SER Chi-restraints excluded: chain R residue 73 VAL Chi-restraints excluded: chain R residue 78 GLU Chi-restraints excluded: chain R residue 145 ASN Chi-restraints excluded: chain S residue 45 ILE Chi-restraints excluded: chain S residue 70 LEU Chi-restraints excluded: chain S residue 116 LYS Chi-restraints excluded: chain S residue 131 VAL Chi-restraints excluded: chain T residue 38 SER Chi-restraints excluded: chain T residue 102 GLU Chi-restraints excluded: chain T residue 147 GLU Chi-restraints excluded: chain V residue 80 ARG Chi-restraints excluded: chain V residue 131 VAL Chi-restraints excluded: chain W residue 60 LEU Chi-restraints excluded: chain W residue 131 VAL Chi-restraints excluded: chain X residue 35 ILE Chi-restraints excluded: chain X residue 45 ILE Chi-restraints excluded: chain X residue 84 SER Chi-restraints excluded: chain X residue 131 VAL Chi-restraints excluded: chain X residue 135 LYS Chi-restraints excluded: chain X residue 138 SER Chi-restraints excluded: chain Y residue 46 SER Chi-restraints excluded: chain Y residue 77 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 184 optimal weight: 3.9990 chunk 263 optimal weight: 6.9990 chunk 266 optimal weight: 7.9990 chunk 257 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 14 optimal weight: 5.9990 chunk 167 optimal weight: 0.9980 chunk 238 optimal weight: 2.9990 chunk 175 optimal weight: 0.8980 chunk 211 optimal weight: 0.0970 chunk 29 optimal weight: 0.6980 overall best weight: 1.1380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN D 145 ASN E 36 GLN F 52 GLN G 52 GLN K 36 GLN K 52 GLN M 52 GLN W 52 GLN Y 36 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.122328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.095446 restraints weight = 33160.057| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 2.70 r_work: 0.3235 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.4917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 22776 Z= 0.127 Angle : 0.577 10.672 30720 Z= 0.293 Chirality : 0.052 0.164 3672 Planarity : 0.003 0.026 3888 Dihedral : 4.221 15.719 3024 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 3.54 % Allowed : 29.99 % Favored : 66.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.87 (0.17), residues: 2856 helix: None (None), residues: 0 sheet: 3.28 (0.15), residues: 1080 loop : -0.13 (0.15), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG T 93 TYR 0.024 0.001 TYR P 106 PHE 0.007 0.001 PHE N 124 TRP 0.003 0.000 TRP Y 59 HIS 0.003 0.001 HIS N 53 Details of bonding type rmsd covalent geometry : bond 0.00303 (22776) covalent geometry : angle 0.57680 (30720) hydrogen bonds : bond 0.03573 ( 962) hydrogen bonds : angle 4.63513 ( 2454) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 642 residues out of total 2544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 552 time to evaluate : 0.967 Fit side-chains REVERT: A 40 LYS cc_start: 0.8572 (ptmt) cc_final: 0.8047 (pttm) REVERT: A 49 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.8037 (tt0) REVERT: A 55 LYS cc_start: 0.8662 (mtpt) cc_final: 0.8448 (mtpp) REVERT: A 78 GLU cc_start: 0.8722 (tt0) cc_final: 0.8297 (tm-30) REVERT: B 52 GLN cc_start: 0.8310 (mt0) cc_final: 0.6997 (tm130) REVERT: B 116 LYS cc_start: 0.7906 (mtmt) cc_final: 0.7655 (mtpp) REVERT: D 28 MET cc_start: 0.4279 (mmt) cc_final: 0.3573 (tpp) REVERT: D 45 ILE cc_start: 0.9163 (OUTLIER) cc_final: 0.8931 (mm) REVERT: D 52 GLN cc_start: 0.8738 (OUTLIER) cc_final: 0.8448 (mp10) REVERT: D 84 SER cc_start: 0.9239 (OUTLIER) cc_final: 0.9014 (p) REVERT: D 110 LYS cc_start: 0.8731 (tttt) cc_final: 0.8319 (ttpp) REVERT: D 142 LYS cc_start: 0.8432 (mmtm) cc_final: 0.8017 (mmtm) REVERT: C 28 MET cc_start: 0.3529 (mmt) cc_final: 0.3081 (mpp) REVERT: C 67 ASP cc_start: 0.8496 (m-30) cc_final: 0.8158 (m-30) REVERT: C 96 TYR cc_start: 0.8939 (t80) cc_final: 0.8594 (t80) REVERT: C 123 LYS cc_start: 0.7747 (mmpt) cc_final: 0.7367 (mppt) REVERT: C 142 LYS cc_start: 0.7639 (mmtm) cc_final: 0.7364 (mmmm) REVERT: E 78 GLU cc_start: 0.8845 (OUTLIER) cc_final: 0.8404 (pp20) REVERT: E 80 ARG cc_start: 0.8583 (mtm-85) cc_final: 0.7844 (mtm-85) REVERT: E 142 LYS cc_start: 0.8517 (mppt) cc_final: 0.8263 (mmtm) REVERT: F 40 LYS cc_start: 0.8178 (ptmt) cc_final: 0.7937 (pttt) REVERT: G 28 MET cc_start: 0.4583 (mmt) cc_final: 0.3940 (tpp) REVERT: G 78 GLU cc_start: 0.8611 (tt0) cc_final: 0.8229 (tm-30) REVERT: G 96 TYR cc_start: 0.9060 (t80) cc_final: 0.8834 (t80) REVERT: G 116 LYS cc_start: 0.8494 (mtmt) cc_final: 0.8275 (mtpt) REVERT: H 28 MET cc_start: 0.4831 (mmt) cc_final: 0.4220 (tpp) REVERT: H 40 LYS cc_start: 0.7655 (ptmm) cc_final: 0.7294 (ptmt) REVERT: H 78 GLU cc_start: 0.8538 (tt0) cc_final: 0.8027 (tm-30) REVERT: I 45 ILE cc_start: 0.8744 (mt) cc_final: 0.8448 (mm) REVERT: I 52 GLN cc_start: 0.7768 (mm-40) cc_final: 0.6992 (tm-30) REVERT: I 78 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7156 (pp20) REVERT: I 80 ARG cc_start: 0.8049 (mtm-85) cc_final: 0.7475 (mtm-85) REVERT: J 28 MET cc_start: 0.3781 (mmt) cc_final: 0.3282 (tpp) REVERT: J 36 GLN cc_start: 0.8468 (mt0) cc_final: 0.7995 (mm-40) REVERT: J 93 ARG cc_start: 0.8446 (OUTLIER) cc_final: 0.7141 (ptp-170) REVERT: J 110 LYS cc_start: 0.9135 (tptt) cc_final: 0.8864 (tptt) REVERT: J 123 LYS cc_start: 0.8903 (OUTLIER) cc_final: 0.8608 (mttm) REVERT: K 40 LYS cc_start: 0.8242 (pttm) cc_final: 0.8005 (pttp) REVERT: K 55 LYS cc_start: 0.8217 (ttpt) cc_final: 0.7912 (tppp) REVERT: K 75 ASP cc_start: 0.8896 (p0) cc_final: 0.8471 (p0) REVERT: K 123 LYS cc_start: 0.8335 (mtmm) cc_final: 0.8131 (mttm) REVERT: L 65 LYS cc_start: 0.8852 (OUTLIER) cc_final: 0.8572 (tttm) REVERT: L 80 ARG cc_start: 0.8742 (OUTLIER) cc_final: 0.8399 (mtm-85) REVERT: L 110 LYS cc_start: 0.8952 (tppt) cc_final: 0.8308 (tptt) REVERT: M 36 GLN cc_start: 0.8081 (mt0) cc_final: 0.7194 (tt0) REVERT: M 40 LYS cc_start: 0.8425 (ptmt) cc_final: 0.7571 (pttm) REVERT: M 43 MET cc_start: 0.9101 (ttm) cc_final: 0.8791 (ttp) REVERT: M 75 ASP cc_start: 0.8785 (p0) cc_final: 0.8426 (p0) REVERT: M 76 THR cc_start: 0.8976 (m) cc_final: 0.8672 (p) REVERT: M 78 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.8244 (tm-30) REVERT: M 96 TYR cc_start: 0.9300 (t80) cc_final: 0.9021 (t80) REVERT: M 110 LYS cc_start: 0.8731 (OUTLIER) cc_final: 0.8184 (ttpp) REVERT: N 28 MET cc_start: 0.5178 (tpp) cc_final: 0.4485 (tpp) REVERT: N 77 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8846 (tp) REVERT: N 145 ASN cc_start: 0.8451 (OUTLIER) cc_final: 0.7933 (t0) REVERT: N 147 GLU cc_start: 0.7279 (OUTLIER) cc_final: 0.7046 (mp0) REVERT: O 52 GLN cc_start: 0.8413 (mm110) cc_final: 0.8129 (mm-40) REVERT: O 105 ILE cc_start: 0.9003 (pt) cc_final: 0.8617 (pp) REVERT: O 106 TYR cc_start: 0.7855 (p90) cc_final: 0.7626 (p90) REVERT: P 67 ASP cc_start: 0.8573 (m-30) cc_final: 0.7701 (t0) REVERT: P 78 GLU cc_start: 0.8304 (tt0) cc_final: 0.8041 (tt0) REVERT: Q 102 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.7968 (pm20) REVERT: R 43 MET cc_start: 0.9072 (ttm) cc_final: 0.8548 (ttm) REVERT: R 80 ARG cc_start: 0.7885 (mtm180) cc_final: 0.7519 (mtm110) REVERT: R 90 GLU cc_start: 0.8253 (mt-10) cc_final: 0.8011 (tp30) REVERT: R 103 GLU cc_start: 0.8231 (tt0) cc_final: 0.7879 (tt0) REVERT: R 123 LYS cc_start: 0.8094 (mtpt) cc_final: 0.7371 (mtpp) REVERT: S 75 ASP cc_start: 0.8692 (p0) cc_final: 0.8279 (p0) REVERT: S 78 GLU cc_start: 0.8302 (tm-30) cc_final: 0.7964 (tm-30) REVERT: S 123 LYS cc_start: 0.8808 (mttt) cc_final: 0.8473 (mttm) REVERT: T 28 MET cc_start: 0.5748 (mmt) cc_final: 0.5113 (mpp) REVERT: T 43 MET cc_start: 0.9096 (ttm) cc_final: 0.8783 (ttm) REVERT: T 75 ASP cc_start: 0.8898 (p0) cc_final: 0.8688 (p0) REVERT: T 101 GLU cc_start: 0.8220 (tp30) cc_final: 0.7766 (tm-30) REVERT: T 142 LYS cc_start: 0.8726 (mptt) cc_final: 0.8408 (mptt) REVERT: V 28 MET cc_start: 0.4768 (mmt) cc_final: 0.3470 (mpp) REVERT: V 75 ASP cc_start: 0.8432 (p0) cc_final: 0.8023 (p0) REVERT: V 80 ARG cc_start: 0.8756 (mtp85) cc_final: 0.8533 (mtm180) REVERT: W 28 MET cc_start: 0.5420 (tpp) cc_final: 0.4456 (tpp) REVERT: W 43 MET cc_start: 0.9287 (ttm) cc_final: 0.8780 (ttm) REVERT: W 75 ASP cc_start: 0.8901 (p0) cc_final: 0.8477 (p0) REVERT: W 80 ARG cc_start: 0.8536 (mtm180) cc_final: 0.8324 (mtp180) REVERT: W 110 LYS cc_start: 0.8974 (OUTLIER) cc_final: 0.8715 (tptp) REVERT: W 123 LYS cc_start: 0.8850 (mppt) cc_final: 0.8137 (mtmm) REVERT: W 142 LYS cc_start: 0.7697 (mmpt) cc_final: 0.7221 (mmmt) REVERT: X 82 LYS cc_start: 0.8101 (ptpp) cc_final: 0.7551 (ptpp) REVERT: X 96 TYR cc_start: 0.9244 (t80) cc_final: 0.8705 (t80) REVERT: X 130 SER cc_start: 0.8770 (m) cc_final: 0.8446 (t) REVERT: X 135 LYS cc_start: 0.8185 (OUTLIER) cc_final: 0.7563 (mttm) REVERT: X 145 ASN cc_start: 0.8235 (p0) cc_final: 0.7787 (p0) REVERT: Y 75 ASP cc_start: 0.8635 (p0) cc_final: 0.8057 (p0) REVERT: Y 77 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8505 (tp) REVERT: Y 82 LYS cc_start: 0.8607 (ptmt) cc_final: 0.8332 (ptmm) REVERT: Y 110 LYS cc_start: 0.8968 (ttmm) cc_final: 0.8762 (ttmm) outliers start: 90 outliers final: 50 residues processed: 609 average time/residue: 0.7342 time to fit residues: 496.2684 Evaluate side-chains 607 residues out of total 2544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 538 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain B residue 123 LYS Chi-restraints excluded: chain B residue 147 GLU Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 46 SER Chi-restraints excluded: chain D residue 52 GLN Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 130 SER Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 78 GLU Chi-restraints excluded: chain E residue 110 LYS Chi-restraints excluded: chain F residue 46 SER Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain I residue 46 SER Chi-restraints excluded: chain I residue 78 GLU Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain I residue 102 GLU Chi-restraints excluded: chain J residue 93 ARG Chi-restraints excluded: chain J residue 123 LYS Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 133 LEU Chi-restraints excluded: chain L residue 65 LYS Chi-restraints excluded: chain L residue 80 ARG Chi-restraints excluded: chain L residue 88 ILE Chi-restraints excluded: chain M residue 78 GLU Chi-restraints excluded: chain M residue 110 LYS Chi-restraints excluded: chain M residue 139 SER Chi-restraints excluded: chain M residue 147 GLU Chi-restraints excluded: chain N residue 77 LEU Chi-restraints excluded: chain N residue 121 SER Chi-restraints excluded: chain N residue 125 GLU Chi-restraints excluded: chain N residue 145 ASN Chi-restraints excluded: chain N residue 147 GLU Chi-restraints excluded: chain O residue 46 SER Chi-restraints excluded: chain O residue 73 VAL Chi-restraints excluded: chain P residue 38 SER Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain P residue 97 SER Chi-restraints excluded: chain P residue 131 VAL Chi-restraints excluded: chain Q residue 46 SER Chi-restraints excluded: chain Q residue 77 LEU Chi-restraints excluded: chain Q residue 102 GLU Chi-restraints excluded: chain Q residue 121 SER Chi-restraints excluded: chain S residue 27 THR Chi-restraints excluded: chain S residue 45 ILE Chi-restraints excluded: chain S residue 131 VAL Chi-restraints excluded: chain T residue 102 GLU Chi-restraints excluded: chain V residue 131 VAL Chi-restraints excluded: chain W residue 60 LEU Chi-restraints excluded: chain W residue 110 LYS Chi-restraints excluded: chain X residue 35 ILE Chi-restraints excluded: chain X residue 45 ILE Chi-restraints excluded: chain X residue 84 SER Chi-restraints excluded: chain X residue 102 GLU Chi-restraints excluded: chain X residue 135 LYS Chi-restraints excluded: chain X residue 138 SER Chi-restraints excluded: chain Y residue 46 SER Chi-restraints excluded: chain Y residue 77 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 37 optimal weight: 9.9990 chunk 57 optimal weight: 7.9990 chunk 45 optimal weight: 6.9990 chunk 213 optimal weight: 4.9990 chunk 212 optimal weight: 5.9990 chunk 100 optimal weight: 7.9990 chunk 195 optimal weight: 4.9990 chunk 16 optimal weight: 5.9990 chunk 259 optimal weight: 0.9980 chunk 216 optimal weight: 10.0000 chunk 4 optimal weight: 4.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN D 36 GLN D 145 ASN E 36 GLN G 52 GLN K 52 GLN L 36 GLN M 52 GLN N 30 GLN P 126 ASN W 52 GLN Y 36 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.118788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.091896 restraints weight = 32970.303| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 2.65 r_work: 0.3173 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.5071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.059 22776 Z= 0.387 Angle : 0.743 11.993 30720 Z= 0.380 Chirality : 0.058 0.195 3672 Planarity : 0.004 0.051 3888 Dihedral : 4.993 17.432 3024 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 5.11 % Allowed : 29.05 % Favored : 65.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.34 (0.16), residues: 2856 helix: None (None), residues: 0 sheet: 2.85 (0.16), residues: 1104 loop : -0.50 (0.15), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG T 93 TYR 0.031 0.002 TYR E 106 PHE 0.015 0.003 PHE T 124 TRP 0.006 0.002 TRP B 59 HIS 0.008 0.001 HIS N 53 Details of bonding type rmsd covalent geometry : bond 0.00954 (22776) covalent geometry : angle 0.74287 (30720) hydrogen bonds : bond 0.04897 ( 962) hydrogen bonds : angle 4.97651 ( 2454) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 648 residues out of total 2544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 518 time to evaluate : 0.734 Fit side-chains REVERT: A 40 LYS cc_start: 0.8657 (ptmt) cc_final: 0.8094 (pttm) REVERT: B 52 GLN cc_start: 0.8159 (mt0) cc_final: 0.6526 (tm130) REVERT: B 116 LYS cc_start: 0.7982 (mtmt) cc_final: 0.7742 (mtpp) REVERT: D 28 MET cc_start: 0.4287 (mmt) cc_final: 0.3648 (tpp) REVERT: D 45 ILE cc_start: 0.9203 (OUTLIER) cc_final: 0.8976 (mm) REVERT: D 52 GLN cc_start: 0.8794 (OUTLIER) cc_final: 0.8371 (mp10) REVERT: D 77 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8793 (tp) REVERT: D 93 ARG cc_start: 0.7930 (OUTLIER) cc_final: 0.6646 (pmt170) REVERT: D 101 GLU cc_start: 0.8174 (tp30) cc_final: 0.7827 (tp30) REVERT: D 110 LYS cc_start: 0.8716 (tttt) cc_final: 0.8322 (ttpp) REVERT: D 137 GLU cc_start: 0.7951 (mm-30) cc_final: 0.7630 (tp30) REVERT: D 142 LYS cc_start: 0.8391 (mmtm) cc_final: 0.7970 (mmtm) REVERT: C 28 MET cc_start: 0.3603 (mmt) cc_final: 0.3191 (mpp) REVERT: C 96 TYR cc_start: 0.9018 (t80) cc_final: 0.8700 (t80) REVERT: C 123 LYS cc_start: 0.7932 (mmpt) cc_final: 0.7448 (mppt) REVERT: C 142 LYS cc_start: 0.7724 (mmtm) cc_final: 0.7455 (mmmm) REVERT: E 78 GLU cc_start: 0.8817 (OUTLIER) cc_final: 0.8328 (pp20) REVERT: G 28 MET cc_start: 0.4889 (mmt) cc_final: 0.4141 (tpp) REVERT: G 78 GLU cc_start: 0.8714 (tt0) cc_final: 0.8208 (tm-30) REVERT: G 96 TYR cc_start: 0.9078 (t80) cc_final: 0.8843 (t80) REVERT: G 116 LYS cc_start: 0.8591 (mtmt) cc_final: 0.8347 (mtpt) REVERT: H 28 MET cc_start: 0.4712 (mmt) cc_final: 0.4499 (tpp) REVERT: H 40 LYS cc_start: 0.7704 (ptmm) cc_final: 0.7326 (ptmt) REVERT: I 51 ASP cc_start: 0.8543 (m-30) cc_final: 0.8180 (m-30) REVERT: I 52 GLN cc_start: 0.7732 (mm-40) cc_final: 0.6858 (tm-30) REVERT: I 78 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.7204 (pp20) REVERT: I 80 ARG cc_start: 0.8083 (mtm-85) cc_final: 0.7520 (mtp180) REVERT: J 28 MET cc_start: 0.3830 (mmt) cc_final: 0.3258 (tpt) REVERT: J 36 GLN cc_start: 0.8544 (mt0) cc_final: 0.8037 (mt0) REVERT: J 93 ARG cc_start: 0.8335 (OUTLIER) cc_final: 0.7072 (ptp-170) REVERT: J 110 LYS cc_start: 0.9107 (tptt) cc_final: 0.8610 (tptt) REVERT: J 123 LYS cc_start: 0.8921 (OUTLIER) cc_final: 0.8607 (mttm) REVERT: K 55 LYS cc_start: 0.8386 (ttpt) cc_final: 0.7945 (tppp) REVERT: K 75 ASP cc_start: 0.8958 (p0) cc_final: 0.8527 (p0) REVERT: L 65 LYS cc_start: 0.8946 (OUTLIER) cc_final: 0.8593 (tttm) REVERT: L 80 ARG cc_start: 0.8788 (OUTLIER) cc_final: 0.8459 (mtm-85) REVERT: M 36 GLN cc_start: 0.8271 (mt0) cc_final: 0.7434 (tt0) REVERT: M 40 LYS cc_start: 0.8523 (ptmt) cc_final: 0.7711 (pttm) REVERT: M 43 MET cc_start: 0.9096 (ttm) cc_final: 0.8815 (ttp) REVERT: M 75 ASP cc_start: 0.8859 (p0) cc_final: 0.8518 (p0) REVERT: M 76 THR cc_start: 0.9097 (m) cc_final: 0.8791 (p) REVERT: M 78 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.7743 (tm-30) REVERT: M 80 ARG cc_start: 0.8563 (mtm180) cc_final: 0.7918 (mtm-85) REVERT: M 110 LYS cc_start: 0.8752 (OUTLIER) cc_final: 0.8538 (tmmt) REVERT: N 28 MET cc_start: 0.5194 (tpp) cc_final: 0.4369 (tpp) REVERT: N 77 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8789 (tp) REVERT: N 145 ASN cc_start: 0.8446 (OUTLIER) cc_final: 0.8023 (t0) REVERT: N 147 GLU cc_start: 0.7354 (OUTLIER) cc_final: 0.7064 (mp0) REVERT: O 52 GLN cc_start: 0.8437 (mm110) cc_final: 0.8173 (mm-40) REVERT: O 106 TYR cc_start: 0.7999 (p90) cc_final: 0.7717 (p90) REVERT: P 78 GLU cc_start: 0.8242 (tt0) cc_final: 0.7323 (tm-30) REVERT: Q 102 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.7976 (pm20) REVERT: R 43 MET cc_start: 0.9057 (ttm) cc_final: 0.8552 (ttm) REVERT: R 80 ARG cc_start: 0.7960 (mtm180) cc_final: 0.7604 (mtm110) REVERT: R 103 GLU cc_start: 0.8310 (tt0) cc_final: 0.8046 (tt0) REVERT: S 78 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7857 (tm-30) REVERT: S 123 LYS cc_start: 0.8865 (mttt) cc_final: 0.8512 (mttm) REVERT: T 28 MET cc_start: 0.5843 (mmt) cc_final: 0.5227 (mpp) REVERT: T 43 MET cc_start: 0.9114 (ttm) cc_final: 0.8798 (ttm) REVERT: T 101 GLU cc_start: 0.8180 (tp30) cc_final: 0.7773 (tm-30) REVERT: V 28 MET cc_start: 0.4704 (mmt) cc_final: 0.3536 (mpm) REVERT: V 75 ASP cc_start: 0.8528 (p0) cc_final: 0.8039 (p0) REVERT: V 80 ARG cc_start: 0.8716 (OUTLIER) cc_final: 0.8485 (mpp80) REVERT: W 28 MET cc_start: 0.5526 (tpp) cc_final: 0.4600 (tpp) REVERT: W 43 MET cc_start: 0.9227 (ttm) cc_final: 0.8670 (ttm) REVERT: W 75 ASP cc_start: 0.8915 (p0) cc_final: 0.8548 (p0) REVERT: W 80 ARG cc_start: 0.8497 (OUTLIER) cc_final: 0.7301 (mtm180) REVERT: W 101 GLU cc_start: 0.8670 (mm-30) cc_final: 0.8113 (tp30) REVERT: X 82 LYS cc_start: 0.8342 (ptpp) cc_final: 0.7886 (pttp) REVERT: X 86 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.8059 (tt) REVERT: X 96 TYR cc_start: 0.9326 (t80) cc_final: 0.8850 (t80) REVERT: X 135 LYS cc_start: 0.8269 (OUTLIER) cc_final: 0.7699 (mttm) REVERT: Y 75 ASP cc_start: 0.8596 (p0) cc_final: 0.8029 (p0) REVERT: Y 77 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8667 (tp) outliers start: 130 outliers final: 77 residues processed: 608 average time/residue: 0.7511 time to fit residues: 506.6969 Evaluate side-chains 606 residues out of total 2544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 507 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 123 LYS Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 46 SER Chi-restraints excluded: chain D residue 52 GLN Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 93 ARG Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 130 SER Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 78 GLU Chi-restraints excluded: chain E residue 93 ARG Chi-restraints excluded: chain F residue 40 LYS Chi-restraints excluded: chain F residue 46 SER Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain G residue 147 GLU Chi-restraints excluded: chain H residue 102 GLU Chi-restraints excluded: chain I residue 38 SER Chi-restraints excluded: chain I residue 40 LYS Chi-restraints excluded: chain I residue 46 SER Chi-restraints excluded: chain I residue 78 GLU Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain I residue 102 GLU Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain I residue 121 SER Chi-restraints excluded: chain J residue 73 VAL Chi-restraints excluded: chain J residue 93 ARG Chi-restraints excluded: chain J residue 123 LYS Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 116 LYS Chi-restraints excluded: chain K residue 133 LEU Chi-restraints excluded: chain L residue 65 LYS Chi-restraints excluded: chain L residue 70 LEU Chi-restraints excluded: chain L residue 80 ARG Chi-restraints excluded: chain L residue 88 ILE Chi-restraints excluded: chain M residue 78 GLU Chi-restraints excluded: chain M residue 110 LYS Chi-restraints excluded: chain M residue 147 GLU Chi-restraints excluded: chain N residue 77 LEU Chi-restraints excluded: chain N residue 104 GLU Chi-restraints excluded: chain N residue 121 SER Chi-restraints excluded: chain N residue 125 GLU Chi-restraints excluded: chain N residue 133 LEU Chi-restraints excluded: chain N residue 145 ASN Chi-restraints excluded: chain N residue 147 GLU Chi-restraints excluded: chain O residue 46 SER Chi-restraints excluded: chain O residue 73 VAL Chi-restraints excluded: chain O residue 76 THR Chi-restraints excluded: chain P residue 38 SER Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain P residue 97 SER Chi-restraints excluded: chain P residue 131 VAL Chi-restraints excluded: chain Q residue 46 SER Chi-restraints excluded: chain Q residue 77 LEU Chi-restraints excluded: chain Q residue 102 GLU Chi-restraints excluded: chain Q residue 108 THR Chi-restraints excluded: chain Q residue 110 LYS Chi-restraints excluded: chain Q residue 121 SER Chi-restraints excluded: chain R residue 73 VAL Chi-restraints excluded: chain S residue 27 THR Chi-restraints excluded: chain S residue 45 ILE Chi-restraints excluded: chain S residue 70 LEU Chi-restraints excluded: chain S residue 78 GLU Chi-restraints excluded: chain S residue 116 LYS Chi-restraints excluded: chain S residue 131 VAL Chi-restraints excluded: chain T residue 38 SER Chi-restraints excluded: chain T residue 102 GLU Chi-restraints excluded: chain V residue 80 ARG Chi-restraints excluded: chain V residue 131 VAL Chi-restraints excluded: chain V residue 147 GLU Chi-restraints excluded: chain W residue 60 LEU Chi-restraints excluded: chain W residue 80 ARG Chi-restraints excluded: chain W residue 131 VAL Chi-restraints excluded: chain X residue 35 ILE Chi-restraints excluded: chain X residue 45 ILE Chi-restraints excluded: chain X residue 84 SER Chi-restraints excluded: chain X residue 86 LEU Chi-restraints excluded: chain X residue 135 LYS Chi-restraints excluded: chain X residue 138 SER Chi-restraints excluded: chain Y residue 46 SER Chi-restraints excluded: chain Y residue 77 LEU Chi-restraints excluded: chain Y residue 138 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 259 optimal weight: 0.9980 chunk 128 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 199 optimal weight: 2.9990 chunk 117 optimal weight: 0.7980 chunk 55 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 165 optimal weight: 3.9990 chunk 258 optimal weight: 0.7980 chunk 220 optimal weight: 0.8980 chunk 149 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN D 145 ASN E 36 GLN G 52 GLN K 36 GLN L 36 GLN M 52 GLN W 52 GLN Y 36 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.121836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.095083 restraints weight = 33214.884| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 2.69 r_work: 0.3228 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.5063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22776 Z= 0.119 Angle : 0.606 12.210 30720 Z= 0.306 Chirality : 0.053 0.174 3672 Planarity : 0.003 0.029 3888 Dihedral : 4.292 16.063 3024 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 3.30 % Allowed : 31.17 % Favored : 65.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.60 (0.17), residues: 2856 helix: None (None), residues: 0 sheet: 2.40 (0.14), residues: 1368 loop : -0.30 (0.17), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG T 93 TYR 0.029 0.001 TYR P 106 PHE 0.006 0.001 PHE N 124 TRP 0.002 0.000 TRP X 59 HIS 0.003 0.001 HIS N 53 Details of bonding type rmsd covalent geometry : bond 0.00280 (22776) covalent geometry : angle 0.60629 (30720) hydrogen bonds : bond 0.03616 ( 962) hydrogen bonds : angle 4.65139 ( 2454) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 624 residues out of total 2544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 540 time to evaluate : 0.902 Fit side-chains REVERT: A 40 LYS cc_start: 0.8578 (ptmt) cc_final: 0.8039 (pttm) REVERT: A 78 GLU cc_start: 0.8721 (tt0) cc_final: 0.8283 (tm-30) REVERT: B 52 GLN cc_start: 0.8309 (mt0) cc_final: 0.6953 (tm130) REVERT: B 116 LYS cc_start: 0.7902 (mtmt) cc_final: 0.7643 (mtpp) REVERT: D 28 MET cc_start: 0.4114 (mmt) cc_final: 0.3515 (tpp) REVERT: D 45 ILE cc_start: 0.9167 (mt) cc_final: 0.8898 (mm) REVERT: D 52 GLN cc_start: 0.8793 (OUTLIER) cc_final: 0.8501 (mp10) REVERT: D 84 SER cc_start: 0.9255 (OUTLIER) cc_final: 0.9032 (p) REVERT: D 93 ARG cc_start: 0.7835 (OUTLIER) cc_final: 0.6549 (pmt170) REVERT: D 101 GLU cc_start: 0.8037 (tp30) cc_final: 0.7759 (tp30) REVERT: D 110 LYS cc_start: 0.8714 (tttt) cc_final: 0.8304 (ttpp) REVERT: D 142 LYS cc_start: 0.8438 (mmtm) cc_final: 0.8022 (mmtm) REVERT: C 28 MET cc_start: 0.3881 (mmt) cc_final: 0.3305 (mpp) REVERT: C 96 TYR cc_start: 0.8939 (t80) cc_final: 0.8616 (t80) REVERT: C 123 LYS cc_start: 0.7742 (mmpt) cc_final: 0.7355 (mppt) REVERT: C 142 LYS cc_start: 0.7713 (mmtm) cc_final: 0.7432 (mmmm) REVERT: E 78 GLU cc_start: 0.8812 (OUTLIER) cc_final: 0.8407 (pp20) REVERT: E 80 ARG cc_start: 0.8565 (mtm-85) cc_final: 0.7865 (mtm-85) REVERT: E 142 LYS cc_start: 0.8518 (mppt) cc_final: 0.8258 (mmtm) REVERT: G 28 MET cc_start: 0.4995 (mmt) cc_final: 0.4248 (tpp) REVERT: G 78 GLU cc_start: 0.8592 (tt0) cc_final: 0.8204 (tm-30) REVERT: G 116 LYS cc_start: 0.8522 (mtmt) cc_final: 0.8310 (mtpt) REVERT: H 28 MET cc_start: 0.4639 (mmt) cc_final: 0.4364 (tpp) REVERT: H 40 LYS cc_start: 0.7678 (ptmm) cc_final: 0.7236 (ptmt) REVERT: H 78 GLU cc_start: 0.8616 (tt0) cc_final: 0.8176 (tt0) REVERT: I 45 ILE cc_start: 0.8740 (mt) cc_final: 0.8458 (mm) REVERT: I 52 GLN cc_start: 0.7749 (mm-40) cc_final: 0.6926 (tm-30) REVERT: I 78 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7336 (pp20) REVERT: J 28 MET cc_start: 0.3645 (mmt) cc_final: 0.3216 (tpt) REVERT: J 36 GLN cc_start: 0.8403 (mt0) cc_final: 0.7905 (mm-40) REVERT: J 93 ARG cc_start: 0.8396 (OUTLIER) cc_final: 0.7109 (ptp-170) REVERT: J 123 LYS cc_start: 0.8894 (OUTLIER) cc_final: 0.8590 (mttm) REVERT: K 36 GLN cc_start: 0.8419 (mt0) cc_final: 0.8141 (mt0) REVERT: K 55 LYS cc_start: 0.8227 (ttpt) cc_final: 0.7917 (tppp) REVERT: K 75 ASP cc_start: 0.8898 (p0) cc_final: 0.8462 (p0) REVERT: L 65 LYS cc_start: 0.8891 (OUTLIER) cc_final: 0.8572 (tttm) REVERT: L 80 ARG cc_start: 0.8751 (OUTLIER) cc_final: 0.8196 (mtt90) REVERT: L 110 LYS cc_start: 0.8895 (tppt) cc_final: 0.8319 (tptt) REVERT: M 36 GLN cc_start: 0.8141 (mt0) cc_final: 0.7177 (tt0) REVERT: M 40 LYS cc_start: 0.8451 (ptmt) cc_final: 0.7599 (pttm) REVERT: M 43 MET cc_start: 0.9126 (ttm) cc_final: 0.8890 (ttp) REVERT: M 75 ASP cc_start: 0.8879 (p0) cc_final: 0.8487 (p0) REVERT: M 76 THR cc_start: 0.8964 (m) cc_final: 0.8672 (p) REVERT: M 78 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.8231 (tm-30) REVERT: M 96 TYR cc_start: 0.9250 (t80) cc_final: 0.8788 (t80) REVERT: M 110 LYS cc_start: 0.8706 (OUTLIER) cc_final: 0.8227 (ttpp) REVERT: N 28 MET cc_start: 0.5096 (OUTLIER) cc_final: 0.4432 (tpp) REVERT: N 77 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8853 (tp) REVERT: N 145 ASN cc_start: 0.8422 (OUTLIER) cc_final: 0.7909 (t0) REVERT: N 147 GLU cc_start: 0.7267 (OUTLIER) cc_final: 0.7039 (mp0) REVERT: O 52 GLN cc_start: 0.8441 (mm110) cc_final: 0.8173 (mm-40) REVERT: O 105 ILE cc_start: 0.9010 (pt) cc_final: 0.8623 (pp) REVERT: P 78 GLU cc_start: 0.8307 (tt0) cc_final: 0.8051 (tt0) REVERT: P 82 LYS cc_start: 0.8015 (ptpt) cc_final: 0.7713 (ptmm) REVERT: Q 28 MET cc_start: 0.3711 (mpm) cc_final: 0.3067 (mpp) REVERT: Q 102 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.7902 (pm20) REVERT: R 28 MET cc_start: 0.4941 (mmp) cc_final: 0.4266 (mpp) REVERT: R 43 MET cc_start: 0.9058 (ttm) cc_final: 0.8510 (ttm) REVERT: R 80 ARG cc_start: 0.7903 (mtm180) cc_final: 0.7525 (mtm110) REVERT: R 103 GLU cc_start: 0.8188 (tt0) cc_final: 0.7941 (tt0) REVERT: R 123 LYS cc_start: 0.8089 (mtpt) cc_final: 0.7350 (mtpp) REVERT: S 78 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.8066 (tm-30) REVERT: S 123 LYS cc_start: 0.8825 (mttt) cc_final: 0.8472 (mttm) REVERT: T 28 MET cc_start: 0.5838 (mmt) cc_final: 0.5198 (mpp) REVERT: T 43 MET cc_start: 0.9157 (ttm) cc_final: 0.8799 (ttm) REVERT: T 101 GLU cc_start: 0.8241 (tp30) cc_final: 0.7778 (tm-30) REVERT: V 28 MET cc_start: 0.4654 (mmt) cc_final: 0.3423 (mpp) REVERT: V 75 ASP cc_start: 0.8444 (p0) cc_final: 0.7950 (p0) REVERT: W 28 MET cc_start: 0.5493 (tpp) cc_final: 0.4458 (tpp) REVERT: W 75 ASP cc_start: 0.8861 (p0) cc_final: 0.8476 (p0) REVERT: W 142 LYS cc_start: 0.7731 (mmpt) cc_final: 0.7282 (mmmt) REVERT: X 82 LYS cc_start: 0.8157 (ptpp) cc_final: 0.7590 (ptpp) REVERT: X 86 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.7830 (tt) REVERT: X 96 TYR cc_start: 0.9246 (t80) cc_final: 0.8712 (t80) REVERT: X 130 SER cc_start: 0.8756 (m) cc_final: 0.8449 (t) REVERT: X 135 LYS cc_start: 0.8193 (OUTLIER) cc_final: 0.7569 (mttm) REVERT: X 145 ASN cc_start: 0.8290 (p0) cc_final: 0.7891 (p0) REVERT: Y 75 ASP cc_start: 0.8629 (p0) cc_final: 0.8041 (p0) REVERT: Y 82 LYS cc_start: 0.8600 (ptmt) cc_final: 0.8304 (ptmm) outliers start: 84 outliers final: 46 residues processed: 591 average time/residue: 0.7731 time to fit residues: 506.3810 Evaluate side-chains 593 residues out of total 2544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 528 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 123 LYS Chi-restraints excluded: chain D residue 52 GLN Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 93 ARG Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 130 SER Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain E residue 78 GLU Chi-restraints excluded: chain E residue 110 LYS Chi-restraints excluded: chain F residue 46 SER Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain I residue 46 SER Chi-restraints excluded: chain I residue 78 GLU Chi-restraints excluded: chain I residue 102 GLU Chi-restraints excluded: chain J residue 93 ARG Chi-restraints excluded: chain J residue 123 LYS Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 133 LEU Chi-restraints excluded: chain L residue 65 LYS Chi-restraints excluded: chain L residue 80 ARG Chi-restraints excluded: chain M residue 78 GLU Chi-restraints excluded: chain M residue 110 LYS Chi-restraints excluded: chain M residue 147 GLU Chi-restraints excluded: chain N residue 28 MET Chi-restraints excluded: chain N residue 77 LEU Chi-restraints excluded: chain N residue 121 SER Chi-restraints excluded: chain N residue 145 ASN Chi-restraints excluded: chain N residue 147 GLU Chi-restraints excluded: chain O residue 46 SER Chi-restraints excluded: chain O residue 73 VAL Chi-restraints excluded: chain O residue 76 THR Chi-restraints excluded: chain P residue 38 SER Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain Q residue 46 SER Chi-restraints excluded: chain Q residue 77 LEU Chi-restraints excluded: chain Q residue 102 GLU Chi-restraints excluded: chain Q residue 121 SER Chi-restraints excluded: chain S residue 27 THR Chi-restraints excluded: chain S residue 45 ILE Chi-restraints excluded: chain S residue 78 GLU Chi-restraints excluded: chain S residue 110 LYS Chi-restraints excluded: chain S residue 131 VAL Chi-restraints excluded: chain T residue 102 GLU Chi-restraints excluded: chain V residue 131 VAL Chi-restraints excluded: chain V residue 147 GLU Chi-restraints excluded: chain W residue 60 LEU Chi-restraints excluded: chain W residue 131 VAL Chi-restraints excluded: chain X residue 35 ILE Chi-restraints excluded: chain X residue 45 ILE Chi-restraints excluded: chain X residue 84 SER Chi-restraints excluded: chain X residue 86 LEU Chi-restraints excluded: chain X residue 135 LYS Chi-restraints excluded: chain Y residue 46 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 241 optimal weight: 0.7980 chunk 90 optimal weight: 0.3980 chunk 105 optimal weight: 6.9990 chunk 141 optimal weight: 7.9990 chunk 125 optimal weight: 0.4980 chunk 69 optimal weight: 3.9990 chunk 205 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 chunk 253 optimal weight: 0.6980 chunk 80 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN D 145 ASN E 30 GLN G 52 GLN H 30 GLN M 52 GLN N 52 GLN O 119 ASN T 126 ASN Y 36 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.121788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.095110 restraints weight = 33347.303| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 2.70 r_work: 0.3232 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.5089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 22776 Z= 0.129 Angle : 0.613 12.987 30720 Z= 0.307 Chirality : 0.053 0.171 3672 Planarity : 0.003 0.029 3888 Dihedral : 4.173 15.407 3024 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.71 % Allowed : 31.41 % Favored : 65.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.77 (0.17), residues: 2856 helix: None (None), residues: 0 sheet: 2.60 (0.14), residues: 1344 loop : -0.22 (0.17), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG T 93 TYR 0.030 0.002 TYR Q 106 PHE 0.006 0.001 PHE N 124 TRP 0.003 0.000 TRP P 59 HIS 0.003 0.001 HIS N 53 Details of bonding type rmsd covalent geometry : bond 0.00308 (22776) covalent geometry : angle 0.61297 (30720) hydrogen bonds : bond 0.03574 ( 962) hydrogen bonds : angle 4.57255 ( 2454) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 611 residues out of total 2544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 542 time to evaluate : 0.766 Fit side-chains REVERT: A 40 LYS cc_start: 0.8561 (ptmt) cc_final: 0.8029 (pttm) REVERT: A 78 GLU cc_start: 0.8728 (tt0) cc_final: 0.8308 (tm-30) REVERT: B 52 GLN cc_start: 0.8311 (mt0) cc_final: 0.6964 (tm130) REVERT: B 116 LYS cc_start: 0.7951 (mtmt) cc_final: 0.7693 (mtpp) REVERT: D 28 MET cc_start: 0.4390 (mmt) cc_final: 0.3725 (tpp) REVERT: D 45 ILE cc_start: 0.9137 (mt) cc_final: 0.8892 (mm) REVERT: D 52 GLN cc_start: 0.8791 (OUTLIER) cc_final: 0.8505 (mp10) REVERT: D 93 ARG cc_start: 0.7865 (OUTLIER) cc_final: 0.6629 (pmt170) REVERT: D 101 GLU cc_start: 0.7953 (tp30) cc_final: 0.7708 (tp30) REVERT: D 110 LYS cc_start: 0.8731 (tttt) cc_final: 0.8311 (ttpp) REVERT: D 142 LYS cc_start: 0.8436 (mmtm) cc_final: 0.8018 (mmtm) REVERT: C 28 MET cc_start: 0.3878 (mmt) cc_final: 0.3383 (mpp) REVERT: C 75 ASP cc_start: 0.8073 (p0) cc_final: 0.7716 (p0) REVERT: C 96 TYR cc_start: 0.8925 (t80) cc_final: 0.8582 (t80) REVERT: C 123 LYS cc_start: 0.7744 (mmpt) cc_final: 0.7397 (mppt) REVERT: C 142 LYS cc_start: 0.7622 (mmtm) cc_final: 0.7340 (mmmm) REVERT: E 78 GLU cc_start: 0.8816 (OUTLIER) cc_final: 0.8397 (pp20) REVERT: E 80 ARG cc_start: 0.8572 (mtm-85) cc_final: 0.8116 (mtm-85) REVERT: E 142 LYS cc_start: 0.8524 (mppt) cc_final: 0.8269 (mmtm) REVERT: F 40 LYS cc_start: 0.8195 (ptmt) cc_final: 0.7956 (pttt) REVERT: G 28 MET cc_start: 0.5062 (mmt) cc_final: 0.4292 (tpp) REVERT: G 78 GLU cc_start: 0.8574 (tt0) cc_final: 0.8177 (tm-30) REVERT: G 116 LYS cc_start: 0.8505 (mtmt) cc_final: 0.8292 (mtpt) REVERT: H 40 LYS cc_start: 0.7711 (ptmm) cc_final: 0.7315 (ptmt) REVERT: H 78 GLU cc_start: 0.8537 (tt0) cc_final: 0.8052 (tm-30) REVERT: I 45 ILE cc_start: 0.8753 (mt) cc_final: 0.8451 (mm) REVERT: I 52 GLN cc_start: 0.7743 (mm-40) cc_final: 0.6917 (tm-30) REVERT: I 78 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7470 (pp20) REVERT: J 28 MET cc_start: 0.3773 (mmt) cc_final: 0.3191 (tpt) REVERT: J 36 GLN cc_start: 0.8443 (mt0) cc_final: 0.7925 (mm-40) REVERT: J 93 ARG cc_start: 0.8400 (OUTLIER) cc_final: 0.7223 (ptp-170) REVERT: J 110 LYS cc_start: 0.9255 (tptt) cc_final: 0.9021 (tptt) REVERT: J 123 LYS cc_start: 0.8922 (OUTLIER) cc_final: 0.8623 (mttm) REVERT: K 36 GLN cc_start: 0.8405 (mt0) cc_final: 0.8183 (mt0) REVERT: K 55 LYS cc_start: 0.8213 (ttpt) cc_final: 0.7913 (tppp) REVERT: K 75 ASP cc_start: 0.8889 (p0) cc_final: 0.8469 (p0) REVERT: L 65 LYS cc_start: 0.8901 (OUTLIER) cc_final: 0.8581 (tttm) REVERT: L 80 ARG cc_start: 0.8751 (OUTLIER) cc_final: 0.8387 (mtm-85) REVERT: L 110 LYS cc_start: 0.8900 (tppt) cc_final: 0.8356 (tptt) REVERT: M 36 GLN cc_start: 0.8110 (mt0) cc_final: 0.7196 (tt0) REVERT: M 40 LYS cc_start: 0.8408 (ptmt) cc_final: 0.7542 (pttm) REVERT: M 43 MET cc_start: 0.9128 (ttm) cc_final: 0.8864 (ttp) REVERT: M 75 ASP cc_start: 0.8874 (p0) cc_final: 0.8535 (p0) REVERT: M 76 THR cc_start: 0.8950 (m) cc_final: 0.8657 (p) REVERT: M 96 TYR cc_start: 0.9227 (t80) cc_final: 0.8735 (t80) REVERT: M 123 LYS cc_start: 0.8703 (mtmt) cc_final: 0.8354 (mtmp) REVERT: N 77 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8859 (tp) REVERT: N 145 ASN cc_start: 0.8470 (OUTLIER) cc_final: 0.7960 (t0) REVERT: N 147 GLU cc_start: 0.7260 (OUTLIER) cc_final: 0.7036 (mp0) REVERT: O 52 GLN cc_start: 0.8453 (mm110) cc_final: 0.8228 (mm-40) REVERT: O 105 ILE cc_start: 0.8985 (pt) cc_final: 0.8616 (pp) REVERT: O 123 LYS cc_start: 0.8597 (mtpp) cc_final: 0.8026 (mmtm) REVERT: P 78 GLU cc_start: 0.8358 (tt0) cc_final: 0.7316 (tm-30) REVERT: Q 28 MET cc_start: 0.3830 (mpm) cc_final: 0.3177 (mpp) REVERT: Q 102 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.7880 (pm20) REVERT: R 43 MET cc_start: 0.9051 (ttm) cc_final: 0.8503 (ttm) REVERT: R 80 ARG cc_start: 0.7874 (mtm180) cc_final: 0.7496 (mtm110) REVERT: R 103 GLU cc_start: 0.8231 (tt0) cc_final: 0.7887 (tt0) REVERT: S 52 GLN cc_start: 0.8273 (mm-40) cc_final: 0.8071 (mm-40) REVERT: S 78 GLU cc_start: 0.8365 (tm-30) cc_final: 0.8013 (tm-30) REVERT: S 123 LYS cc_start: 0.8816 (mttt) cc_final: 0.8484 (mttm) REVERT: T 28 MET cc_start: 0.6074 (mmt) cc_final: 0.5355 (mpp) REVERT: T 43 MET cc_start: 0.9180 (ttm) cc_final: 0.8817 (ttm) REVERT: T 101 GLU cc_start: 0.8261 (tp30) cc_final: 0.7792 (tm-30) REVERT: T 110 LYS cc_start: 0.8812 (tptp) cc_final: 0.8466 (tptp) REVERT: V 28 MET cc_start: 0.4633 (mmt) cc_final: 0.3419 (mpp) REVERT: V 40 LYS cc_start: 0.8643 (ptmm) cc_final: 0.8302 (pttp) REVERT: V 75 ASP cc_start: 0.8530 (p0) cc_final: 0.8061 (p0) REVERT: V 123 LYS cc_start: 0.8489 (mtpp) cc_final: 0.7898 (mtmm) REVERT: W 28 MET cc_start: 0.5358 (tpp) cc_final: 0.4361 (tpp) REVERT: W 43 MET cc_start: 0.9095 (ttp) cc_final: 0.8597 (ttm) REVERT: W 75 ASP cc_start: 0.8855 (p0) cc_final: 0.8471 (p0) REVERT: W 142 LYS cc_start: 0.7732 (mmpt) cc_final: 0.6982 (mmmt) REVERT: X 82 LYS cc_start: 0.8125 (ptpp) cc_final: 0.7539 (ptpp) REVERT: X 86 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7810 (tt) REVERT: X 96 TYR cc_start: 0.9240 (t80) cc_final: 0.8694 (t80) REVERT: X 130 SER cc_start: 0.8739 (m) cc_final: 0.8434 (t) REVERT: X 135 LYS cc_start: 0.8214 (OUTLIER) cc_final: 0.7560 (mttm) REVERT: X 145 ASN cc_start: 0.8434 (p0) cc_final: 0.8021 (p0) REVERT: Y 75 ASP cc_start: 0.8598 (p0) cc_final: 0.8125 (p0) REVERT: Y 82 LYS cc_start: 0.8603 (ptmt) cc_final: 0.8305 (ptmm) REVERT: Y 110 LYS cc_start: 0.8944 (ttmm) cc_final: 0.8505 (tmmt) outliers start: 69 outliers final: 46 residues processed: 584 average time/residue: 0.7674 time to fit residues: 497.4748 Evaluate side-chains 595 residues out of total 2544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 535 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 123 LYS Chi-restraints excluded: chain D residue 52 GLN Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 93 ARG Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 130 SER Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain E residue 78 GLU Chi-restraints excluded: chain E residue 110 LYS Chi-restraints excluded: chain F residue 46 SER Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain H residue 52 GLN Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain I residue 40 LYS Chi-restraints excluded: chain I residue 46 SER Chi-restraints excluded: chain I residue 78 GLU Chi-restraints excluded: chain I residue 102 GLU Chi-restraints excluded: chain J residue 93 ARG Chi-restraints excluded: chain J residue 123 LYS Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 133 LEU Chi-restraints excluded: chain L residue 65 LYS Chi-restraints excluded: chain L residue 73 VAL Chi-restraints excluded: chain L residue 80 ARG Chi-restraints excluded: chain L residue 88 ILE Chi-restraints excluded: chain M residue 139 SER Chi-restraints excluded: chain M residue 147 GLU Chi-restraints excluded: chain N residue 77 LEU Chi-restraints excluded: chain N residue 121 SER Chi-restraints excluded: chain N residue 145 ASN Chi-restraints excluded: chain N residue 147 GLU Chi-restraints excluded: chain O residue 46 SER Chi-restraints excluded: chain O residue 73 VAL Chi-restraints excluded: chain O residue 76 THR Chi-restraints excluded: chain P residue 38 SER Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain Q residue 46 SER Chi-restraints excluded: chain Q residue 77 LEU Chi-restraints excluded: chain Q residue 102 GLU Chi-restraints excluded: chain Q residue 121 SER Chi-restraints excluded: chain S residue 27 THR Chi-restraints excluded: chain S residue 110 LYS Chi-restraints excluded: chain S residue 131 VAL Chi-restraints excluded: chain T residue 102 GLU Chi-restraints excluded: chain V residue 131 VAL Chi-restraints excluded: chain V residue 147 GLU Chi-restraints excluded: chain X residue 35 ILE Chi-restraints excluded: chain X residue 45 ILE Chi-restraints excluded: chain X residue 84 SER Chi-restraints excluded: chain X residue 86 LEU Chi-restraints excluded: chain X residue 135 LYS Chi-restraints excluded: chain Y residue 46 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 65 optimal weight: 0.9980 chunk 90 optimal weight: 0.9990 chunk 268 optimal weight: 0.7980 chunk 37 optimal weight: 9.9990 chunk 143 optimal weight: 7.9990 chunk 42 optimal weight: 4.9990 chunk 9 optimal weight: 8.9990 chunk 193 optimal weight: 2.9990 chunk 263 optimal weight: 6.9990 chunk 21 optimal weight: 10.0000 chunk 6 optimal weight: 0.0470 overall best weight: 1.1682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN D 36 GLN D 145 ASN G 52 GLN M 52 GLN O 119 ASN Y 36 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.122037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.095333 restraints weight = 33149.853| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 2.68 r_work: 0.3234 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.5139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22776 Z= 0.134 Angle : 0.621 11.337 30720 Z= 0.310 Chirality : 0.053 0.170 3672 Planarity : 0.003 0.031 3888 Dihedral : 4.154 15.468 3024 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.99 % Allowed : 31.68 % Favored : 65.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.79 (0.17), residues: 2856 helix: None (None), residues: 0 sheet: 2.61 (0.14), residues: 1344 loop : -0.21 (0.17), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG T 93 TYR 0.031 0.002 TYR P 106 PHE 0.007 0.001 PHE N 124 TRP 0.003 0.001 TRP Y 59 HIS 0.003 0.001 HIS N 53 Details of bonding type rmsd covalent geometry : bond 0.00323 (22776) covalent geometry : angle 0.62064 (30720) hydrogen bonds : bond 0.03589 ( 962) hydrogen bonds : angle 4.55990 ( 2454) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9289.99 seconds wall clock time: 158 minutes 12.41 seconds (9492.41 seconds total)