Starting phenix.real_space_refine on Thu Jun 19 07:31:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nvc_49832/06_2025/9nvc_49832.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nvc_49832/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9nvc_49832/06_2025/9nvc_49832.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nvc_49832/06_2025/9nvc_49832.map" model { file = "/net/cci-nas-00/data/ceres_data/9nvc_49832/06_2025/9nvc_49832.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nvc_49832/06_2025/9nvc_49832.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 12.73, per 1000 atoms: 0.57 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: 4.88 Conformation dependent library (CDL) restraints added in 2.8 seconds 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: 4.06 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: 7.93 Time building geometry restraints manager: 5.63 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: 0.01 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: 0.930 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: 0.020 Extract box with map and model: 0.730 Check model and map are aligned: 0.150 Set scattering table: 0.190 Process input model: 49.290 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.140 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:13.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.020 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.012 0.001 TRP L 59 HIS 0.005 0.001 HIS N 53 PHE 0.016 0.001 PHE L 124 TYR 0.017 0.002 TYR E 106 ARG 0.004 0.001 ARG Q 80 Details of bonding type rmsd hydrogen bonds : bond 0.22427 ( 962) hydrogen bonds : angle 5.80643 ( 2454) covalent geometry : bond 0.00418 (22776) covalent geometry : angle 0.63779 (30720) *********************** 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 : 2.774 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: 1.5999 time to fit residues: 1478.3989 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 : 2.574 ------------------------------------------------------------------------------- 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 243 optimal weight: 2.9990 chunk 218 optimal weight: 3.9990 chunk 121 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 147 optimal weight: 3.9990 chunk 116 optimal weight: 0.6980 chunk 225 optimal weight: 6.9990 chunk 87 optimal weight: 5.9990 chunk 137 optimal weight: 5.9990 chunk 168 optimal weight: 0.0370 chunk 261 optimal weight: 4.9990 overall best weight: 2.3464 ------------------------------------------------------------------------------- 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 30 GLN L 52 GLN N 30 GLN N 119 ASN O 71 ASN O 119 ASN P 30 GLN Q 36 GLN R 119 ASN 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 = 0.3727 r_free = 0.3727 target = 0.122656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.095596 restraints weight = 32964.784| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 2.70 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: 0.8025 moved from start: 0.3736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 22776 Z= 0.223 Angle : 0.653 8.305 30720 Z= 0.342 Chirality : 0.055 0.185 3672 Planarity : 0.004 0.033 3888 Dihedral : 4.923 24.760 3026 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 4.76 % Allowed : 23.55 % Favored : 71.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.16), residues: 2856 helix: None (None), residues: 0 sheet: 2.90 (0.15), residues: 1104 loop : -0.12 (0.15), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 59 HIS 0.006 0.001 HIS N 53 PHE 0.013 0.002 PHE N 124 TYR 0.014 0.002 TYR P 106 ARG 0.005 0.001 ARG B 107 Details of bonding type rmsd hydrogen bonds : bond 0.04647 ( 962) hydrogen bonds : angle 4.92020 ( 2454) covalent geometry : bond 0.00547 (22776) covalent geometry : angle 0.65330 (30720) *********************** 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 739 residues out of total 2544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 618 time to evaluate : 2.486 Fit side-chains revert: symmetry clash REVERT: A 40 LYS cc_start: 0.8473 (ptmm) cc_final: 0.7987 (pttm) REVERT: A 102 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7476 (pm20) REVERT: D 52 GLN cc_start: 0.8669 (OUTLIER) cc_final: 0.8230 (mp10) REVERT: D 84 SER cc_start: 0.9081 (m) cc_final: 0.8567 (t) REVERT: D 93 ARG cc_start: 0.7686 (ptp90) cc_final: 0.6852 (pmt170) REVERT: C 28 MET cc_start: 0.3133 (mmt) cc_final: 0.2707 (mpp) REVERT: C 42 PHE cc_start: 0.8631 (t80) cc_final: 0.8380 (t80) REVERT: C 67 ASP cc_start: 0.8493 (m-30) cc_final: 0.8130 (m-30) REVERT: C 96 TYR cc_start: 0.8877 (t80) cc_final: 0.8571 (t80) REVERT: C 123 LYS cc_start: 0.7563 (mmpt) cc_final: 0.7233 (mppt) REVERT: C 142 LYS cc_start: 0.7746 (mmtm) cc_final: 0.7494 (mmmm) REVERT: E 28 MET cc_start: 0.4497 (mmp) cc_final: 0.3507 (mmt) REVERT: E 36 GLN cc_start: 0.8446 (mt0) cc_final: 0.8182 (mt0) REVERT: E 43 MET cc_start: 0.8857 (ttm) cc_final: 0.8545 (ttm) REVERT: E 87 MET cc_start: 0.7572 (OUTLIER) cc_final: 0.7318 (pmm) REVERT: E 101 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.7524 (mp0) REVERT: F 116 LYS cc_start: 0.8289 (mtmt) cc_final: 0.7848 (mtmt) REVERT: G 28 MET cc_start: 0.3878 (mmt) cc_final: 0.3425 (tpp) REVERT: G 43 MET cc_start: 0.9097 (ttm) cc_final: 0.8734 (ttm) REVERT: G 51 ASP cc_start: 0.8881 (OUTLIER) cc_final: 0.8648 (t0) REVERT: G 55 LYS cc_start: 0.8782 (tttt) cc_final: 0.8420 (tttp) REVERT: G 67 ASP cc_start: 0.9013 (m-30) cc_final: 0.8786 (m-30) REVERT: G 78 GLU cc_start: 0.8790 (tt0) cc_final: 0.8346 (tm-30) REVERT: G 96 TYR cc_start: 0.9102 (t80) cc_final: 0.8875 (t80) REVERT: G 104 GLU cc_start: 0.7461 (tp30) cc_final: 0.7235 (tp30) REVERT: H 28 MET cc_start: 0.4435 (mmt) cc_final: 0.3701 (tpp) REVERT: H 104 GLU cc_start: 0.8847 (OUTLIER) cc_final: 0.8214 (mt-10) REVERT: H 141 LYS cc_start: 0.8698 (mttt) cc_final: 0.8444 (mttp) REVERT: H 145 ASN cc_start: 0.8698 (OUTLIER) cc_final: 0.8407 (m110) REVERT: I 45 ILE cc_start: 0.8702 (mt) cc_final: 0.8439 (mm) REVERT: I 51 ASP cc_start: 0.8344 (m-30) cc_final: 0.7763 (m-30) REVERT: I 52 GLN cc_start: 0.8043 (mm-40) cc_final: 0.7072 (tm130) REVERT: J 28 MET cc_start: 0.3734 (mmt) cc_final: 0.2880 (tpp) REVERT: J 36 GLN cc_start: 0.8632 (mt0) cc_final: 0.8108 (mt0) REVERT: J 123 LYS cc_start: 0.8883 (OUTLIER) cc_final: 0.8626 (mttm) REVERT: J 141 LYS cc_start: 0.8471 (OUTLIER) cc_final: 0.8186 (mttt) REVERT: K 75 ASP cc_start: 0.8873 (p0) cc_final: 0.8639 (p0) REVERT: L 65 LYS cc_start: 0.8818 (OUTLIER) cc_final: 0.8486 (tttm) REVERT: L 80 ARG cc_start: 0.8761 (mtp180) cc_final: 0.8365 (mtm-85) REVERT: L 84 SER cc_start: 0.8708 (m) cc_final: 0.8305 (p) REVERT: L 110 LYS cc_start: 0.8861 (tppt) cc_final: 0.8238 (tppt) REVERT: M 43 MET cc_start: 0.9174 (ttm) cc_final: 0.8883 (ttp) REVERT: M 55 LYS cc_start: 0.8679 (ttmt) cc_final: 0.8475 (ttmt) REVERT: M 76 THR cc_start: 0.9079 (m) cc_final: 0.8748 (p) REVERT: M 96 TYR cc_start: 0.9250 (t80) cc_final: 0.8994 (t80) REVERT: M 125 GLU cc_start: 0.8331 (tt0) cc_final: 0.8047 (mp0) REVERT: N 145 ASN cc_start: 0.8376 (t0) cc_final: 0.7855 (t0) REVERT: O 80 ARG cc_start: 0.7964 (mtp85) cc_final: 0.7738 (mtm-85) REVERT: O 106 TYR cc_start: 0.8074 (p90) cc_final: 0.7823 (p90) REVERT: O 110 LYS cc_start: 0.8251 (tmmm) cc_final: 0.7967 (tmmm) REVERT: O 123 LYS cc_start: 0.8439 (mmtp) cc_final: 0.8182 (mtpp) REVERT: P 55 LYS cc_start: 0.8389 (tttt) cc_final: 0.8148 (mtpm) REVERT: P 67 ASP cc_start: 0.8740 (m-30) cc_final: 0.7695 (t0) REVERT: P 78 GLU cc_start: 0.8420 (tt0) cc_final: 0.7342 (tm-30) REVERT: P 121 SER cc_start: 0.8571 (p) cc_final: 0.8338 (t) REVERT: Q 55 LYS cc_start: 0.8762 (tttt) cc_final: 0.8537 (tttt) REVERT: R 49 GLU cc_start: 0.8066 (tt0) cc_final: 0.7739 (tt0) REVERT: R 75 ASP cc_start: 0.8234 (p0) cc_final: 0.7395 (p0) REVERT: S 40 LYS cc_start: 0.8280 (ptmm) cc_final: 0.7990 (ptmt) REVERT: S 75 ASP cc_start: 0.8643 (p0) cc_final: 0.8114 (p0) REVERT: S 80 ARG cc_start: 0.8619 (mtm180) cc_final: 0.8341 (mtm180) REVERT: T 28 MET cc_start: 0.5766 (mmt) cc_final: 0.5040 (mpp) REVERT: T 75 ASP cc_start: 0.8922 (p0) cc_final: 0.8690 (p0) REVERT: T 101 GLU cc_start: 0.8334 (tp30) cc_final: 0.7890 (tm-30) REVERT: T 110 LYS cc_start: 0.8666 (tptp) cc_final: 0.8312 (tptp) REVERT: T 142 LYS cc_start: 0.8696 (mttp) cc_final: 0.8459 (mptt) REVERT: V 28 MET cc_start: 0.5428 (mmt) cc_final: 0.3963 (mpt) REVERT: V 75 ASP cc_start: 0.8155 (p0) cc_final: 0.7755 (p0) REVERT: W 28 MET cc_start: 0.4358 (tpp) cc_final: 0.3531 (tpp) REVERT: W 75 ASP cc_start: 0.8825 (p0) cc_final: 0.8456 (p0) REVERT: W 80 ARG cc_start: 0.8459 (mtm180) cc_final: 0.8147 (mtp180) REVERT: W 94 ILE cc_start: 0.9054 (mt) cc_final: 0.8792 (mp) REVERT: W 110 LYS cc_start: 0.8635 (OUTLIER) cc_final: 0.8409 (tptp) REVERT: X 49 GLU cc_start: 0.7842 (tt0) cc_final: 0.7519 (tt0) REVERT: X 87 MET cc_start: 0.7732 (pmm) cc_final: 0.7481 (ppp) REVERT: X 130 SER cc_start: 0.8772 (m) cc_final: 0.8464 (t) REVERT: X 135 LYS cc_start: 0.8020 (OUTLIER) cc_final: 0.7135 (mtmm) REVERT: Y 75 ASP cc_start: 0.8661 (p0) cc_final: 0.7989 (p0) REVERT: Y 78 GLU cc_start: 0.8767 (tt0) cc_final: 0.8402 (pt0) REVERT: Y 110 LYS cc_start: 0.8794 (OUTLIER) cc_final: 0.8462 (ttmm) outliers start: 121 outliers final: 44 residues processed: 681 average time/residue: 1.6078 time to fit residues: 1217.0272 Evaluate side-chains 611 residues out of total 2544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 554 time to evaluate : 2.448 ------------------------------------------------------------------------------- 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 B residue 123 LYS 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 E residue 87 MET Chi-restraints excluded: chain E residue 101 GLU 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 84 SER Chi-restraints excluded: chain H residue 104 GLU Chi-restraints excluded: chain H residue 145 ASN 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 133 LEU Chi-restraints excluded: chain L residue 65 LYS Chi-restraints excluded: chain M residue 51 ASP Chi-restraints excluded: chain M residue 110 LYS Chi-restraints excluded: chain M residue 139 SER Chi-restraints excluded: chain O residue 28 MET Chi-restraints excluded: chain O residue 46 SER Chi-restraints excluded: chain O residue 73 VAL 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 82 LYS 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 125 GLU 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 105 ILE Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain V residue 131 VAL Chi-restraints excluded: chain W residue 110 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 115 VAL 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 153 optimal weight: 0.6980 chunk 280 optimal weight: 3.9990 chunk 234 optimal weight: 0.1980 chunk 7 optimal weight: 6.9990 chunk 275 optimal weight: 0.4980 chunk 72 optimal weight: 7.9990 chunk 45 optimal weight: 0.8980 chunk 57 optimal weight: 4.9990 chunk 249 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 145 ASN E 52 GLN F 52 GLN G 36 GLN H 52 GLN I 119 ASN K 36 GLN K 52 GLN M 52 GLN O 71 ASN 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: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.124699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.097771 restraints weight = 32664.216| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 2.69 r_work: 0.3261 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.4084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 22776 Z= 0.109 Angle : 0.541 8.940 30720 Z= 0.280 Chirality : 0.052 0.168 3672 Planarity : 0.002 0.026 3888 Dihedral : 4.265 15.224 3024 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 4.28 % Allowed : 25.94 % Favored : 69.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.07 (0.16), residues: 2856 helix: None (None), residues: 0 sheet: 3.22 (0.15), residues: 1080 loop : 0.16 (0.15), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP F 59 HIS 0.003 0.001 HIS N 53 PHE 0.007 0.001 PHE C 42 TYR 0.016 0.001 TYR Y 106 ARG 0.006 0.000 ARG T 93 Details of bonding type rmsd hydrogen bonds : bond 0.03632 ( 962) hydrogen bonds : angle 4.68593 ( 2454) covalent geometry : bond 0.00255 (22776) covalent geometry : angle 0.54147 (30720) *********************** 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 713 residues out of total 2544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 604 time to evaluate : 2.528 Fit side-chains revert: symmetry clash REVERT: A 40 LYS cc_start: 0.8314 (ptmm) cc_final: 0.7904 (pttm) REVERT: A 78 GLU cc_start: 0.8720 (tt0) cc_final: 0.8246 (tm-30) REVERT: A 102 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7391 (pm20) REVERT: B 52 GLN cc_start: 0.8132 (mt0) cc_final: 0.6686 (tm130) REVERT: B 116 LYS cc_start: 0.7799 (mtmt) cc_final: 0.7536 (mtpp) REVERT: D 28 MET cc_start: 0.4970 (mmm) cc_final: 0.3731 (tpp) REVERT: D 45 ILE cc_start: 0.9087 (mt) cc_final: 0.8859 (mm) REVERT: D 52 GLN cc_start: 0.8654 (OUTLIER) cc_final: 0.8336 (mp10) REVERT: D 84 SER cc_start: 0.9051 (m) cc_final: 0.8567 (t) REVERT: D 87 MET cc_start: 0.8241 (pmm) cc_final: 0.7887 (ppp) REVERT: D 93 ARG cc_start: 0.7595 (ptp90) cc_final: 0.7135 (pmt170) REVERT: D 110 LYS cc_start: 0.8615 (tttt) cc_final: 0.8290 (ttpp) REVERT: D 142 LYS cc_start: 0.8388 (mmtm) cc_final: 0.7861 (mmtm) REVERT: C 28 MET cc_start: 0.3137 (mmt) cc_final: 0.2826 (mpp) REVERT: C 42 PHE cc_start: 0.8454 (t80) cc_final: 0.8186 (t80) REVERT: C 67 ASP cc_start: 0.8483 (m-30) cc_final: 0.8134 (m-30) REVERT: C 93 ARG cc_start: 0.7523 (ptt-90) cc_final: 0.6753 (pmt170) REVERT: C 96 TYR cc_start: 0.8823 (t80) cc_final: 0.8536 (t80) REVERT: C 123 LYS cc_start: 0.7445 (mmpt) cc_final: 0.7200 (mppt) REVERT: C 142 LYS cc_start: 0.7568 (mmtm) cc_final: 0.7276 (mmmm) REVERT: E 43 MET cc_start: 0.8814 (ttm) cc_final: 0.8462 (ttm) REVERT: E 87 MET cc_start: 0.7524 (OUTLIER) cc_final: 0.7287 (pmm) REVERT: G 28 MET cc_start: 0.3730 (mmt) cc_final: 0.3438 (tpp) REVERT: G 43 MET cc_start: 0.9084 (ttm) cc_final: 0.8592 (ttm) REVERT: G 45 ILE cc_start: 0.9189 (OUTLIER) cc_final: 0.8972 (mm) REVERT: G 78 GLU cc_start: 0.8729 (tt0) cc_final: 0.8391 (tm-30) REVERT: G 96 TYR cc_start: 0.8937 (t80) cc_final: 0.8657 (t80) REVERT: H 28 MET cc_start: 0.4539 (mmt) cc_final: 0.3910 (tpp) REVERT: H 40 LYS cc_start: 0.7547 (ptmm) cc_final: 0.6909 (ptmm) REVERT: H 141 LYS cc_start: 0.8710 (mttt) cc_final: 0.8405 (mttp) REVERT: I 52 GLN cc_start: 0.7853 (mm-40) cc_final: 0.7205 (tm130) REVERT: I 78 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.7126 (pp20) REVERT: I 80 ARG cc_start: 0.7917 (mtm-85) cc_final: 0.7597 (mtm-85) REVERT: I 147 GLU cc_start: 0.7492 (OUTLIER) cc_final: 0.7230 (pp20) REVERT: J 28 MET cc_start: 0.3732 (mmt) cc_final: 0.3144 (tpp) REVERT: J 36 GLN cc_start: 0.8486 (mt0) cc_final: 0.7945 (mm-40) REVERT: J 55 LYS cc_start: 0.8588 (tttp) cc_final: 0.8340 (mtpp) REVERT: J 110 LYS cc_start: 0.9167 (tptt) cc_final: 0.8956 (tptt) REVERT: J 123 LYS cc_start: 0.8859 (OUTLIER) cc_final: 0.8614 (mttm) REVERT: K 36 GLN cc_start: 0.8191 (mt0) cc_final: 0.7942 (mt0) REVERT: K 75 ASP cc_start: 0.8987 (p0) cc_final: 0.8649 (p0) REVERT: K 78 GLU cc_start: 0.8588 (OUTLIER) cc_final: 0.7846 (tt0) REVERT: K 86 LEU cc_start: 0.8970 (tt) cc_final: 0.8726 (mt) REVERT: K 147 GLU cc_start: 0.6820 (OUTLIER) cc_final: 0.5901 (pm20) REVERT: L 65 LYS cc_start: 0.8794 (tttp) cc_final: 0.8466 (tttm) REVERT: L 80 ARG cc_start: 0.8699 (OUTLIER) cc_final: 0.8307 (mtm-85) REVERT: L 84 SER cc_start: 0.8766 (m) cc_final: 0.8402 (p) REVERT: L 110 LYS cc_start: 0.8852 (tppt) cc_final: 0.8265 (tptt) REVERT: M 40 LYS cc_start: 0.8385 (OUTLIER) cc_final: 0.7651 (pttm) REVERT: M 43 MET cc_start: 0.9147 (ttm) cc_final: 0.8838 (ttp) REVERT: M 76 THR cc_start: 0.9084 (m) cc_final: 0.8710 (p) REVERT: M 78 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.8068 (tm-30) REVERT: M 96 TYR cc_start: 0.9281 (t80) cc_final: 0.9034 (t80) REVERT: M 110 LYS cc_start: 0.8561 (OUTLIER) cc_final: 0.8229 (ttpp) REVERT: M 123 LYS cc_start: 0.8599 (mtmt) cc_final: 0.8250 (mtmp) REVERT: M 125 GLU cc_start: 0.8330 (tt0) cc_final: 0.8067 (mt-10) REVERT: N 145 ASN cc_start: 0.8353 (OUTLIER) cc_final: 0.7833 (t0) REVERT: O 52 GLN cc_start: 0.8467 (mm110) cc_final: 0.8159 (tp40) REVERT: O 55 LYS cc_start: 0.8355 (mtpp) cc_final: 0.7881 (tttt) REVERT: O 106 TYR cc_start: 0.7772 (p90) cc_final: 0.7484 (p90) REVERT: P 67 ASP cc_start: 0.8715 (m-30) cc_final: 0.7705 (t0) REVERT: P 78 GLU cc_start: 0.8301 (tt0) cc_final: 0.8043 (tt0) REVERT: P 119 ASN cc_start: 0.8856 (m-40) cc_final: 0.8190 (m110) REVERT: P 130 SER cc_start: 0.9104 (m) cc_final: 0.8757 (p) REVERT: Q 55 LYS cc_start: 0.8723 (tttt) cc_final: 0.8509 (tttt) REVERT: Q 75 ASP cc_start: 0.9095 (p0) cc_final: 0.8646 (p0) REVERT: R 43 MET cc_start: 0.9049 (ttm) cc_final: 0.8564 (ttm) REVERT: R 49 GLU cc_start: 0.8037 (tt0) cc_final: 0.7749 (tt0) REVERT: R 77 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8160 (tp) REVERT: R 80 ARG cc_start: 0.7763 (mtm180) cc_final: 0.7454 (mtm110) REVERT: R 123 LYS cc_start: 0.8120 (mtmt) cc_final: 0.7270 (mtpp) REVERT: S 36 GLN cc_start: 0.8178 (mt0) cc_final: 0.7973 (mt0) REVERT: S 75 ASP cc_start: 0.8626 (p0) cc_final: 0.8132 (p0) REVERT: S 78 GLU cc_start: 0.8284 (tt0) cc_final: 0.8019 (tm-30) REVERT: S 80 ARG cc_start: 0.8651 (mtm180) cc_final: 0.8431 (mtm110) REVERT: T 28 MET cc_start: 0.5703 (mmt) cc_final: 0.5020 (mpp) REVERT: T 43 MET cc_start: 0.8815 (ttm) cc_final: 0.8540 (ttm) REVERT: T 75 ASP cc_start: 0.8926 (p0) cc_final: 0.8695 (p0) REVERT: T 101 GLU cc_start: 0.8271 (tp30) cc_final: 0.7940 (tm-30) REVERT: T 142 LYS cc_start: 0.8699 (mttp) cc_final: 0.8485 (mptt) REVERT: V 28 MET cc_start: 0.5334 (mmt) cc_final: 0.3959 (mpt) REVERT: V 75 ASP cc_start: 0.8270 (p0) cc_final: 0.7924 (p0) REVERT: W 28 MET cc_start: 0.4704 (tpp) cc_final: 0.3840 (tpp) REVERT: W 51 ASP cc_start: 0.8041 (m-30) cc_final: 0.7817 (m-30) REVERT: W 65 LYS cc_start: 0.8272 (ttpt) cc_final: 0.8011 (tttt) REVERT: W 75 ASP cc_start: 0.8812 (p0) cc_final: 0.8450 (p0) REVERT: W 80 ARG cc_start: 0.8443 (mtm180) cc_final: 0.8077 (mtp180) REVERT: W 93 ARG cc_start: 0.7993 (ptp90) cc_final: 0.7696 (ptp90) REVERT: W 94 ILE cc_start: 0.9046 (mt) cc_final: 0.8771 (mp) REVERT: W 110 LYS cc_start: 0.8691 (OUTLIER) cc_final: 0.8418 (tptp) REVERT: W 142 LYS cc_start: 0.7463 (mmpt) cc_final: 0.6793 (mmmt) REVERT: X 49 GLU cc_start: 0.7579 (tt0) cc_final: 0.7306 (tt0) REVERT: X 82 LYS cc_start: 0.8141 (ptpp) cc_final: 0.7502 (pttp) REVERT: X 96 TYR cc_start: 0.9238 (t80) cc_final: 0.8826 (t80) REVERT: X 130 SER cc_start: 0.8734 (m) cc_final: 0.8439 (t) REVERT: X 135 LYS cc_start: 0.7895 (OUTLIER) cc_final: 0.7302 (mttm) REVERT: Y 40 LYS cc_start: 0.8200 (ptmm) cc_final: 0.7972 (ptmt) REVERT: Y 75 ASP cc_start: 0.8636 (p0) cc_final: 0.8119 (p0) REVERT: Y 77 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8610 (tp) REVERT: Y 82 LYS cc_start: 0.8506 (ptmt) cc_final: 0.8247 (ptmm) REVERT: Y 102 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7828 (pm20) outliers start: 109 outliers final: 34 residues processed: 663 average time/residue: 1.6189 time to fit residues: 1197.1253 Evaluate side-chains 606 residues out of total 2544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 553 time to evaluate : 2.996 ------------------------------------------------------------------------------- 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 D residue 52 GLN Chi-restraints excluded: chain D residue 76 THR 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 87 MET 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 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 147 GLU Chi-restraints excluded: chain J residue 97 SER Chi-restraints excluded: chain J residue 123 LYS Chi-restraints excluded: chain K residue 78 GLU Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 147 GLU Chi-restraints excluded: chain L residue 80 ARG 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 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 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 110 LYS Chi-restraints excluded: chain Q residue 121 SER Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain R residue 145 ASN Chi-restraints excluded: chain T residue 52 GLN Chi-restraints excluded: chain V residue 131 VAL Chi-restraints excluded: chain V residue 147 GLU 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 135 LYS Chi-restraints excluded: chain Y residue 38 SER Chi-restraints excluded: chain Y residue 77 LEU Chi-restraints excluded: chain Y residue 84 SER Chi-restraints excluded: chain Y residue 102 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 118 optimal weight: 4.9990 chunk 143 optimal weight: 6.9990 chunk 262 optimal weight: 4.9990 chunk 92 optimal weight: 7.9990 chunk 207 optimal weight: 4.9990 chunk 231 optimal weight: 1.9990 chunk 24 optimal weight: 10.0000 chunk 41 optimal weight: 4.9990 chunk 181 optimal weight: 6.9990 chunk 232 optimal weight: 0.5980 chunk 168 optimal weight: 4.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 36 GLN D 145 ASN F 52 GLN G 36 GLN H 126 ASN K 52 GLN K 126 ASN L 30 GLN O 71 ASN P 30 GLN R 30 GLN R 119 ASN T 36 GLN W 52 GLN Y 36 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.119761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.092984 restraints weight = 33330.733| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 2.66 r_work: 0.3189 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.4623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.046 22776 Z= 0.313 Angle : 0.675 10.205 30720 Z= 0.350 Chirality : 0.056 0.183 3672 Planarity : 0.004 0.047 3888 Dihedral : 4.881 16.152 3024 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 5.46 % Allowed : 26.30 % Favored : 68.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.16), residues: 2856 helix: None (None), residues: 0 sheet: 3.21 (0.15), residues: 1080 loop : -0.18 (0.15), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP N 59 HIS 0.009 0.002 HIS N 53 PHE 0.013 0.002 PHE T 124 TYR 0.024 0.002 TYR Q 106 ARG 0.007 0.001 ARG T 93 Details of bonding type rmsd hydrogen bonds : bond 0.04764 ( 962) hydrogen bonds : angle 4.90848 ( 2454) covalent geometry : bond 0.00774 (22776) covalent geometry : angle 0.67451 (30720) *********************** 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 679 residues out of total 2544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 540 time to evaluate : 2.495 Fit side-chains revert: symmetry clash REVERT: A 40 LYS cc_start: 0.8344 (ptmm) cc_final: 0.7877 (pttp) REVERT: A 102 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7571 (pm20) REVERT: B 52 GLN cc_start: 0.8087 (mt0) cc_final: 0.6632 (tm130) REVERT: B 87 MET cc_start: 0.7164 (ppp) cc_final: 0.6701 (pmm) REVERT: B 116 LYS cc_start: 0.7932 (mtmt) cc_final: 0.7681 (mtpp) REVERT: D 28 MET cc_start: 0.5049 (mmm) cc_final: 0.3610 (tpp) REVERT: D 35 ILE cc_start: 0.8121 (OUTLIER) cc_final: 0.7884 (pt) REVERT: D 45 ILE cc_start: 0.9180 (OUTLIER) cc_final: 0.8951 (mm) REVERT: D 52 GLN cc_start: 0.8766 (OUTLIER) cc_final: 0.8347 (mp10) REVERT: D 77 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8924 (tp) REVERT: D 87 MET cc_start: 0.8342 (pmm) cc_final: 0.7931 (ppp) REVERT: D 110 LYS cc_start: 0.8706 (tttt) cc_final: 0.8424 (ttpp) REVERT: D 142 LYS cc_start: 0.8423 (mmtm) cc_final: 0.7837 (mmtm) REVERT: C 28 MET cc_start: 0.3172 (mmt) cc_final: 0.2840 (mpp) REVERT: C 48 ILE cc_start: 0.8181 (OUTLIER) cc_final: 0.7934 (mp) REVERT: C 67 ASP cc_start: 0.8583 (m-30) cc_final: 0.8183 (m-30) REVERT: C 93 ARG cc_start: 0.7678 (ptt-90) cc_final: 0.6747 (pmt170) REVERT: C 96 TYR cc_start: 0.9010 (t80) cc_final: 0.8727 (t80) REVERT: C 123 LYS cc_start: 0.7861 (mmpt) cc_final: 0.7533 (mppt) REVERT: C 142 LYS cc_start: 0.7705 (mmtm) cc_final: 0.7471 (mmmm) REVERT: E 43 MET cc_start: 0.8828 (ttm) cc_final: 0.8596 (ttm) REVERT: E 78 GLU cc_start: 0.8858 (OUTLIER) cc_final: 0.8447 (pp20) REVERT: E 87 MET cc_start: 0.7662 (OUTLIER) cc_final: 0.7450 (pmm) REVERT: E 102 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7830 (pt0) REVERT: G 28 MET cc_start: 0.4331 (mmt) cc_final: 0.3636 (tpp) REVERT: G 51 ASP cc_start: 0.8951 (OUTLIER) cc_final: 0.8685 (t0) REVERT: G 67 ASP cc_start: 0.8956 (m-30) cc_final: 0.8738 (m-30) REVERT: G 78 GLU cc_start: 0.8759 (tt0) cc_final: 0.8297 (tm-30) REVERT: G 96 TYR cc_start: 0.8967 (t80) cc_final: 0.8726 (t80) REVERT: H 28 MET cc_start: 0.4620 (mmt) cc_final: 0.3866 (tpp) REVERT: H 142 LYS cc_start: 0.8494 (mmtm) cc_final: 0.8135 (mptt) REVERT: I 52 GLN cc_start: 0.7815 (mm-40) cc_final: 0.7343 (tm-30) REVERT: I 78 GLU cc_start: 0.7698 (pt0) cc_final: 0.7209 (pp20) REVERT: I 80 ARG cc_start: 0.7958 (mtm-85) cc_final: 0.7491 (mtm-85) REVERT: J 28 MET cc_start: 0.3680 (mmt) cc_final: 0.3158 (tpt) REVERT: J 36 GLN cc_start: 0.8508 (mt0) cc_final: 0.7995 (mt0) REVERT: J 93 ARG cc_start: 0.8343 (OUTLIER) cc_final: 0.7102 (ptp-170) REVERT: J 123 LYS cc_start: 0.8898 (OUTLIER) cc_final: 0.8596 (mttm) REVERT: J 141 LYS cc_start: 0.8453 (OUTLIER) cc_final: 0.8195 (mttt) REVERT: K 75 ASP cc_start: 0.8967 (p0) cc_final: 0.8556 (p0) REVERT: L 65 LYS cc_start: 0.8836 (OUTLIER) cc_final: 0.8508 (tttm) REVERT: L 80 ARG cc_start: 0.8781 (mtp180) cc_final: 0.8383 (mtm-85) REVERT: L 110 LYS cc_start: 0.8907 (tppt) cc_final: 0.8272 (tptt) REVERT: M 40 LYS cc_start: 0.8483 (ptmt) cc_final: 0.7656 (pttm) REVERT: M 43 MET cc_start: 0.9087 (ttm) cc_final: 0.8867 (ttp) REVERT: M 76 THR cc_start: 0.9148 (m) cc_final: 0.8781 (p) REVERT: M 78 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.8151 (tm-30) REVERT: M 110 LYS cc_start: 0.8693 (OUTLIER) cc_final: 0.8472 (tmmt) REVERT: N 77 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8798 (tp) REVERT: N 145 ASN cc_start: 0.8396 (OUTLIER) cc_final: 0.7921 (t0) REVERT: O 52 GLN cc_start: 0.8449 (mm110) cc_final: 0.8130 (mm-40) REVERT: O 78 GLU cc_start: 0.8026 (tt0) cc_final: 0.7398 (tm-30) REVERT: O 93 ARG cc_start: 0.8265 (OUTLIER) cc_final: 0.7341 (ptp90) REVERT: O 106 TYR cc_start: 0.7987 (p90) cc_final: 0.7766 (p90) REVERT: P 67 ASP cc_start: 0.8660 (m-30) cc_final: 0.7588 (t0) REVERT: P 78 GLU cc_start: 0.8445 (tt0) cc_final: 0.7374 (tm-30) REVERT: Q 55 LYS cc_start: 0.8792 (tttt) cc_final: 0.8543 (tttt) REVERT: Q 102 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.7915 (pm20) REVERT: R 55 LYS cc_start: 0.8182 (tttt) cc_final: 0.7781 (mtpp) REVERT: R 103 GLU cc_start: 0.8172 (tt0) cc_final: 0.7869 (tt0) REVERT: R 135 LYS cc_start: 0.8142 (OUTLIER) cc_final: 0.7711 (mmtm) REVERT: R 147 GLU cc_start: 0.7412 (OUTLIER) cc_final: 0.6600 (pp20) REVERT: S 36 GLN cc_start: 0.8485 (mt0) cc_final: 0.8231 (mt0) REVERT: T 28 MET cc_start: 0.5727 (mmt) cc_final: 0.4990 (mpp) REVERT: T 43 MET cc_start: 0.9057 (ttm) cc_final: 0.8757 (ttm) REVERT: T 75 ASP cc_start: 0.8919 (p0) cc_final: 0.8688 (p0) REVERT: T 101 GLU cc_start: 0.8276 (tp30) cc_final: 0.7796 (tm-30) REVERT: T 142 LYS cc_start: 0.8795 (mttp) cc_final: 0.8532 (mptt) REVERT: V 28 MET cc_start: 0.5122 (mmt) cc_final: 0.4187 (tpt) REVERT: V 37 ILE cc_start: 0.9176 (OUTLIER) cc_final: 0.8968 (mm) REVERT: V 75 ASP cc_start: 0.8347 (p0) cc_final: 0.8134 (p0) REVERT: V 123 LYS cc_start: 0.8642 (mtpp) cc_final: 0.8182 (mttm) REVERT: W 28 MET cc_start: 0.4948 (tpp) cc_final: 0.3804 (tpp) REVERT: W 51 ASP cc_start: 0.8066 (m-30) cc_final: 0.7759 (m-30) REVERT: W 65 LYS cc_start: 0.8453 (ttpt) cc_final: 0.8151 (tttt) REVERT: W 75 ASP cc_start: 0.8856 (p0) cc_final: 0.8521 (p0) REVERT: W 80 ARG cc_start: 0.8555 (OUTLIER) cc_final: 0.8234 (mtp180) REVERT: W 110 LYS cc_start: 0.8652 (OUTLIER) cc_final: 0.8418 (tptp) REVERT: X 49 GLU cc_start: 0.7847 (tt0) cc_final: 0.7632 (tt0) REVERT: X 82 LYS cc_start: 0.8366 (ptpp) cc_final: 0.7798 (ptpp) REVERT: X 96 TYR cc_start: 0.9273 (t80) cc_final: 0.8791 (t80) REVERT: X 130 SER cc_start: 0.8787 (m) cc_final: 0.8401 (t) REVERT: X 135 LYS cc_start: 0.8135 (OUTLIER) cc_final: 0.7609 (mttm) REVERT: Y 75 ASP cc_start: 0.8663 (p0) cc_final: 0.8045 (p0) REVERT: Y 77 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8678 (tp) REVERT: Y 78 GLU cc_start: 0.8688 (tt0) cc_final: 0.8485 (pt0) REVERT: Y 102 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.7981 (pm20) outliers start: 139 outliers final: 75 residues processed: 633 average time/residue: 1.9765 time to fit residues: 1391.3516 Evaluate side-chains 617 residues out of total 2544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 514 time to evaluate : 2.919 ------------------------------------------------------------------------------- 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 76 THR 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 121 SER Chi-restraints excluded: chain D residue 130 SER Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 80 ARG Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain E residue 78 GLU Chi-restraints excluded: chain E residue 87 MET Chi-restraints excluded: chain E residue 102 GLU Chi-restraints excluded: chain F residue 46 SER Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain F residue 78 GLU 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 79 ILE Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain I residue 121 SER Chi-restraints excluded: chain J residue 77 LEU 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 78 GLU Chi-restraints excluded: chain K residue 116 LYS Chi-restraints excluded: chain K residue 133 LEU Chi-restraints excluded: chain K residue 147 GLU Chi-restraints excluded: chain L residue 35 ILE Chi-restraints excluded: chain L residue 65 LYS Chi-restraints excluded: chain L residue 70 LEU Chi-restraints excluded: chain L residue 88 ILE Chi-restraints excluded: chain M residue 78 GLU Chi-restraints excluded: chain M residue 101 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 104 GLU 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 73 VAL Chi-restraints excluded: chain O residue 76 THR Chi-restraints excluded: chain O residue 93 ARG Chi-restraints excluded: chain O residue 145 ASN 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 46 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 Q residue 130 SER Chi-restraints excluded: chain R residue 46 SER Chi-restraints excluded: chain R residue 78 GLU Chi-restraints excluded: chain R residue 135 LYS Chi-restraints excluded: chain R residue 145 ASN Chi-restraints excluded: chain R residue 147 GLU 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 52 GLN Chi-restraints excluded: chain T residue 102 GLU Chi-restraints excluded: chain T residue 105 ILE Chi-restraints excluded: chain V residue 37 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 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 38 SER Chi-restraints excluded: chain Y residue 46 SER Chi-restraints excluded: chain Y residue 77 LEU Chi-restraints excluded: chain Y residue 84 SER Chi-restraints excluded: chain Y residue 102 GLU Chi-restraints excluded: chain Y residue 138 SER Chi-restraints excluded: chain Y residue 139 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 146 optimal weight: 0.9990 chunk 78 optimal weight: 0.9990 chunk 254 optimal weight: 5.9990 chunk 141 optimal weight: 1.9990 chunk 104 optimal weight: 0.8980 chunk 172 optimal weight: 0.7980 chunk 126 optimal weight: 1.9990 chunk 260 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 15 optimal weight: 0.0770 chunk 186 optimal weight: 1.9990 overall best weight: 0.7542 ------------------------------------------------------------------------------- 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 E 36 GLN F 52 GLN G 36 GLN G 52 GLN K 36 GLN K 52 GLN L 36 GLN L 52 GLN W 52 GLN X 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 = 0.3742 r_free = 0.3742 target = 0.123868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.096485 restraints weight = 32906.965| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 2.71 r_work: 0.3262 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.4697 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= 0.103 Angle : 0.543 9.441 30720 Z= 0.280 Chirality : 0.052 0.162 3672 Planarity : 0.002 0.031 3888 Dihedral : 4.173 15.589 3024 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 3.97 % Allowed : 28.50 % Favored : 67.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.17), residues: 2856 helix: None (None), residues: 0 sheet: 3.32 (0.15), residues: 1080 loop : -0.03 (0.15), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP I 59 HIS 0.002 0.001 HIS N 53 PHE 0.005 0.001 PHE F 42 TYR 0.015 0.001 TYR J 106 ARG 0.006 0.000 ARG T 93 Details of bonding type rmsd hydrogen bonds : bond 0.03452 ( 962) hydrogen bonds : angle 4.63847 ( 2454) covalent geometry : bond 0.00238 (22776) covalent geometry : angle 0.54304 (30720) *********************** 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 674 residues out of total 2544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 573 time to evaluate : 2.471 Fit side-chains revert: symmetry clash REVERT: A 40 LYS cc_start: 0.8274 (ptmm) cc_final: 0.7738 (pttp) REVERT: A 78 GLU cc_start: 0.8736 (tt0) cc_final: 0.8306 (tm-30) REVERT: B 52 GLN cc_start: 0.8239 (mt0) cc_final: 0.6892 (tm130) REVERT: B 87 MET cc_start: 0.7433 (ppp) cc_final: 0.7061 (pmm) REVERT: B 88 ILE cc_start: 0.8832 (pt) cc_final: 0.8332 (pp) REVERT: B 116 LYS cc_start: 0.7909 (mtmt) cc_final: 0.7642 (mtpp) REVERT: D 28 MET cc_start: 0.4960 (mmm) cc_final: 0.3550 (tpp) REVERT: D 45 ILE cc_start: 0.9144 (mt) cc_final: 0.8920 (mm) REVERT: D 52 GLN cc_start: 0.8712 (OUTLIER) cc_final: 0.8419 (mp10) REVERT: D 84 SER cc_start: 0.9217 (OUTLIER) cc_final: 0.8979 (p) REVERT: D 87 MET cc_start: 0.8397 (pmm) cc_final: 0.7956 (ppp) REVERT: D 110 LYS cc_start: 0.8692 (tttt) cc_final: 0.8366 (ttpp) REVERT: D 123 LYS cc_start: 0.8581 (OUTLIER) cc_final: 0.8257 (mttp) REVERT: D 142 LYS cc_start: 0.8465 (mmtm) cc_final: 0.7929 (mmtm) REVERT: C 28 MET cc_start: 0.3261 (mmt) cc_final: 0.2710 (mpp) REVERT: C 45 ILE cc_start: 0.9010 (mt) cc_final: 0.8729 (mp) REVERT: C 67 ASP cc_start: 0.8498 (m-30) cc_final: 0.8161 (m-30) REVERT: C 96 TYR cc_start: 0.8936 (t80) cc_final: 0.8653 (t80) REVERT: C 116 LYS cc_start: 0.7711 (mtpt) cc_final: 0.7454 (mtpp) REVERT: C 123 LYS cc_start: 0.7574 (mmpt) cc_final: 0.7156 (mppt) REVERT: C 142 LYS cc_start: 0.7698 (mmtm) cc_final: 0.7393 (mmmm) REVERT: E 43 MET cc_start: 0.8793 (ttm) cc_final: 0.8553 (ttm) REVERT: E 78 GLU cc_start: 0.8715 (OUTLIER) cc_final: 0.8281 (pp20) REVERT: E 80 ARG cc_start: 0.8558 (mtm-85) cc_final: 0.8330 (mtm-85) REVERT: E 87 MET cc_start: 0.7629 (OUTLIER) cc_final: 0.7427 (pmm) REVERT: E 102 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7993 (pt0) REVERT: G 28 MET cc_start: 0.4331 (mmt) cc_final: 0.3839 (tpp) REVERT: G 78 GLU cc_start: 0.8647 (tt0) cc_final: 0.8251 (tm-30) REVERT: H 28 MET cc_start: 0.4593 (mmt) cc_final: 0.3793 (tpp) REVERT: H 40 LYS cc_start: 0.7670 (ptmm) cc_final: 0.7089 (ptmm) REVERT: H 78 GLU cc_start: 0.8537 (tt0) cc_final: 0.8048 (tm-30) REVERT: I 52 GLN cc_start: 0.7892 (mm-40) cc_final: 0.7384 (tm-30) REVERT: I 55 LYS cc_start: 0.8827 (mtpp) cc_final: 0.8564 (mmmm) REVERT: I 78 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7309 (pp20) REVERT: I 80 ARG cc_start: 0.7836 (mtm-85) cc_final: 0.7393 (mtm-85) REVERT: J 28 MET cc_start: 0.3731 (mmt) cc_final: 0.3237 (tpt) REVERT: J 36 GLN cc_start: 0.8355 (mt0) cc_final: 0.7819 (mm-40) REVERT: J 55 LYS cc_start: 0.8585 (tttp) cc_final: 0.8276 (mtpp) REVERT: J 110 LYS cc_start: 0.9276 (tptt) cc_final: 0.9072 (tptt) REVERT: J 123 LYS cc_start: 0.8896 (OUTLIER) cc_final: 0.8602 (mttm) REVERT: K 36 GLN cc_start: 0.8451 (mt0) cc_final: 0.8226 (mt0) REVERT: K 75 ASP cc_start: 0.8896 (p0) cc_final: 0.8466 (p0) REVERT: K 123 LYS cc_start: 0.8381 (mtmm) cc_final: 0.8145 (mttm) REVERT: K 147 GLU cc_start: 0.6563 (OUTLIER) cc_final: 0.5746 (pm20) REVERT: L 64 ASN cc_start: 0.8541 (m-40) cc_final: 0.8307 (m-40) REVERT: L 65 LYS cc_start: 0.8824 (OUTLIER) cc_final: 0.8543 (tttm) REVERT: L 80 ARG cc_start: 0.8737 (OUTLIER) cc_final: 0.8244 (mtt90) REVERT: L 110 LYS cc_start: 0.8927 (tppt) cc_final: 0.8279 (tptt) REVERT: M 36 GLN cc_start: 0.7774 (mt0) cc_final: 0.7074 (tt0) REVERT: M 40 LYS cc_start: 0.8384 (ptmt) cc_final: 0.7552 (pttm) REVERT: M 43 MET cc_start: 0.9106 (ttm) cc_final: 0.8793 (ttp) REVERT: M 76 THR cc_start: 0.9132 (m) cc_final: 0.8672 (p) REVERT: M 78 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.8137 (tm-30) REVERT: M 96 TYR cc_start: 0.9267 (t80) cc_final: 0.8937 (t80) REVERT: M 110 LYS cc_start: 0.8760 (OUTLIER) cc_final: 0.8290 (ttpp) REVERT: M 123 LYS cc_start: 0.8634 (mtmt) cc_final: 0.8301 (mtmp) REVERT: N 145 ASN cc_start: 0.8426 (OUTLIER) cc_final: 0.7939 (t0) REVERT: O 52 GLN cc_start: 0.8406 (mm110) cc_final: 0.8045 (mm-40) REVERT: O 55 LYS cc_start: 0.8519 (mtpp) cc_final: 0.8153 (tttt) REVERT: O 93 ARG cc_start: 0.8158 (OUTLIER) cc_final: 0.7909 (ptp90) REVERT: O 105 ILE cc_start: 0.8934 (pt) cc_final: 0.8512 (pp) REVERT: O 106 TYR cc_start: 0.7830 (p90) cc_final: 0.7595 (p90) REVERT: O 110 LYS cc_start: 0.8520 (tmmm) cc_final: 0.8102 (tmmm) REVERT: P 52 GLN cc_start: 0.8260 (mp10) cc_final: 0.8058 (mp10) REVERT: P 67 ASP cc_start: 0.8585 (m-30) cc_final: 0.7656 (t0) REVERT: P 78 GLU cc_start: 0.8376 (tt0) cc_final: 0.8142 (tt0) REVERT: P 130 SER cc_start: 0.9130 (m) cc_final: 0.8871 (p) REVERT: R 43 MET cc_start: 0.9075 (ttm) cc_final: 0.8537 (ttm) REVERT: R 49 GLU cc_start: 0.8092 (tt0) cc_final: 0.7786 (tt0) REVERT: R 80 ARG cc_start: 0.7821 (mtm180) cc_final: 0.7535 (mtm110) REVERT: R 103 GLU cc_start: 0.8098 (tt0) cc_final: 0.7816 (tt0) REVERT: R 123 LYS cc_start: 0.8140 (mtmt) cc_final: 0.7280 (mtpp) REVERT: S 36 GLN cc_start: 0.8321 (mt0) cc_final: 0.8114 (mt0) REVERT: S 78 GLU cc_start: 0.8346 (tm-30) cc_final: 0.8100 (tm-30) REVERT: T 28 MET cc_start: 0.5557 (mmt) cc_final: 0.4820 (mpp) REVERT: T 43 MET cc_start: 0.9026 (ttm) cc_final: 0.8677 (ttm) REVERT: T 75 ASP cc_start: 0.8980 (p0) cc_final: 0.8697 (p0) REVERT: T 101 GLU cc_start: 0.8278 (tp30) cc_final: 0.7783 (tm-30) REVERT: T 142 LYS cc_start: 0.8702 (mttp) cc_final: 0.8469 (mptt) REVERT: V 28 MET cc_start: 0.4919 (mmt) cc_final: 0.3816 (mpt) REVERT: V 75 ASP cc_start: 0.8408 (p0) cc_final: 0.8000 (p0) REVERT: V 80 ARG cc_start: 0.8656 (mtp85) cc_final: 0.8449 (mtm180) REVERT: V 123 LYS cc_start: 0.8606 (mtpp) cc_final: 0.8027 (mtmm) REVERT: W 28 MET cc_start: 0.5303 (tpp) cc_final: 0.4043 (tpp) REVERT: W 75 ASP cc_start: 0.8861 (p0) cc_final: 0.8541 (p0) REVERT: W 80 ARG cc_start: 0.8474 (OUTLIER) cc_final: 0.8131 (mtp180) REVERT: W 142 LYS cc_start: 0.7755 (OUTLIER) cc_final: 0.7277 (mmmt) REVERT: X 49 GLU cc_start: 0.7819 (tt0) cc_final: 0.7564 (tt0) REVERT: X 82 LYS cc_start: 0.8112 (ptpp) cc_final: 0.7489 (ptpp) REVERT: X 86 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.7853 (tt) REVERT: X 96 TYR cc_start: 0.9232 (t80) cc_final: 0.8678 (t80) REVERT: X 130 SER cc_start: 0.8738 (m) cc_final: 0.8432 (t) REVERT: X 135 LYS cc_start: 0.8089 (OUTLIER) cc_final: 0.7497 (mttm) REVERT: X 145 ASN cc_start: 0.8185 (p0) cc_final: 0.7731 (p0) REVERT: Y 40 LYS cc_start: 0.8323 (ptmm) cc_final: 0.8045 (ptmt) REVERT: Y 75 ASP cc_start: 0.8656 (p0) cc_final: 0.8072 (p0) REVERT: Y 82 LYS cc_start: 0.8547 (ptmt) cc_final: 0.8247 (ptmm) outliers start: 101 outliers final: 40 residues processed: 633 average time/residue: 1.8587 time to fit residues: 1308.7271 Evaluate side-chains 606 residues out of total 2544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 547 time to evaluate : 3.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER 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 84 SER Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 123 LYS 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 87 MET Chi-restraints excluded: chain E residue 102 GLU 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 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 97 SER Chi-restraints excluded: chain J residue 123 LYS Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 147 GLU 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 147 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 O residue 93 ARG Chi-restraints excluded: chain P residue 28 MET 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 46 SER Chi-restraints excluded: chain Q residue 77 LEU 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 T residue 102 GLU Chi-restraints excluded: chain V residue 131 VAL Chi-restraints excluded: chain W residue 80 ARG Chi-restraints excluded: chain W residue 142 LYS 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 131 VAL Chi-restraints excluded: chain X residue 135 LYS Chi-restraints excluded: chain Y residue 38 SER Chi-restraints excluded: chain Y residue 46 SER Chi-restraints excluded: chain Y residue 84 SER Chi-restraints excluded: chain Y residue 139 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 1 optimal weight: 0.8980 chunk 155 optimal weight: 2.9990 chunk 206 optimal weight: 3.9990 chunk 183 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 220 optimal weight: 6.9990 chunk 286 optimal weight: 4.9990 chunk 99 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 36 GLN D 145 ASN E 36 GLN G 36 GLN G 52 GLN G 126 ASN L 36 GLN L 52 GLN M 52 GLN O 119 ASN P 119 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 = 0.3696 r_free = 0.3696 target = 0.120954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.093990 restraints weight = 33216.815| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 2.67 r_work: 0.3224 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.4840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 22776 Z= 0.205 Angle : 0.603 10.380 30720 Z= 0.310 Chirality : 0.054 0.168 3672 Planarity : 0.003 0.029 3888 Dihedral : 4.484 15.848 3024 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 4.72 % Allowed : 28.69 % Favored : 66.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.17), residues: 2856 helix: None (None), residues: 0 sheet: 3.10 (0.15), residues: 1128 loop : -0.13 (0.16), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP N 59 HIS 0.006 0.001 HIS N 53 PHE 0.009 0.001 PHE N 124 TYR 0.028 0.002 TYR Q 106 ARG 0.008 0.001 ARG T 93 Details of bonding type rmsd hydrogen bonds : bond 0.04106 ( 962) hydrogen bonds : angle 4.71378 ( 2454) covalent geometry : bond 0.00500 (22776) covalent geometry : angle 0.60268 (30720) *********************** 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 665 residues out of total 2544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 545 time to evaluate : 2.567 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 LYS cc_start: 0.8331 (ptmm) cc_final: 0.7862 (pttp) REVERT: A 78 GLU cc_start: 0.8715 (tt0) cc_final: 0.8287 (tm-30) REVERT: B 52 GLN cc_start: 0.8223 (mt0) cc_final: 0.6625 (tm130) REVERT: B 116 LYS cc_start: 0.7937 (mtmt) cc_final: 0.7691 (mtpp) REVERT: D 28 MET cc_start: 0.5112 (mmm) cc_final: 0.3660 (tpp) REVERT: D 45 ILE cc_start: 0.9193 (mt) cc_final: 0.8927 (mm) REVERT: D 52 GLN cc_start: 0.8752 (OUTLIER) cc_final: 0.8439 (mp10) REVERT: D 84 SER cc_start: 0.9276 (OUTLIER) cc_final: 0.9059 (p) REVERT: D 87 MET cc_start: 0.8417 (pmm) cc_final: 0.7986 (ppp) REVERT: D 110 LYS cc_start: 0.8732 (tttt) cc_final: 0.8405 (ttpp) REVERT: D 123 LYS cc_start: 0.8595 (OUTLIER) cc_final: 0.8225 (mttp) REVERT: D 142 LYS cc_start: 0.8449 (mmtm) cc_final: 0.7879 (mmtm) REVERT: C 28 MET cc_start: 0.3640 (mmt) cc_final: 0.3141 (mpp) REVERT: C 48 ILE cc_start: 0.8152 (OUTLIER) cc_final: 0.7924 (mp) REVERT: C 67 ASP cc_start: 0.8517 (m-30) cc_final: 0.8163 (m-30) REVERT: C 96 TYR cc_start: 0.8958 (t80) cc_final: 0.8640 (t80) REVERT: C 123 LYS cc_start: 0.7796 (mmpt) cc_final: 0.7411 (mppt) REVERT: C 142 LYS cc_start: 0.7637 (mmtm) cc_final: 0.7353 (mmmm) REVERT: E 43 MET cc_start: 0.8834 (ttm) cc_final: 0.8583 (ttm) REVERT: E 78 GLU cc_start: 0.8655 (OUTLIER) cc_final: 0.8206 (pp20) REVERT: E 80 ARG cc_start: 0.8550 (mtm-85) cc_final: 0.8266 (mtm-85) REVERT: E 87 MET cc_start: 0.7615 (OUTLIER) cc_final: 0.7400 (pmm) REVERT: E 93 ARG cc_start: 0.8159 (ptp90) cc_final: 0.7872 (ptp90) REVERT: E 102 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7870 (pt0) REVERT: E 142 LYS cc_start: 0.8552 (mppt) cc_final: 0.8268 (mmtm) REVERT: G 28 MET cc_start: 0.4581 (mmt) cc_final: 0.4043 (tpp) REVERT: G 78 GLU cc_start: 0.8700 (tt0) cc_final: 0.8223 (tm-30) REVERT: G 80 ARG cc_start: 0.8581 (mtm-85) cc_final: 0.8222 (mtm-85) REVERT: H 28 MET cc_start: 0.4901 (mmt) cc_final: 0.4283 (tpp) REVERT: H 78 GLU cc_start: 0.8688 (tt0) cc_final: 0.8196 (tm-30) REVERT: I 52 GLN cc_start: 0.7878 (mm-40) cc_final: 0.7385 (tm-30) REVERT: I 78 GLU cc_start: 0.7660 (pt0) cc_final: 0.7193 (pp20) REVERT: I 80 ARG cc_start: 0.7887 (mtm-85) cc_final: 0.7384 (mtm-85) REVERT: J 28 MET cc_start: 0.3772 (mmt) cc_final: 0.3228 (tpt) REVERT: J 36 GLN cc_start: 0.8490 (mt0) cc_final: 0.8006 (mt0) REVERT: J 123 LYS cc_start: 0.8931 (OUTLIER) cc_final: 0.8636 (mttm) REVERT: J 141 LYS cc_start: 0.8416 (OUTLIER) cc_final: 0.8131 (mttt) REVERT: K 36 GLN cc_start: 0.8489 (mt0) cc_final: 0.8274 (mt0) REVERT: K 75 ASP cc_start: 0.8888 (p0) cc_final: 0.8419 (p0) REVERT: K 147 GLU cc_start: 0.6474 (OUTLIER) cc_final: 0.5723 (pm20) REVERT: L 65 LYS cc_start: 0.8859 (OUTLIER) cc_final: 0.8574 (tttm) REVERT: L 80 ARG cc_start: 0.8772 (OUTLIER) cc_final: 0.8366 (mtm-85) REVERT: L 110 LYS cc_start: 0.8929 (tppt) cc_final: 0.8340 (tppt) REVERT: L 123 LYS cc_start: 0.8202 (mttp) cc_final: 0.7887 (mtpp) REVERT: M 36 GLN cc_start: 0.7887 (mt0) cc_final: 0.7188 (tt0) REVERT: M 40 LYS cc_start: 0.8447 (ptmt) cc_final: 0.7668 (pttm) REVERT: M 43 MET cc_start: 0.9104 (ttm) cc_final: 0.8810 (ttp) REVERT: M 75 ASP cc_start: 0.8852 (p0) cc_final: 0.8520 (p0) REVERT: M 76 THR cc_start: 0.8963 (m) cc_final: 0.8676 (p) REVERT: M 78 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.8095 (tm-30) REVERT: M 96 TYR cc_start: 0.9264 (t80) cc_final: 0.8898 (t80) REVERT: M 110 LYS cc_start: 0.8776 (OUTLIER) cc_final: 0.8240 (ttpp) REVERT: N 77 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8822 (tp) REVERT: N 145 ASN cc_start: 0.8432 (OUTLIER) cc_final: 0.7939 (t0) REVERT: O 52 GLN cc_start: 0.8408 (mm110) cc_final: 0.8042 (mm-40) REVERT: O 93 ARG cc_start: 0.8268 (OUTLIER) cc_final: 0.7615 (ptp90) REVERT: O 105 ILE cc_start: 0.9005 (pt) cc_final: 0.8603 (pp) REVERT: O 106 TYR cc_start: 0.7916 (p90) cc_final: 0.7689 (p90) REVERT: P 52 GLN cc_start: 0.8250 (mp10) cc_final: 0.7971 (mp10) REVERT: P 67 ASP cc_start: 0.8566 (m-30) cc_final: 0.7658 (t0) REVERT: P 78 GLU cc_start: 0.8320 (tt0) cc_final: 0.8068 (tt0) REVERT: Q 102 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.7918 (pm20) REVERT: R 43 MET cc_start: 0.9053 (ttm) cc_final: 0.8487 (ttm) REVERT: R 49 GLU cc_start: 0.8156 (tt0) cc_final: 0.7897 (tt0) REVERT: R 55 LYS cc_start: 0.8181 (tttt) cc_final: 0.7797 (mtpp) REVERT: R 103 GLU cc_start: 0.8163 (tt0) cc_final: 0.7824 (tt0) REVERT: S 36 GLN cc_start: 0.8399 (mt0) cc_final: 0.8117 (mt0) REVERT: S 78 GLU cc_start: 0.8362 (tm-30) cc_final: 0.8057 (tm-30) REVERT: S 110 LYS cc_start: 0.8892 (tmtp) cc_final: 0.8580 (tptp) REVERT: S 123 LYS cc_start: 0.8873 (mttt) cc_final: 0.8374 (mttp) REVERT: T 28 MET cc_start: 0.5683 (mmt) cc_final: 0.5022 (mpp) REVERT: T 43 MET cc_start: 0.9099 (ttm) cc_final: 0.8773 (ttm) REVERT: T 101 GLU cc_start: 0.8259 (tp30) cc_final: 0.7778 (tm-30) REVERT: T 142 LYS cc_start: 0.8796 (mttp) cc_final: 0.8541 (mptt) REVERT: V 28 MET cc_start: 0.4895 (mmt) cc_final: 0.3714 (mpp) REVERT: V 75 ASP cc_start: 0.8411 (p0) cc_final: 0.7930 (p0) REVERT: V 80 ARG cc_start: 0.8697 (OUTLIER) cc_final: 0.8438 (mtm180) REVERT: V 123 LYS cc_start: 0.8624 (mtpp) cc_final: 0.8232 (mtpp) REVERT: W 28 MET cc_start: 0.5434 (tpp) cc_final: 0.4501 (tpp) REVERT: W 75 ASP cc_start: 0.8929 (p0) cc_final: 0.8620 (p0) REVERT: W 80 ARG cc_start: 0.8535 (mtm180) cc_final: 0.8204 (mtp180) REVERT: W 142 LYS cc_start: 0.7733 (mmpt) cc_final: 0.7232 (mmmt) REVERT: X 49 GLU cc_start: 0.7855 (tt0) cc_final: 0.7645 (tt0) REVERT: X 82 LYS cc_start: 0.8120 (ptpp) cc_final: 0.7502 (ptpp) REVERT: X 86 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.7898 (tt) REVERT: X 96 TYR cc_start: 0.9266 (t80) cc_final: 0.8770 (t80) REVERT: X 130 SER cc_start: 0.8739 (m) cc_final: 0.8402 (t) REVERT: X 135 LYS cc_start: 0.8182 (OUTLIER) cc_final: 0.7573 (mttm) REVERT: X 145 ASN cc_start: 0.8171 (p0) cc_final: 0.7711 (p0) REVERT: Y 40 LYS cc_start: 0.8323 (ptmm) cc_final: 0.8030 (ptmt) REVERT: Y 75 ASP cc_start: 0.8629 (p0) cc_final: 0.8092 (p0) REVERT: Y 77 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8578 (tp) REVERT: Y 82 LYS cc_start: 0.8607 (ptmt) cc_final: 0.8327 (ptmm) REVERT: Y 110 LYS cc_start: 0.8972 (ttmm) cc_final: 0.8495 (tmmt) outliers start: 120 outliers final: 63 residues processed: 625 average time/residue: 1.6183 time to fit residues: 1125.5555 Evaluate side-chains 615 residues out of total 2544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 530 time to evaluate : 2.883 ------------------------------------------------------------------------------- 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 84 SER Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 123 LYS Chi-restraints excluded: chain D residue 130 SER Chi-restraints excluded: chain C residue 48 ILE 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 87 MET Chi-restraints excluded: chain E residue 102 GLU 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 78 GLU Chi-restraints excluded: chain F residue 84 SER 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 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 97 SER Chi-restraints excluded: chain J residue 123 LYS Chi-restraints excluded: chain J residue 141 LYS Chi-restraints excluded: chain K residue 133 LEU Chi-restraints excluded: chain K residue 147 GLU Chi-restraints excluded: chain L residue 35 ILE 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 121 SER Chi-restraints excluded: chain N residue 133 LEU 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 O residue 93 ARG 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 46 SER Chi-restraints excluded: chain Q residue 77 LEU 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 46 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 R residue 147 GLU Chi-restraints excluded: chain S residue 45 ILE 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 80 ARG Chi-restraints excluded: chain V 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 38 SER Chi-restraints excluded: chain Y residue 46 SER Chi-restraints excluded: chain Y residue 77 LEU Chi-restraints excluded: chain Y residue 84 SER Chi-restraints excluded: chain Y residue 139 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 93 optimal weight: 7.9990 chunk 190 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 123 optimal weight: 2.9990 chunk 209 optimal weight: 0.6980 chunk 104 optimal weight: 0.7980 chunk 172 optimal weight: 0.7980 chunk 247 optimal weight: 0.1980 chunk 125 optimal weight: 0.7980 chunk 243 optimal weight: 0.9980 chunk 129 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 145 ASN E 36 GLN F 52 GLN G 36 GLN G 52 GLN L 36 GLN M 52 GLN O 119 ASN W 52 GLN X 52 GLN Y 36 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.123362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.096518 restraints weight = 33072.710| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.69 r_work: 0.3259 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.4871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 22776 Z= 0.100 Angle : 0.560 10.534 30720 Z= 0.284 Chirality : 0.052 0.170 3672 Planarity : 0.002 0.025 3888 Dihedral : 4.036 15.400 3024 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 3.22 % Allowed : 30.39 % Favored : 66.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.98 (0.17), residues: 2856 helix: None (None), residues: 0 sheet: 3.34 (0.15), residues: 1080 loop : -0.04 (0.16), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP D 59 HIS 0.002 0.001 HIS N 53 PHE 0.004 0.001 PHE N 124 TYR 0.015 0.001 TYR V 106 ARG 0.006 0.000 ARG T 93 Details of bonding type rmsd hydrogen bonds : bond 0.03359 ( 962) hydrogen bonds : angle 4.54933 ( 2454) covalent geometry : bond 0.00232 (22776) covalent geometry : angle 0.56026 (30720) *********************** 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 641 residues out of total 2544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 559 time to evaluate : 2.629 Fit side-chains REVERT: A 40 LYS cc_start: 0.8330 (ptmm) cc_final: 0.7771 (pttm) REVERT: A 78 GLU cc_start: 0.8687 (tt0) cc_final: 0.8278 (tm-30) REVERT: B 52 GLN cc_start: 0.8313 (mt0) cc_final: 0.6963 (tm130) REVERT: B 116 LYS cc_start: 0.7887 (mtmt) cc_final: 0.7635 (mtpp) REVERT: D 28 MET cc_start: 0.5012 (mmm) cc_final: 0.3606 (tpp) REVERT: D 45 ILE cc_start: 0.9126 (mt) cc_final: 0.8881 (mm) REVERT: D 49 GLU cc_start: 0.8458 (tt0) cc_final: 0.8249 (tt0) REVERT: D 52 GLN cc_start: 0.8705 (OUTLIER) cc_final: 0.8434 (mp10) REVERT: D 87 MET cc_start: 0.8413 (pmm) cc_final: 0.7974 (ppp) REVERT: D 110 LYS cc_start: 0.8650 (tttt) cc_final: 0.8252 (ttpp) REVERT: D 142 LYS cc_start: 0.8450 (mmtm) cc_final: 0.7893 (mmtm) REVERT: C 28 MET cc_start: 0.3480 (mmt) cc_final: 0.2954 (mpp) REVERT: C 45 ILE cc_start: 0.9025 (mt) cc_final: 0.8740 (mp) REVERT: C 67 ASP cc_start: 0.8461 (m-30) cc_final: 0.8152 (m-30) REVERT: C 96 TYR cc_start: 0.8886 (t80) cc_final: 0.8599 (t80) REVERT: C 116 LYS cc_start: 0.7763 (mtpt) cc_final: 0.7505 (mtpp) REVERT: C 123 LYS cc_start: 0.7727 (mmpt) cc_final: 0.7343 (mppt) REVERT: C 142 LYS cc_start: 0.7605 (mmtm) cc_final: 0.7249 (mmmm) REVERT: E 43 MET cc_start: 0.8767 (ttm) cc_final: 0.8504 (ttm) REVERT: E 78 GLU cc_start: 0.8731 (OUTLIER) cc_final: 0.8307 (pp20) REVERT: E 80 ARG cc_start: 0.8531 (mtm-85) cc_final: 0.8216 (mtm-85) REVERT: E 87 MET cc_start: 0.7564 (OUTLIER) cc_final: 0.7356 (pmm) REVERT: E 93 ARG cc_start: 0.8170 (ptp90) cc_final: 0.7776 (ptp90) REVERT: E 102 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7904 (pt0) REVERT: E 142 LYS cc_start: 0.8495 (mppt) cc_final: 0.8221 (mmtm) REVERT: F 40 LYS cc_start: 0.8114 (ptmt) cc_final: 0.7873 (pttt) REVERT: G 28 MET cc_start: 0.4564 (mmt) cc_final: 0.4005 (tpp) REVERT: G 75 ASP cc_start: 0.8700 (p0) cc_final: 0.8498 (p0) REVERT: G 78 GLU cc_start: 0.8655 (tt0) cc_final: 0.8322 (tm-30) REVERT: H 28 MET cc_start: 0.4888 (mmt) cc_final: 0.4261 (tpp) REVERT: H 40 LYS cc_start: 0.7623 (ptmm) cc_final: 0.7289 (ptmt) REVERT: H 78 GLU cc_start: 0.8541 (tt0) cc_final: 0.8038 (tm-30) REVERT: I 52 GLN cc_start: 0.7886 (mm-40) cc_final: 0.7340 (tm-30) REVERT: I 55 LYS cc_start: 0.8815 (mtpp) cc_final: 0.8565 (mmmm) REVERT: I 78 GLU cc_start: 0.7719 (pt0) cc_final: 0.7213 (pp20) REVERT: I 80 ARG cc_start: 0.7798 (mtm-85) cc_final: 0.7303 (mtm-85) REVERT: J 28 MET cc_start: 0.3802 (mmt) cc_final: 0.3249 (tpt) REVERT: J 36 GLN cc_start: 0.8321 (mt0) cc_final: 0.7795 (mm-40) REVERT: J 55 LYS cc_start: 0.8627 (tttp) cc_final: 0.8327 (mtpp) REVERT: J 123 LYS cc_start: 0.8910 (OUTLIER) cc_final: 0.8613 (mttm) REVERT: K 36 GLN cc_start: 0.8422 (mt0) cc_final: 0.8196 (mt0) REVERT: K 75 ASP cc_start: 0.8897 (p0) cc_final: 0.8464 (p0) REVERT: K 123 LYS cc_start: 0.8377 (mtmm) cc_final: 0.8160 (mttm) REVERT: K 147 GLU cc_start: 0.6528 (OUTLIER) cc_final: 0.5730 (pm20) REVERT: L 65 LYS cc_start: 0.8832 (OUTLIER) cc_final: 0.8547 (tttm) REVERT: L 80 ARG cc_start: 0.8733 (OUTLIER) cc_final: 0.8244 (mtt90) REVERT: L 110 LYS cc_start: 0.8890 (tppt) cc_final: 0.8223 (tptt) REVERT: L 123 LYS cc_start: 0.8123 (mttp) cc_final: 0.7751 (mtpp) REVERT: M 36 GLN cc_start: 0.7841 (mt0) cc_final: 0.7165 (tt0) REVERT: M 40 LYS cc_start: 0.8368 (ptmt) cc_final: 0.7518 (pttm) REVERT: M 43 MET cc_start: 0.9107 (ttm) cc_final: 0.8791 (ttp) REVERT: M 75 ASP cc_start: 0.8793 (p0) cc_final: 0.8436 (p0) REVERT: M 76 THR cc_start: 0.8926 (m) cc_final: 0.8596 (p) REVERT: M 78 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.8171 (tm-30) REVERT: M 96 TYR cc_start: 0.9248 (t80) cc_final: 0.8849 (t80) REVERT: M 123 LYS cc_start: 0.8698 (mtmt) cc_final: 0.8387 (mtmp) REVERT: N 145 ASN cc_start: 0.8406 (OUTLIER) cc_final: 0.7907 (t0) REVERT: O 52 GLN cc_start: 0.8379 (mm110) cc_final: 0.8068 (mm-40) REVERT: O 93 ARG cc_start: 0.8230 (OUTLIER) cc_final: 0.7985 (ptp90) REVERT: O 105 ILE cc_start: 0.8973 (pt) cc_final: 0.8586 (pp) REVERT: O 106 TYR cc_start: 0.7840 (p90) cc_final: 0.7593 (p90) REVERT: P 52 GLN cc_start: 0.8271 (mp10) cc_final: 0.7992 (mp10) REVERT: P 67 ASP cc_start: 0.8523 (m-30) cc_final: 0.7703 (t0) REVERT: P 78 GLU cc_start: 0.8321 (tt0) cc_final: 0.8060 (tt0) REVERT: P 130 SER cc_start: 0.9139 (m) cc_final: 0.8924 (p) REVERT: R 28 MET cc_start: 0.5117 (mmp) cc_final: 0.4418 (mpp) REVERT: R 43 MET cc_start: 0.9051 (ttm) cc_final: 0.8479 (ttm) REVERT: R 49 GLU cc_start: 0.8051 (tt0) cc_final: 0.7668 (tt0) REVERT: R 103 GLU cc_start: 0.8153 (tt0) cc_final: 0.7834 (tt0) REVERT: S 78 GLU cc_start: 0.8403 (tm-30) cc_final: 0.8043 (tm-30) REVERT: S 123 LYS cc_start: 0.8835 (mttt) cc_final: 0.8330 (mttp) REVERT: T 28 MET cc_start: 0.5623 (mmt) cc_final: 0.4951 (mpp) REVERT: T 43 MET cc_start: 0.9097 (ttm) cc_final: 0.8721 (ttm) REVERT: T 101 GLU cc_start: 0.8270 (tp30) cc_final: 0.7780 (tm-30) REVERT: T 142 LYS cc_start: 0.8692 (mttp) cc_final: 0.8453 (mptt) REVERT: V 28 MET cc_start: 0.4910 (mmt) cc_final: 0.3667 (mpp) REVERT: V 75 ASP cc_start: 0.8386 (p0) cc_final: 0.7996 (p0) REVERT: V 80 ARG cc_start: 0.8653 (mtp85) cc_final: 0.8428 (mtm180) REVERT: V 123 LYS cc_start: 0.8599 (mtpp) cc_final: 0.7977 (mtmm) REVERT: W 28 MET cc_start: 0.5229 (tpp) cc_final: 0.4244 (tpp) REVERT: W 43 MET cc_start: 0.8991 (ttp) cc_final: 0.8752 (ttm) REVERT: W 75 ASP cc_start: 0.8905 (p0) cc_final: 0.8591 (p0) REVERT: W 80 ARG cc_start: 0.8495 (OUTLIER) cc_final: 0.8292 (mtp180) REVERT: W 142 LYS cc_start: 0.7749 (OUTLIER) cc_final: 0.7273 (mmmt) REVERT: X 28 MET cc_start: 0.3595 (mmt) cc_final: 0.3028 (mpp) REVERT: X 49 GLU cc_start: 0.7773 (tt0) cc_final: 0.7532 (tt0) REVERT: X 82 LYS cc_start: 0.8048 (ptpp) cc_final: 0.7465 (ptpp) REVERT: X 86 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.7829 (tt) REVERT: X 96 TYR cc_start: 0.9232 (t80) cc_final: 0.8634 (t80) REVERT: X 130 SER cc_start: 0.8720 (m) cc_final: 0.8426 (t) REVERT: X 135 LYS cc_start: 0.8127 (OUTLIER) cc_final: 0.7526 (mttm) REVERT: X 145 ASN cc_start: 0.8264 (p0) cc_final: 0.7774 (p0) REVERT: Y 40 LYS cc_start: 0.8314 (ptmm) cc_final: 0.8022 (ptmt) REVERT: Y 75 ASP cc_start: 0.8629 (p0) cc_final: 0.8164 (p0) REVERT: Y 82 LYS cc_start: 0.8627 (ptmt) cc_final: 0.8344 (ptmm) REVERT: Y 110 LYS cc_start: 0.9004 (ttmm) cc_final: 0.8479 (tmmt) outliers start: 82 outliers final: 40 residues processed: 606 average time/residue: 1.6691 time to fit residues: 1121.5774 Evaluate side-chains 594 residues out of total 2544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 539 time to evaluate : 2.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A 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 E residue 87 MET Chi-restraints excluded: chain E residue 102 GLU Chi-restraints excluded: chain F residue 46 SER Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain I residue 46 SER Chi-restraints excluded: chain I residue 102 GLU Chi-restraints excluded: chain J residue 123 LYS Chi-restraints excluded: chain K residue 133 LEU Chi-restraints excluded: chain K residue 147 GLU 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 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 46 SER Chi-restraints excluded: chain O residue 73 VAL Chi-restraints excluded: chain O residue 93 ARG Chi-restraints excluded: chain O residue 145 ASN 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 46 SER Chi-restraints excluded: chain Q residue 77 LEU 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 T residue 40 LYS Chi-restraints excluded: chain T residue 52 GLN Chi-restraints excluded: chain T residue 102 GLU Chi-restraints excluded: chain V residue 131 VAL Chi-restraints excluded: chain W residue 80 ARG Chi-restraints excluded: chain W residue 142 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 86 LEU Chi-restraints excluded: chain X residue 131 VAL Chi-restraints excluded: chain X residue 135 LYS Chi-restraints excluded: chain Y residue 38 SER Chi-restraints excluded: chain Y residue 46 SER Chi-restraints excluded: chain Y residue 84 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 191 optimal weight: 6.9990 chunk 199 optimal weight: 5.9990 chunk 128 optimal weight: 4.9990 chunk 149 optimal weight: 5.9990 chunk 239 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 chunk 192 optimal weight: 20.0000 chunk 135 optimal weight: 0.0270 chunk 187 optimal weight: 5.9990 chunk 139 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 overall best weight: 3.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 36 GLN D 145 ASN E 36 GLN G 36 GLN G 52 GLN J 30 GLN J 36 GLN N 30 GLN O 126 ASN P 119 ASN R 126 ASN X 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 = 0.3682 r_free = 0.3682 target = 0.119628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.092974 restraints weight = 33363.336| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 2.64 r_work: 0.3192 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.4983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.059 22776 Z= 0.321 Angle : 0.690 11.895 30720 Z= 0.352 Chirality : 0.056 0.178 3672 Planarity : 0.004 0.044 3888 Dihedral : 4.731 16.637 3024 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 4.68 % Allowed : 29.48 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.16), residues: 2856 helix: None (None), residues: 0 sheet: 3.02 (0.15), residues: 1128 loop : -0.35 (0.15), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 59 HIS 0.008 0.001 HIS N 53 PHE 0.013 0.002 PHE N 124 TYR 0.032 0.002 TYR E 106 ARG 0.010 0.001 ARG T 93 Details of bonding type rmsd hydrogen bonds : bond 0.04601 ( 962) hydrogen bonds : angle 4.82876 ( 2454) covalent geometry : bond 0.00791 (22776) covalent geometry : angle 0.68954 (30720) *********************** 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 643 residues out of total 2544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 524 time to evaluate : 2.605 Fit side-chains REVERT: A 40 LYS cc_start: 0.8401 (ptmm) cc_final: 0.7968 (pttm) REVERT: B 52 GLN cc_start: 0.8197 (mt0) cc_final: 0.6546 (tm130) REVERT: B 116 LYS cc_start: 0.7996 (mtmt) cc_final: 0.7755 (mtpp) REVERT: D 28 MET cc_start: 0.5226 (mmm) cc_final: 0.3750 (tpp) REVERT: D 45 ILE cc_start: 0.9218 (OUTLIER) cc_final: 0.8986 (mm) REVERT: D 52 GLN cc_start: 0.8798 (OUTLIER) cc_final: 0.8432 (mp10) REVERT: D 77 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8816 (tp) REVERT: D 110 LYS cc_start: 0.8698 (tttt) cc_final: 0.8359 (ttpp) REVERT: D 142 LYS cc_start: 0.8475 (mmtm) cc_final: 0.7904 (mmtm) REVERT: C 28 MET cc_start: 0.3674 (mmt) cc_final: 0.3115 (mpp) REVERT: C 67 ASP cc_start: 0.8559 (m-30) cc_final: 0.8166 (m-30) REVERT: C 96 TYR cc_start: 0.9010 (t80) cc_final: 0.8718 (t80) REVERT: C 123 LYS cc_start: 0.7851 (mmpt) cc_final: 0.7476 (mppt) REVERT: C 142 LYS cc_start: 0.7645 (mmtm) cc_final: 0.7384 (mmmm) REVERT: C 145 ASN cc_start: 0.8289 (OUTLIER) cc_final: 0.7749 (t0) REVERT: E 43 MET cc_start: 0.8863 (ttm) cc_final: 0.8610 (ttm) REVERT: E 78 GLU cc_start: 0.8821 (OUTLIER) cc_final: 0.8414 (pp20) REVERT: E 87 MET cc_start: 0.7667 (OUTLIER) cc_final: 0.7445 (pmm) REVERT: E 94 ILE cc_start: 0.9425 (mt) cc_final: 0.9175 (mp) REVERT: E 102 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7840 (pt0) REVERT: E 142 LYS cc_start: 0.8574 (mppt) cc_final: 0.8279 (mmtm) REVERT: G 28 MET cc_start: 0.4917 (mmt) cc_final: 0.4282 (tpp) REVERT: G 78 GLU cc_start: 0.8704 (tt0) cc_final: 0.8244 (tm-30) REVERT: G 142 LYS cc_start: 0.8893 (mptt) cc_final: 0.8680 (mmtt) REVERT: H 28 MET cc_start: 0.4763 (mmt) cc_final: 0.4527 (tpp) REVERT: H 40 LYS cc_start: 0.7780 (ptmm) cc_final: 0.7353 (ptmt) REVERT: I 52 GLN cc_start: 0.7836 (mm-40) cc_final: 0.6978 (tm-30) REVERT: I 78 GLU cc_start: 0.7670 (pt0) cc_final: 0.7195 (pp20) REVERT: I 80 ARG cc_start: 0.7892 (mtm-85) cc_final: 0.7274 (mtm-85) REVERT: J 28 MET cc_start: 0.3849 (mmt) cc_final: 0.3253 (tpt) REVERT: J 36 GLN cc_start: 0.8584 (mt0) cc_final: 0.8012 (mt0) REVERT: J 93 ARG cc_start: 0.8286 (OUTLIER) cc_final: 0.7072 (ptp-170) REVERT: J 123 LYS cc_start: 0.8934 (OUTLIER) cc_final: 0.8630 (mttm) REVERT: K 75 ASP cc_start: 0.8983 (p0) cc_final: 0.8527 (p0) REVERT: K 147 GLU cc_start: 0.6496 (OUTLIER) cc_final: 0.5762 (pm20) REVERT: L 65 LYS cc_start: 0.8893 (OUTLIER) cc_final: 0.8584 (tttm) REVERT: L 80 ARG cc_start: 0.8787 (OUTLIER) cc_final: 0.8380 (mtm-85) REVERT: L 123 LYS cc_start: 0.8233 (mttp) cc_final: 0.7951 (mtpp) REVERT: M 36 GLN cc_start: 0.7900 (mt0) cc_final: 0.7127 (tt0) REVERT: M 40 LYS cc_start: 0.8522 (ptmt) cc_final: 0.7733 (pttm) REVERT: M 43 MET cc_start: 0.9101 (ttm) cc_final: 0.8895 (ttp) REVERT: M 75 ASP cc_start: 0.8906 (p0) cc_final: 0.8570 (p0) REVERT: M 76 THR cc_start: 0.9111 (m) cc_final: 0.8803 (p) REVERT: M 78 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.8160 (tt0) REVERT: M 96 TYR cc_start: 0.9276 (t80) cc_final: 0.9003 (t80) REVERT: M 110 LYS cc_start: 0.8855 (ttpt) cc_final: 0.8397 (ttpp) REVERT: N 101 GLU cc_start: 0.8201 (mp0) cc_final: 0.7954 (mp0) REVERT: N 145 ASN cc_start: 0.8440 (OUTLIER) cc_final: 0.7960 (t0) REVERT: O 52 GLN cc_start: 0.8429 (mm110) cc_final: 0.8135 (mm-40) REVERT: O 93 ARG cc_start: 0.8303 (OUTLIER) cc_final: 0.7418 (ptp90) REVERT: O 105 ILE cc_start: 0.9063 (pt) cc_final: 0.8682 (pp) REVERT: O 106 TYR cc_start: 0.8020 (p90) cc_final: 0.7724 (p90) REVERT: P 52 GLN cc_start: 0.8283 (mp10) cc_final: 0.8012 (mp10) REVERT: P 67 ASP cc_start: 0.8599 (m-30) cc_final: 0.7695 (t0) REVERT: P 78 GLU cc_start: 0.8328 (tt0) cc_final: 0.7356 (tm-30) REVERT: R 49 GLU cc_start: 0.8150 (tt0) cc_final: 0.7927 (tt0) REVERT: R 55 LYS cc_start: 0.8279 (tttt) cc_final: 0.7912 (mtpp) REVERT: R 80 ARG cc_start: 0.7935 (mtm180) cc_final: 0.7554 (mtm110) REVERT: R 103 GLU cc_start: 0.8286 (tt0) cc_final: 0.7961 (tt0) REVERT: R 147 GLU cc_start: 0.7416 (OUTLIER) cc_final: 0.6686 (pp20) REVERT: S 52 GLN cc_start: 0.8360 (mm-40) cc_final: 0.8145 (mm-40) REVERT: S 110 LYS cc_start: 0.8923 (tmtp) cc_final: 0.8593 (tptp) REVERT: T 28 MET cc_start: 0.5845 (mmt) cc_final: 0.5254 (mpp) REVERT: T 43 MET cc_start: 0.9121 (ttm) cc_final: 0.8797 (ttm) REVERT: T 101 GLU cc_start: 0.8310 (tp30) cc_final: 0.7855 (tm-30) REVERT: T 142 LYS cc_start: 0.8808 (mttp) cc_final: 0.8532 (mptt) REVERT: V 28 MET cc_start: 0.4784 (mmt) cc_final: 0.3600 (mpp) REVERT: V 75 ASP cc_start: 0.8516 (p0) cc_final: 0.8063 (p0) REVERT: V 80 ARG cc_start: 0.8716 (mtp85) cc_final: 0.8450 (mtm180) REVERT: V 123 LYS cc_start: 0.8615 (mtpp) cc_final: 0.8222 (mtpp) REVERT: W 28 MET cc_start: 0.5521 (tpp) cc_final: 0.4530 (tpp) REVERT: W 75 ASP cc_start: 0.8916 (p0) cc_final: 0.8600 (p0) REVERT: W 80 ARG cc_start: 0.8547 (OUTLIER) cc_final: 0.8245 (mtp180) REVERT: W 142 LYS cc_start: 0.7695 (OUTLIER) cc_final: 0.6972 (mmmt) REVERT: X 82 LYS cc_start: 0.8317 (ptpp) cc_final: 0.7859 (ptpp) REVERT: X 96 TYR cc_start: 0.9316 (t80) cc_final: 0.8846 (t80) REVERT: X 135 LYS cc_start: 0.8293 (OUTLIER) cc_final: 0.7660 (mttm) REVERT: X 145 ASN cc_start: 0.8160 (p0) cc_final: 0.7686 (p0) REVERT: Y 40 LYS cc_start: 0.8379 (ptmm) cc_final: 0.8108 (ptmt) REVERT: Y 75 ASP cc_start: 0.8594 (p0) cc_final: 0.8011 (p0) outliers start: 119 outliers final: 70 residues processed: 599 average time/residue: 1.8698 time to fit residues: 1244.2505 Evaluate side-chains 603 residues out of total 2544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 514 time to evaluate : 2.659 ------------------------------------------------------------------------------- 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 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 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 C residue 145 ASN 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 87 MET Chi-restraints excluded: chain E residue 102 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 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 38 SER Chi-restraints excluded: chain I residue 40 LYS Chi-restraints excluded: chain I residue 46 SER 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 K residue 147 GLU 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 35 ILE Chi-restraints excluded: chain M residue 78 GLU Chi-restraints excluded: chain M residue 101 GLU Chi-restraints excluded: chain M residue 147 GLU Chi-restraints excluded: chain N residue 40 LYS Chi-restraints excluded: chain N residue 104 GLU 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 46 SER Chi-restraints excluded: chain O residue 73 VAL Chi-restraints excluded: chain O residue 76 THR Chi-restraints excluded: chain O residue 93 ARG 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 46 SER 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 46 SER Chi-restraints excluded: chain R residue 73 VAL Chi-restraints excluded: chain R residue 145 ASN Chi-restraints excluded: chain R residue 147 GLU Chi-restraints excluded: chain S residue 45 ILE Chi-restraints excluded: chain S residue 70 LEU 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 80 ARG Chi-restraints excluded: chain W residue 142 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 131 VAL Chi-restraints excluded: chain X residue 135 LYS Chi-restraints excluded: chain Y residue 38 SER Chi-restraints excluded: chain Y residue 46 SER Chi-restraints excluded: chain Y residue 76 THR Chi-restraints excluded: chain Y residue 84 SER Chi-restraints excluded: chain Y residue 139 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 219 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 105 optimal weight: 7.9990 chunk 82 optimal weight: 0.8980 chunk 135 optimal weight: 1.9990 chunk 247 optimal weight: 0.0070 chunk 120 optimal weight: 0.0020 chunk 59 optimal weight: 0.9980 chunk 281 optimal weight: 0.9990 chunk 20 optimal weight: 6.9990 chunk 128 optimal weight: 0.9990 overall best weight: 0.5808 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 145 ASN E 30 GLN G 36 GLN G 52 GLN K 36 GLN O 119 ASN X 52 GLN Y 36 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.123299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.096381 restraints weight = 33073.503| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.69 r_work: 0.3255 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.5001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 22776 Z= 0.101 Angle : 0.586 12.134 30720 Z= 0.293 Chirality : 0.052 0.165 3672 Planarity : 0.002 0.027 3888 Dihedral : 4.050 15.485 3024 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 2.63 % Allowed : 31.84 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.17), residues: 2856 helix: None (None), residues: 0 sheet: 2.64 (0.14), residues: 1344 loop : -0.17 (0.17), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP L 59 HIS 0.002 0.001 HIS N 53 PHE 0.004 0.001 PHE G 42 TYR 0.016 0.001 TYR J 106 ARG 0.007 0.000 ARG T 93 Details of bonding type rmsd hydrogen bonds : bond 0.03361 ( 962) hydrogen bonds : angle 4.55152 ( 2454) covalent geometry : bond 0.00238 (22776) covalent geometry : angle 0.58635 (30720) *********************** 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 620 residues out of total 2544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 553 time to evaluate : 2.839 Fit side-chains REVERT: A 40 LYS cc_start: 0.8348 (ptmm) cc_final: 0.7940 (pttp) REVERT: A 78 GLU cc_start: 0.8700 (tt0) cc_final: 0.8275 (tm-30) REVERT: B 52 GLN cc_start: 0.8309 (mt0) cc_final: 0.6983 (tm130) REVERT: B 116 LYS cc_start: 0.7908 (mtmt) cc_final: 0.7651 (mtpp) REVERT: D 28 MET cc_start: 0.5023 (mmm) cc_final: 0.3614 (tpp) REVERT: D 45 ILE cc_start: 0.9140 (mt) cc_final: 0.8890 (mm) REVERT: D 52 GLN cc_start: 0.8752 (OUTLIER) cc_final: 0.8454 (mp10) REVERT: D 110 LYS cc_start: 0.8678 (tttt) cc_final: 0.8268 (ttpp) REVERT: D 142 LYS cc_start: 0.8454 (mmtm) cc_final: 0.7919 (mmtm) REVERT: C 28 MET cc_start: 0.3628 (mmt) cc_final: 0.3147 (mpp) REVERT: C 45 ILE cc_start: 0.9015 (mt) cc_final: 0.8734 (mp) REVERT: C 67 ASP cc_start: 0.8460 (m-30) cc_final: 0.8151 (m-30) REVERT: C 96 TYR cc_start: 0.8891 (t80) cc_final: 0.8556 (t80) REVERT: C 116 LYS cc_start: 0.7781 (mtpt) cc_final: 0.7545 (mtpp) REVERT: C 123 LYS cc_start: 0.7720 (mmpt) cc_final: 0.7330 (mppt) REVERT: C 142 LYS cc_start: 0.7607 (mmtm) cc_final: 0.7252 (mmmm) REVERT: C 145 ASN cc_start: 0.8210 (OUTLIER) cc_final: 0.7660 (t0) REVERT: E 78 GLU cc_start: 0.8711 (OUTLIER) cc_final: 0.8296 (pp20) REVERT: E 80 ARG cc_start: 0.8565 (mtm-85) cc_final: 0.8123 (mtm-85) REVERT: E 87 MET cc_start: 0.7607 (OUTLIER) cc_final: 0.7376 (pmm) REVERT: E 93 ARG cc_start: 0.8291 (ptp90) cc_final: 0.8019 (ptp90) REVERT: E 94 ILE cc_start: 0.9398 (mt) cc_final: 0.9103 (mp) REVERT: E 102 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7870 (pt0) REVERT: E 142 LYS cc_start: 0.8506 (mppt) cc_final: 0.8223 (mmtm) REVERT: F 40 LYS cc_start: 0.8159 (OUTLIER) cc_final: 0.7924 (pttt) REVERT: G 28 MET cc_start: 0.4771 (mmt) cc_final: 0.4200 (tpp) REVERT: G 78 GLU cc_start: 0.8579 (tt0) cc_final: 0.8246 (tm-30) REVERT: H 28 MET cc_start: 0.4813 (mmt) cc_final: 0.4524 (tpp) REVERT: H 40 LYS cc_start: 0.7620 (ptmm) cc_final: 0.7281 (ptmt) REVERT: H 78 GLU cc_start: 0.8532 (tt0) cc_final: 0.8013 (tm-30) REVERT: I 52 GLN cc_start: 0.7785 (mm-40) cc_final: 0.7172 (tm-30) REVERT: I 55 LYS cc_start: 0.8841 (mtpp) cc_final: 0.8603 (mmmm) REVERT: I 78 GLU cc_start: 0.7753 (pt0) cc_final: 0.7305 (pp20) REVERT: I 80 ARG cc_start: 0.7736 (mtm-85) cc_final: 0.7240 (mtm-85) REVERT: I 110 LYS cc_start: 0.8109 (ttpp) cc_final: 0.7805 (ttpp) REVERT: J 28 MET cc_start: 0.3672 (mmt) cc_final: 0.3266 (tpt) REVERT: J 36 GLN cc_start: 0.8415 (mt0) cc_final: 0.7901 (mt0) REVERT: J 55 LYS cc_start: 0.8604 (tttp) cc_final: 0.8312 (mtpp) REVERT: J 93 ARG cc_start: 0.8450 (OUTLIER) cc_final: 0.7243 (ptp-170) REVERT: J 123 LYS cc_start: 0.8905 (OUTLIER) cc_final: 0.8600 (mttm) REVERT: K 36 GLN cc_start: 0.8333 (mt0) cc_final: 0.8088 (mt0) REVERT: K 75 ASP cc_start: 0.8924 (p0) cc_final: 0.8514 (p0) REVERT: K 147 GLU cc_start: 0.6513 (OUTLIER) cc_final: 0.5704 (pm20) REVERT: L 65 LYS cc_start: 0.8893 (tttp) cc_final: 0.8573 (tttm) REVERT: L 80 ARG cc_start: 0.8729 (OUTLIER) cc_final: 0.8443 (mtt90) REVERT: L 110 LYS cc_start: 0.8901 (tppt) cc_final: 0.8355 (tptt) REVERT: L 123 LYS cc_start: 0.8125 (mttp) cc_final: 0.7787 (mtpp) REVERT: M 36 GLN cc_start: 0.7813 (mt0) cc_final: 0.7063 (tt0) REVERT: M 40 LYS cc_start: 0.8382 (ptmt) cc_final: 0.7535 (pttm) REVERT: M 43 MET cc_start: 0.9110 (ttm) cc_final: 0.8862 (ttp) REVERT: M 75 ASP cc_start: 0.8772 (p0) cc_final: 0.8424 (p0) REVERT: M 76 THR cc_start: 0.8956 (m) cc_final: 0.8634 (p) REVERT: M 78 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.8133 (tm-30) REVERT: M 96 TYR cc_start: 0.9273 (t80) cc_final: 0.8884 (t80) REVERT: M 123 LYS cc_start: 0.8674 (mtmt) cc_final: 0.8361 (mtmp) REVERT: N 145 ASN cc_start: 0.8391 (OUTLIER) cc_final: 0.7881 (t0) REVERT: N 147 GLU cc_start: 0.7313 (OUTLIER) cc_final: 0.7085 (mp0) REVERT: O 52 GLN cc_start: 0.8402 (mm110) cc_final: 0.8093 (mm-40) REVERT: O 93 ARG cc_start: 0.8193 (OUTLIER) cc_final: 0.7969 (ptp90) REVERT: O 105 ILE cc_start: 0.8988 (pt) cc_final: 0.8604 (pp) REVERT: O 106 TYR cc_start: 0.7838 (p90) cc_final: 0.7610 (p90) REVERT: O 123 LYS cc_start: 0.8539 (mtpp) cc_final: 0.8265 (ptpt) REVERT: P 52 GLN cc_start: 0.8283 (mp10) cc_final: 0.7943 (mp10) REVERT: P 67 ASP cc_start: 0.8562 (m-30) cc_final: 0.7731 (t0) REVERT: P 78 GLU cc_start: 0.8325 (tt0) cc_final: 0.8066 (tt0) REVERT: Q 28 MET cc_start: 0.3895 (mpm) cc_final: 0.3260 (mpp) REVERT: Q 82 LYS cc_start: 0.8405 (pttt) cc_final: 0.8199 (ptpt) REVERT: R 28 MET cc_start: 0.5127 (mmp) cc_final: 0.4489 (mpp) REVERT: R 43 MET cc_start: 0.9057 (ttm) cc_final: 0.8559 (ttm) REVERT: R 49 GLU cc_start: 0.8067 (tt0) cc_final: 0.7798 (tt0) REVERT: R 103 GLU cc_start: 0.8194 (tt0) cc_final: 0.7872 (tt0) REVERT: S 123 LYS cc_start: 0.8821 (mttt) cc_final: 0.8311 (mttp) REVERT: T 28 MET cc_start: 0.5798 (mmt) cc_final: 0.5188 (mpp) REVERT: T 43 MET cc_start: 0.9100 (ttm) cc_final: 0.8720 (ttm) REVERT: T 52 GLN cc_start: 0.8614 (mm-40) cc_final: 0.8331 (mm110) REVERT: T 101 GLU cc_start: 0.8298 (tp30) cc_final: 0.7805 (tm-30) REVERT: T 142 LYS cc_start: 0.8712 (mttp) cc_final: 0.8467 (mptt) REVERT: V 28 MET cc_start: 0.4741 (mmt) cc_final: 0.3501 (mpp) REVERT: V 40 LYS cc_start: 0.8586 (ptmm) cc_final: 0.8296 (pttp) REVERT: V 75 ASP cc_start: 0.8393 (p0) cc_final: 0.7965 (p0) REVERT: V 80 ARG cc_start: 0.8664 (mtp85) cc_final: 0.8423 (mtm180) REVERT: V 123 LYS cc_start: 0.8567 (mtpp) cc_final: 0.7889 (mtmm) REVERT: W 28 MET cc_start: 0.5281 (tpp) cc_final: 0.4262 (tpp) REVERT: W 75 ASP cc_start: 0.8868 (p0) cc_final: 0.8545 (p0) REVERT: W 80 ARG cc_start: 0.8501 (OUTLIER) cc_final: 0.8162 (mtp180) REVERT: W 142 LYS cc_start: 0.7762 (mmpt) cc_final: 0.7297 (mmmt) REVERT: X 49 GLU cc_start: 0.7737 (tt0) cc_final: 0.7499 (tt0) REVERT: X 82 LYS cc_start: 0.8040 (ptpp) cc_final: 0.7467 (ptpp) REVERT: X 96 TYR cc_start: 0.9240 (t80) cc_final: 0.8648 (t80) REVERT: X 130 SER cc_start: 0.8744 (m) cc_final: 0.8435 (t) REVERT: X 135 LYS cc_start: 0.8122 (OUTLIER) cc_final: 0.7414 (mttm) REVERT: X 145 ASN cc_start: 0.8239 (p0) cc_final: 0.7735 (p0) REVERT: Y 75 ASP cc_start: 0.8584 (p0) cc_final: 0.8151 (p0) REVERT: Y 110 LYS cc_start: 0.8909 (ttmm) cc_final: 0.8451 (tmmt) outliers start: 67 outliers final: 34 residues processed: 592 average time/residue: 1.6358 time to fit residues: 1077.5506 Evaluate side-chains 590 residues out of total 2544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 540 time to evaluate : 2.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A 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 130 SER Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 145 ASN Chi-restraints excluded: chain E residue 78 GLU Chi-restraints excluded: chain E residue 87 MET Chi-restraints excluded: chain E residue 102 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 84 SER Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain I residue 40 LYS Chi-restraints excluded: chain I residue 46 SER Chi-restraints excluded: chain J residue 93 ARG Chi-restraints excluded: chain J residue 123 LYS Chi-restraints excluded: chain K residue 133 LEU Chi-restraints excluded: chain K residue 147 GLU 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 35 ILE Chi-restraints excluded: chain M residue 78 GLU Chi-restraints excluded: chain M residue 147 GLU Chi-restraints excluded: chain N residue 104 GLU 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 93 ARG 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 46 SER Chi-restraints excluded: chain R residue 145 ASN Chi-restraints excluded: chain T residue 102 GLU Chi-restraints excluded: chain V residue 131 VAL Chi-restraints excluded: chain W residue 80 ARG Chi-restraints excluded: chain X residue 35 ILE Chi-restraints excluded: chain X residue 45 ILE Chi-restraints excluded: chain X residue 135 LYS Chi-restraints excluded: chain Y residue 38 SER Chi-restraints excluded: chain Y residue 46 SER Chi-restraints excluded: chain Y residue 84 SER Chi-restraints excluded: chain Y residue 139 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 38 optimal weight: 7.9990 chunk 263 optimal weight: 0.3980 chunk 153 optimal weight: 4.9990 chunk 149 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 168 optimal weight: 4.9990 chunk 107 optimal weight: 5.9990 chunk 163 optimal weight: 2.9990 chunk 208 optimal weight: 2.9990 chunk 166 optimal weight: 3.9990 overall best weight: 2.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 145 ASN G 52 GLN H 30 GLN S 30 GLN X 52 GLN Y 36 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.119815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.092962 restraints weight = 33459.266| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 2.67 r_work: 0.3205 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.5070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 22776 Z= 0.247 Angle : 0.670 12.073 30720 Z= 0.339 Chirality : 0.055 0.183 3672 Planarity : 0.003 0.032 3888 Dihedral : 4.538 16.179 3024 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.67 % Allowed : 32.04 % Favored : 65.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.16), residues: 2856 helix: None (None), residues: 0 sheet: 3.07 (0.15), residues: 1128 loop : -0.26 (0.15), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 59 HIS 0.007 0.001 HIS N 53 PHE 0.012 0.002 PHE N 124 TYR 0.032 0.002 TYR E 106 ARG 0.009 0.001 ARG T 93 Details of bonding type rmsd hydrogen bonds : bond 0.04255 ( 962) hydrogen bonds : angle 4.72885 ( 2454) covalent geometry : bond 0.00607 (22776) covalent geometry : angle 0.66953 (30720) ********************** 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 592 residues out of total 2544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 524 time to evaluate : 2.822 Fit side-chains REVERT: A 40 LYS cc_start: 0.8347 (ptmm) cc_final: 0.7869 (pttp) REVERT: A 78 GLU cc_start: 0.8724 (tt0) cc_final: 0.8282 (tm-30) REVERT: B 52 GLN cc_start: 0.8172 (mt0) cc_final: 0.6513 (tm130) REVERT: B 116 LYS cc_start: 0.7932 (mtmt) cc_final: 0.7689 (mtpp) REVERT: D 28 MET cc_start: 0.5325 (mmm) cc_final: 0.3880 (tpp) REVERT: D 52 GLN cc_start: 0.8776 (OUTLIER) cc_final: 0.8445 (mp10) REVERT: D 101 GLU cc_start: 0.8088 (tp30) cc_final: 0.7740 (tp30) REVERT: D 110 LYS cc_start: 0.8660 (tttt) cc_final: 0.8311 (ttpp) REVERT: D 142 LYS cc_start: 0.8453 (mmtm) cc_final: 0.7919 (mmtm) REVERT: C 28 MET cc_start: 0.3885 (mmt) cc_final: 0.3322 (mpp) REVERT: C 67 ASP cc_start: 0.8508 (m-30) cc_final: 0.8141 (m-30) REVERT: C 96 TYR cc_start: 0.9007 (t80) cc_final: 0.8669 (t80) REVERT: C 110 LYS cc_start: 0.8299 (ptpt) cc_final: 0.7757 (ptmt) REVERT: C 123 LYS cc_start: 0.7792 (mmpt) cc_final: 0.7393 (mppt) REVERT: C 142 LYS cc_start: 0.7636 (mmtm) cc_final: 0.7362 (mmmm) REVERT: C 145 ASN cc_start: 0.8265 (OUTLIER) cc_final: 0.7703 (t0) REVERT: E 78 GLU cc_start: 0.8783 (OUTLIER) cc_final: 0.8367 (pp20) REVERT: E 87 MET cc_start: 0.7659 (OUTLIER) cc_final: 0.7428 (pmm) REVERT: E 93 ARG cc_start: 0.8301 (ptp90) cc_final: 0.7919 (ptp90) REVERT: E 94 ILE cc_start: 0.9401 (mt) cc_final: 0.9125 (mp) REVERT: E 102 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7915 (pt0) REVERT: E 142 LYS cc_start: 0.8559 (mppt) cc_final: 0.8272 (mmtm) REVERT: G 28 MET cc_start: 0.4960 (mmt) cc_final: 0.4244 (tpp) REVERT: G 78 GLU cc_start: 0.8645 (tt0) cc_final: 0.8215 (tm-30) REVERT: H 28 MET cc_start: 0.4863 (mmt) cc_final: 0.4638 (tpp) REVERT: H 40 LYS cc_start: 0.7729 (ptmm) cc_final: 0.7284 (ptmt) REVERT: I 52 GLN cc_start: 0.7770 (mm-40) cc_final: 0.6967 (tm-30) REVERT: I 78 GLU cc_start: 0.7647 (pt0) cc_final: 0.7170 (pp20) REVERT: I 80 ARG cc_start: 0.7846 (mtm-85) cc_final: 0.7176 (mtm-85) REVERT: J 28 MET cc_start: 0.3749 (mmt) cc_final: 0.3309 (tpt) REVERT: J 36 GLN cc_start: 0.8545 (mt0) cc_final: 0.8067 (mt0) REVERT: J 123 LYS cc_start: 0.8930 (OUTLIER) cc_final: 0.8625 (mttm) REVERT: K 75 ASP cc_start: 0.8888 (p0) cc_final: 0.8433 (p0) REVERT: K 147 GLU cc_start: 0.6462 (OUTLIER) cc_final: 0.5661 (pm20) REVERT: L 65 LYS cc_start: 0.8875 (tttp) cc_final: 0.8579 (tttm) REVERT: L 80 ARG cc_start: 0.8779 (OUTLIER) cc_final: 0.8420 (mtm-85) REVERT: L 110 LYS cc_start: 0.8932 (tppt) cc_final: 0.8348 (tptt) REVERT: L 123 LYS cc_start: 0.8205 (mttp) cc_final: 0.7887 (mtpp) REVERT: L 142 LYS cc_start: 0.8641 (mmtm) cc_final: 0.8215 (mmtt) REVERT: M 36 GLN cc_start: 0.7831 (mt0) cc_final: 0.7114 (tt0) REVERT: M 40 LYS cc_start: 0.8452 (ptmt) cc_final: 0.7648 (pttm) REVERT: M 43 MET cc_start: 0.9105 (ttm) cc_final: 0.8819 (ttp) REVERT: M 75 ASP cc_start: 0.8871 (p0) cc_final: 0.8498 (p0) REVERT: M 76 THR cc_start: 0.9080 (m) cc_final: 0.8757 (p) REVERT: M 78 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.8148 (tm-30) REVERT: M 96 TYR cc_start: 0.9256 (t80) cc_final: 0.8934 (t80) REVERT: M 110 LYS cc_start: 0.8805 (ttpt) cc_final: 0.8342 (ttpp) REVERT: N 145 ASN cc_start: 0.8418 (OUTLIER) cc_final: 0.7921 (t0) REVERT: N 147 GLU cc_start: 0.7348 (OUTLIER) cc_final: 0.7054 (mp0) REVERT: O 52 GLN cc_start: 0.8398 (mm110) cc_final: 0.8088 (mm-40) REVERT: O 93 ARG cc_start: 0.8272 (OUTLIER) cc_final: 0.7372 (ptp90) REVERT: O 105 ILE cc_start: 0.8989 (pt) cc_final: 0.8585 (pp) REVERT: O 106 TYR cc_start: 0.7995 (p90) cc_final: 0.7698 (p90) REVERT: P 52 GLN cc_start: 0.8283 (mp10) cc_final: 0.7953 (mp10) REVERT: P 67 ASP cc_start: 0.8620 (m-30) cc_final: 0.7697 (t0) REVERT: P 78 GLU cc_start: 0.8291 (tt0) cc_final: 0.7325 (tm-30) REVERT: Q 28 MET cc_start: 0.3743 (mpm) cc_final: 0.2946 (mpp) REVERT: R 43 MET cc_start: 0.9026 (ttm) cc_final: 0.8480 (ttm) REVERT: R 49 GLU cc_start: 0.8105 (tt0) cc_final: 0.7785 (tt0) REVERT: R 55 LYS cc_start: 0.8201 (tttt) cc_final: 0.7805 (mtpp) REVERT: R 103 GLU cc_start: 0.8221 (tt0) cc_final: 0.7952 (tt0) REVERT: S 75 ASP cc_start: 0.8669 (p0) cc_final: 0.8246 (p0) REVERT: S 123 LYS cc_start: 0.8850 (mttt) cc_final: 0.8338 (mttp) REVERT: T 28 MET cc_start: 0.6091 (mmt) cc_final: 0.5444 (mpp) REVERT: T 43 MET cc_start: 0.9113 (ttm) cc_final: 0.8708 (ttm) REVERT: T 101 GLU cc_start: 0.8287 (tp30) cc_final: 0.7803 (tm-30) REVERT: T 110 LYS cc_start: 0.8823 (tptp) cc_final: 0.8460 (tptp) REVERT: T 142 LYS cc_start: 0.8787 (mttp) cc_final: 0.8509 (mptt) REVERT: V 28 MET cc_start: 0.4682 (mmt) cc_final: 0.3475 (mpp) REVERT: V 75 ASP cc_start: 0.8454 (p0) cc_final: 0.8006 (p0) REVERT: V 80 ARG cc_start: 0.8731 (OUTLIER) cc_final: 0.8470 (mtm180) REVERT: V 123 LYS cc_start: 0.8613 (mtpp) cc_final: 0.8205 (mtpp) REVERT: W 28 MET cc_start: 0.5495 (tpp) cc_final: 0.4473 (tpp) REVERT: W 75 ASP cc_start: 0.8892 (p0) cc_final: 0.8568 (p0) REVERT: W 80 ARG cc_start: 0.8535 (OUTLIER) cc_final: 0.8212 (mtp180) REVERT: W 142 LYS cc_start: 0.7692 (mmpt) cc_final: 0.6951 (mmmt) REVERT: X 82 LYS cc_start: 0.8155 (ptpp) cc_final: 0.7571 (ptpp) REVERT: X 96 TYR cc_start: 0.9266 (t80) cc_final: 0.8733 (t80) REVERT: X 130 SER cc_start: 0.8865 (m) cc_final: 0.8516 (t) REVERT: X 135 LYS cc_start: 0.8231 (OUTLIER) cc_final: 0.7604 (mttm) REVERT: X 145 ASN cc_start: 0.8242 (p0) cc_final: 0.7726 (p0) REVERT: Y 75 ASP cc_start: 0.8550 (p0) cc_final: 0.8063 (p0) REVERT: Y 110 LYS cc_start: 0.8868 (ttmm) cc_final: 0.8448 (tmmt) outliers start: 68 outliers final: 42 residues processed: 566 average time/residue: 1.6836 time to fit residues: 1057.5661 Evaluate side-chains 572 residues out of total 2544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 515 time to evaluate : 2.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A 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 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 C residue 145 ASN Chi-restraints excluded: chain E residue 78 GLU Chi-restraints excluded: chain E residue 87 MET Chi-restraints excluded: chain E residue 102 GLU 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 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 40 LYS Chi-restraints excluded: chain I residue 46 SER Chi-restraints excluded: chain J residue 123 LYS Chi-restraints excluded: chain K residue 133 LEU Chi-restraints excluded: chain K residue 147 GLU Chi-restraints excluded: chain L residue 35 ILE 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 35 ILE Chi-restraints excluded: chain M residue 78 GLU Chi-restraints excluded: chain M residue 139 SER Chi-restraints excluded: chain M residue 147 GLU Chi-restraints excluded: chain N residue 104 GLU 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 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 O residue 93 ARG 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 46 SER Chi-restraints excluded: chain R residue 145 ASN Chi-restraints excluded: chain S residue 45 ILE 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 W residue 80 ARG Chi-restraints excluded: chain X residue 35 ILE Chi-restraints excluded: chain X residue 45 ILE Chi-restraints excluded: chain X residue 135 LYS Chi-restraints excluded: chain Y residue 38 SER Chi-restraints excluded: chain Y residue 46 SER Chi-restraints excluded: chain Y residue 84 SER Chi-restraints excluded: chain Y residue 139 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 114 optimal weight: 2.9990 chunk 256 optimal weight: 5.9990 chunk 232 optimal weight: 3.9990 chunk 110 optimal weight: 0.5980 chunk 74 optimal weight: 3.9990 chunk 188 optimal weight: 3.9990 chunk 226 optimal weight: 0.9980 chunk 213 optimal weight: 5.9990 chunk 160 optimal weight: 3.9990 chunk 264 optimal weight: 9.9990 chunk 255 optimal weight: 2.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 36 GLN D 145 ASN G 52 GLN K 36 GLN K 52 GLN O 119 ASN X 52 GLN Y 36 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.120020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.093279 restraints weight = 33127.469| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 2.65 r_work: 0.3215 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.5079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 22776 Z= 0.219 Angle : 0.657 11.854 30720 Z= 0.332 Chirality : 0.054 0.179 3672 Planarity : 0.003 0.033 3888 Dihedral : 4.524 16.263 3024 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.83 % Allowed : 31.88 % Favored : 65.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.17), residues: 2856 helix: None (None), residues: 0 sheet: 2.85 (0.15), residues: 1152 loop : -0.30 (0.15), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP Y 59 HIS 0.006 0.001 HIS N 53 PHE 0.011 0.001 PHE N 124 TYR 0.020 0.002 TYR O 96 ARG 0.009 0.001 ARG T 93 Details of bonding type rmsd hydrogen bonds : bond 0.04120 ( 962) hydrogen bonds : angle 4.73222 ( 2454) covalent geometry : bond 0.00536 (22776) covalent geometry : angle 0.65714 (30720) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21412.00 seconds wall clock time: 371 minutes 14.75 seconds (22274.75 seconds total)