Starting phenix.real_space_refine on Tue Sep 15 16:09:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w6g_65690/09_2026/9w6g_65690.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w6g_65690/09_2026/9w6g_65690.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9w6g_65690/09_2026/9w6g_65690.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w6g_65690/09_2026/9w6g_65690.map" model { file = "/net/cci-nas-00/data/ceres_data/9w6g_65690/09_2026/9w6g_65690.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w6g_65690/09_2026/9w6g_65690.cif" } resolution = 4.02 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 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: 5 Type Number sf(0) Gaussians P 944 5.49 5 S 56 5.16 5 C 23105 2.51 5 N 7711 2.21 5 O 9559 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 41375 Number of models: 1 Model: "" Number of chains: 40 Chain: "A" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 790 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 614 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 1, 'TRANS': 75} Chain: "C" Number of atoms: 701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 701 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 4, 'TRANS': 86} Chain: "D" Number of atoms: 679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 679 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 2, 'TRANS': 84} Chain: "E" Number of atoms: 739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 739 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "F" Number of atoms: 602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 602 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "G" Number of atoms: 707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 707 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "H" Number of atoms: 672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 672 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 2, 'TRANS': 83} Chain: "I" Number of atoms: 2433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 2433 Classifications: {'DNA': 118} Link IDs: {'rna3p': 117} Chain: "J" Number of atoms: 2405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 2405 Classifications: {'DNA': 118} Link IDs: {'rna3p': 117} Chain: "K" Number of atoms: 732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 732 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "L" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 610 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 1, 'TRANS': 74} Chain: "M" Number of atoms: 741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 741 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain: "N" Number of atoms: 679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 679 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 2, 'TRANS': 84} Chain: "O" Number of atoms: 709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 709 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 2, 'TRANS': 83} Chain: "P" Number of atoms: 614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 614 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 1, 'TRANS': 75} Chain: "Q" Number of atoms: 663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 663 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 3, 'TRANS': 82} Chain: "R" Number of atoms: 672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 672 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 2, 'TRANS': 83} Chain: "S" Number of atoms: 2433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 2433 Classifications: {'DNA': 118} Link IDs: {'rna3p': 117} Chain: "T" Number of atoms: 2405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 2405 Classifications: {'DNA': 118} Link IDs: {'rna3p': 117} Chain: "U" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 790 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "V" Number of atoms: 614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 614 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 1, 'TRANS': 75} Chain: "W" Number of atoms: 711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 711 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "X" Number of atoms: 679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 679 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 2, 'TRANS': 84} Chain: "Y" Number of atoms: 732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 732 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "Z" Number of atoms: 614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 614 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 1, 'TRANS': 75} Chain: "a" Number of atoms: 700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 700 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 4, 'TRANS': 86} Chain: "b" Number of atoms: 672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 672 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 2, 'TRANS': 83} Chain: "c" Number of atoms: 2433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 2433 Classifications: {'DNA': 118} Link IDs: {'rna3p': 117} Chain: "d" Number of atoms: 2405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 2405 Classifications: {'DNA': 118} Link IDs: {'rna3p': 117} Chain: "e" Number of atoms: 728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 728 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 2, 'TRANS': 86} Chain: "f" Number of atoms: 606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 606 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 1, 'TRANS': 74} Chain: "g" Number of atoms: 778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 778 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "h" Number of atoms: 679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 679 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 2, 'TRANS': 84} Chain: "i" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 783 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "j" Number of atoms: 606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 606 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 1, 'TRANS': 74} Chain: "k" Number of atoms: 728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 728 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "l" Number of atoms: 679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 679 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 2, 'TRANS': 84} Chain: "m" Number of atoms: 2433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 2433 Classifications: {'DNA': 118} Link IDs: {'rna3p': 117} Chain: "n" Number of atoms: 2405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 2405 Classifications: {'DNA': 118} Link IDs: {'rna3p': 117} Time building chain proxies: 9.58, per 1000 atoms: 0.23 Number of scatterers: 41375 At special positions: 0 Unit cell: (178.2, 214.5, 184.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 56 16.00 P 944 15.00 O 9559 8.00 N 7711 7.00 C 23105 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: 3.61 Conformation dependent library (CDL) restraints added in 1.3 seconds 5432 Ramachandran restraints generated. 2716 Oldfield, 0 Emsley, 2716 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5176 Finding SS restraints... Secondary structure from input PDB file: 126 helices and 28 sheets defined 74.8% alpha, 2.2% beta 469 base pairs and 700 stacking pairs defined. Time for finding SS restraints: 5.86 Creating SS restraints... Processing helix chain 'A' and resid 45 through 55 Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.618A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 114 removed outlier: 3.666A pdb=" N LEU A 109 " --> pdb=" O GLU A 105 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N CYS A 110 " --> pdb=" O ASP A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.077A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.420A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 91 through 97 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 56 through 84 removed outlier: 3.693A pdb=" N GLY D 60 " --> pdb=" O SER D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 104 through 122 removed outlier: 3.759A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N HIS D 109 " --> pdb=" O GLU D 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.612A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 30 through 42 removed outlier: 3.521A pdb=" N GLY F 41 " --> pdb=" O LEU F 37 " (cutoff:3.500A) Processing helix chain 'F' and resid 50 through 76 Processing helix chain 'F' and resid 82 through 94 Processing helix chain 'G' and resid 27 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.001A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASN G 73 " --> pdb=" O ALA G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 91 through 97 Processing helix chain 'H' and resid 37 through 47 removed outlier: 3.705A pdb=" N TYR H 42 " --> pdb=" O SER H 38 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS H 43 " --> pdb=" O ILE H 39 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLN H 47 " --> pdb=" O LYS H 43 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 104 through 121 removed outlier: 3.792A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 55 removed outlier: 3.759A pdb=" N ARG K 49 " --> pdb=" O THR K 45 " (cutoff:3.500A) Processing helix chain 'K' and resid 63 through 77 removed outlier: 3.531A pdb=" N PHE K 67 " --> pdb=" O ARG K 63 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ASP K 77 " --> pdb=" O GLU K 73 " (cutoff:3.500A) Processing helix chain 'K' and resid 85 through 114 Processing helix chain 'K' and resid 120 through 131 Processing helix chain 'L' and resid 25 through 29 removed outlier: 3.638A pdb=" N ILE L 29 " --> pdb=" O ILE L 26 " (cutoff:3.500A) Processing helix chain 'L' and resid 30 through 41 Processing helix chain 'L' and resid 49 through 76 removed outlier: 4.083A pdb=" N GLU L 53 " --> pdb=" O LEU L 49 " (cutoff:3.500A) Processing helix chain 'L' and resid 82 through 93 Processing helix chain 'M' and resid 17 through 21 Processing helix chain 'M' and resid 26 through 37 Processing helix chain 'M' and resid 46 through 73 removed outlier: 3.679A pdb=" N ASN M 68 " --> pdb=" O GLU M 64 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA M 69 " --> pdb=" O LEU M 65 " (cutoff:3.500A) Processing helix chain 'M' and resid 79 through 90 Processing helix chain 'M' and resid 91 through 97 Processing helix chain 'N' and resid 38 through 49 removed outlier: 3.800A pdb=" N VAL N 44 " --> pdb=" O TYR N 40 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN N 47 " --> pdb=" O LYS N 43 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL N 48 " --> pdb=" O VAL N 44 " (cutoff:3.500A) Processing helix chain 'N' and resid 55 through 84 Processing helix chain 'N' and resid 90 through 102 Processing helix chain 'N' and resid 104 through 122 removed outlier: 3.690A pdb=" N LYS N 108 " --> pdb=" O GLY N 104 " (cutoff:3.500A) Processing helix chain 'O' and resid 49 through 54 Processing helix chain 'O' and resid 63 through 78 removed outlier: 3.521A pdb=" N PHE O 67 " --> pdb=" O ARG O 63 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASP O 77 " --> pdb=" O GLU O 73 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE O 78 " --> pdb=" O ILE O 74 " (cutoff:3.500A) Processing helix chain 'O' and resid 85 through 114 removed outlier: 3.617A pdb=" N ALA O 114 " --> pdb=" O CYS O 110 " (cutoff:3.500A) Processing helix chain 'O' and resid 120 through 132 removed outlier: 3.626A pdb=" N ILE O 124 " --> pdb=" O MET O 120 " (cutoff:3.500A) Processing helix chain 'P' and resid 25 through 29 removed outlier: 3.565A pdb=" N ILE P 29 " --> pdb=" O ILE P 26 " (cutoff:3.500A) Processing helix chain 'P' and resid 30 through 42 Processing helix chain 'P' and resid 49 through 76 removed outlier: 3.735A pdb=" N GLU P 53 " --> pdb=" O LEU P 49 " (cutoff:3.500A) Processing helix chain 'P' and resid 82 through 94 removed outlier: 3.726A pdb=" N VAL P 86 " --> pdb=" O THR P 82 " (cutoff:3.500A) Processing helix chain 'Q' and resid 27 through 36 Processing helix chain 'Q' and resid 45 through 74 removed outlier: 4.424A pdb=" N VAL Q 49 " --> pdb=" O ALA Q 45 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASP Q 72 " --> pdb=" O ASN Q 68 " (cutoff:3.500A) Processing helix chain 'Q' and resid 79 through 90 Processing helix chain 'Q' and resid 91 through 97 Processing helix chain 'R' and resid 37 through 49 Processing helix chain 'R' and resid 55 through 84 Processing helix chain 'R' and resid 90 through 102 removed outlier: 3.503A pdb=" N ILE R 94 " --> pdb=" O THR R 90 " (cutoff:3.500A) Processing helix chain 'R' and resid 104 through 120 Processing helix chain 'U' and resid 45 through 57 removed outlier: 3.620A pdb=" N LYS U 56 " --> pdb=" O ARG U 52 " (cutoff:3.500A) Processing helix chain 'U' and resid 63 through 78 removed outlier: 3.719A pdb=" N ASP U 77 " --> pdb=" O GLU U 73 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N PHE U 78 " --> pdb=" O ILE U 74 " (cutoff:3.500A) Processing helix chain 'U' and resid 85 through 114 Processing helix chain 'U' and resid 120 through 132 removed outlier: 3.522A pdb=" N ILE U 124 " --> pdb=" O MET U 120 " (cutoff:3.500A) Processing helix chain 'V' and resid 25 through 29 removed outlier: 3.785A pdb=" N ILE V 29 " --> pdb=" O ILE V 26 " (cutoff:3.500A) Processing helix chain 'V' and resid 30 through 42 removed outlier: 3.607A pdb=" N GLY V 41 " --> pdb=" O LEU V 37 " (cutoff:3.500A) Processing helix chain 'V' and resid 50 through 76 removed outlier: 3.709A pdb=" N ASP V 68 " --> pdb=" O ASN V 64 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA V 76 " --> pdb=" O TYR V 72 " (cutoff:3.500A) Processing helix chain 'V' and resid 82 through 94 removed outlier: 3.597A pdb=" N VAL V 86 " --> pdb=" O THR V 82 " (cutoff:3.500A) Processing helix chain 'W' and resid 26 through 37 Processing helix chain 'W' and resid 46 through 73 removed outlier: 3.608A pdb=" N TYR W 50 " --> pdb=" O GLY W 46 " (cutoff:3.500A) Processing helix chain 'W' and resid 79 through 90 Processing helix chain 'W' and resid 91 through 97 removed outlier: 3.975A pdb=" N LYS W 95 " --> pdb=" O GLU W 91 " (cutoff:3.500A) Processing helix chain 'X' and resid 37 through 47 removed outlier: 3.509A pdb=" N LYS X 46 " --> pdb=" O TYR X 42 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLN X 47 " --> pdb=" O LYS X 43 " (cutoff:3.500A) Processing helix chain 'X' and resid 55 through 84 Processing helix chain 'X' and resid 90 through 102 removed outlier: 3.751A pdb=" N ILE X 94 " --> pdb=" O THR X 90 " (cutoff:3.500A) Processing helix chain 'X' and resid 103 through 122 removed outlier: 3.829A pdb=" N HIS X 109 " --> pdb=" O GLU X 105 " (cutoff:3.500A) Processing helix chain 'Y' and resid 45 through 57 removed outlier: 3.788A pdb=" N LYS Y 56 " --> pdb=" O ARG Y 52 " (cutoff:3.500A) Processing helix chain 'Y' and resid 63 through 79 removed outlier: 3.815A pdb=" N ASP Y 77 " --> pdb=" O GLU Y 73 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N PHE Y 78 " --> pdb=" O ILE Y 74 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS Y 79 " --> pdb=" O ALA Y 75 " (cutoff:3.500A) Processing helix chain 'Y' and resid 85 through 114 removed outlier: 3.546A pdb=" N ALA Y 114 " --> pdb=" O CYS Y 110 " (cutoff:3.500A) Processing helix chain 'Y' and resid 120 through 132 removed outlier: 3.866A pdb=" N GLY Y 132 " --> pdb=" O ARG Y 128 " (cutoff:3.500A) Processing helix chain 'Z' and resid 25 through 29 removed outlier: 3.542A pdb=" N ILE Z 29 " --> pdb=" O ILE Z 26 " (cutoff:3.500A) Processing helix chain 'Z' and resid 30 through 41 Processing helix chain 'Z' and resid 49 through 76 removed outlier: 4.030A pdb=" N GLU Z 53 " --> pdb=" O LEU Z 49 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ARG Z 55 " --> pdb=" O TYR Z 51 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY Z 56 " --> pdb=" O GLU Z 52 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N THR Z 71 " --> pdb=" O ARG Z 67 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TYR Z 72 " --> pdb=" O ASP Z 68 " (cutoff:3.500A) Processing helix chain 'Z' and resid 82 through 93 removed outlier: 3.529A pdb=" N GLN Z 93 " --> pdb=" O ALA Z 89 " (cutoff:3.500A) Processing helix chain 'a' and resid 28 through 37 Processing helix chain 'a' and resid 46 through 73 removed outlier: 3.774A pdb=" N ASP a 72 " --> pdb=" O ASN a 68 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ASN a 73 " --> pdb=" O ALA a 69 " (cutoff:3.500A) Processing helix chain 'a' and resid 79 through 89 Processing helix chain 'a' and resid 91 through 97 Processing helix chain 'b' and resid 37 through 47 removed outlier: 3.707A pdb=" N LYS b 46 " --> pdb=" O TYR b 42 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLN b 47 " --> pdb=" O LYS b 43 " (cutoff:3.500A) Processing helix chain 'b' and resid 55 through 84 removed outlier: 3.766A pdb=" N ASN b 84 " --> pdb=" O LEU b 80 " (cutoff:3.500A) Processing helix chain 'b' and resid 90 through 102 removed outlier: 3.665A pdb=" N ILE b 94 " --> pdb=" O THR b 90 " (cutoff:3.500A) Processing helix chain 'b' and resid 104 through 121 removed outlier: 3.811A pdb=" N LYS b 108 " --> pdb=" O GLY b 104 " (cutoff:3.500A) Processing helix chain 'e' and resid 46 through 55 Processing helix chain 'e' and resid 63 through 79 removed outlier: 3.528A pdb=" N ASP e 77 " --> pdb=" O GLU e 73 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N PHE e 78 " --> pdb=" O ILE e 74 " (cutoff:3.500A) Processing helix chain 'e' and resid 85 through 114 Processing helix chain 'e' and resid 120 through 132 removed outlier: 3.792A pdb=" N ILE e 124 " --> pdb=" O MET e 120 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN e 125 " --> pdb=" O PRO e 121 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG e 131 " --> pdb=" O ALA e 127 " (cutoff:3.500A) Processing helix chain 'f' and resid 30 through 42 Processing helix chain 'f' and resid 50 through 77 Processing helix chain 'f' and resid 82 through 94 Processing helix chain 'g' and resid 17 through 22 Processing helix chain 'g' and resid 26 through 36 Processing helix chain 'g' and resid 45 through 73 removed outlier: 4.288A pdb=" N VAL g 49 " --> pdb=" O ALA g 45 " (cutoff:3.500A) Processing helix chain 'g' and resid 79 through 88 Processing helix chain 'g' and resid 91 through 97 Processing helix chain 'h' and resid 37 through 49 Processing helix chain 'h' and resid 55 through 84 Processing helix chain 'h' and resid 90 through 102 Processing helix chain 'h' and resid 104 through 122 Processing helix chain 'i' and resid 44 through 55 removed outlier: 3.942A pdb=" N LEU i 48 " --> pdb=" O GLY i 44 " (cutoff:3.500A) Processing helix chain 'i' and resid 63 through 79 removed outlier: 4.007A pdb=" N ASP i 77 " --> pdb=" O GLU i 73 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N PHE i 78 " --> pdb=" O ILE i 74 " (cutoff:3.500A) Processing helix chain 'i' and resid 85 through 114 removed outlier: 3.995A pdb=" N VAL i 89 " --> pdb=" O GLN i 85 " (cutoff:3.500A) Processing helix chain 'i' and resid 120 through 132 Processing helix chain 'j' and resid 30 through 42 Processing helix chain 'j' and resid 49 through 77 removed outlier: 3.759A pdb=" N GLU j 53 " --> pdb=" O LEU j 49 " (cutoff:3.500A) Processing helix chain 'j' and resid 82 through 94 removed outlier: 3.548A pdb=" N GLY j 94 " --> pdb=" O LEU j 90 " (cutoff:3.500A) Processing helix chain 'k' and resid 26 through 37 Processing helix chain 'k' and resid 45 through 74 removed outlier: 4.234A pdb=" N VAL k 49 " --> pdb=" O ALA k 45 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASP k 72 " --> pdb=" O ASN k 68 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASN k 73 " --> pdb=" O ALA k 69 " (cutoff:3.500A) Processing helix chain 'k' and resid 79 through 90 removed outlier: 3.550A pdb=" N ASP k 90 " --> pdb=" O ALA k 86 " (cutoff:3.500A) Processing helix chain 'k' and resid 90 through 97 Processing helix chain 'l' and resid 37 through 49 removed outlier: 3.666A pdb=" N TYR l 42 " --> pdb=" O SER l 38 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS l 43 " --> pdb=" O ILE l 39 " (cutoff:3.500A) Processing helix chain 'l' and resid 55 through 84 Processing helix chain 'l' and resid 90 through 102 removed outlier: 3.564A pdb=" N ILE l 94 " --> pdb=" O THR l 90 " (cutoff:3.500A) Processing helix chain 'l' and resid 104 through 122 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.829A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 removed outlier: 3.610A pdb=" N ILE A 119 " --> pdb=" O ARG B 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.067A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.992A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.536A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AA9, first strand: chain 'K' and resid 83 through 84 removed outlier: 7.644A pdb=" N ARG K 83 " --> pdb=" O VAL L 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'K' and resid 118 through 119 removed outlier: 3.557A pdb=" N ILE K 119 " --> pdb=" O ARG L 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'L' and resid 96 through 97 removed outlier: 6.318A pdb=" N THR L 96 " --> pdb=" O THR Q 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'M' and resid 77 through 78 Processing sheet with id=AB4, first strand: chain 'M' and resid 100 through 102 Processing sheet with id=AB5, first strand: chain 'O' and resid 83 through 84 removed outlier: 6.564A pdb=" N ARG O 83 " --> pdb=" O VAL P 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'Q' and resid 42 through 43 removed outlier: 7.341A pdb=" N ARG Q 42 " --> pdb=" O ILE R 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'U' and resid 83 through 84 removed outlier: 6.915A pdb=" N ARG U 83 " --> pdb=" O VAL V 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'U' and resid 118 through 119 Processing sheet with id=AB9, first strand: chain 'W' and resid 77 through 78 removed outlier: 3.609A pdb=" N ILE W 78 " --> pdb=" O GLY X 53 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'W' and resid 101 through 102 removed outlier: 7.523A pdb=" N THR W 101 " --> pdb=" O TYR Z 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'Y' and resid 83 through 84 removed outlier: 7.178A pdb=" N ARG Y 83 " --> pdb=" O VAL Z 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'a' and resid 42 through 43 removed outlier: 7.316A pdb=" N ARG a 42 " --> pdb=" O ILE b 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'a' and resid 77 through 78 Processing sheet with id=AC5, first strand: chain 'e' and resid 83 through 84 removed outlier: 7.572A pdb=" N ARG e 83 " --> pdb=" O VAL f 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'e' and resid 118 through 119 Processing sheet with id=AC7, first strand: chain 'g' and resid 100 through 102 removed outlier: 6.803A pdb=" N THR g 101 " --> pdb=" O TYR j 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'i' and resid 83 through 84 removed outlier: 7.342A pdb=" N ARG i 83 " --> pdb=" O VAL j 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'k' and resid 42 through 43 removed outlier: 7.243A pdb=" N ARG k 42 " --> pdb=" O ILE l 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'k' and resid 77 through 78 1493 hydrogen bonds defined for protein. 4467 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1213 hydrogen bonds 2410 hydrogen bond angles 0 basepair planarities 469 basepair parallelities 700 stacking parallelities Total time for adding SS restraints: 9.18 Time building geometry restraints manager: 4.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6982 1.33 - 1.45: 14607 1.45 - 1.57: 20452 1.57 - 1.69: 1880 1.69 - 1.81: 96 Bond restraints: 44017 Sorted by residual: bond pdb=" C3' DA S -14 " pdb=" C2' DA S -14 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.23e+01 bond pdb=" C3' DG c 0 " pdb=" C2' DG c 0 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.13e+01 bond pdb=" C3' DC I 68 " pdb=" C2' DC I 68 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.11e+01 bond pdb=" C3' DC S -43 " pdb=" C2' DC S -43 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.11e+01 bond pdb=" C3' DG J -60 " pdb=" C2' DG J -60 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.09e+01 ... (remaining 44012 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.21: 58957 1.21 - 2.42: 4002 2.42 - 3.63: 494 3.63 - 4.84: 28 4.84 - 6.05: 8 Bond angle restraints: 63489 Sorted by residual: angle pdb=" O4' DC m 61 " pdb=" C4' DC m 61 " pdb=" C3' DC m 61 " ideal model delta sigma weight residual 106.00 103.15 2.85 6.00e-01 2.78e+00 2.25e+01 angle pdb=" O4' DG c 20 " pdb=" C1' DG c 20 " pdb=" N9 DG c 20 " ideal model delta sigma weight residual 108.00 111.16 -3.16 7.00e-01 2.04e+00 2.04e+01 angle pdb=" N3 DT J -26 " pdb=" C4 DT J -26 " pdb=" O4 DT J -26 " ideal model delta sigma weight residual 119.90 122.55 -2.65 6.00e-01 2.78e+00 1.94e+01 angle pdb=" N3 DT S 31 " pdb=" C4 DT S 31 " pdb=" O4 DT S 31 " ideal model delta sigma weight residual 119.90 122.54 -2.64 6.00e-01 2.78e+00 1.93e+01 angle pdb=" O4' DT I -32 " pdb=" C4' DT I -32 " pdb=" C3' DT I -32 " ideal model delta sigma weight residual 106.00 103.37 2.63 6.00e-01 2.78e+00 1.92e+01 ... (remaining 63484 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.47: 18327 23.47 - 46.94: 3493 46.94 - 70.41: 2091 70.41 - 93.88: 55 93.88 - 117.34: 1 Dihedral angle restraints: 23967 sinusoidal: 15928 harmonic: 8039 Sorted by residual: dihedral pdb=" C4' DG S 20 " pdb=" C3' DG S 20 " pdb=" O3' DG S 20 " pdb=" P DG S 21 " ideal model delta sinusoidal sigma weight residual 220.00 102.66 117.34 1 3.50e+01 8.16e-04 1.14e+01 dihedral pdb=" CA LYS N 46 " pdb=" CB LYS N 46 " pdb=" CG LYS N 46 " pdb=" CD LYS N 46 " ideal model delta sinusoidal sigma weight residual 60.00 118.50 -58.50 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" CA GLU j 53 " pdb=" CB GLU j 53 " pdb=" CG GLU j 53 " pdb=" CD GLU j 53 " ideal model delta sinusoidal sigma weight residual 60.00 111.97 -51.97 3 1.50e+01 4.44e-03 9.07e+00 ... (remaining 23964 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 3905 0.029 - 0.059: 2286 0.059 - 0.088: 759 0.088 - 0.118: 301 0.118 - 0.147: 14 Chirality restraints: 7265 Sorted by residual: chirality pdb=" CA ILE g 79 " pdb=" N ILE g 79 " pdb=" C ILE g 79 " pdb=" CB ILE g 79 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.40e-01 chirality pdb=" CA ILE M 79 " pdb=" N ILE M 79 " pdb=" C ILE M 79 " pdb=" CB ILE M 79 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.80e-01 chirality pdb=" CA ILE k 79 " pdb=" N ILE k 79 " pdb=" C ILE k 79 " pdb=" CB ILE k 79 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.12e-01 ... (remaining 7262 not shown) Planarity restraints: 4746 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE g 79 " 0.035 5.00e-02 4.00e+02 5.27e-02 4.45e+00 pdb=" N PRO g 80 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO g 80 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO g 80 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE k 79 " 0.029 5.00e-02 4.00e+02 4.39e-02 3.08e+00 pdb=" N PRO k 80 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO k 80 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO k 80 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE M 79 " 0.028 5.00e-02 4.00e+02 4.17e-02 2.78e+00 pdb=" N PRO M 80 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO M 80 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO M 80 " 0.023 5.00e-02 4.00e+02 ... (remaining 4743 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 6257 2.77 - 3.30: 36621 3.30 - 3.83: 78520 3.83 - 4.37: 83998 4.37 - 4.90: 127580 Nonbonded interactions: 332976 Sorted by model distance: nonbonded pdb=" OD1 ASP f 85 " pdb=" OH TYR h 83 " model vdw 2.235 3.040 nonbonded pdb=" OG SER U 57 " pdb=" OE1 GLU U 59 " model vdw 2.240 3.040 nonbonded pdb=" NH2 ARG K 69 " pdb=" OP1 DA S 17 " model vdw 2.244 3.120 nonbonded pdb=" OD1 ASP B 85 " pdb=" OH TYR D 83 " model vdw 2.274 3.040 nonbonded pdb=" OG SER Z 47 " pdb=" OP1 DC d 7 " model vdw 2.274 3.040 ... (remaining 332971 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 48 through 133) selection = (chain 'E' and resid 48 through 133) selection = (chain 'K' and resid 48 through 133) selection = chain 'O' selection = (chain 'U' and resid 48 through 133) selection = (chain 'Y' and resid 48 through 133) selection = (chain 'e' and resid 48 through 133) selection = (chain 'i' and resid 48 through 133) } ncs_group { reference = (chain 'B' and resid 26 through 100) selection = chain 'F' selection = (chain 'L' and resid 26 through 100) selection = (chain 'P' and resid 26 through 100) selection = (chain 'V' and resid 26 through 100) selection = (chain 'Z' and resid 26 through 100) selection = (chain 'f' and resid 26 through 100) selection = (chain 'j' and resid 26 through 100) } ncs_group { reference = (chain 'C' and resid 27 through 109) selection = (chain 'G' and resid 27 through 109) selection = (chain 'M' and resid 27 through 109) selection = (chain 'Q' and resid 27 through 109) selection = (chain 'W' and resid 27 through 109) selection = (chain 'a' and resid 27 through 109) selection = (chain 'g' and resid 27 through 109) selection = (chain 'k' and resid 27 through 109) } ncs_group { reference = (chain 'D' and resid 36 through 121) selection = chain 'H' selection = (chain 'N' and resid 36 through 121) selection = chain 'R' selection = (chain 'X' and resid 36 through 121) selection = chain 'b' selection = (chain 'h' and resid 36 through 121) selection = (chain 'l' and resid 36 through 121) } ncs_group { reference = chain 'I' selection = chain 'S' selection = chain 'c' selection = chain 'm' } ncs_group { reference = chain 'J' selection = chain 'T' selection = chain 'd' selection = chain 'n' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 1.100 Check model and map are aligned: 0.170 Set scattering table: 0.150 Process input model: 42.760 Find NCS groups from input model: 1.020 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6544 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 : 0.005 0.039 44017 Z= 0.475 Angle : 0.633 6.049 63489 Z= 0.595 Chirality : 0.041 0.147 7265 Planarity : 0.003 0.053 4746 Dihedral : 24.819 117.344 18791 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.53 (0.17), residues: 2716 helix: 3.66 (0.11), residues: 1945 sheet: None (None), residues: 0 loop : -1.45 (0.21), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG V 78 TYR 0.010 0.001 TYR g 50 PHE 0.007 0.001 PHE N 70 HIS 0.002 0.000 HIS f 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00496 / 0.48 (44017) covalent geometry : angle 0.63303 / 0.60 (63489) hydrogen bonds : bond 0.10096 / 6.94 ( 2706) hydrogen bonds : angle 3.13939 / 2.24 ( 6877) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5432 Ramachandran restraints generated. 2716 Oldfield, 0 Emsley, 2716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5432 Ramachandran restraints generated. 2716 Oldfield, 0 Emsley, 2716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 871 residues out of total 2317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 871 time to evaluate : 1.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 59 LYS cc_start: 0.7359 (tttt) cc_final: 0.7148 (tttt) REVERT: B 88 TYR cc_start: 0.6773 (m-80) cc_final: 0.6402 (m-80) REVERT: C 99 LYS cc_start: 0.7979 (ptpt) cc_final: 0.7647 (ptpt) REVERT: D 54 ILE cc_start: 0.8571 (mt) cc_final: 0.8069 (mt) REVERT: D 79 ARG cc_start: 0.7648 (mtt180) cc_final: 0.7409 (ttm110) REVERT: D 101 LEU cc_start: 0.7851 (tp) cc_final: 0.7641 (mp) REVERT: F 50 ILE cc_start: 0.6773 (mm) cc_final: 0.6547 (mm) REVERT: F 100 PHE cc_start: 0.7602 (m-80) cc_final: 0.7100 (m-80) REVERT: G 36 LYS cc_start: 0.6244 (mttt) cc_final: 0.5883 (mttt) REVERT: G 73 ASN cc_start: 0.8166 (t0) cc_final: 0.7958 (t0) REVERT: H 52 THR cc_start: 0.7607 (m) cc_final: 0.7388 (p) REVERT: H 111 VAL cc_start: 0.7647 (t) cc_final: 0.7293 (p) REVERT: K 60 LEU cc_start: 0.6918 (mp) cc_final: 0.6277 (mt) REVERT: K 84 PHE cc_start: 0.6263 (m-10) cc_final: 0.5910 (m-10) REVERT: K 97 GLU cc_start: 0.7158 (mt-10) cc_final: 0.6848 (mt-10) REVERT: K 130 ILE cc_start: 0.8334 (mt) cc_final: 0.8072 (mt) REVERT: L 27 GLN cc_start: 0.7985 (mt0) cc_final: 0.7727 (mp10) REVERT: L 29 ILE cc_start: 0.6765 (mm) cc_final: 0.6191 (tt) REVERT: L 44 LYS cc_start: 0.6137 (mttt) cc_final: 0.5800 (ptpt) REVERT: L 59 LYS cc_start: 0.8226 (pttt) cc_final: 0.7896 (pttt) REVERT: M 49 VAL cc_start: 0.7545 (p) cc_final: 0.7297 (p) REVERT: M 58 LEU cc_start: 0.7211 (mt) cc_final: 0.6982 (mt) REVERT: M 95 LYS cc_start: 0.7613 (tttt) cc_final: 0.7398 (tppt) REVERT: M 99 LYS cc_start: 0.6754 (mttt) cc_final: 0.5466 (mmtt) REVERT: M 104 GLN cc_start: 0.7493 (mt0) cc_final: 0.7188 (mm-40) REVERT: N 48 VAL cc_start: 0.8077 (t) cc_final: 0.7781 (m) REVERT: O 73 GLU cc_start: 0.7771 (tt0) cc_final: 0.7536 (tm-30) REVERT: O 76 GLN cc_start: 0.6727 (mt0) cc_final: 0.6185 (mm110) REVERT: O 115 LYS cc_start: 0.6406 (mttt) cc_final: 0.5982 (mmtt) REVERT: Q 33 LEU cc_start: 0.7433 (mt) cc_final: 0.7205 (mt) REVERT: Q 74 LYS cc_start: 0.6578 (mttt) cc_final: 0.5976 (mmtp) REVERT: Q 95 LYS cc_start: 0.7087 (mttt) cc_final: 0.6578 (mtmm) REVERT: Q 99 LYS cc_start: 0.6698 (mttt) cc_final: 0.6354 (mttm) REVERT: R 45 LEU cc_start: 0.6511 (tp) cc_final: 0.6096 (tp) REVERT: U 80 THR cc_start: 0.7833 (p) cc_final: 0.7582 (t) REVERT: V 84 MET cc_start: 0.6539 (mmm) cc_final: 0.5870 (tpp) REVERT: Y 49 ARG cc_start: 0.6631 (ttp-110) cc_final: 0.6259 (ttt-90) REVERT: a 33 LEU cc_start: 0.7885 (mt) cc_final: 0.7617 (mm) REVERT: a 36 LYS cc_start: 0.7014 (mttt) cc_final: 0.6728 (ptpt) REVERT: a 38 ASN cc_start: 0.7158 (m-40) cc_final: 0.6923 (m110) REVERT: a 39 TYR cc_start: 0.7643 (m-80) cc_final: 0.7081 (m-80) REVERT: b 67 ASN cc_start: 0.7872 (m-40) cc_final: 0.7202 (t0) REVERT: e 49 ARG cc_start: 0.6052 (mtt-85) cc_final: 0.5725 (mtp-110) REVERT: e 63 ARG cc_start: 0.5486 (mtt-85) cc_final: 0.4504 (mmp-170) REVERT: e 73 GLU cc_start: 0.6538 (tt0) cc_final: 0.5932 (tm-30) REVERT: e 90 MET cc_start: 0.6585 (mmm) cc_final: 0.6193 (mmp) REVERT: e 120 MET cc_start: 0.6798 (mtp) cc_final: 0.6446 (mmt) REVERT: e 133 GLU cc_start: 0.6400 (tt0) cc_final: 0.6192 (tm-30) REVERT: f 39 ARG cc_start: 0.6866 (mmt180) cc_final: 0.6342 (mtt90) REVERT: g 36 LYS cc_start: 0.5700 (mttt) cc_final: 0.5298 (tttt) REVERT: g 42 ARG cc_start: 0.5668 (ttt-90) cc_final: 0.5431 (tpp-160) REVERT: g 84 GLN cc_start: 0.7873 (tp40) cc_final: 0.7493 (tp40) REVERT: h 40 TYR cc_start: 0.7474 (m-80) cc_final: 0.7174 (m-80) REVERT: h 85 LYS cc_start: 0.7942 (mttt) cc_final: 0.7561 (mmtm) REVERT: i 112 ILE cc_start: 0.8117 (mm) cc_final: 0.7892 (mm) REVERT: i 130 ILE cc_start: 0.8908 (mm) cc_final: 0.8407 (mt) REVERT: j 45 ARG cc_start: 0.6994 (mtt180) cc_final: 0.6308 (mtt-85) REVERT: j 79 LYS cc_start: 0.6978 (mttt) cc_final: 0.6305 (mmtm) REVERT: j 88 TYR cc_start: 0.7050 (m-10) cc_final: 0.6551 (m-10) REVERT: l 40 TYR cc_start: 0.7094 (m-80) cc_final: 0.6770 (m-80) REVERT: l 44 VAL cc_start: 0.8283 (t) cc_final: 0.8062 (t) REVERT: l 83 TYR cc_start: 0.7384 (t80) cc_final: 0.7172 (t80) outliers start: 0 outliers final: 0 residues processed: 871 average time/residue: 0.3079 time to fit residues: 404.6287 Evaluate side-chains 459 residues out of total 2317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 459 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 197 optimal weight: 0.0870 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 50.0000 chunk 248 optimal weight: 50.0000 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 50.0000 chunk 244 optimal weight: 50.0000 chunk 183 optimal weight: 9.9990 chunk 298 optimal weight: 7.9990 overall best weight: 1.6164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN B 25 ASN B 27 GLN D 84 ASN D 95 GLN E 125 GLN H 63 ASN L 25 ASN ** L 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 73 ASN ** N 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 49 HIS R 95 GLN ** V 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 25 ASN a 104 GLN e 68 GLN h 95 GLN i 68 GLN k 24 GLN l 49 HIS l 84 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.130853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.101640 restraints weight = 139651.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.101185 restraints weight = 188253.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.101931 restraints weight = 175531.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.103018 restraints weight = 121953.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.103089 restraints weight = 111897.260| |-----------------------------------------------------------------------------| r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6591 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.065 44017 Z= 0.150 Angle : 0.536 7.918 63489 Z= 0.334 Chirality : 0.038 0.205 7265 Planarity : 0.004 0.052 4746 Dihedral : 29.000 111.667 13347 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.17 % Allowed : 2.81 % Favored : 97.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.16 (0.16), residues: 2716 helix: 3.27 (0.11), residues: 1988 sheet: None (None), residues: 0 loop : -1.55 (0.21), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG j 92 TYR 0.035 0.001 TYR M 39 PHE 0.018 0.001 PHE M 25 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.15 (44017) covalent geometry : angle 0.53580 / 0.33 (63489) hydrogen bonds : bond 0.05167 / 3.47 ( 2706) hydrogen bonds : angle 2.86514 / 2.07 ( 6877) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5432 Ramachandran restraints generated. 2716 Oldfield, 0 Emsley, 2716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5432 Ramachandran restraints generated. 2716 Oldfield, 0 Emsley, 2716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 607 residues out of total 2317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 603 time to evaluate : 1.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.7138 (tm-30) cc_final: 0.6773 (tp30) REVERT: C 50 TYR cc_start: 0.4678 (t80) cc_final: 0.3748 (t80) REVERT: C 99 LYS cc_start: 0.7834 (ptpt) cc_final: 0.7573 (ptpt) REVERT: D 52 THR cc_start: 0.5839 (p) cc_final: 0.5627 (p) REVERT: D 54 ILE cc_start: 0.8700 (mt) cc_final: 0.8438 (mt) REVERT: D 62 MET cc_start: 0.8005 (mmm) cc_final: 0.7526 (tpp) REVERT: D 101 LEU cc_start: 0.8046 (tp) cc_final: 0.7759 (mp) REVERT: E 120 MET cc_start: 0.6473 (mtm) cc_final: 0.6246 (mtm) REVERT: F 50 ILE cc_start: 0.6669 (mm) cc_final: 0.6329 (mm) REVERT: F 84 MET cc_start: 0.6610 (tpp) cc_final: 0.5989 (tpp) REVERT: F 100 PHE cc_start: 0.7569 (m-80) cc_final: 0.7041 (m-80) REVERT: K 84 PHE cc_start: 0.6734 (m-10) cc_final: 0.6266 (m-10) REVERT: K 113 HIS cc_start: 0.6084 (t-90) cc_final: 0.5878 (t-90) REVERT: K 130 ILE cc_start: 0.8175 (mt) cc_final: 0.7912 (mt) REVERT: L 27 GLN cc_start: 0.8029 (mt0) cc_final: 0.7760 (mp10) REVERT: L 29 ILE cc_start: 0.6342 (mm) cc_final: 0.5960 (tt) REVERT: L 44 LYS cc_start: 0.6014 (mttt) cc_final: 0.5805 (ptpt) REVERT: L 59 LYS cc_start: 0.8194 (pttt) cc_final: 0.7892 (pttt) REVERT: L 68 ASP cc_start: 0.7277 (m-30) cc_final: 0.6847 (m-30) REVERT: M 39 TYR cc_start: 0.6375 (m-10) cc_final: 0.6081 (m-10) REVERT: M 63 LEU cc_start: 0.8437 (mm) cc_final: 0.8096 (mt) REVERT: M 99 LYS cc_start: 0.6996 (mttt) cc_final: 0.5682 (mmtt) REVERT: N 44 VAL cc_start: 0.8159 (t) cc_final: 0.7878 (t) REVERT: N 48 VAL cc_start: 0.7784 (t) cc_final: 0.7459 (m) REVERT: O 76 GLN cc_start: 0.6474 (mt0) cc_final: 0.6127 (mm110) REVERT: O 115 LYS cc_start: 0.6256 (mttt) cc_final: 0.5982 (mmtt) REVERT: Q 74 LYS cc_start: 0.6398 (mttt) cc_final: 0.6151 (mmtp) REVERT: Q 95 LYS cc_start: 0.7116 (mttt) cc_final: 0.6697 (mtmm) REVERT: Q 99 LYS cc_start: 0.6926 (mttt) cc_final: 0.6597 (mttm) REVERT: R 100 LEU cc_start: 0.7926 (mt) cc_final: 0.7723 (mt) REVERT: U 80 THR cc_start: 0.7913 (p) cc_final: 0.7707 (t) REVERT: U 120 MET cc_start: 0.7574 (mtt) cc_final: 0.7236 (mtm) REVERT: V 84 MET cc_start: 0.6162 (mmm) cc_final: 0.5760 (mmt) REVERT: Y 50 GLU cc_start: 0.7053 (mm-30) cc_final: 0.6011 (tm-30) REVERT: Z 92 ARG cc_start: 0.7436 (tpt-90) cc_final: 0.6795 (ttt180) REVERT: a 39 TYR cc_start: 0.7341 (m-80) cc_final: 0.6851 (m-80) REVERT: a 65 LEU cc_start: 0.7503 (mt) cc_final: 0.7136 (mt) REVERT: b 67 ASN cc_start: 0.7488 (m-40) cc_final: 0.7246 (t0) REVERT: b 93 GLU cc_start: 0.7535 (mp0) cc_final: 0.7276 (mp0) REVERT: e 49 ARG cc_start: 0.6211 (mtt-85) cc_final: 0.5970 (mtp-110) REVERT: e 63 ARG cc_start: 0.5346 (mtt-85) cc_final: 0.4492 (mmm160) REVERT: e 90 MET cc_start: 0.6123 (mmm) cc_final: 0.5890 (mmm) REVERT: e 105 GLU cc_start: 0.6921 (tm-30) cc_final: 0.6584 (tp30) REVERT: e 107 THR cc_start: 0.8762 (m) cc_final: 0.8460 (p) REVERT: e 120 MET cc_start: 0.7090 (mtp) cc_final: 0.6516 (mmt) REVERT: f 39 ARG cc_start: 0.7196 (mmt180) cc_final: 0.6858 (mtt90) REVERT: g 36 LYS cc_start: 0.5526 (mttt) cc_final: 0.5209 (tttt) REVERT: g 64 GLU cc_start: 0.7144 (pp20) cc_final: 0.6726 (pp20) REVERT: h 85 LYS cc_start: 0.7878 (mttt) cc_final: 0.7643 (mmtm) REVERT: i 81 ASP cc_start: 0.7288 (m-30) cc_final: 0.7064 (m-30) REVERT: i 112 ILE cc_start: 0.8283 (mm) cc_final: 0.8060 (mm) REVERT: i 130 ILE cc_start: 0.8538 (mm) cc_final: 0.8208 (mt) REVERT: j 45 ARG cc_start: 0.6713 (mtt180) cc_final: 0.6407 (mtt-85) REVERT: j 79 LYS cc_start: 0.6905 (mttt) cc_final: 0.6283 (mmtm) REVERT: j 88 TYR cc_start: 0.7133 (m-10) cc_final: 0.6764 (m-10) outliers start: 4 outliers final: 0 residues processed: 605 average time/residue: 0.2540 time to fit residues: 245.9944 Evaluate side-chains 420 residues out of total 2317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 420 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 226 optimal weight: 1.9990 chunk 138 optimal weight: 10.0000 chunk 322 optimal weight: 9.9990 chunk 11 optimal weight: 4.9990 chunk 313 optimal weight: 5.9990 chunk 160 optimal weight: 50.0000 chunk 63 optimal weight: 0.7980 chunk 251 optimal weight: 50.0000 chunk 135 optimal weight: 1.9990 chunk 158 optimal weight: 50.0000 chunk 66 optimal weight: 50.0000 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN C 84 GLN D 63 ASN D 84 ASN F 75 HIS L 25 ASN L 75 HIS ** N 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 75 HIS U 93 GLN V 25 ASN ** Y 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 25 ASN a 104 GLN b 63 ASN k 84 GLN k 110 ASN l 84 ASN l 95 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.128864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.098651 restraints weight = 138275.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.098546 restraints weight = 191768.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.099185 restraints weight = 178886.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.100418 restraints weight = 123123.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.100448 restraints weight = 109659.213| |-----------------------------------------------------------------------------| r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6669 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 44017 Z= 0.158 Angle : 0.561 8.863 63489 Z= 0.341 Chirality : 0.039 0.271 7265 Planarity : 0.005 0.060 4746 Dihedral : 29.229 106.704 13347 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 0.26 % Allowed : 3.32 % Favored : 96.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.66 (0.16), residues: 2716 helix: 2.95 (0.11), residues: 1990 sheet: None (None), residues: 0 loop : -1.92 (0.20), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG H 92 TYR 0.025 0.002 TYR l 40 PHE 0.027 0.002 PHE e 67 HIS 0.007 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.16 (44017) covalent geometry : angle 0.56106 / 0.34 (63489) hydrogen bonds : bond 0.05295 / 3.60 ( 2706) hydrogen bonds : angle 2.88564 / 2.08 ( 6877) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5432 Ramachandran restraints generated. 2716 Oldfield, 0 Emsley, 2716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5432 Ramachandran restraints generated. 2716 Oldfield, 0 Emsley, 2716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 550 residues out of total 2317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 544 time to evaluate : 1.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.7191 (tm-30) cc_final: 0.6782 (tp30) REVERT: A 106 ASP cc_start: 0.6443 (m-30) cc_final: 0.6229 (m-30) REVERT: B 84 MET cc_start: 0.6334 (mmt) cc_final: 0.6128 (mmt) REVERT: C 99 LYS cc_start: 0.7887 (ptpt) cc_final: 0.7639 (ptpt) REVERT: F 100 PHE cc_start: 0.7675 (m-80) cc_final: 0.7274 (m-80) REVERT: G 39 TYR cc_start: 0.7944 (m-80) cc_final: 0.7586 (m-80) REVERT: K 105 GLU cc_start: 0.6771 (tm-30) cc_final: 0.6539 (tm-30) REVERT: K 130 ILE cc_start: 0.8099 (mt) cc_final: 0.7888 (mt) REVERT: L 29 ILE cc_start: 0.6262 (mm) cc_final: 0.5911 (tt) REVERT: L 44 LYS cc_start: 0.6285 (mttt) cc_final: 0.5906 (ptpt) REVERT: L 59 LYS cc_start: 0.8091 (pttt) cc_final: 0.7846 (pttt) REVERT: L 68 ASP cc_start: 0.7171 (m-30) cc_final: 0.6858 (m-30) REVERT: M 63 LEU cc_start: 0.8438 (mm) cc_final: 0.8124 (mt) REVERT: M 99 LYS cc_start: 0.6992 (mttt) cc_final: 0.5683 (mmtt) REVERT: N 48 VAL cc_start: 0.7833 (t) cc_final: 0.7447 (m) REVERT: O 76 GLN cc_start: 0.6758 (mt0) cc_final: 0.6237 (mm110) REVERT: P 45 ARG cc_start: 0.7017 (mtt180) cc_final: 0.6655 (mtp180) REVERT: Q 42 ARG cc_start: 0.7464 (mtp85) cc_final: 0.6827 (ttp-110) REVERT: Q 74 LYS cc_start: 0.6515 (mttt) cc_final: 0.6170 (mmtp) REVERT: Q 95 LYS cc_start: 0.7185 (mttt) cc_final: 0.6845 (mtmm) REVERT: U 80 THR cc_start: 0.7914 (p) cc_final: 0.7703 (t) REVERT: V 84 MET cc_start: 0.6143 (mmm) cc_final: 0.5719 (mmt) REVERT: W 64 GLU cc_start: 0.6463 (tt0) cc_final: 0.6199 (tt0) REVERT: Y 50 GLU cc_start: 0.7076 (mm-30) cc_final: 0.5974 (tm-30) REVERT: Y 130 ILE cc_start: 0.8491 (OUTLIER) cc_final: 0.8245 (mp) REVERT: Z 92 ARG cc_start: 0.7506 (tpt-90) cc_final: 0.6797 (ttt180) REVERT: a 39 TYR cc_start: 0.7336 (m-80) cc_final: 0.7092 (m-80) REVERT: e 63 ARG cc_start: 0.5219 (mtt-85) cc_final: 0.4537 (mmm160) REVERT: e 105 GLU cc_start: 0.7001 (tm-30) cc_final: 0.6618 (tp30) REVERT: e 107 THR cc_start: 0.8869 (m) cc_final: 0.8531 (p) REVERT: f 39 ARG cc_start: 0.7329 (mmt180) cc_final: 0.6825 (mtt90) REVERT: f 63 GLU cc_start: 0.8133 (tm-30) cc_final: 0.7825 (tm-30) REVERT: g 36 LYS cc_start: 0.5692 (mttt) cc_final: 0.5184 (tttt) REVERT: h 85 LYS cc_start: 0.7826 (mttt) cc_final: 0.7582 (mmtm) REVERT: i 130 ILE cc_start: 0.8542 (mm) cc_final: 0.8217 (mt) REVERT: j 45 ARG cc_start: 0.6868 (mtt180) cc_final: 0.6469 (mtt-85) REVERT: j 79 LYS cc_start: 0.7190 (mttt) cc_final: 0.6567 (mmtm) REVERT: l 68 ASP cc_start: 0.6907 (t70) cc_final: 0.6584 (t70) outliers start: 6 outliers final: 0 residues processed: 547 average time/residue: 0.2504 time to fit residues: 219.4894 Evaluate side-chains 392 residues out of total 2317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 391 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 286 optimal weight: 20.0000 chunk 40 optimal weight: 8.9990 chunk 289 optimal weight: 1.9990 chunk 188 optimal weight: 10.0000 chunk 10 optimal weight: 0.5980 chunk 239 optimal weight: 8.9990 chunk 313 optimal weight: 0.8980 chunk 230 optimal weight: 0.2980 chunk 184 optimal weight: 3.9990 chunk 124 optimal weight: 8.9990 chunk 193 optimal weight: 6.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN B 25 ASN D 49 HIS D 63 ASN D 84 ASN ** N 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 25 ASN ** Y 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 104 GLN b 47 GLN e 55 GLN i 93 GLN k 110 ASN l 84 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.129387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.099360 restraints weight = 138596.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.099139 restraints weight = 197365.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.099877 restraints weight = 176920.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.100901 restraints weight = 123254.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.100996 restraints weight = 113430.590| |-----------------------------------------------------------------------------| r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6653 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 44017 Z= 0.135 Angle : 0.514 7.000 63489 Z= 0.319 Chirality : 0.037 0.177 7265 Planarity : 0.004 0.063 4746 Dihedral : 29.253 107.963 13347 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.30 % Allowed : 2.72 % Favored : 96.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.79 (0.16), residues: 2716 helix: 3.08 (0.11), residues: 1990 sheet: None (None), residues: 0 loop : -1.96 (0.20), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG F 35 TYR 0.033 0.001 TYR K 54 PHE 0.016 0.001 PHE W 25 HIS 0.012 0.001 HIS V 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00210 / 0.14 (44017) covalent geometry : angle 0.51429 / 0.32 (63489) hydrogen bonds : bond 0.04719 / 3.19 ( 2706) hydrogen bonds : angle 2.74956 / 2.00 ( 6877) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5432 Ramachandran restraints generated. 2716 Oldfield, 0 Emsley, 2716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5432 Ramachandran restraints generated. 2716 Oldfield, 0 Emsley, 2716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 2317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 527 time to evaluate : 1.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.7164 (tm-30) cc_final: 0.6776 (tp30) REVERT: C 99 LYS cc_start: 0.7875 (ptpt) cc_final: 0.7638 (ptpt) REVERT: F 52 GLU cc_start: 0.5965 (mm-30) cc_final: 0.5757 (mm-30) REVERT: F 84 MET cc_start: 0.6653 (tpp) cc_final: 0.6431 (tpp) REVERT: F 100 PHE cc_start: 0.7637 (m-80) cc_final: 0.7261 (m-80) REVERT: G 39 TYR cc_start: 0.7922 (m-80) cc_final: 0.7556 (m-80) REVERT: K 105 GLU cc_start: 0.6831 (tm-30) cc_final: 0.6625 (tm-30) REVERT: K 130 ILE cc_start: 0.7987 (mt) cc_final: 0.7695 (mt) REVERT: L 29 ILE cc_start: 0.6237 (mm) cc_final: 0.5877 (tt) REVERT: L 44 LYS cc_start: 0.6110 (mttt) cc_final: 0.5757 (ptpt) REVERT: L 68 ASP cc_start: 0.7089 (m-30) cc_final: 0.6875 (m-30) REVERT: M 58 LEU cc_start: 0.7268 (mt) cc_final: 0.7030 (mt) REVERT: M 99 LYS cc_start: 0.7044 (mttt) cc_final: 0.5712 (mmtt) REVERT: N 48 VAL cc_start: 0.7836 (t) cc_final: 0.7450 (m) REVERT: O 76 GLN cc_start: 0.6660 (mt0) cc_final: 0.6112 (mm110) REVERT: Q 74 LYS cc_start: 0.6513 (mttt) cc_final: 0.6146 (mmtp) REVERT: Q 95 LYS cc_start: 0.7073 (mttt) cc_final: 0.6637 (mtmm) REVERT: U 80 THR cc_start: 0.7903 (p) cc_final: 0.7692 (t) REVERT: V 68 ASP cc_start: 0.7373 (m-30) cc_final: 0.7170 (m-30) REVERT: V 84 MET cc_start: 0.6050 (mmm) cc_final: 0.5567 (mmt) REVERT: Y 50 GLU cc_start: 0.7040 (mm-30) cc_final: 0.5910 (tm-30) REVERT: Y 130 ILE cc_start: 0.8364 (OUTLIER) cc_final: 0.8085 (mp) REVERT: Z 92 ARG cc_start: 0.7534 (tpt-90) cc_final: 0.6883 (ttt180) REVERT: a 39 TYR cc_start: 0.7347 (m-80) cc_final: 0.6961 (m-80) REVERT: e 63 ARG cc_start: 0.5270 (mtt-85) cc_final: 0.4528 (mmp-170) REVERT: e 105 GLU cc_start: 0.6997 (tm-30) cc_final: 0.6617 (tp30) REVERT: e 107 THR cc_start: 0.8820 (m) cc_final: 0.8349 (p) REVERT: f 39 ARG cc_start: 0.7302 (mmt180) cc_final: 0.6905 (mtt90) REVERT: f 62 LEU cc_start: 0.8337 (mt) cc_final: 0.8084 (mt) REVERT: g 36 LYS cc_start: 0.5668 (mttt) cc_final: 0.5208 (tttt) REVERT: h 101 LEU cc_start: 0.7103 (OUTLIER) cc_final: 0.6891 (mp) REVERT: i 130 ILE cc_start: 0.8486 (mm) cc_final: 0.8178 (mt) REVERT: j 45 ARG cc_start: 0.6687 (mtt180) cc_final: 0.6252 (mtt-85) REVERT: j 79 LYS cc_start: 0.6911 (mttt) cc_final: 0.6298 (mmtm) outliers start: 7 outliers final: 1 residues processed: 531 average time/residue: 0.2469 time to fit residues: 212.2352 Evaluate side-chains 383 residues out of total 2317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 380 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 93 optimal weight: 6.9990 chunk 2 optimal weight: 6.9990 chunk 30 optimal weight: 6.9990 chunk 170 optimal weight: 50.0000 chunk 271 optimal weight: 8.9990 chunk 176 optimal weight: 9.9990 chunk 225 optimal weight: 5.9990 chunk 43 optimal weight: 10.0000 chunk 79 optimal weight: 50.0000 chunk 241 optimal weight: 50.0000 chunk 269 optimal weight: 2.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** D 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 ASN D 84 ASN F 75 HIS ** N 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 68 GLN O 108 ASN R 84 ASN ** V 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 63 ASN ** Y 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 104 GLN b 47 GLN b 63 ASN e 55 GLN i 93 GLN ** j 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 84 GLN k 110 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.125788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.095089 restraints weight = 137216.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.095546 restraints weight = 204411.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.096148 restraints weight = 180225.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.097586 restraints weight = 125400.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.097594 restraints weight = 106046.536| |-----------------------------------------------------------------------------| r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6764 moved from start: 0.3303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 44017 Z= 0.213 Angle : 0.691 10.519 63489 Z= 0.394 Chirality : 0.044 0.208 7265 Planarity : 0.006 0.079 4746 Dihedral : 29.535 98.006 13347 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 0.13 % Allowed : 3.93 % Favored : 95.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.54 (0.15), residues: 2716 helix: 2.15 (0.11), residues: 1980 sheet: None (None), residues: 0 loop : -2.32 (0.19), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 92 TYR 0.033 0.003 TYR l 40 PHE 0.025 0.003 PHE e 67 HIS 0.013 0.002 HIS Q 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.21 (44017) covalent geometry : angle 0.69077 / 0.39 (63489) hydrogen bonds : bond 0.06901 / 4.69 ( 2706) hydrogen bonds : angle 3.31364 / 2.38 ( 6877) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5432 Ramachandran restraints generated. 2716 Oldfield, 0 Emsley, 2716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5432 Ramachandran restraints generated. 2716 Oldfield, 0 Emsley, 2716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 2317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 479 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.7299 (tm-30) cc_final: 0.7087 (tm-30) REVERT: C 99 LYS cc_start: 0.7931 (ptpt) cc_final: 0.7658 (ptpt) REVERT: D 57 LYS cc_start: 0.7143 (mttt) cc_final: 0.6914 (mttp) REVERT: F 78 ARG cc_start: 0.8369 (mtt180) cc_final: 0.8126 (mtt-85) REVERT: F 79 LYS cc_start: 0.6654 (tppt) cc_final: 0.6453 (tptp) REVERT: F 100 PHE cc_start: 0.7763 (m-80) cc_final: 0.7410 (m-80) REVERT: G 39 TYR cc_start: 0.8058 (m-80) cc_final: 0.7647 (m-80) REVERT: G 74 LYS cc_start: 0.5717 (pttm) cc_final: 0.5243 (mmtt) REVERT: K 123 ASP cc_start: 0.6651 (t70) cc_final: 0.6421 (t70) REVERT: K 130 ILE cc_start: 0.8281 (mt) cc_final: 0.8066 (mt) REVERT: L 29 ILE cc_start: 0.6157 (mm) cc_final: 0.5709 (tt) REVERT: L 44 LYS cc_start: 0.6185 (mttt) cc_final: 0.5823 (ptpt) REVERT: M 99 LYS cc_start: 0.7185 (mttt) cc_final: 0.5733 (mmtt) REVERT: N 43 LYS cc_start: 0.8321 (ttpt) cc_final: 0.8108 (ttmt) REVERT: N 48 VAL cc_start: 0.7885 (t) cc_final: 0.7579 (m) REVERT: O 76 GLN cc_start: 0.6719 (mt0) cc_final: 0.6245 (mm110) REVERT: O 115 LYS cc_start: 0.6473 (mttt) cc_final: 0.6070 (mmtt) REVERT: P 45 ARG cc_start: 0.7086 (mtt180) cc_final: 0.6836 (mtp180) REVERT: Q 74 LYS cc_start: 0.6655 (mttt) cc_final: 0.6355 (mmtp) REVERT: Q 95 LYS cc_start: 0.7210 (mttt) cc_final: 0.6846 (mtmm) REVERT: V 84 MET cc_start: 0.6202 (mmm) cc_final: 0.5617 (mmt) REVERT: W 107 VAL cc_start: 0.5780 (p) cc_final: 0.5561 (m) REVERT: Y 130 ILE cc_start: 0.8645 (OUTLIER) cc_final: 0.8354 (mp) REVERT: a 42 ARG cc_start: 0.5366 (mtt90) cc_final: 0.4712 (mtm180) REVERT: a 95 LYS cc_start: 0.7837 (mptt) cc_final: 0.7631 (tttp) REVERT: e 63 ARG cc_start: 0.5327 (mtt-85) cc_final: 0.4663 (mmm160) REVERT: e 105 GLU cc_start: 0.7265 (tm-30) cc_final: 0.6787 (tp30) REVERT: g 32 ARG cc_start: 0.5608 (tmm-80) cc_final: 0.5356 (ttp-170) REVERT: g 36 LYS cc_start: 0.5816 (mttt) cc_final: 0.5184 (tttt) REVERT: h 83 TYR cc_start: 0.6586 (t80) cc_final: 0.6322 (t80) REVERT: i 100 LEU cc_start: 0.8770 (mm) cc_final: 0.8532 (mm) REVERT: j 45 ARG cc_start: 0.7115 (mtt180) cc_final: 0.6467 (mtt-85) REVERT: j 63 GLU cc_start: 0.7526 (tm-30) cc_final: 0.7222 (tm-30) REVERT: j 79 LYS cc_start: 0.7258 (mttt) cc_final: 0.6724 (mmtm) REVERT: j 88 TYR cc_start: 0.7343 (m-80) cc_final: 0.7043 (m-10) REVERT: k 110 ASN cc_start: 0.6976 (m110) cc_final: 0.6774 (m-40) REVERT: l 52 THR cc_start: 0.4248 (p) cc_final: 0.4002 (t) REVERT: l 68 ASP cc_start: 0.7076 (t70) cc_final: 0.6837 (t70) REVERT: l 83 TYR cc_start: 0.7173 (t80) cc_final: 0.6834 (t80) outliers start: 3 outliers final: 0 residues processed: 480 average time/residue: 0.2597 time to fit residues: 199.5179 Evaluate side-chains 366 residues out of total 2317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 365 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 286 optimal weight: 8.9990 chunk 121 optimal weight: 8.9990 chunk 120 optimal weight: 10.0000 chunk 208 optimal weight: 3.9990 chunk 266 optimal weight: 3.9990 chunk 80 optimal weight: 50.0000 chunk 231 optimal weight: 20.0000 chunk 282 optimal weight: 4.9990 chunk 136 optimal weight: 0.0970 chunk 256 optimal weight: 40.0000 chunk 12 optimal weight: 1.9990 overall best weight: 3.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 63 ASN H 109 HIS ** N 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 95 GLN P 75 HIS R 84 ASN ** V 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 47 GLN b 63 ASN ** i 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.126802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.096434 restraints weight = 137240.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.096373 restraints weight = 186826.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.097044 restraints weight = 176338.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.098071 restraints weight = 120490.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.098173 restraints weight = 107259.157| |-----------------------------------------------------------------------------| r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6743 moved from start: 0.3342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 44017 Z= 0.150 Angle : 0.565 9.172 63489 Z= 0.339 Chirality : 0.039 0.174 7265 Planarity : 0.004 0.061 4746 Dihedral : 29.532 100.368 13347 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 0.09 % Allowed : 1.77 % Favored : 98.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.11 (0.16), residues: 2716 helix: 2.63 (0.11), residues: 1975 sheet: None (None), residues: 0 loop : -2.28 (0.19), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG k 35 TYR 0.022 0.002 TYR l 40 PHE 0.024 0.002 PHE e 67 HIS 0.008 0.001 HIS P 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.15 (44017) covalent geometry : angle 0.56498 / 0.34 (63489) hydrogen bonds : bond 0.05412 / 3.69 ( 2706) hydrogen bonds : angle 2.98807 / 2.16 ( 6877) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5432 Ramachandran restraints generated. 2716 Oldfield, 0 Emsley, 2716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5432 Ramachandran restraints generated. 2716 Oldfield, 0 Emsley, 2716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 2317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 493 time to evaluate : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.7189 (tm-30) cc_final: 0.6806 (tp30) REVERT: F 79 LYS cc_start: 0.6644 (tppt) cc_final: 0.6351 (tptp) REVERT: F 84 MET cc_start: 0.7083 (tpt) cc_final: 0.6640 (tpp) REVERT: F 100 PHE cc_start: 0.7781 (m-80) cc_final: 0.7362 (m-80) REVERT: G 39 TYR cc_start: 0.8062 (m-80) cc_final: 0.7688 (m-80) REVERT: G 74 LYS cc_start: 0.5756 (pttm) cc_final: 0.5256 (mmtt) REVERT: K 90 MET cc_start: 0.5762 (mtp) cc_final: 0.5557 (mtp) REVERT: K 130 ILE cc_start: 0.8213 (mt) cc_final: 0.7931 (mt) REVERT: L 29 ILE cc_start: 0.6187 (mm) cc_final: 0.5843 (tt) REVERT: L 44 LYS cc_start: 0.6151 (mttt) cc_final: 0.5803 (ptpt) REVERT: M 99 LYS cc_start: 0.7049 (mttt) cc_final: 0.5837 (mmtt) REVERT: N 43 LYS cc_start: 0.8304 (ttpt) cc_final: 0.8084 (ttmt) REVERT: N 48 VAL cc_start: 0.7742 (t) cc_final: 0.7439 (m) REVERT: O 76 GLN cc_start: 0.6711 (mt0) cc_final: 0.6324 (mm110) REVERT: O 115 LYS cc_start: 0.6575 (mttt) cc_final: 0.6101 (mmtt) REVERT: Q 74 LYS cc_start: 0.6623 (mttt) cc_final: 0.6292 (mmtp) REVERT: Q 95 LYS cc_start: 0.7197 (mttt) cc_final: 0.6821 (mtmm) REVERT: V 84 MET cc_start: 0.6141 (mmm) cc_final: 0.5534 (mmt) REVERT: W 107 VAL cc_start: 0.5852 (p) cc_final: 0.5591 (m) REVERT: X 59 MET cc_start: 0.5087 (tpp) cc_final: 0.4867 (tpp) REVERT: X 106 LEU cc_start: 0.7642 (mt) cc_final: 0.7411 (mt) REVERT: Y 105 GLU cc_start: 0.7356 (tm-30) cc_final: 0.6766 (tp30) REVERT: a 95 LYS cc_start: 0.7816 (mptt) cc_final: 0.7592 (tttp) REVERT: e 63 ARG cc_start: 0.5253 (mtt-85) cc_final: 0.4623 (mmm160) REVERT: e 105 GLU cc_start: 0.7250 (tm-30) cc_final: 0.6778 (tp30) REVERT: g 32 ARG cc_start: 0.5617 (tmm-80) cc_final: 0.5392 (ttp-170) REVERT: g 36 LYS cc_start: 0.5675 (mttt) cc_final: 0.5128 (tttt) REVERT: h 40 TYR cc_start: 0.7402 (m-80) cc_final: 0.7149 (m-80) REVERT: h 83 TYR cc_start: 0.6604 (t80) cc_final: 0.6265 (t80) REVERT: j 45 ARG cc_start: 0.6873 (mtt180) cc_final: 0.6391 (mtt-85) REVERT: j 63 GLU cc_start: 0.7602 (tm-30) cc_final: 0.7295 (tm-30) REVERT: j 79 LYS cc_start: 0.7075 (mttt) cc_final: 0.6402 (mmtm) REVERT: l 68 ASP cc_start: 0.6852 (t70) cc_final: 0.6535 (t70) outliers start: 2 outliers final: 0 residues processed: 493 average time/residue: 0.2518 time to fit residues: 199.0045 Evaluate side-chains 372 residues out of total 2317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 372 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 180 optimal weight: 7.9990 chunk 49 optimal weight: 8.9990 chunk 221 optimal weight: 0.9990 chunk 233 optimal weight: 10.0000 chunk 296 optimal weight: 20.0000 chunk 114 optimal weight: 6.9990 chunk 344 optimal weight: 40.0000 chunk 124 optimal weight: 10.0000 chunk 120 optimal weight: 6.9990 chunk 300 optimal weight: 7.9990 chunk 69 optimal weight: 50.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN D 63 ASN G 110 ASN ** L 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 68 GLN Q 84 GLN R 84 ASN ** U 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 47 GLN g 89 ASN ** i 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 95 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.124920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.093973 restraints weight = 136519.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.094339 restraints weight = 193326.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.094919 restraints weight = 178907.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.095065 restraints weight = 122928.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.096457 restraints weight = 116965.577| |-----------------------------------------------------------------------------| r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6804 moved from start: 0.3921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 44017 Z= 0.206 Angle : 0.684 8.423 63489 Z= 0.392 Chirality : 0.044 0.207 7265 Planarity : 0.006 0.144 4746 Dihedral : 29.756 94.379 13347 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 0.13 % Allowed : 2.55 % Favored : 97.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.16), residues: 2716 helix: 2.03 (0.11), residues: 1970 sheet: None (None), residues: 0 loop : -2.54 (0.19), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.041 0.001 ARG E 116 TYR 0.031 0.003 TYR B 72 PHE 0.024 0.002 PHE X 65 HIS 0.010 0.002 HIS V 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.21 (44017) covalent geometry : angle 0.68442 / 0.39 (63489) hydrogen bonds : bond 0.06758 / 4.62 ( 2706) hydrogen bonds : angle 3.36044 / 2.42 ( 6877) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5432 Ramachandran restraints generated. 2716 Oldfield, 0 Emsley, 2716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5432 Ramachandran restraints generated. 2716 Oldfield, 0 Emsley, 2716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 2317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 451 time to evaluate : 1.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.7274 (tm-30) cc_final: 0.6878 (tp30) REVERT: A 120 MET cc_start: 0.7770 (mtm) cc_final: 0.7483 (mtm) REVERT: D 57 LYS cc_start: 0.7158 (mttt) cc_final: 0.6788 (mttp) REVERT: F 78 ARG cc_start: 0.8159 (mtt180) cc_final: 0.7866 (mtt-85) REVERT: F 79 LYS cc_start: 0.6908 (tppt) cc_final: 0.6528 (tptp) REVERT: F 100 PHE cc_start: 0.7779 (m-80) cc_final: 0.7519 (m-80) REVERT: G 74 LYS cc_start: 0.5687 (pttm) cc_final: 0.5098 (mmtt) REVERT: K 130 ILE cc_start: 0.8258 (mt) cc_final: 0.7967 (mt) REVERT: L 29 ILE cc_start: 0.6169 (mm) cc_final: 0.5843 (tt) REVERT: M 99 LYS cc_start: 0.7032 (mttt) cc_final: 0.5817 (mmtt) REVERT: N 48 VAL cc_start: 0.7891 (t) cc_final: 0.7572 (m) REVERT: N 59 MET cc_start: 0.7467 (tpp) cc_final: 0.6887 (ttp) REVERT: O 115 LYS cc_start: 0.6578 (mttt) cc_final: 0.6069 (mmtt) REVERT: Q 74 LYS cc_start: 0.6674 (mttt) cc_final: 0.6327 (mmtp) REVERT: Q 95 LYS cc_start: 0.7210 (mttt) cc_final: 0.6802 (mtmm) REVERT: U 123 ASP cc_start: 0.8484 (m-30) cc_final: 0.8270 (m-30) REVERT: a 95 LYS cc_start: 0.7891 (mptt) cc_final: 0.7664 (tttp) REVERT: e 63 ARG cc_start: 0.5446 (mtt-85) cc_final: 0.4805 (mmm160) REVERT: e 105 GLU cc_start: 0.7223 (tm-30) cc_final: 0.6768 (tp30) REVERT: g 36 LYS cc_start: 0.5905 (mttt) cc_final: 0.5181 (tttt) REVERT: h 40 TYR cc_start: 0.7517 (m-80) cc_final: 0.7298 (m-80) REVERT: j 45 ARG cc_start: 0.7102 (mtt180) cc_final: 0.6556 (mtt-85) REVERT: j 79 LYS cc_start: 0.6854 (mttt) cc_final: 0.6253 (mmtm) REVERT: l 68 ASP cc_start: 0.7074 (t70) cc_final: 0.6732 (t70) outliers start: 3 outliers final: 0 residues processed: 451 average time/residue: 0.2441 time to fit residues: 178.5368 Evaluate side-chains 353 residues out of total 2317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 353 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 190 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 204 optimal weight: 5.9990 chunk 98 optimal weight: 0.9980 chunk 50 optimal weight: 9.9990 chunk 185 optimal weight: 6.9990 chunk 62 optimal weight: 7.9990 chunk 154 optimal weight: 40.0000 chunk 288 optimal weight: 0.0870 chunk 198 optimal weight: 7.9990 chunk 346 optimal weight: 50.0000 overall best weight: 3.0164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN D 63 ASN K 108 ASN ** N 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 84 ASN ** V 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 47 GLN ** i 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 95 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.125743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.095403 restraints weight = 137091.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.095675 restraints weight = 198973.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.096340 restraints weight = 179357.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.096487 restraints weight = 122939.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.097949 restraints weight = 117015.788| |-----------------------------------------------------------------------------| r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6762 moved from start: 0.3937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 44017 Z= 0.153 Angle : 0.589 8.745 63489 Z= 0.351 Chirality : 0.040 0.184 7265 Planarity : 0.004 0.063 4746 Dihedral : 29.736 95.450 13347 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 0.09 % Allowed : 1.29 % Favored : 98.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.79 (0.16), residues: 2716 helix: 2.41 (0.11), residues: 1976 sheet: None (None), residues: 0 loop : -2.44 (0.19), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG k 35 TYR 0.026 0.002 TYR a 39 PHE 0.022 0.002 PHE W 25 HIS 0.007 0.001 HIS h 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.15 (44017) covalent geometry : angle 0.58934 / 0.35 (63489) hydrogen bonds : bond 0.05590 / 3.82 ( 2706) hydrogen bonds : angle 3.09506 / 2.24 ( 6877) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5432 Ramachandran restraints generated. 2716 Oldfield, 0 Emsley, 2716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5432 Ramachandran restraints generated. 2716 Oldfield, 0 Emsley, 2716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 2317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 462 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.7371 (tm-30) cc_final: 0.7017 (tp30) REVERT: D 57 LYS cc_start: 0.7281 (mttt) cc_final: 0.6891 (mttp) REVERT: F 78 ARG cc_start: 0.8119 (mtt180) cc_final: 0.7855 (mtt-85) REVERT: F 100 PHE cc_start: 0.7740 (m-80) cc_final: 0.7428 (m-80) REVERT: G 39 TYR cc_start: 0.8092 (m-80) cc_final: 0.7626 (m-80) REVERT: G 74 LYS cc_start: 0.5460 (pttm) cc_final: 0.4940 (mmtt) REVERT: K 130 ILE cc_start: 0.8243 (mt) cc_final: 0.7894 (mt) REVERT: L 29 ILE cc_start: 0.6093 (mm) cc_final: 0.5776 (tt) REVERT: M 99 LYS cc_start: 0.7007 (mttt) cc_final: 0.5696 (mmtt) REVERT: N 48 VAL cc_start: 0.7834 (t) cc_final: 0.7548 (m) REVERT: N 59 MET cc_start: 0.7477 (tpp) cc_final: 0.6998 (ttp) REVERT: O 115 LYS cc_start: 0.6565 (mttt) cc_final: 0.6120 (mmtt) REVERT: Q 74 LYS cc_start: 0.6429 (mttt) cc_final: 0.6154 (mmtp) REVERT: Q 95 LYS cc_start: 0.7225 (mttt) cc_final: 0.6834 (mtmm) REVERT: R 59 MET cc_start: 0.6393 (tpp) cc_final: 0.5847 (tpp) REVERT: U 94 GLU cc_start: 0.6602 (mt-10) cc_final: 0.6347 (mt-10) REVERT: U 123 ASP cc_start: 0.8493 (m-30) cc_final: 0.8265 (m-30) REVERT: V 84 MET cc_start: 0.6776 (tpp) cc_final: 0.5656 (mmt) REVERT: W 107 VAL cc_start: 0.6046 (p) cc_final: 0.5832 (m) REVERT: a 38 ASN cc_start: 0.7707 (p0) cc_final: 0.7428 (p0) REVERT: e 63 ARG cc_start: 0.5319 (mtt-85) cc_final: 0.4757 (mmm160) REVERT: e 105 GLU cc_start: 0.7260 (tm-30) cc_final: 0.6754 (tp30) REVERT: e 107 THR cc_start: 0.8737 (m) cc_final: 0.8451 (p) REVERT: g 36 LYS cc_start: 0.5719 (mttt) cc_final: 0.5123 (tttt) REVERT: h 40 TYR cc_start: 0.7595 (m-80) cc_final: 0.7284 (m-80) REVERT: j 45 ARG cc_start: 0.7042 (mtt180) cc_final: 0.6557 (mtt-85) REVERT: j 63 GLU cc_start: 0.7372 (tm-30) cc_final: 0.7129 (tm-30) REVERT: j 79 LYS cc_start: 0.6857 (mttt) cc_final: 0.6114 (mmtm) REVERT: l 68 ASP cc_start: 0.6869 (t70) cc_final: 0.6577 (t70) outliers start: 2 outliers final: 0 residues processed: 462 average time/residue: 0.2564 time to fit residues: 189.7254 Evaluate side-chains 366 residues out of total 2317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 366 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 239 optimal weight: 2.9990 chunk 328 optimal weight: 50.0000 chunk 148 optimal weight: 6.9990 chunk 62 optimal weight: 5.9990 chunk 250 optimal weight: 50.0000 chunk 49 optimal weight: 4.9990 chunk 140 optimal weight: 6.9990 chunk 186 optimal weight: 3.9990 chunk 263 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 92 optimal weight: 9.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN D 63 ASN K 108 ASN ** N 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 84 ASN ** V 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 47 GLN j 75 HIS ** j 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.125455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.095159 restraints weight = 137381.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.095247 restraints weight = 198668.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.095929 restraints weight = 182380.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.097373 restraints weight = 124787.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.097402 restraints weight = 106077.407| |-----------------------------------------------------------------------------| r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6771 moved from start: 0.4055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 44017 Z= 0.157 Angle : 0.596 8.881 63489 Z= 0.351 Chirality : 0.040 0.188 7265 Planarity : 0.005 0.072 4746 Dihedral : 29.737 93.128 13347 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 0.09 % Allowed : 0.78 % Favored : 99.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.85 (0.16), residues: 2716 helix: 2.46 (0.11), residues: 1974 sheet: None (None), residues: 0 loop : -2.43 (0.19), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG k 35 TYR 0.026 0.002 TYR a 39 PHE 0.021 0.002 PHE X 65 HIS 0.008 0.001 HIS V 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.16 (44017) covalent geometry : angle 0.59551 / 0.35 (63489) hydrogen bonds : bond 0.05562 / 3.80 ( 2706) hydrogen bonds : angle 3.09415 / 2.24 ( 6877) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5432 Ramachandran restraints generated. 2716 Oldfield, 0 Emsley, 2716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5432 Ramachandran restraints generated. 2716 Oldfield, 0 Emsley, 2716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 2317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 447 time to evaluate : 1.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.7389 (tm-30) cc_final: 0.7055 (tp30) REVERT: A 120 MET cc_start: 0.7534 (mtm) cc_final: 0.7140 (mtm) REVERT: B 88 TYR cc_start: 0.6719 (m-80) cc_final: 0.6473 (m-80) REVERT: F 62 LEU cc_start: 0.8740 (mt) cc_final: 0.8523 (mt) REVERT: F 78 ARG cc_start: 0.8190 (mtt180) cc_final: 0.7897 (mtt-85) REVERT: F 100 PHE cc_start: 0.7769 (m-80) cc_final: 0.7430 (m-80) REVERT: G 39 TYR cc_start: 0.8141 (m-80) cc_final: 0.7523 (m-80) REVERT: G 74 LYS cc_start: 0.5301 (pttm) cc_final: 0.4781 (mmtt) REVERT: L 29 ILE cc_start: 0.6218 (mm) cc_final: 0.5780 (tt) REVERT: M 99 LYS cc_start: 0.7042 (mttt) cc_final: 0.5737 (mmtt) REVERT: N 48 VAL cc_start: 0.7826 (t) cc_final: 0.7524 (m) REVERT: N 59 MET cc_start: 0.7367 (tpp) cc_final: 0.6978 (ttp) REVERT: O 115 LYS cc_start: 0.6491 (mttt) cc_final: 0.6031 (mmtt) REVERT: Q 74 LYS cc_start: 0.6434 (mttt) cc_final: 0.6147 (mmtp) REVERT: Q 95 LYS cc_start: 0.7187 (mttt) cc_final: 0.6822 (mtmm) REVERT: R 59 MET cc_start: 0.6340 (tpp) cc_final: 0.5777 (tpp) REVERT: U 94 GLU cc_start: 0.6615 (mt-10) cc_final: 0.6400 (mt-10) REVERT: U 123 ASP cc_start: 0.8517 (m-30) cc_final: 0.8291 (m-30) REVERT: V 84 MET cc_start: 0.6890 (tpp) cc_final: 0.5682 (mmt) REVERT: W 107 VAL cc_start: 0.6079 (p) cc_final: 0.5865 (m) REVERT: a 64 GLU cc_start: 0.6066 (mt-10) cc_final: 0.5845 (mt-10) REVERT: e 63 ARG cc_start: 0.5408 (mtt-85) cc_final: 0.4846 (mmm160) REVERT: e 105 GLU cc_start: 0.7360 (tm-30) cc_final: 0.6875 (tp30) REVERT: e 107 THR cc_start: 0.8756 (m) cc_final: 0.8441 (p) REVERT: e 120 MET cc_start: 0.7981 (mpp) cc_final: 0.7689 (mpp) REVERT: g 36 LYS cc_start: 0.5853 (mttt) cc_final: 0.5168 (tttt) REVERT: g 42 ARG cc_start: 0.6402 (tpp-160) cc_final: 0.6157 (tpp-160) REVERT: h 40 TYR cc_start: 0.7510 (m-80) cc_final: 0.7289 (m-80) REVERT: j 45 ARG cc_start: 0.7095 (mtt180) cc_final: 0.6504 (mtt-85) REVERT: j 63 GLU cc_start: 0.7468 (tm-30) cc_final: 0.7203 (tm-30) REVERT: j 79 LYS cc_start: 0.6824 (mttt) cc_final: 0.6098 (mmtm) REVERT: k 35 ARG cc_start: 0.6866 (mmm160) cc_final: 0.6649 (mmm160) REVERT: l 68 ASP cc_start: 0.6875 (t70) cc_final: 0.6590 (t70) REVERT: l 83 TYR cc_start: 0.7304 (t80) cc_final: 0.7090 (t80) outliers start: 2 outliers final: 0 residues processed: 447 average time/residue: 0.2410 time to fit residues: 175.4180 Evaluate side-chains 360 residues out of total 2317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 360 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 74 optimal weight: 50.0000 chunk 87 optimal weight: 50.0000 chunk 84 optimal weight: 50.0000 chunk 166 optimal weight: 50.0000 chunk 205 optimal weight: 6.9990 chunk 238 optimal weight: 5.9990 chunk 306 optimal weight: 3.9990 chunk 164 optimal weight: 50.0000 chunk 282 optimal weight: 7.9990 chunk 256 optimal weight: 40.0000 chunk 35 optimal weight: 1.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN D 63 ASN K 108 ASN ** N 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 47 GLN ** j 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.124416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.093611 restraints weight = 136285.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.093965 restraints weight = 202105.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.094616 restraints weight = 182420.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.095647 restraints weight = 125848.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.095766 restraints weight = 113436.008| |-----------------------------------------------------------------------------| r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6816 moved from start: 0.4401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 44017 Z= 0.191 Angle : 0.660 8.737 63489 Z= 0.380 Chirality : 0.043 0.259 7265 Planarity : 0.006 0.084 4746 Dihedral : 29.872 88.608 13347 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 0.04 % Allowed : 0.65 % Favored : 99.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.16), residues: 2716 helix: 2.09 (0.11), residues: 1970 sheet: None (None), residues: 0 loop : -2.54 (0.19), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG k 35 TYR 0.035 0.002 TYR j 88 PHE 0.028 0.002 PHE X 65 HIS 0.009 0.002 HIS V 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.19 (44017) covalent geometry : angle 0.65967 / 0.38 (63489) hydrogen bonds : bond 0.06346 / 4.33 ( 2706) hydrogen bonds : angle 3.33853 / 2.40 ( 6877) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5432 Ramachandran restraints generated. 2716 Oldfield, 0 Emsley, 2716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5432 Ramachandran restraints generated. 2716 Oldfield, 0 Emsley, 2716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 2317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 430 time to evaluate : 1.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.7318 (tm-30) cc_final: 0.6944 (tp30) REVERT: A 120 MET cc_start: 0.7591 (mtm) cc_final: 0.7307 (mtm) REVERT: D 57 LYS cc_start: 0.7231 (mttt) cc_final: 0.6823 (mttp) REVERT: D 71 GLU cc_start: 0.7101 (mp0) cc_final: 0.6888 (mp0) REVERT: F 79 LYS cc_start: 0.7016 (mmtm) cc_final: 0.6750 (mmtm) REVERT: F 100 PHE cc_start: 0.7825 (m-80) cc_final: 0.7440 (m-80) REVERT: G 39 TYR cc_start: 0.8163 (m-80) cc_final: 0.7940 (m-80) REVERT: G 74 LYS cc_start: 0.5331 (pttm) cc_final: 0.4723 (mmtt) REVERT: K 58 THR cc_start: 0.6752 (p) cc_final: 0.6241 (t) REVERT: L 29 ILE cc_start: 0.6343 (mm) cc_final: 0.5917 (tt) REVERT: M 99 LYS cc_start: 0.7082 (mttt) cc_final: 0.5772 (mmtt) REVERT: N 48 VAL cc_start: 0.7908 (t) cc_final: 0.7687 (m) REVERT: O 115 LYS cc_start: 0.6526 (mttt) cc_final: 0.6108 (mmtt) REVERT: Q 74 LYS cc_start: 0.6680 (mttt) cc_final: 0.6356 (mmtp) REVERT: Q 95 LYS cc_start: 0.7247 (mttt) cc_final: 0.6833 (mtmm) REVERT: R 59 MET cc_start: 0.6537 (tpp) cc_final: 0.5975 (tpp) REVERT: U 94 GLU cc_start: 0.6728 (mt-10) cc_final: 0.6503 (mt-10) REVERT: V 84 MET cc_start: 0.6887 (tpp) cc_final: 0.5818 (mmt) REVERT: X 59 MET cc_start: 0.5088 (tpp) cc_final: 0.4843 (tpp) REVERT: Z 92 ARG cc_start: 0.7587 (tpt-90) cc_final: 0.6918 (ttt180) REVERT: e 63 ARG cc_start: 0.5501 (mtt-85) cc_final: 0.4933 (mmm160) REVERT: e 105 GLU cc_start: 0.7246 (tm-30) cc_final: 0.6721 (tp30) REVERT: g 36 LYS cc_start: 0.5968 (mttt) cc_final: 0.5208 (tttt) REVERT: j 45 ARG cc_start: 0.7127 (mtt180) cc_final: 0.6524 (mtt-85) REVERT: j 63 GLU cc_start: 0.7540 (tm-30) cc_final: 0.7301 (tm-30) REVERT: j 79 LYS cc_start: 0.6773 (mttt) cc_final: 0.6048 (mmtm) outliers start: 1 outliers final: 0 residues processed: 430 average time/residue: 0.2549 time to fit residues: 178.9400 Evaluate side-chains 355 residues out of total 2317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 355 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 300 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 241 optimal weight: 50.0000 chunk 211 optimal weight: 8.9990 chunk 122 optimal weight: 2.9990 chunk 280 optimal weight: 7.9990 chunk 25 optimal weight: 0.9990 chunk 85 optimal weight: 50.0000 chunk 47 optimal weight: 4.9990 chunk 173 optimal weight: 40.0000 chunk 58 optimal weight: 5.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN D 63 ASN K 108 ASN ** N 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 84 ASN ** Y 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 47 GLN ** i 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 110 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.125244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.098004 restraints weight = 136902.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.096471 restraints weight = 177428.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.097383 restraints weight = 198757.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.097482 restraints weight = 138324.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.098802 restraints weight = 115572.920| |-----------------------------------------------------------------------------| r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6763 moved from start: 0.4379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 44017 Z= 0.148 Angle : 0.590 8.602 63489 Z= 0.350 Chirality : 0.040 0.191 7265 Planarity : 0.004 0.063 4746 Dihedral : 29.828 89.813 13347 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 0.09 % Allowed : 0.47 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.82 (0.16), residues: 2716 helix: 2.44 (0.11), residues: 1968 sheet: None (None), residues: 0 loop : -2.41 (0.19), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG k 35 TYR 0.031 0.002 TYR j 88 PHE 0.022 0.002 PHE M 25 HIS 0.007 0.001 HIS V 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.15 (44017) covalent geometry : angle 0.58990 / 0.35 (63489) hydrogen bonds : bond 0.05508 / 3.76 ( 2706) hydrogen bonds : angle 3.11047 / 2.25 ( 6877) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6541.30 seconds wall clock time: 113 minutes 33.87 seconds (6813.87 seconds total)