Starting phenix.real_space_refine on Sun Sep 13 04:32:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w6e_65684/09_2026/9w6e_65684.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w6e_65684/09_2026/9w6e_65684.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9w6e_65684/09_2026/9w6e_65684.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w6e_65684/09_2026/9w6e_65684.map" model { file = "/net/cci-nas-00/data/ceres_data/9w6e_65684/09_2026/9w6e_65684.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w6e_65684/09_2026/9w6e_65684.cif" } resolution = 3.7 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= 0.002 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 472 5.49 5 S 28 5.16 5 C 11589 2.51 5 N 3871 2.21 5 O 4799 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20759 Number of models: 1 Model: "" Number of chains: 20 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: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 785 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 5, 'TRANS': 96} Chain: "D" Number of atoms: 691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 691 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 2, 'TRANS': 86} Chain: "E" Number of atoms: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 773 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 3, 'TRANS': 90} Chain: "F" 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: "G" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 785 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 5, '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: "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: 614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 614 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 1, 'TRANS': 75} Chain: "M" Number of atoms: 632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 632 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "N" Number of atoms: 691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 691 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 2, 'TRANS': 86} Chain: "O" 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: "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: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 658 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 4, 'TRANS': 80} Chain: "R" 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: 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: "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} Time building chain proxies: 3.15, per 1000 atoms: 0.15 Number of scatterers: 20759 At special positions: 0 Unit cell: (171.6, 157.3, 129.8, 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 28 16.00 P 472 15.00 O 4799 8.00 N 3871 7.00 C 11589 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.72 Conformation dependent library (CDL) restraints added in 430.2 milliseconds 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2606 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 11 sheets defined 76.1% alpha, 1.9% beta 214 base pairs and 335 stacking pairs defined. Time for finding SS restraints: 2.79 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.732A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 115 removed outlier: 4.212A pdb=" N ALA A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS A 115 " --> pdb=" O ALA A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 25 through 29 removed outlier: 3.796A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.500A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 removed outlier: 3.549A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 22 Processing helix chain 'C' and resid 26 through 36 removed outlier: 3.519A pdb=" N VAL C 30 " --> pdb=" O PRO C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 73 Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 91 through 97 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.506A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.616A pdb=" N ILE D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 124 Processing helix chain 'E' and resid 44 through 57 removed outlier: 3.584A pdb=" N LEU E 48 " --> pdb=" O GLY E 44 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N SER E 57 " --> pdb=" O ARG E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.809A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.657A pdb=" N VAL E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N MET E 90 " --> pdb=" O SER E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 131 Processing helix chain 'F' and resid 25 through 29 removed outlier: 3.535A pdb=" N ILE F 29 " --> pdb=" O ILE F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.805A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 94 removed outlier: 3.511A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 17 through 22 Processing helix chain 'G' and resid 27 through 36 Processing helix chain 'G' and resid 45 through 74 removed outlier: 4.584A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASP G 72 " --> pdb=" O ASN G 68 " (cutoff:3.500A) removed outlier: 3.882A 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 49 Processing helix chain 'H' and resid 57 through 84 Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.975A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLN H 95 " --> pdb=" O SER H 91 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N THR H 96 " --> pdb=" O ARG H 92 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 122 removed outlier: 3.692A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 56 removed outlier: 3.872A pdb=" N ARG K 49 " --> pdb=" O THR K 45 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ILE K 51 " --> pdb=" O ALA K 47 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ARG K 52 " --> pdb=" O LEU K 48 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ARG K 53 " --> pdb=" O ARG K 49 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LYS K 56 " --> pdb=" O ARG K 52 " (cutoff:3.500A) Processing helix chain 'K' and resid 63 through 79 removed outlier: 3.873A pdb=" N ASP K 77 " --> pdb=" O GLU K 73 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N PHE K 78 " --> pdb=" O ILE K 74 " (cutoff:3.500A) Processing helix chain 'K' and resid 85 through 114 Processing helix chain 'K' and resid 120 through 132 Processing helix chain 'L' and resid 30 through 41 Processing helix chain 'L' and resid 50 through 76 removed outlier: 3.887A pdb=" N ASP L 68 " --> pdb=" O ASN L 64 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N THR L 71 " --> pdb=" O ARG L 67 " (cutoff:3.500A) Processing helix chain 'L' and resid 82 through 94 removed outlier: 3.564A pdb=" N GLN L 93 " --> pdb=" O ALA L 89 " (cutoff:3.500A) Processing helix chain 'M' and resid 27 through 37 Processing helix chain 'M' and resid 45 through 73 removed outlier: 4.634A pdb=" N VAL M 49 " --> pdb=" O ALA M 45 " (cutoff:3.500A) Processing helix chain 'M' and resid 79 through 89 Processing helix chain 'M' and resid 90 through 97 Processing helix chain 'N' and resid 37 through 49 Processing helix chain 'N' and resid 55 through 84 Processing helix chain 'N' and resid 90 through 102 removed outlier: 3.620A pdb=" N ILE N 94 " --> pdb=" O THR N 90 " (cutoff:3.500A) Processing helix chain 'N' and resid 104 through 124 removed outlier: 4.087A pdb=" N LYS N 108 " --> pdb=" O GLY N 104 " (cutoff:3.500A) Processing helix chain 'O' and resid 45 through 57 removed outlier: 3.564A pdb=" N LYS O 56 " --> pdb=" O ARG O 52 " (cutoff:3.500A) Processing helix chain 'O' and resid 63 through 79 removed outlier: 4.080A pdb=" N ASP O 77 " --> pdb=" O GLU O 73 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N PHE O 78 " --> pdb=" O ILE O 74 " (cutoff:3.500A) Processing helix chain 'O' and resid 85 through 114 Processing helix chain 'O' and resid 120 through 132 Processing helix chain 'P' and resid 25 through 29 removed outlier: 3.721A pdb=" N ILE P 29 " --> pdb=" O ILE P 26 " (cutoff:3.500A) Processing helix chain 'P' and resid 30 through 41 Processing helix chain 'P' and resid 49 through 76 removed outlier: 3.991A pdb=" N GLU P 53 " --> pdb=" O LEU P 49 " (cutoff:3.500A) Processing helix chain 'P' and resid 82 through 94 removed outlier: 3.642A pdb=" N GLY P 94 " --> pdb=" O LEU P 90 " (cutoff:3.500A) Processing helix chain 'Q' and resid 26 through 37 Processing helix chain 'Q' and resid 45 through 74 removed outlier: 4.521A pdb=" N VAL Q 49 " --> pdb=" O ALA Q 45 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ASP Q 72 " --> pdb=" O ASN Q 68 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ASN Q 73 " --> pdb=" O ALA Q 69 " (cutoff:3.500A) Processing helix chain 'Q' and resid 79 through 90 Processing helix chain 'Q' and resid 90 through 97 Processing helix chain 'R' and resid 37 through 49 Processing helix chain 'R' and resid 55 through 84 removed outlier: 3.768A pdb=" N ASN R 84 " --> pdb=" O LEU R 80 " (cutoff:3.500A) Processing helix chain 'R' and resid 90 through 102 Processing helix chain 'R' and resid 103 through 122 Processing sheet with id=AA1, first strand: chain 'A' and resid 118 through 119 removed outlier: 3.515A pdb=" N ILE A 119 " --> pdb=" O ARG B 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 96 through 97 removed outlier: 6.311A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (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: 7.514A 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: 6.775A 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 'E' and resid 118 through 119 removed outlier: 3.729A pdb=" N ILE E 119 " --> pdb=" O ARG F 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.379A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB1, first strand: chain 'L' and resid 96 through 98 removed outlier: 5.572A pdb=" N THR L 96 " --> pdb=" O THR Q 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'Q' and resid 42 through 43 removed outlier: 7.617A pdb=" N ARG Q 42 " --> pdb=" O ILE R 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 759 hydrogen bonds defined for protein. 2268 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 562 hydrogen bonds 1124 hydrogen bond angles 0 basepair planarities 214 basepair parallelities 335 stacking parallelities Total time for adding SS restraints: 3.70 Time building geometry restraints manager: 2.35 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: 3055 1.33 - 1.45: 7725 1.45 - 1.57: 10313 1.57 - 1.69: 940 1.69 - 1.81: 48 Bond restraints: 22081 Sorted by residual: bond pdb=" C3' DC T 21 " pdb=" C2' DC T 21 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.24e+01 bond pdb=" C3' DA S -30 " pdb=" C2' DA S -30 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.10e+01 bond pdb=" C3' DC T 36 " pdb=" C2' DC T 36 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.09e+01 bond pdb=" C3' DA I 42 " pdb=" C2' DA I 42 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.09e+01 bond pdb=" C3' DT I 33 " pdb=" C2' DT I 33 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.05e+01 ... (remaining 22076 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.42: 29945 1.42 - 2.83: 1840 2.83 - 4.25: 41 4.25 - 5.67: 10 5.67 - 7.08: 6 Bond angle restraints: 31842 Sorted by residual: angle pdb=" O4' DG S -33 " pdb=" C4' DG S -33 " pdb=" C3' DG S -33 " ideal model delta sigma weight residual 106.00 102.90 3.10 6.00e-01 2.78e+00 2.68e+01 angle pdb=" O4' DA J -9 " pdb=" C4' DA J -9 " pdb=" C3' DA J -9 " ideal model delta sigma weight residual 106.00 102.92 3.08 6.00e-01 2.78e+00 2.63e+01 angle pdb=" O4' DA J 32 " pdb=" C4' DA J 32 " pdb=" C3' DA J 32 " ideal model delta sigma weight residual 106.00 103.20 2.80 6.00e-01 2.78e+00 2.18e+01 angle pdb=" N3 DT I 9 " pdb=" C4 DT I 9 " pdb=" O4 DT I 9 " ideal model delta sigma weight residual 119.90 122.61 -2.71 6.00e-01 2.78e+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 119.90 122.60 -2.70 6.00e-01 2.78e+00 2.02e+01 ... (remaining 31837 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 8740 17.88 - 35.75: 1490 35.75 - 53.63: 1372 53.63 - 71.50: 395 71.50 - 89.38: 30 Dihedral angle restraints: 12027 sinusoidal: 7978 harmonic: 4049 Sorted by residual: dihedral pdb=" CA PRO D 103 " pdb=" C PRO D 103 " pdb=" N GLY D 104 " pdb=" CA GLY D 104 " ideal model delta harmonic sigma weight residual 180.00 161.89 18.11 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" N GLU H 113 " pdb=" CA GLU H 113 " pdb=" CB GLU H 113 " pdb=" CG GLU H 113 " ideal model delta sinusoidal sigma weight residual 180.00 -124.24 -55.76 3 1.50e+01 4.44e-03 9.36e+00 dihedral pdb=" N ARG Q 71 " pdb=" CA ARG Q 71 " pdb=" CB ARG Q 71 " pdb=" CG ARG Q 71 " ideal model delta sinusoidal sigma weight residual -60.00 -113.77 53.77 3 1.50e+01 4.44e-03 9.23e+00 ... (remaining 12024 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 1639 0.025 - 0.050: 1281 0.050 - 0.075: 419 0.075 - 0.100: 233 0.100 - 0.125: 70 Chirality restraints: 3642 Sorted by residual: chirality pdb=" C3' DC J -48 " pdb=" C4' DC J -48 " pdb=" O3' DC J -48 " pdb=" C2' DC J -48 " both_signs ideal model delta sigma weight residual False -2.73 -2.61 -0.12 2.00e-01 2.50e+01 3.88e-01 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 2.56 -0.12 2.00e-01 2.50e+01 3.80e-01 chirality pdb=" C3' DC S 24 " pdb=" C4' DC S 24 " pdb=" O3' DC S 24 " pdb=" C2' DC S 24 " both_signs ideal model delta sigma weight residual False -2.73 -2.61 -0.12 2.00e-01 2.50e+01 3.60e-01 ... (remaining 3639 not shown) Planarity restraints: 2387 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG S -33 " -0.024 2.00e-02 2.50e+03 1.03e-02 3.19e+00 pdb=" N9 DG S -33 " 0.022 2.00e-02 2.50e+03 pdb=" C8 DG S -33 " 0.005 2.00e-02 2.50e+03 pdb=" N7 DG S -33 " 0.004 2.00e-02 2.50e+03 pdb=" C5 DG S -33 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DG S -33 " -0.004 2.00e-02 2.50e+03 pdb=" O6 DG S -33 " -0.007 2.00e-02 2.50e+03 pdb=" N1 DG S -33 " -0.003 2.00e-02 2.50e+03 pdb=" C2 DG S -33 " -0.004 2.00e-02 2.50e+03 pdb=" N2 DG S -33 " 0.008 2.00e-02 2.50e+03 pdb=" N3 DG S -33 " 0.003 2.00e-02 2.50e+03 pdb=" C4 DG S -33 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA J 32 " -0.018 2.00e-02 2.50e+03 8.55e-03 2.01e+00 pdb=" N9 DA J 32 " 0.020 2.00e-02 2.50e+03 pdb=" C8 DA J 32 " 0.002 2.00e-02 2.50e+03 pdb=" N7 DA J 32 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DA J 32 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DA J 32 " -0.001 2.00e-02 2.50e+03 pdb=" N6 DA J 32 " -0.004 2.00e-02 2.50e+03 pdb=" N1 DA J 32 " -0.004 2.00e-02 2.50e+03 pdb=" C2 DA J 32 " 0.004 2.00e-02 2.50e+03 pdb=" N3 DA J 32 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DA J 32 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU K 65 " 0.023 5.00e-02 4.00e+02 3.49e-02 1.95e+00 pdb=" N PRO K 66 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO K 66 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO K 66 " 0.020 5.00e-02 4.00e+02 ... (remaining 2384 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 3018 2.77 - 3.30: 18893 3.30 - 3.83: 39374 3.83 - 4.37: 42725 4.37 - 4.90: 64126 Nonbonded interactions: 168136 Sorted by model distance: nonbonded pdb=" N6 DA S 42 " pdb=" O6 DG T -41 " model vdw 2.232 3.120 nonbonded pdb=" OG1 THR O 118 " pdb=" OP1 DG J -3 " model vdw 2.256 3.040 nonbonded pdb=" NE2 HIS K 113 " pdb=" OD1 ASP O 123 " model vdw 2.297 3.120 nonbonded pdb=" NZ LYS K 79 " pdb=" O ASP K 81 " model vdw 2.305 3.120 nonbonded pdb=" NH2 ARG K 53 " pdb=" OP1 DT J -65 " model vdw 2.312 3.120 ... (remaining 168131 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 44 through 133) selection = (chain 'E' and resid 44 through 133) selection = chain 'K' selection = chain 'O' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'L' selection = chain 'P' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 36 through 122) selection = chain 'H' selection = (chain 'N' and resid 36 through 122) selection = chain 'R' } ncs_group { reference = chain 'I' selection = chain 'S' } ncs_group { reference = chain 'J' selection = chain 'T' } ncs_group { reference = chain 'M' selection = (chain 'Q' and resid 26 through 107) } 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: 1.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 18.130 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.040 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:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6372 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 0.033 22081 Z= 0.494 Angle : 0.651 7.084 31842 Z= 0.608 Chirality : 0.041 0.125 3642 Planarity : 0.003 0.035 2387 Dihedral : 24.725 89.379 9421 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % 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: 3.12 (0.23), residues: 1369 helix: 3.12 (0.16), residues: 996 sheet: None (None), residues: 0 loop : -1.07 (0.30), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 99 TYR 0.007 0.001 TYR G 50 PHE 0.004 0.001 PHE D 70 HIS 0.003 0.000 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00511 / 0.49 (22081) covalent geometry : angle 0.65085 / 0.61 (31842) hydrogen bonds : bond 0.09898 / 6.91 ( 1321) hydrogen bonds : angle 3.07206 / 2.20 ( 3392) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 357 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 THR cc_start: 0.8551 (p) cc_final: 0.7621 (p) REVERT: B 39 ARG cc_start: 0.7354 (mtt180) cc_final: 0.6951 (mmt180) REVERT: C 64 GLU cc_start: 0.7453 (tt0) cc_final: 0.6879 (tp30) REVERT: D 68 ASP cc_start: 0.7339 (t70) cc_final: 0.7089 (t0) REVERT: F 79 LYS cc_start: 0.8550 (mttt) cc_final: 0.8230 (mmtm) REVERT: G 36 LYS cc_start: 0.8307 (mttt) cc_final: 0.8101 (mttm) REVERT: K 52 ARG cc_start: 0.6343 (mtt180) cc_final: 0.5571 (mmm160) REVERT: K 60 LEU cc_start: 0.6568 (mt) cc_final: 0.6308 (pp) REVERT: K 118 THR cc_start: 0.3660 (m) cc_final: 0.2869 (t) REVERT: L 74 GLU cc_start: 0.5904 (mm-30) cc_final: 0.5415 (tp30) REVERT: M 95 LYS cc_start: 0.6566 (mmmt) cc_final: 0.5755 (mttt) REVERT: N 70 PHE cc_start: 0.6769 (t80) cc_final: 0.6490 (t80) REVERT: O 74 ILE cc_start: 0.5746 (mt) cc_final: 0.5509 (mt) REVERT: P 34 ILE cc_start: 0.5696 (mt) cc_final: 0.5392 (mp) REVERT: P 59 LYS cc_start: 0.7578 (tppt) cc_final: 0.7210 (ttmt) REVERT: Q 35 ARG cc_start: 0.5827 (mtm180) cc_final: 0.5017 (mmp-170) outliers start: 0 outliers final: 0 residues processed: 357 average time/residue: 0.2404 time to fit residues: 115.3094 Evaluate side-chains 200 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 30.0000 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 50.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 HIS C 73 ASN C 112 GLN D 84 ASN F 75 HIS G 31 HIS ** N 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 95 GLN P 93 GLN Q 84 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.165187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.136449 restraints weight = 56506.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.139334 restraints weight = 134926.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.138915 restraints weight = 75615.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.139265 restraints weight = 66806.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.139717 restraints weight = 52847.022| |-----------------------------------------------------------------------------| r_work (final): 0.4111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6568 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 22081 Z= 0.208 Angle : 0.646 9.874 31842 Z= 0.389 Chirality : 0.043 0.242 3642 Planarity : 0.006 0.092 2387 Dihedral : 28.895 89.334 6687 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.66 % Allowed : 10.03 % Favored : 87.32 % 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: 2.37 (0.23), residues: 1369 helix: 2.59 (0.16), residues: 1000 sheet: None (None), residues: 0 loop : -1.48 (0.30), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG L 55 TYR 0.030 0.002 TYR C 57 PHE 0.017 0.002 PHE O 67 HIS 0.009 0.002 HIS D 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.21 (22081) covalent geometry : angle 0.64551 / 0.39 (31842) hydrogen bonds : bond 0.05752 / 3.85 ( 1321) hydrogen bonds : angle 3.11889 / 2.23 ( 3392) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 219 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 THR cc_start: 0.8385 (p) cc_final: 0.8052 (t) REVERT: E 90 MET cc_start: 0.7824 (mmp) cc_final: 0.7564 (mmm) REVERT: G 93 LEU cc_start: 0.8791 (mt) cc_final: 0.8564 (mt) REVERT: K 126 LEU cc_start: 0.6298 (OUTLIER) cc_final: 0.6067 (mm) REVERT: L 74 GLU cc_start: 0.5054 (mm-30) cc_final: 0.4735 (tp30) REVERT: M 95 LYS cc_start: 0.6810 (mmmt) cc_final: 0.5935 (mttt) REVERT: N 59 MET cc_start: 0.6216 (mmm) cc_final: 0.5798 (tpp) REVERT: O 74 ILE cc_start: 0.5696 (mt) cc_final: 0.5267 (mt) REVERT: P 67 ARG cc_start: 0.6287 (ttm170) cc_final: 0.5697 (ttt90) REVERT: Q 35 ARG cc_start: 0.5829 (mtm180) cc_final: 0.5068 (mmp-170) REVERT: R 100 LEU cc_start: 0.6354 (tp) cc_final: 0.5847 (tp) outliers start: 31 outliers final: 20 residues processed: 239 average time/residue: 0.1906 time to fit residues: 66.0118 Evaluate side-chains 214 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 193 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 95 GLN Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain K residue 99 TYR Chi-restraints excluded: chain K residue 103 LEU Chi-restraints excluded: chain K residue 125 GLN Chi-restraints excluded: chain K residue 126 LEU Chi-restraints excluded: chain L residue 87 VAL Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain M residue 55 LEU Chi-restraints excluded: chain M residue 107 VAL Chi-restraints excluded: chain O residue 117 VAL Chi-restraints excluded: chain P residue 93 GLN Chi-restraints excluded: chain R residue 71 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 84 optimal weight: 20.0000 chunk 85 optimal weight: 0.6980 chunk 100 optimal weight: 5.9990 chunk 152 optimal weight: 50.0000 chunk 151 optimal weight: 50.0000 chunk 82 optimal weight: 10.0000 chunk 37 optimal weight: 4.9990 chunk 128 optimal weight: 8.9990 chunk 87 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 169 optimal weight: 40.0000 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 55 GLN ** K 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 125 GLN ** N 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 93 GLN ** Q 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.164100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.135281 restraints weight = 55886.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.138307 restraints weight = 136891.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.137867 restraints weight = 77659.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.138341 restraints weight = 65692.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.138528 restraints weight = 54138.210| |-----------------------------------------------------------------------------| r_work (final): 0.4086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6615 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 22081 Z= 0.200 Angle : 0.623 10.674 31842 Z= 0.374 Chirality : 0.041 0.258 3642 Planarity : 0.005 0.061 2387 Dihedral : 29.161 88.008 6687 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 3.94 % Allowed : 11.31 % Favored : 84.75 % 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: 1.97 (0.22), residues: 1369 helix: 2.32 (0.16), residues: 1000 sheet: None (None), residues: 0 loop : -1.70 (0.29), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 36 TYR 0.025 0.002 TYR N 83 PHE 0.028 0.003 PHE O 67 HIS 0.007 0.001 HIS D 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.20 (22081) covalent geometry : angle 0.62253 / 0.37 (31842) hydrogen bonds : bond 0.05574 / 3.74 ( 1321) hydrogen bonds : angle 3.09223 / 2.21 ( 3392) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 203 time to evaluate : 0.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 59 MET cc_start: 0.7214 (tpt) cc_final: 0.6529 (tpt) REVERT: E 90 MET cc_start: 0.7926 (mmp) cc_final: 0.7702 (mmm) REVERT: F 92 ARG cc_start: 0.8433 (OUTLIER) cc_final: 0.7444 (ttp80) REVERT: G 93 LEU cc_start: 0.8721 (mt) cc_final: 0.8506 (mt) REVERT: K 126 LEU cc_start: 0.6086 (OUTLIER) cc_final: 0.5855 (mm) REVERT: L 74 GLU cc_start: 0.5201 (mm-30) cc_final: 0.4868 (tp30) REVERT: M 95 LYS cc_start: 0.6819 (mmmt) cc_final: 0.6053 (mttt) REVERT: N 59 MET cc_start: 0.5956 (mmm) cc_final: 0.5689 (tpp) REVERT: N 83 TYR cc_start: 0.6508 (t80) cc_final: 0.6196 (t80) outliers start: 46 outliers final: 25 residues processed: 232 average time/residue: 0.1597 time to fit residues: 56.4227 Evaluate side-chains 212 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 185 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain K residue 71 VAL Chi-restraints excluded: chain K residue 103 LEU Chi-restraints excluded: chain K residue 126 LEU Chi-restraints excluded: chain L residue 58 LEU Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain M residue 55 LEU Chi-restraints excluded: chain M residue 107 VAL Chi-restraints excluded: chain N residue 62 MET Chi-restraints excluded: chain N residue 63 ASN Chi-restraints excluded: chain O residue 117 VAL Chi-restraints excluded: chain P residue 86 VAL Chi-restraints excluded: chain P residue 93 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 54 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 138 optimal weight: 50.0000 chunk 41 optimal weight: 2.9990 chunk 109 optimal weight: 10.0000 chunk 65 optimal weight: 0.8980 chunk 95 optimal weight: 7.9990 chunk 161 optimal weight: 30.0000 chunk 34 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 31 optimal weight: 8.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 73 ASN ** K 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 93 GLN ** Q 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.164844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.136402 restraints weight = 56132.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.137483 restraints weight = 134012.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.137997 restraints weight = 71668.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.138432 restraints weight = 60006.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.138535 restraints weight = 52871.327| |-----------------------------------------------------------------------------| r_work (final): 0.4100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6595 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 22081 Z= 0.152 Angle : 0.569 8.911 31842 Z= 0.348 Chirality : 0.039 0.225 3642 Planarity : 0.004 0.038 2387 Dihedral : 29.224 89.058 6687 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.91 % Allowed : 13.28 % Favored : 83.80 % 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 (0.23), residues: 1369 helix: 2.46 (0.16), residues: 1000 sheet: None (None), residues: 0 loop : -1.74 (0.29), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 36 TYR 0.021 0.002 TYR P 88 PHE 0.027 0.002 PHE O 67 HIS 0.006 0.001 HIS M 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.15 (22081) covalent geometry : angle 0.56941 / 0.35 (31842) hydrogen bonds : bond 0.04781 / 3.21 ( 1321) hydrogen bonds : angle 2.95534 / 2.11 ( 3392) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 201 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 THR cc_start: 0.8516 (p) cc_final: 0.8269 (t) REVERT: C 64 GLU cc_start: 0.7149 (tm-30) cc_final: 0.6884 (tp30) REVERT: C 73 ASN cc_start: 0.7105 (OUTLIER) cc_final: 0.6882 (t0) REVERT: D 59 MET cc_start: 0.7218 (tpt) cc_final: 0.6583 (tpt) REVERT: E 56 LYS cc_start: 0.7033 (pttp) cc_final: 0.6682 (mptt) REVERT: F 92 ARG cc_start: 0.8370 (OUTLIER) cc_final: 0.7325 (ttp80) REVERT: M 95 LYS cc_start: 0.6786 (mmmt) cc_final: 0.6020 (mttt) REVERT: P 39 ARG cc_start: 0.6022 (tpp-160) cc_final: 0.5758 (tpp-160) REVERT: R 63 ASN cc_start: 0.4362 (t0) cc_final: 0.4097 (t0) REVERT: R 67 ASN cc_start: 0.4360 (OUTLIER) cc_final: 0.4131 (m-40) outliers start: 34 outliers final: 20 residues processed: 221 average time/residue: 0.1731 time to fit residues: 56.5046 Evaluate side-chains 209 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 186 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 47 GLN Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 99 LYS Chi-restraints excluded: chain K residue 71 VAL Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain M residue 55 LEU Chi-restraints excluded: chain M residue 107 VAL Chi-restraints excluded: chain N residue 62 MET Chi-restraints excluded: chain N residue 63 ASN Chi-restraints excluded: chain O residue 117 VAL Chi-restraints excluded: chain P residue 86 VAL Chi-restraints excluded: chain P residue 93 GLN Chi-restraints excluded: chain R residue 67 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 27 optimal weight: 6.9990 chunk 172 optimal weight: 30.0000 chunk 88 optimal weight: 10.0000 chunk 28 optimal weight: 0.6980 chunk 110 optimal weight: 8.9990 chunk 67 optimal weight: 3.9990 chunk 148 optimal weight: 50.0000 chunk 121 optimal weight: 20.0000 chunk 158 optimal weight: 40.0000 chunk 34 optimal weight: 6.9990 chunk 60 optimal weight: 0.9980 overall best weight: 3.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 93 GLN ** Q 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.162533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.130578 restraints weight = 56066.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.129500 restraints weight = 98301.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.127790 restraints weight = 82399.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.127057 restraints weight = 86420.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.126725 restraints weight = 73667.960| |-----------------------------------------------------------------------------| r_work (final): 0.3943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6870 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 22081 Z= 0.193 Angle : 0.626 9.143 31842 Z= 0.371 Chirality : 0.042 0.392 3642 Planarity : 0.005 0.041 2387 Dihedral : 29.456 88.920 6687 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 3.43 % Allowed : 13.97 % Favored : 82.60 % 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: 1.69 (0.22), residues: 1369 helix: 2.11 (0.16), residues: 1009 sheet: None (None), residues: 0 loop : -1.88 (0.29), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG L 36 TYR 0.018 0.002 TYR M 57 PHE 0.012 0.002 PHE P 100 HIS 0.007 0.001 HIS D 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.19 (22081) covalent geometry : angle 0.62578 / 0.37 (31842) hydrogen bonds : bond 0.05563 / 3.73 ( 1321) hydrogen bonds : angle 3.11757 / 2.23 ( 3392) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 191 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 47 GLN cc_start: 0.7507 (OUTLIER) cc_final: 0.7126 (tt0) REVERT: D 59 MET cc_start: 0.7591 (tpt) cc_final: 0.6951 (tpt) REVERT: E 56 LYS cc_start: 0.7050 (pttp) cc_final: 0.6696 (mptt) REVERT: F 92 ARG cc_start: 0.8314 (OUTLIER) cc_final: 0.8022 (ttp80) REVERT: G 93 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8674 (mt) REVERT: M 95 LYS cc_start: 0.6855 (mmmt) cc_final: 0.6076 (mttt) REVERT: R 63 ASN cc_start: 0.4704 (t0) cc_final: 0.4483 (t0) outliers start: 40 outliers final: 29 residues processed: 214 average time/residue: 0.1749 time to fit residues: 54.9596 Evaluate side-chains 215 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 183 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 47 GLN Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 99 LYS Chi-restraints excluded: chain K residue 71 VAL Chi-restraints excluded: chain L residue 58 LEU Chi-restraints excluded: chain L residue 87 VAL Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain M residue 107 VAL Chi-restraints excluded: chain N residue 62 MET Chi-restraints excluded: chain N residue 63 ASN Chi-restraints excluded: chain O residue 62 ILE Chi-restraints excluded: chain O residue 117 VAL Chi-restraints excluded: chain P residue 30 THR Chi-restraints excluded: chain P residue 86 VAL Chi-restraints excluded: chain P residue 93 GLN Chi-restraints excluded: chain Q residue 49 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 114 optimal weight: 2.9990 chunk 153 optimal weight: 50.0000 chunk 112 optimal weight: 7.9990 chunk 92 optimal weight: 10.0000 chunk 169 optimal weight: 30.0000 chunk 46 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 chunk 35 optimal weight: 9.9990 chunk 30 optimal weight: 4.9990 chunk 126 optimal weight: 5.9990 chunk 137 optimal weight: 50.0000 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN ** K 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 93 GLN ** Q 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.161298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.128962 restraints weight = 56989.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.128078 restraints weight = 103443.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.126595 restraints weight = 85798.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.126214 restraints weight = 82684.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.126078 restraints weight = 75744.725| |-----------------------------------------------------------------------------| r_work (final): 0.3936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6868 moved from start: 0.3247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 22081 Z= 0.172 Angle : 0.604 9.440 31842 Z= 0.360 Chirality : 0.040 0.308 3642 Planarity : 0.004 0.053 2387 Dihedral : 29.556 89.531 6687 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 3.00 % Allowed : 15.85 % Favored : 81.15 % 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: 1.65 (0.22), residues: 1369 helix: 2.09 (0.16), residues: 1009 sheet: None (None), residues: 0 loop : -1.94 (0.28), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG K 53 TYR 0.018 0.002 TYR P 88 PHE 0.039 0.002 PHE O 67 HIS 0.005 0.001 HIS M 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.17 (22081) covalent geometry : angle 0.60374 / 0.36 (31842) hydrogen bonds : bond 0.05190 / 3.50 ( 1321) hydrogen bonds : angle 3.08314 / 2.20 ( 3392) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 194 time to evaluate : 0.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 47 GLN cc_start: 0.7475 (OUTLIER) cc_final: 0.7122 (tt0) REVERT: D 59 MET cc_start: 0.7708 (tpt) cc_final: 0.7085 (tpt) REVERT: E 56 LYS cc_start: 0.7130 (pttp) cc_final: 0.6676 (mptt) REVERT: F 92 ARG cc_start: 0.8311 (OUTLIER) cc_final: 0.7928 (ttp80) REVERT: G 93 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8509 (mt) REVERT: M 81 ARG cc_start: 0.7168 (tpp-160) cc_final: 0.6156 (ttp80) REVERT: M 95 LYS cc_start: 0.6885 (mmmt) cc_final: 0.6109 (mttt) REVERT: Q 35 ARG cc_start: 0.5876 (mtm180) cc_final: 0.5177 (mmp-170) REVERT: Q 73 ASN cc_start: 0.4635 (t0) cc_final: 0.4237 (t0) REVERT: R 63 ASN cc_start: 0.4873 (t0) cc_final: 0.4603 (t0) outliers start: 35 outliers final: 27 residues processed: 215 average time/residue: 0.1844 time to fit residues: 57.7897 Evaluate side-chains 213 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 183 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 47 GLN Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 99 LYS Chi-restraints excluded: chain K residue 71 VAL Chi-restraints excluded: chain L residue 87 VAL Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain M residue 55 LEU Chi-restraints excluded: chain M residue 107 VAL Chi-restraints excluded: chain N residue 62 MET Chi-restraints excluded: chain N residue 63 ASN Chi-restraints excluded: chain O residue 62 ILE Chi-restraints excluded: chain O residue 117 VAL Chi-restraints excluded: chain P residue 86 VAL Chi-restraints excluded: chain P residue 93 GLN Chi-restraints excluded: chain Q residue 49 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 1 optimal weight: 4.9990 chunk 100 optimal weight: 5.9990 chunk 99 optimal weight: 10.0000 chunk 96 optimal weight: 20.0000 chunk 83 optimal weight: 6.9990 chunk 152 optimal weight: 50.0000 chunk 144 optimal weight: 50.0000 chunk 11 optimal weight: 4.9990 chunk 128 optimal weight: 10.0000 chunk 160 optimal weight: 30.0000 chunk 92 optimal weight: 0.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 93 GLN G 38 ASN H 82 HIS ** K 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 55 GLN ** O 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 93 GLN ** Q 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.159542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.129931 restraints weight = 57156.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.126358 restraints weight = 80453.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.124058 restraints weight = 90050.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.123966 restraints weight = 87807.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.123183 restraints weight = 73125.038| |-----------------------------------------------------------------------------| r_work (final): 0.3890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6940 moved from start: 0.3658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 22081 Z= 0.215 Angle : 0.664 7.687 31842 Z= 0.387 Chirality : 0.044 0.263 3642 Planarity : 0.005 0.039 2387 Dihedral : 29.766 89.196 6687 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.70 % Favored : 94.23 % Rotamer: Outliers : 3.77 % Allowed : 16.80 % Favored : 79.43 % 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: 1.18 (0.22), residues: 1369 helix: 1.74 (0.16), residues: 1008 sheet: None (None), residues: 0 loop : -2.07 (0.28), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG L 36 TYR 0.021 0.002 TYR K 99 PHE 0.037 0.003 PHE O 67 HIS 0.007 0.001 HIS D 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.22 (22081) covalent geometry : angle 0.66378 / 0.39 (31842) hydrogen bonds : bond 0.06049 / 4.07 ( 1321) hydrogen bonds : angle 3.31592 / 2.38 ( 3392) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 191 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 47 GLN cc_start: 0.7510 (OUTLIER) cc_final: 0.7146 (tt0) REVERT: D 59 MET cc_start: 0.7787 (tpt) cc_final: 0.7124 (tpt) REVERT: E 56 LYS cc_start: 0.7168 (pttp) cc_final: 0.6708 (mptt) REVERT: F 92 ARG cc_start: 0.8404 (OUTLIER) cc_final: 0.8185 (ttp80) REVERT: M 81 ARG cc_start: 0.6960 (tpp-160) cc_final: 0.6134 (ttp80) REVERT: M 95 LYS cc_start: 0.7017 (mmmt) cc_final: 0.6240 (mttt) REVERT: R 63 ASN cc_start: 0.4618 (t0) cc_final: 0.4389 (t0) outliers start: 44 outliers final: 32 residues processed: 218 average time/residue: 0.1754 time to fit residues: 56.6773 Evaluate side-chains 218 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 184 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 47 GLN Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 105 GLU Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 104 PHE Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 99 LYS Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain K residue 71 VAL Chi-restraints excluded: chain L residue 87 VAL Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain M residue 55 LEU Chi-restraints excluded: chain M residue 107 VAL Chi-restraints excluded: chain N residue 62 MET Chi-restraints excluded: chain N residue 63 ASN Chi-restraints excluded: chain O residue 62 ILE Chi-restraints excluded: chain O residue 117 VAL Chi-restraints excluded: chain P residue 30 THR Chi-restraints excluded: chain P residue 86 VAL Chi-restraints excluded: chain Q residue 49 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 36 optimal weight: 0.9980 chunk 8 optimal weight: 6.9990 chunk 88 optimal weight: 5.9990 chunk 159 optimal weight: 40.0000 chunk 16 optimal weight: 9.9990 chunk 141 optimal weight: 50.0000 chunk 155 optimal weight: 40.0000 chunk 123 optimal weight: 20.0000 chunk 163 optimal weight: 50.0000 chunk 15 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 overall best weight: 3.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 93 GLN ** Q 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.160054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.129015 restraints weight = 56728.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.126473 restraints weight = 94559.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.124178 restraints weight = 93131.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.124223 restraints weight = 101841.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.124256 restraints weight = 73319.686| |-----------------------------------------------------------------------------| r_work (final): 0.3903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6922 moved from start: 0.3836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 22081 Z= 0.174 Angle : 0.624 11.396 31842 Z= 0.367 Chirality : 0.042 0.249 3642 Planarity : 0.004 0.038 2387 Dihedral : 29.803 89.272 6687 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 3.43 % Allowed : 17.74 % Favored : 78.83 % 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: 1.35 (0.22), residues: 1369 helix: 1.86 (0.16), residues: 1009 sheet: None (None), residues: 0 loop : -1.99 (0.28), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG L 36 TYR 0.038 0.002 TYR N 83 PHE 0.037 0.002 PHE O 67 HIS 0.006 0.001 HIS M 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.17 (22081) covalent geometry : angle 0.62413 / 0.37 (31842) hydrogen bonds : bond 0.05318 / 3.59 ( 1321) hydrogen bonds : angle 3.20787 / 2.30 ( 3392) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 193 time to evaluate : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 47 GLN cc_start: 0.7449 (OUTLIER) cc_final: 0.7084 (tt0) REVERT: D 59 MET cc_start: 0.7776 (tpt) cc_final: 0.7184 (tpt) REVERT: E 56 LYS cc_start: 0.7074 (pttp) cc_final: 0.6628 (mptt) REVERT: F 92 ARG cc_start: 0.8397 (OUTLIER) cc_final: 0.8082 (ttp80) REVERT: M 81 ARG cc_start: 0.6896 (tpp-160) cc_final: 0.5996 (ttp80) REVERT: M 95 LYS cc_start: 0.7117 (mmmt) cc_final: 0.6377 (mttt) REVERT: R 63 ASN cc_start: 0.4646 (t0) cc_final: 0.4436 (t0) REVERT: R 69 ILE cc_start: 0.7749 (mm) cc_final: 0.7544 (mm) REVERT: R 99 ARG cc_start: 0.4586 (ppt90) cc_final: 0.3748 (ttp80) outliers start: 40 outliers final: 29 residues processed: 217 average time/residue: 0.1693 time to fit residues: 54.8807 Evaluate side-chains 215 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 184 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 47 GLN Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 104 PHE Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 99 LYS Chi-restraints excluded: chain K residue 71 VAL Chi-restraints excluded: chain L residue 84 MET Chi-restraints excluded: chain L residue 87 VAL Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain M residue 55 LEU Chi-restraints excluded: chain M residue 107 VAL Chi-restraints excluded: chain N residue 63 ASN Chi-restraints excluded: chain O residue 62 ILE Chi-restraints excluded: chain O residue 117 VAL Chi-restraints excluded: chain P residue 86 VAL Chi-restraints excluded: chain Q residue 49 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 57 optimal weight: 0.0970 chunk 158 optimal weight: 40.0000 chunk 33 optimal weight: 4.9990 chunk 10 optimal weight: 10.0000 chunk 131 optimal weight: 5.9990 chunk 135 optimal weight: 50.0000 chunk 121 optimal weight: 20.0000 chunk 93 optimal weight: 6.9990 chunk 173 optimal weight: 30.0000 chunk 63 optimal weight: 0.6980 chunk 65 optimal weight: 0.8980 overall best weight: 2.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 125 GLN ** N 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.160203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.129686 restraints weight = 57045.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.126796 restraints weight = 97855.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.124694 restraints weight = 92321.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.124510 restraints weight = 84428.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.123550 restraints weight = 74577.577| |-----------------------------------------------------------------------------| r_work (final): 0.3897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6934 moved from start: 0.3923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 22081 Z= 0.160 Angle : 0.617 9.994 31842 Z= 0.364 Chirality : 0.041 0.251 3642 Planarity : 0.004 0.043 2387 Dihedral : 29.795 89.933 6687 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 2.74 % Allowed : 18.68 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.22), residues: 1369 helix: 1.93 (0.16), residues: 1008 sheet: None (None), residues: 0 loop : -1.99 (0.28), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG L 36 TYR 0.026 0.002 TYR M 57 PHE 0.066 0.002 PHE K 104 HIS 0.006 0.001 HIS M 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.16 (22081) covalent geometry : angle 0.61658 / 0.36 (31842) hydrogen bonds : bond 0.05133 / 3.46 ( 1321) hydrogen bonds : angle 3.22327 / 2.31 ( 3392) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 189 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 47 GLN cc_start: 0.7443 (OUTLIER) cc_final: 0.7057 (tt0) REVERT: D 59 MET cc_start: 0.7761 (tpt) cc_final: 0.6889 (tpt) REVERT: E 56 LYS cc_start: 0.7129 (pttp) cc_final: 0.6662 (mptt) REVERT: F 92 ARG cc_start: 0.8212 (OUTLIER) cc_final: 0.7849 (ttp80) REVERT: M 81 ARG cc_start: 0.6748 (tpp-160) cc_final: 0.5994 (ttp80) REVERT: M 95 LYS cc_start: 0.7115 (mmmt) cc_final: 0.6394 (mttt) REVERT: N 59 MET cc_start: 0.6169 (tpt) cc_final: 0.5950 (tpp) REVERT: R 63 ASN cc_start: 0.4658 (t0) cc_final: 0.4452 (t0) REVERT: R 99 ARG cc_start: 0.4544 (ppt90) cc_final: 0.3728 (ttp80) outliers start: 32 outliers final: 27 residues processed: 209 average time/residue: 0.1577 time to fit residues: 49.5002 Evaluate side-chains 212 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 183 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 47 GLN Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 104 PHE Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 99 LYS Chi-restraints excluded: chain K residue 71 VAL Chi-restraints excluded: chain L residue 87 VAL Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain M residue 55 LEU Chi-restraints excluded: chain M residue 107 VAL Chi-restraints excluded: chain N residue 63 ASN Chi-restraints excluded: chain O residue 62 ILE Chi-restraints excluded: chain O residue 117 VAL Chi-restraints excluded: chain P residue 86 VAL Chi-restraints excluded: chain Q residue 49 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 41 optimal weight: 1.9990 chunk 146 optimal weight: 50.0000 chunk 123 optimal weight: 7.9990 chunk 127 optimal weight: 0.7980 chunk 87 optimal weight: 5.9990 chunk 136 optimal weight: 50.0000 chunk 49 optimal weight: 0.8980 chunk 50 optimal weight: 10.0000 chunk 170 optimal weight: 30.0000 chunk 24 optimal weight: 5.9990 chunk 4 optimal weight: 8.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 125 GLN ** N 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.159780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.126980 restraints weight = 56911.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.126426 restraints weight = 109174.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.125710 restraints weight = 88077.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.125321 restraints weight = 80495.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.125313 restraints weight = 70410.237| |-----------------------------------------------------------------------------| r_work (final): 0.3927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6891 moved from start: 0.4117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 22081 Z= 0.173 Angle : 0.637 12.165 31842 Z= 0.371 Chirality : 0.042 0.250 3642 Planarity : 0.005 0.037 2387 Dihedral : 29.859 89.747 6687 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.91 % Allowed : 19.02 % Favored : 78.06 % 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 (0.22), residues: 1369 helix: 1.83 (0.16), residues: 1012 sheet: None (None), residues: 0 loop : -2.11 (0.28), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 53 TYR 0.027 0.002 TYR M 57 PHE 0.034 0.002 PHE O 67 HIS 0.006 0.001 HIS M 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.17 (22081) covalent geometry : angle 0.63674 / 0.37 (31842) hydrogen bonds : bond 0.05289 / 3.56 ( 1321) hydrogen bonds : angle 3.25778 / 2.34 ( 3392) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 182 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.7270 (mm-30) cc_final: 0.7023 (mm-30) REVERT: D 47 GLN cc_start: 0.7463 (OUTLIER) cc_final: 0.7098 (tt0) REVERT: D 59 MET cc_start: 0.7746 (tpt) cc_final: 0.6882 (tpt) REVERT: E 56 LYS cc_start: 0.7100 (pttp) cc_final: 0.6663 (mptt) REVERT: F 92 ARG cc_start: 0.8380 (OUTLIER) cc_final: 0.8039 (ttp80) REVERT: M 81 ARG cc_start: 0.6780 (tpp-160) cc_final: 0.6057 (ttp80) REVERT: M 95 LYS cc_start: 0.7200 (mmmt) cc_final: 0.6431 (mttt) REVERT: R 99 ARG cc_start: 0.4455 (ppt90) cc_final: 0.3736 (ttp80) outliers start: 34 outliers final: 27 residues processed: 204 average time/residue: 0.1633 time to fit residues: 49.7485 Evaluate side-chains 208 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 179 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 47 GLN Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 104 PHE Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 99 LYS Chi-restraints excluded: chain K residue 71 VAL Chi-restraints excluded: chain L residue 87 VAL Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain M residue 55 LEU Chi-restraints excluded: chain M residue 107 VAL Chi-restraints excluded: chain N residue 63 ASN Chi-restraints excluded: chain O residue 62 ILE Chi-restraints excluded: chain O residue 117 VAL Chi-restraints excluded: chain P residue 86 VAL Chi-restraints excluded: chain Q residue 49 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 4 optimal weight: 0.0980 chunk 156 optimal weight: 30.0000 chunk 12 optimal weight: 0.0870 chunk 29 optimal weight: 0.8980 chunk 86 optimal weight: 8.9990 chunk 14 optimal weight: 8.9990 chunk 132 optimal weight: 50.0000 chunk 95 optimal weight: 10.0000 chunk 20 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 38 optimal weight: 0.1980 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 125 GLN ** N 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 84 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.161793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.131224 restraints weight = 57156.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.129439 restraints weight = 101958.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.127968 restraints weight = 81069.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.127504 restraints weight = 84878.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.127101 restraints weight = 70963.853| |-----------------------------------------------------------------------------| r_work (final): 0.3954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6839 moved from start: 0.4034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.065 22081 Z= 0.138 Angle : 0.587 10.924 31842 Z= 0.350 Chirality : 0.039 0.249 3642 Planarity : 0.004 0.038 2387 Dihedral : 29.711 88.286 6687 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.80 % Allowed : 20.22 % Favored : 77.98 % 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: 1.70 (0.23), residues: 1369 helix: 2.12 (0.16), residues: 1014 sheet: None (None), residues: 0 loop : -1.97 (0.28), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 36 TYR 0.026 0.001 TYR M 57 PHE 0.027 0.002 PHE O 67 HIS 0.006 0.001 HIS M 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.14 (22081) covalent geometry : angle 0.58674 / 0.35 (31842) hydrogen bonds : bond 0.04366 / 2.93 ( 1321) hydrogen bonds : angle 3.09635 / 2.22 ( 3392) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3046.80 seconds wall clock time: 53 minutes 21.64 seconds (3201.64 seconds total)