Starting phenix.real_space_refine on Thu Aug 6 06:41:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dby_46728/08_2026/9dby_46728.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dby_46728/08_2026/9dby_46728.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9dby_46728/08_2026/9dby_46728.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dby_46728/08_2026/9dby_46728.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9dby_46728/08_2026/9dby_46728.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dby_46728/08_2026/9dby_46728.map" } resolution = 2.8 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= 0.008 sd= 0.052 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: 6 Type Number sf(0) Gaussians Zn 5 6.06 5 P 296 5.49 5 S 35 5.16 5 C 8103 2.51 5 N 2666 2.21 5 O 3263 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14368 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 801 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 658 Classifications: {'peptide': 83} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 81} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 811 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "D" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 718 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "E" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 779 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 91} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 668 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 83} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "G" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 821 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 102} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "H" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 3054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 3054 Classifications: {'DNA': 148} Link IDs: {'rna3p': 147} Chain: "J" Number of atoms: 3014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 3014 Classifications: {'DNA': 148} Link IDs: {'rna3p': 147} Chain: "K" Number of atoms: 774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 774 Classifications: {'peptide': 102} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 5, 'TRANS': 96} Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 54 Planarities with less than four sites: {'ARG:plan': 4, 'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "L" Number of atoms: 766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 766 Classifications: {'peptide': 101} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 7, 'TRANS': 93} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "M" Number of atoms: 312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 312 Classifications: {'peptide': 42} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 40} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 15 Chain: "N" Number of atoms: 461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 461 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 3, 'TRANS': 70} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 136 Unresolved non-hydrogen angles: 167 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 3, 'PHE:plan': 2, 'GLU:plan': 6, 'ASN:plan1': 2, 'ASP:plan': 3, 'ARG:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 80 Chain: "K" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12177 SG CYS K 18 44.857 30.580 26.339 1.00145.64 S ATOM 12198 SG CYS K 21 45.062 28.682 23.183 1.00156.22 S ATOM 12336 SG CYS K 39 48.050 28.903 25.456 1.00151.87 S ATOM 12358 SG CYS K 42 46.963 31.939 23.256 1.00142.44 S ATOM 12295 SG CYS K 34 44.556 39.992 36.127 1.00132.24 S ATOM 12439 SG CYS K 53 42.704 39.676 32.791 1.00134.96 S ATOM 12460 SG CYS K 56 40.745 40.482 35.983 1.00131.92 S ATOM 13093 SG CYS L 51 53.439 25.162 52.648 1.00155.30 S ATOM 13114 SG CYS L 54 52.143 22.750 54.897 1.00157.82 S ATOM 13255 SG CYS L 72 49.628 25.167 53.402 1.00134.45 S ATOM 13274 SG CYS L 75 52.103 26.347 56.132 1.00132.62 S ATOM 13209 SG CYS L 67 58.703 34.972 44.952 1.00120.44 S ATOM 13363 SG CYS L 87 59.811 32.804 47.899 1.00132.41 S ATOM 13383 SG CYS L 90 62.338 33.718 45.169 1.00128.23 S ATOM 13638 SG CYS M 27 82.978 95.202 65.944 1.00146.07 S ATOM 13657 SG CYS M 30 86.649 95.173 67.082 1.00146.70 S ATOM 13741 SG CYS M 41 85.854 95.649 63.506 1.00145.31 S ATOM 13761 SG CYS M 44 85.287 92.274 64.927 1.00149.57 S Time building chain proxies: 2.71, per 1000 atoms: 0.19 Number of scatterers: 14368 At special positions: 0 Unit cell: (124.499, 119.086, 119.086, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 5 29.99 S 35 16.00 P 296 15.00 O 3263 8.00 N 2666 7.00 C 8103 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: 0.80 Conformation dependent library (CDL) restraints added in 478.4 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K 401 " pdb="ZN ZN K 401 " - pdb=" SG CYS K 21 " pdb="ZN ZN K 401 " - pdb=" SG CYS K 39 " pdb="ZN ZN K 401 " - pdb=" SG CYS K 18 " pdb="ZN ZN K 401 " - pdb=" SG CYS K 42 " pdb=" ZN K 402 " pdb="ZN ZN K 402 " - pdb=" ND1 HIS K 36 " pdb="ZN ZN K 402 " - pdb=" SG CYS K 34 " pdb="ZN ZN K 402 " - pdb=" SG CYS K 56 " pdb="ZN ZN K 402 " - pdb=" SG CYS K 53 " pdb=" ZN L 401 " pdb="ZN ZN L 401 " - pdb=" SG CYS L 54 " pdb="ZN ZN L 401 " - pdb=" SG CYS L 51 " pdb="ZN ZN L 401 " - pdb=" SG CYS L 72 " pdb="ZN ZN L 401 " - pdb=" SG CYS L 75 " pdb=" ZN L 402 " pdb="ZN ZN L 402 " - pdb=" ND1 HIS L 69 " pdb="ZN ZN L 402 " - pdb=" SG CYS L 87 " pdb="ZN ZN L 402 " - pdb=" SG CYS L 67 " pdb="ZN ZN L 402 " - pdb=" SG CYS L 90 " pdb=" ZN M 301 " pdb="ZN ZN M 301 " - pdb=" SG CYS M 41 " pdb="ZN ZN M 301 " - pdb=" SG CYS M 30 " pdb="ZN ZN M 301 " - pdb=" SG CYS M 44 " pdb="ZN ZN M 301 " - pdb=" SG CYS M 27 " Number of angles added : 24 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2046 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 15 sheets defined 59.1% alpha, 5.7% beta 148 base pairs and 264 stacking pairs defined. Time for finding SS restraints: 1.89 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 Processing helix chain 'B' and resid 82 through 94 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 73 removed outlier: 3.687A pdb=" N TYR C 50 " --> pdb=" O GLY C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 101 through 120 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.706A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 46 through 73 Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 101 through 121 Processing helix chain 'K' and resid 9 through 13 Processing helix chain 'K' and resid 40 through 48 removed outlier: 3.653A pdb=" N GLU K 48 " --> pdb=" O VAL K 44 " (cutoff:3.500A) Processing helix chain 'K' and resid 64 through 67 Processing helix chain 'K' and resid 72 through 83 Processing helix chain 'K' and resid 85 through 99 Processing helix chain 'L' and resid 45 through 50 Processing helix chain 'L' and resid 73 through 83 Processing helix chain 'L' and resid 96 through 98 No H-bonds generated for 'chain 'L' and resid 96 through 98' Processing helix chain 'L' and resid 103 through 114 Processing helix chain 'N' and resid 22 through 35 Processing helix chain 'N' and resid 37 through 39 No H-bonds generated for 'chain 'N' and resid 37 through 39' Processing helix chain 'N' and resid 55 through 60 removed outlier: 3.710A pdb=" N TYR N 59 " --> pdb=" O THR N 55 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.862A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.266A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.866A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.735A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.354A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'K' and resid 5 through 8 Processing sheet with id=AB3, first strand: chain 'K' and resid 36 through 39 Processing sheet with id=AB4, first strand: chain 'L' and resid 70 through 72 Processing sheet with id=AB5, first strand: chain 'M' and resid 25 through 26 Processing sheet with id=AB6, first strand: chain 'N' and resid 12 through 16 removed outlier: 7.709A pdb=" N GLN N 2 " --> pdb=" O SER N 65 " (cutoff:3.500A) removed outlier: 8.794A pdb=" N LEU N 67 " --> pdb=" O GLN N 2 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N PHE N 4 " --> pdb=" O LEU N 67 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N LEU N 69 " --> pdb=" O PHE N 4 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LYS N 6 " --> pdb=" O LEU N 69 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N LEU N 71 " --> pdb=" O LYS N 6 " (cutoff:3.500A) 490 hydrogen bonds defined for protein. 1449 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 379 hydrogen bonds 758 hydrogen bond angles 0 basepair planarities 148 basepair parallelities 264 stacking parallelities Total time for adding SS restraints: 2.28 Time building geometry restraints manager: 1.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3424 1.34 - 1.46: 4344 1.46 - 1.58: 6811 1.58 - 1.70: 590 1.70 - 1.82: 49 Bond restraints: 15218 Sorted by residual: bond pdb=" C3' DC J 115 " pdb=" C2' DC J 115 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.13e+01 bond pdb=" C3' DC J 164 " pdb=" C2' DC J 164 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.02e+01 bond pdb=" C3' DG J 54 " pdb=" C2' DG J 54 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.01e+01 bond pdb=" C3' DC J 73 " pdb=" C2' DC J 73 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.64e+00 bond pdb=" N ILE K 26 " pdb=" CA ILE K 26 " ideal model delta sigma weight residual 1.458 1.495 -0.036 1.17e-02 7.31e+03 9.59e+00 ... (remaining 15213 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 21164 2.17 - 4.33: 660 4.33 - 6.50: 38 6.50 - 8.67: 6 8.67 - 10.83: 1 Bond angle restraints: 21869 Sorted by residual: angle pdb=" N GLN B 27 " pdb=" CA GLN B 27 " pdb=" C GLN B 27 " ideal model delta sigma weight residual 114.64 103.81 10.83 1.52e+00 4.33e-01 5.08e+01 angle pdb=" N ASN G 73 " pdb=" CA ASN G 73 " pdb=" C ASN G 73 " ideal model delta sigma weight residual 113.28 107.16 6.12 1.22e+00 6.72e-01 2.52e+01 angle pdb=" N3 DT J 55 " pdb=" C4 DT J 55 " pdb=" O4 DT J 55 " ideal model delta sigma weight residual 119.90 122.55 -2.65 6.00e-01 2.78e+00 1.95e+01 angle pdb=" N3 DT I 78 " pdb=" C4 DT I 78 " pdb=" O4 DT I 78 " ideal model delta sigma weight residual 119.90 122.54 -2.64 6.00e-01 2.78e+00 1.93e+01 angle pdb=" N3 DT I 103 " pdb=" C4 DT I 103 " pdb=" O4 DT I 103 " ideal model delta sigma weight residual 119.90 122.52 -2.62 6.00e-01 2.78e+00 1.91e+01 ... (remaining 21864 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.53: 6381 26.53 - 53.07: 1695 53.07 - 79.60: 317 79.60 - 106.14: 2 106.14 - 132.67: 2 Dihedral angle restraints: 8397 sinusoidal: 5245 harmonic: 3152 Sorted by residual: dihedral pdb=" CA ILE B 26 " pdb=" C ILE B 26 " pdb=" N GLN B 27 " pdb=" CA GLN B 27 " ideal model delta harmonic sigma weight residual 180.00 160.27 19.73 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA PRO H 100 " pdb=" C PRO H 100 " pdb=" N GLY H 101 " pdb=" CA GLY H 101 " ideal model delta harmonic sigma weight residual 180.00 161.25 18.75 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" C4' DC I 36 " pdb=" C3' DC I 36 " pdb=" O3' DC I 36 " pdb=" P DT I 37 " ideal model delta sinusoidal sigma weight residual 220.00 87.33 132.67 1 3.50e+01 8.16e-04 1.31e+01 ... (remaining 8394 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 2494 0.111 - 0.222: 34 0.222 - 0.333: 1 0.333 - 0.444: 0 0.444 - 0.555: 6 Chirality restraints: 2535 Sorted by residual: chirality pdb=" P DT I 35 " pdb=" OP1 DT I 35 " pdb=" OP2 DT I 35 " pdb=" O5' DT I 35 " both_signs ideal model delta sigma weight residual True 2.34 -2.89 -0.56 2.00e-01 2.50e+01 7.71e+00 chirality pdb=" P DA J 151 " pdb=" OP1 DA J 151 " pdb=" OP2 DA J 151 " pdb=" O5' DA J 151 " both_signs ideal model delta sigma weight residual True 2.34 -2.87 -0.54 2.00e-01 2.50e+01 7.19e+00 chirality pdb=" P DT I 37 " pdb=" OP1 DT I 37 " pdb=" OP2 DT I 37 " pdb=" O5' DT I 37 " both_signs ideal model delta sigma weight residual True 2.34 -2.87 -0.53 2.00e-01 2.50e+01 7.14e+00 ... (remaining 2532 not shown) Planarity restraints: 1744 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU D 99 " 0.034 5.00e-02 4.00e+02 5.17e-02 4.28e+00 pdb=" N PRO D 100 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO D 100 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO D 100 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU H 99 " -0.033 5.00e-02 4.00e+02 5.05e-02 4.08e+00 pdb=" N PRO H 100 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO H 100 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO H 100 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL K 83 " 0.032 5.00e-02 4.00e+02 4.87e-02 3.79e+00 pdb=" N PRO K 84 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO K 84 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO K 84 " 0.027 5.00e-02 4.00e+02 ... (remaining 1741 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2456 2.78 - 3.31: 12479 3.31 - 3.84: 26673 3.84 - 4.37: 31022 4.37 - 4.90: 45681 Nonbonded interactions: 118311 Sorted by model distance: nonbonded pdb=" O LEU L 80 " pdb=" NZ LYS L 85 " model vdw 2.249 3.120 nonbonded pdb=" OG1 THR D 87 " pdb=" OE1 GLU D 90 " model vdw 2.284 3.040 nonbonded pdb=" N GLN L 25 " pdb=" OE1 GLN L 25 " model vdw 2.291 3.120 nonbonded pdb=" O GLU N 16 " pdb=" NZ LYS N 29 " model vdw 2.334 3.120 nonbonded pdb=" OH TYR B 98 " pdb=" OD2 ASP H 65 " model vdw 2.337 3.040 ... (remaining 118306 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 40 through 134) selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 19 through 101) } ncs_group { reference = (chain 'C' and (resid 12 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB )) or resid 75 through 118)) selection = (chain 'G' and ((resid 12 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 35 or (resid 36 and (name N or name CA or name \ C or name O or name CB )) or resid 37 through 117 or resid 119)) } ncs_group { reference = chain 'D' selection = (chain 'H' and (resid 29 through 30 or (resid 31 and (name N or name CA or name \ C or name O or name CB )) or resid 32 through 53 or (resid 54 through 55 and (na \ me N or name CA or name C or name O or name CB )) or resid 56 through 121)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.490 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: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 14.990 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 15238 Z= 0.505 Angle : 0.798 10.831 21893 Z= 0.659 Chirality : 0.052 0.555 2535 Planarity : 0.005 0.056 1744 Dihedral : 26.421 132.669 6351 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.23 % Allowed : 16.65 % Favored : 83.12 % 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: 2.14 (0.26), residues: 1057 helix: 2.53 (0.22), residues: 613 sheet: 1.95 (0.99), residues: 26 loop : -0.32 (0.28), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 129 TYR 0.009 0.001 TYR L 114 PHE 0.014 0.001 PHE M 32 TRP 0.006 0.001 TRP M 25 HIS 0.002 0.001 HIS D 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00584 / 0.51 (15218) covalent geometry : angle 0.78999 / 0.66 (21869) hydrogen bonds : bond 0.06965 / 4.72 ( 869) hydrogen bonds : angle 3.45656 / 2.44 ( 2207) metal coordination : bond 0.00585 / 0.38 ( 20) metal coordination : angle 3.53762 / 2.27 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 316 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 ASP cc_start: 0.7256 (t0) cc_final: 0.6843 (t0) REVERT: H 73 GLU cc_start: 0.6836 (tp30) cc_final: 0.6496 (tp30) REVERT: L 50 MET cc_start: 0.5528 (mmp) cc_final: 0.4848 (mmt) outliers start: 2 outliers final: 1 residues processed: 316 average time/residue: 0.5627 time to fit residues: 193.7546 Evaluate side-chains 197 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 196 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 98 optimal weight: 20.0000 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 50.0000 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 40.0000 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 10.0000 chunk 55 optimal weight: 4.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 HIS D 44 GLN D 81 ASN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 76 GLN K 89 ASN L 29 GLN ** N 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.071516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.044459 restraints weight = 69911.075| |-----------------------------------------------------------------------------| r_work (start): 0.2844 rms_B_bonded: 3.82 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8855 moved from start: 0.5168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.133 15238 Z= 0.360 Angle : 0.962 13.062 21893 Z= 0.520 Chirality : 0.059 0.357 2535 Planarity : 0.008 0.098 1744 Dihedral : 29.312 124.652 4422 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 6.45 % Allowed : 22.16 % Favored : 71.40 % 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: 0.44 (0.24), residues: 1057 helix: 0.85 (0.19), residues: 612 sheet: 2.08 (0.93), residues: 25 loop : -0.57 (0.28), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG N 72 TYR 0.053 0.004 TYR D 80 PHE 0.025 0.003 PHE M 39 TRP 0.007 0.002 TRP M 25 HIS 0.009 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00772 / 0.36 (15218) covalent geometry : angle 0.95235 / 0.52 (21869) hydrogen bonds : bond 0.09106 / 6.11 ( 869) hydrogen bonds : angle 4.23487 / 3.07 ( 2207) metal coordination : bond 0.03358 / 1.17 ( 20) metal coordination : angle 4.23071 / 2.62 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 172 time to evaluate : 0.262 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.8707 (m-30) cc_final: 0.8449 (m-30) REVERT: A 90 MET cc_start: 0.9114 (OUTLIER) cc_final: 0.8753 (mmm) REVERT: A 94 GLU cc_start: 0.8797 (OUTLIER) cc_final: 0.7983 (mp0) REVERT: D 84 SER cc_start: 0.9023 (OUTLIER) cc_final: 0.8795 (m) REVERT: E 50 GLU cc_start: 0.9019 (OUTLIER) cc_final: 0.8793 (mt-10) REVERT: E 56 LYS cc_start: 0.9299 (ttpp) cc_final: 0.9092 (ttmm) REVERT: E 120 MET cc_start: 0.8805 (OUTLIER) cc_final: 0.8520 (mtm) REVERT: G 41 GLU cc_start: 0.8691 (tm-30) cc_final: 0.8279 (tm-30) REVERT: G 90 ASP cc_start: 0.8088 (t70) cc_final: 0.7689 (t0) REVERT: G 111 ILE cc_start: 0.8561 (OUTLIER) cc_final: 0.8245 (tt) REVERT: H 31 LYS cc_start: 0.9092 (ptpp) cc_final: 0.8880 (ptpp) REVERT: H 65 ASP cc_start: 0.9019 (t0) cc_final: 0.8776 (t0) REVERT: L 50 MET cc_start: 0.7303 (mmp) cc_final: 0.6660 (mmt) REVERT: M 32 PHE cc_start: 0.8686 (t80) cc_final: 0.8356 (t80) outliers start: 55 outliers final: 17 residues processed: 206 average time/residue: 0.6381 time to fit residues: 142.0571 Evaluate side-chains 173 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 150 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain L residue 66 GLU Chi-restraints excluded: chain L residue 85 LYS Chi-restraints excluded: chain L residue 87 CYS Chi-restraints excluded: chain L residue 105 ASN Chi-restraints excluded: chain M residue 35 SER Chi-restraints excluded: chain M residue 52 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 119 optimal weight: 0.0670 chunk 24 optimal weight: 2.9990 chunk 115 optimal weight: 7.9990 chunk 121 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 105 optimal weight: 0.0980 chunk 45 optimal weight: 7.9990 chunk 28 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 overall best weight: 1.0324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN F 25 ASN G 104 GLN K 2 HIS K 89 ASN L 29 GLN ** N 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.072284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.045221 restraints weight = 70008.461| |-----------------------------------------------------------------------------| r_work (start): 0.2864 rms_B_bonded: 3.88 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8831 moved from start: 0.5319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15238 Z= 0.156 Angle : 0.658 7.856 21893 Z= 0.377 Chirality : 0.045 0.244 2535 Planarity : 0.005 0.039 1744 Dihedral : 29.279 119.160 4419 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.52 % Allowed : 25.67 % Favored : 70.81 % 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: 1.64 (0.25), residues: 1057 helix: 2.10 (0.21), residues: 613 sheet: 0.58 (0.91), residues: 35 loop : -0.44 (0.29), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 91 TYR 0.012 0.001 TYR B 88 PHE 0.011 0.001 PHE A 67 TRP 0.005 0.001 TRP M 25 HIS 0.009 0.001 HIS L 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.16 (15218) covalent geometry : angle 0.64926 / 0.38 (21869) hydrogen bonds : bond 0.05298 / 3.52 ( 869) hydrogen bonds : angle 3.35193 / 2.40 ( 2207) metal coordination : bond 0.00997 / 0.46 ( 20) metal coordination : angle 3.28096 / 2.01 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 162 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.8673 (m-30) cc_final: 0.8438 (m-30) REVERT: A 90 MET cc_start: 0.9043 (OUTLIER) cc_final: 0.8644 (mmp) REVERT: A 94 GLU cc_start: 0.8786 (OUTLIER) cc_final: 0.8065 (mp0) REVERT: E 50 GLU cc_start: 0.9029 (OUTLIER) cc_final: 0.8810 (mt-10) REVERT: E 120 MET cc_start: 0.8739 (OUTLIER) cc_final: 0.8432 (mtm) REVERT: F 59 LYS cc_start: 0.9300 (tttm) cc_final: 0.9065 (tttp) REVERT: G 41 GLU cc_start: 0.8558 (tm-30) cc_final: 0.8094 (tm-30) REVERT: G 90 ASP cc_start: 0.8059 (t70) cc_final: 0.7590 (t70) REVERT: G 111 ILE cc_start: 0.8580 (OUTLIER) cc_final: 0.8375 (tt) REVERT: H 65 ASP cc_start: 0.9015 (t0) cc_final: 0.8811 (t0) REVERT: L 50 MET cc_start: 0.7091 (mmp) cc_final: 0.6375 (mmt) outliers start: 30 outliers final: 14 residues processed: 178 average time/residue: 0.6412 time to fit residues: 123.4757 Evaluate side-chains 170 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 151 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain L residue 105 ASN Chi-restraints excluded: chain M residue 35 SER Chi-restraints excluded: chain M residue 50 THR Chi-restraints excluded: chain M residue 52 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 96 optimal weight: 20.0000 chunk 98 optimal weight: 20.0000 chunk 43 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 chunk 7 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 25 optimal weight: 6.9990 chunk 113 optimal weight: 40.0000 chunk 47 optimal weight: 5.9990 chunk 87 optimal weight: 50.0000 chunk 1 optimal weight: 0.8980 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 GLN B 25 ASN C 24 GLN D 44 GLN H 46 HIS ** N 31 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 = 0.3660 r_free = 0.3660 target = 0.071558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.044422 restraints weight = 69653.079| |-----------------------------------------------------------------------------| r_work (start): 0.2834 rms_B_bonded: 3.89 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8876 moved from start: 0.5767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 15238 Z= 0.185 Angle : 0.664 8.727 21893 Z= 0.375 Chirality : 0.045 0.227 2535 Planarity : 0.005 0.053 1744 Dihedral : 29.285 114.119 4419 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.75 % Allowed : 26.14 % Favored : 70.11 % 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: 1.84 (0.25), residues: 1057 helix: 2.29 (0.21), residues: 612 sheet: 1.98 (0.91), residues: 25 loop : -0.46 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 30 TYR 0.010 0.001 TYR K 80 PHE 0.014 0.002 PHE C 25 TRP 0.008 0.001 TRP M 25 HIS 0.006 0.001 HIS L 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.18 (15218) covalent geometry : angle 0.65760 / 0.37 (21869) hydrogen bonds : bond 0.05552 / 3.67 ( 869) hydrogen bonds : angle 3.34642 / 2.40 ( 2207) metal coordination : bond 0.01401 / 0.51 ( 20) metal coordination : angle 2.81825 / 1.73 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 155 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.8794 (m-30) cc_final: 0.8541 (m-30) REVERT: D 84 SER cc_start: 0.9059 (OUTLIER) cc_final: 0.8783 (m) REVERT: E 93 GLN cc_start: 0.9286 (OUTLIER) cc_final: 0.9070 (mt0) REVERT: E 97 GLU cc_start: 0.8789 (mm-30) cc_final: 0.8501 (mp0) REVERT: E 120 MET cc_start: 0.8874 (OUTLIER) cc_final: 0.8621 (mtt) REVERT: F 59 LYS cc_start: 0.9282 (OUTLIER) cc_final: 0.9079 (tttm) REVERT: F 63 GLU cc_start: 0.8349 (pt0) cc_final: 0.8135 (pt0) REVERT: G 41 GLU cc_start: 0.8574 (tm-30) cc_final: 0.8085 (tm-30) REVERT: G 90 ASP cc_start: 0.8188 (t70) cc_final: 0.7715 (t0) REVERT: H 65 ASP cc_start: 0.9111 (t0) cc_final: 0.8832 (t0) REVERT: H 90 GLU cc_start: 0.8711 (mp0) cc_final: 0.8507 (mp0) REVERT: K 16 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8660 (pt) REVERT: L 50 MET cc_start: 0.7088 (mmp) cc_final: 0.6440 (mmt) outliers start: 32 outliers final: 14 residues processed: 173 average time/residue: 0.6231 time to fit residues: 116.5763 Evaluate side-chains 163 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 144 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain E residue 93 GLN Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain L residue 68 LEU Chi-restraints excluded: chain L residue 105 ASN Chi-restraints excluded: chain M residue 50 THR Chi-restraints excluded: chain M residue 52 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 125 optimal weight: 40.0000 chunk 73 optimal weight: 30.0000 chunk 76 optimal weight: 20.0000 chunk 54 optimal weight: 0.5980 chunk 17 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 81 optimal weight: 10.0000 chunk 30 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN C 24 GLN E 93 GLN ** N 31 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 = 0.3652 r_free = 0.3652 target = 0.071143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.044095 restraints weight = 69453.828| |-----------------------------------------------------------------------------| r_work (start): 0.2822 rms_B_bonded: 3.88 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8896 moved from start: 0.6137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 15238 Z= 0.172 Angle : 0.643 8.694 21893 Z= 0.364 Chirality : 0.045 0.264 2535 Planarity : 0.004 0.046 1744 Dihedral : 29.290 107.419 4419 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.93 % Allowed : 27.67 % Favored : 69.40 % 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: 1.94 (0.25), residues: 1057 helix: 2.40 (0.21), residues: 614 sheet: 1.99 (0.93), residues: 25 loop : -0.48 (0.28), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 99 TYR 0.014 0.001 TYR K 46 PHE 0.009 0.001 PHE F 61 TRP 0.008 0.001 TRP M 25 HIS 0.004 0.001 HIS H 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.17 (15218) covalent geometry : angle 0.63795 / 0.36 (21869) hydrogen bonds : bond 0.05154 / 3.41 ( 869) hydrogen bonds : angle 3.23871 / 2.32 ( 2207) metal coordination : bond 0.00731 / 0.44 ( 20) metal coordination : angle 2.55317 / 1.57 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 150 time to evaluate : 0.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 91 LYS cc_start: 0.9603 (ttmt) cc_final: 0.9367 (ttpp) REVERT: D 84 SER cc_start: 0.9043 (OUTLIER) cc_final: 0.8671 (p) REVERT: D 102 GLU cc_start: 0.8704 (mp0) cc_final: 0.8421 (mm-30) REVERT: E 59 GLU cc_start: 0.7977 (pm20) cc_final: 0.7541 (pm20) REVERT: E 120 MET cc_start: 0.8903 (OUTLIER) cc_final: 0.8664 (mtt) REVERT: F 63 GLU cc_start: 0.8339 (pt0) cc_final: 0.8115 (pt0) REVERT: G 41 GLU cc_start: 0.8548 (tm-30) cc_final: 0.8032 (tm-30) REVERT: G 90 ASP cc_start: 0.8297 (t70) cc_final: 0.7988 (t0) REVERT: H 65 ASP cc_start: 0.9134 (t0) cc_final: 0.8836 (t0) REVERT: H 90 GLU cc_start: 0.8756 (mp0) cc_final: 0.8423 (mp0) REVERT: K 17 MET cc_start: 0.9491 (mmm) cc_final: 0.9170 (tpp) REVERT: M 32 PHE cc_start: 0.8023 (t80) cc_final: 0.7804 (t80) outliers start: 25 outliers final: 13 residues processed: 164 average time/residue: 0.6050 time to fit residues: 106.6697 Evaluate side-chains 159 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 144 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain K residue 43 ILE Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain L residue 85 LYS Chi-restraints excluded: chain L residue 105 ASN Chi-restraints excluded: chain M residue 52 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 32 optimal weight: 4.9990 chunk 123 optimal weight: 50.0000 chunk 90 optimal weight: 20.0000 chunk 98 optimal weight: 20.0000 chunk 119 optimal weight: 8.9990 chunk 79 optimal weight: 10.0000 chunk 125 optimal weight: 30.0000 chunk 16 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN ** N 31 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 = 0.3626 r_free = 0.3626 target = 0.070244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.042911 restraints weight = 68566.383| |-----------------------------------------------------------------------------| r_work (start): 0.2776 rms_B_bonded: 3.80 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8940 moved from start: 0.6675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 15238 Z= 0.210 Angle : 0.678 9.060 21893 Z= 0.378 Chirality : 0.045 0.246 2535 Planarity : 0.005 0.088 1744 Dihedral : 29.300 101.874 4419 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.52 % Allowed : 27.20 % Favored : 69.28 % 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: 1.89 (0.25), residues: 1057 helix: 2.36 (0.21), residues: 614 sheet: 2.13 (0.97), residues: 25 loop : -0.52 (0.28), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 99 TYR 0.019 0.002 TYR K 80 PHE 0.023 0.002 PHE M 32 TRP 0.020 0.004 TRP M 25 HIS 0.007 0.001 HIS L 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.21 (15218) covalent geometry : angle 0.67007 / 0.38 (21869) hydrogen bonds : bond 0.05981 / 3.96 ( 869) hydrogen bonds : angle 3.46118 / 2.46 ( 2207) metal coordination : bond 0.01289 / 0.59 ( 20) metal coordination : angle 3.19298 / 2.12 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 157 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 91 LYS cc_start: 0.9631 (ttmt) cc_final: 0.9395 (ttpp) REVERT: D 84 SER cc_start: 0.9144 (OUTLIER) cc_final: 0.8798 (p) REVERT: D 102 GLU cc_start: 0.8749 (mp0) cc_final: 0.8469 (mm-30) REVERT: E 59 GLU cc_start: 0.8210 (pm20) cc_final: 0.7780 (pm20) REVERT: E 120 MET cc_start: 0.8944 (OUTLIER) cc_final: 0.8731 (mtt) REVERT: F 63 GLU cc_start: 0.8491 (pt0) cc_final: 0.8252 (pt0) REVERT: G 41 GLU cc_start: 0.8526 (tm-30) cc_final: 0.8018 (tm-30) REVERT: G 64 GLU cc_start: 0.8931 (tt0) cc_final: 0.8729 (tt0) REVERT: G 90 ASP cc_start: 0.8491 (t70) cc_final: 0.7920 (t0) REVERT: H 90 GLU cc_start: 0.8815 (mp0) cc_final: 0.8390 (mp0) REVERT: K 17 MET cc_start: 0.9477 (mmm) cc_final: 0.9058 (tpp) REVERT: K 24 TYR cc_start: 0.8887 (m-10) cc_final: 0.8345 (m-80) outliers start: 30 outliers final: 15 residues processed: 179 average time/residue: 0.5942 time to fit residues: 114.6106 Evaluate side-chains 160 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 143 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain K residue 13 ASN Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain L residue 85 LYS Chi-restraints excluded: chain L residue 105 ASN Chi-restraints excluded: chain M residue 35 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 60 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 chunk 93 optimal weight: 10.0000 chunk 10 optimal weight: 0.7980 chunk 120 optimal weight: 20.0000 chunk 113 optimal weight: 5.9990 chunk 29 optimal weight: 0.9990 chunk 19 optimal weight: 5.9990 chunk 95 optimal weight: 10.0000 chunk 72 optimal weight: 50.0000 chunk 117 optimal weight: 5.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN ** N 31 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 = 0.3628 r_free = 0.3628 target = 0.070332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.043218 restraints weight = 68364.254| |-----------------------------------------------------------------------------| r_work (start): 0.2786 rms_B_bonded: 3.79 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8933 moved from start: 0.6839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15238 Z= 0.178 Angle : 0.656 10.094 21893 Z= 0.367 Chirality : 0.044 0.272 2535 Planarity : 0.004 0.033 1744 Dihedral : 29.262 99.119 4419 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.05 % Allowed : 27.43 % Favored : 69.52 % 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: 1.95 (0.26), residues: 1057 helix: 2.47 (0.21), residues: 615 sheet: 2.11 (0.99), residues: 25 loop : -0.59 (0.28), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG M 33 TYR 0.011 0.001 TYR F 51 PHE 0.009 0.001 PHE F 61 TRP 0.003 0.001 TRP M 25 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.18 (15218) covalent geometry : angle 0.65071 / 0.37 (21869) hydrogen bonds : bond 0.05328 / 3.52 ( 869) hydrogen bonds : angle 3.33459 / 2.39 ( 2207) metal coordination : bond 0.01167 / 0.52 ( 20) metal coordination : angle 2.63287 / 1.66 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 149 time to evaluate : 0.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 91 LYS cc_start: 0.9629 (ttmt) cc_final: 0.9400 (ttpp) REVERT: D 84 SER cc_start: 0.9136 (OUTLIER) cc_final: 0.8884 (p) REVERT: D 102 GLU cc_start: 0.8736 (mp0) cc_final: 0.8464 (mm-30) REVERT: E 59 GLU cc_start: 0.8248 (pm20) cc_final: 0.7813 (pm20) REVERT: E 97 GLU cc_start: 0.8876 (mm-30) cc_final: 0.8663 (mp0) REVERT: E 120 MET cc_start: 0.8935 (OUTLIER) cc_final: 0.8715 (mtt) REVERT: F 63 GLU cc_start: 0.8505 (pt0) cc_final: 0.8260 (pt0) REVERT: G 41 GLU cc_start: 0.8521 (tm-30) cc_final: 0.7994 (tm-30) REVERT: G 90 ASP cc_start: 0.8435 (t70) cc_final: 0.7934 (t0) REVERT: H 68 GLU cc_start: 0.8528 (tp30) cc_final: 0.8213 (tp30) REVERT: H 90 GLU cc_start: 0.8826 (mp0) cc_final: 0.8424 (mp0) REVERT: K 17 MET cc_start: 0.9440 (mmm) cc_final: 0.9041 (tpp) REVERT: K 24 TYR cc_start: 0.8872 (m-10) cc_final: 0.8347 (m-80) outliers start: 26 outliers final: 14 residues processed: 167 average time/residue: 0.5989 time to fit residues: 107.9858 Evaluate side-chains 159 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 143 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain K residue 13 ASN Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain L residue 85 LYS Chi-restraints excluded: chain L residue 105 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 101 optimal weight: 50.0000 chunk 47 optimal weight: 5.9990 chunk 90 optimal weight: 20.0000 chunk 50 optimal weight: 0.9990 chunk 63 optimal weight: 5.9990 chunk 91 optimal weight: 10.0000 chunk 46 optimal weight: 0.0670 chunk 40 optimal weight: 1.9990 chunk 80 optimal weight: 10.0000 chunk 73 optimal weight: 30.0000 chunk 33 optimal weight: 0.9980 overall best weight: 2.0124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 31 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 = 0.3632 r_free = 0.3632 target = 0.070276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.043300 restraints weight = 68691.984| |-----------------------------------------------------------------------------| r_work (start): 0.2797 rms_B_bonded: 3.81 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8932 moved from start: 0.6981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15238 Z= 0.162 Angle : 0.645 10.506 21893 Z= 0.363 Chirality : 0.043 0.257 2535 Planarity : 0.004 0.043 1744 Dihedral : 29.186 95.198 4419 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.46 % Allowed : 28.72 % Favored : 68.82 % 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: 2.02 (0.26), residues: 1057 helix: 2.53 (0.21), residues: 616 sheet: 2.14 (0.98), residues: 25 loop : -0.59 (0.28), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG M 33 TYR 0.012 0.001 TYR D 39 PHE 0.009 0.001 PHE F 61 TRP 0.007 0.001 TRP M 25 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.16 (15218) covalent geometry : angle 0.64020 / 0.36 (21869) hydrogen bonds : bond 0.05069 / 3.35 ( 869) hydrogen bonds : angle 3.23745 / 2.32 ( 2207) metal coordination : bond 0.01037 / 0.47 ( 20) metal coordination : angle 2.51540 / 1.61 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 149 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 91 LYS cc_start: 0.9635 (ttmt) cc_final: 0.9399 (ttpp) REVERT: D 84 SER cc_start: 0.9095 (OUTLIER) cc_final: 0.8890 (p) REVERT: D 102 GLU cc_start: 0.8710 (mp0) cc_final: 0.8427 (mm-30) REVERT: E 59 GLU cc_start: 0.8226 (pm20) cc_final: 0.7826 (pm20) REVERT: E 97 GLU cc_start: 0.8853 (mm-30) cc_final: 0.8646 (mp0) REVERT: E 120 MET cc_start: 0.8914 (OUTLIER) cc_final: 0.8699 (mtt) REVERT: F 63 GLU cc_start: 0.8510 (pt0) cc_final: 0.8258 (pt0) REVERT: G 41 GLU cc_start: 0.8526 (tm-30) cc_final: 0.7989 (tm-30) REVERT: G 90 ASP cc_start: 0.8409 (t70) cc_final: 0.8050 (t0) REVERT: H 68 GLU cc_start: 0.8578 (tp30) cc_final: 0.8258 (tp30) REVERT: H 90 GLU cc_start: 0.8845 (mp0) cc_final: 0.8407 (mp0) REVERT: K 17 MET cc_start: 0.9391 (mmm) cc_final: 0.9035 (tpp) REVERT: K 24 TYR cc_start: 0.8891 (m-10) cc_final: 0.8418 (m-80) REVERT: K 43 ILE cc_start: 0.8610 (tp) cc_final: 0.8317 (mt) outliers start: 21 outliers final: 13 residues processed: 163 average time/residue: 0.6575 time to fit residues: 115.6257 Evaluate side-chains 158 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 143 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain K residue 13 ASN Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain M residue 35 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 25 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 127 optimal weight: 0.0010 chunk 12 optimal weight: 2.9990 chunk 55 optimal weight: 0.2980 chunk 45 optimal weight: 0.7980 chunk 43 optimal weight: 0.5980 chunk 81 optimal weight: 10.0000 chunk 112 optimal weight: 40.0000 chunk 130 optimal weight: 50.0000 chunk 31 optimal weight: 1.9990 overall best weight: 0.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 31 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 = 0.3652 r_free = 0.3652 target = 0.070936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.044199 restraints weight = 68948.502| |-----------------------------------------------------------------------------| r_work (start): 0.2833 rms_B_bonded: 3.92 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8913 moved from start: 0.7033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 15238 Z= 0.134 Angle : 0.637 11.053 21893 Z= 0.358 Chirality : 0.043 0.274 2535 Planarity : 0.004 0.050 1744 Dihedral : 29.108 91.949 4419 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.11 % Allowed : 29.31 % Favored : 68.58 % 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: 2.18 (0.26), residues: 1057 helix: 2.66 (0.21), residues: 614 sheet: 2.18 (0.99), residues: 25 loop : -0.50 (0.28), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG M 33 TYR 0.012 0.001 TYR D 39 PHE 0.008 0.001 PHE F 61 TRP 0.007 0.001 TRP M 25 HIS 0.003 0.000 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.13 (15218) covalent geometry : angle 0.63229 / 0.36 (21869) hydrogen bonds : bond 0.04504 / 2.99 ( 869) hydrogen bonds : angle 3.08736 / 2.21 ( 2207) metal coordination : bond 0.00781 / 0.35 ( 20) metal coordination : angle 2.31726 / 1.49 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 158 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 91 LYS cc_start: 0.9618 (ttmt) cc_final: 0.9385 (ttpp) REVERT: D 102 GLU cc_start: 0.8658 (mp0) cc_final: 0.8369 (mm-30) REVERT: E 59 GLU cc_start: 0.8208 (pm20) cc_final: 0.7779 (pm20) REVERT: E 120 MET cc_start: 0.8881 (OUTLIER) cc_final: 0.8663 (mtt) REVERT: F 63 GLU cc_start: 0.8456 (pt0) cc_final: 0.8193 (pt0) REVERT: G 90 ASP cc_start: 0.8404 (t70) cc_final: 0.7922 (t0) REVERT: H 68 GLU cc_start: 0.8571 (tp30) cc_final: 0.8207 (tp30) REVERT: H 90 GLU cc_start: 0.8833 (mp0) cc_final: 0.8385 (mp0) REVERT: H 113 LYS cc_start: 0.9315 (ttpp) cc_final: 0.9097 (ttmm) REVERT: K 17 MET cc_start: 0.9373 (mmm) cc_final: 0.9028 (tpp) REVERT: K 24 TYR cc_start: 0.8843 (m-10) cc_final: 0.8349 (m-80) REVERT: K 43 ILE cc_start: 0.8595 (tp) cc_final: 0.8236 (mt) outliers start: 18 outliers final: 11 residues processed: 170 average time/residue: 0.5963 time to fit residues: 109.7052 Evaluate side-chains 160 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 148 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain K residue 13 ASN Chi-restraints excluded: chain K residue 38 PHE Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain L residue 64 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 39 optimal weight: 3.9990 chunk 121 optimal weight: 20.0000 chunk 25 optimal weight: 2.9990 chunk 36 optimal weight: 0.4980 chunk 67 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 89 optimal weight: 20.0000 chunk 65 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 109 optimal weight: 8.9990 chunk 92 optimal weight: 10.0000 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN C 73 ASN E 125 GLN G 104 GLN ** N 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.070352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.043485 restraints weight = 68727.055| |-----------------------------------------------------------------------------| r_work (start): 0.2808 rms_B_bonded: 3.84 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8929 moved from start: 0.7146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15238 Z= 0.172 Angle : 0.657 11.037 21893 Z= 0.368 Chirality : 0.043 0.253 2535 Planarity : 0.004 0.036 1744 Dihedral : 29.119 88.520 4419 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.34 % Allowed : 29.31 % Favored : 68.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.13 (0.26), residues: 1057 helix: 2.64 (0.21), residues: 616 sheet: 2.18 (0.99), residues: 25 loop : -0.59 (0.28), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG M 33 TYR 0.016 0.001 TYR K 46 PHE 0.015 0.001 PHE M 32 TRP 0.005 0.001 TRP M 25 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.17 (15218) covalent geometry : angle 0.65330 / 0.37 (21869) hydrogen bonds : bond 0.04934 / 3.27 ( 869) hydrogen bonds : angle 3.20999 / 2.30 ( 2207) metal coordination : bond 0.01036 / 0.45 ( 20) metal coordination : angle 2.22305 / 1.37 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 151 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 23 ARG cc_start: 0.8721 (pmt-80) cc_final: 0.8487 (pmt-80) REVERT: B 24 ASP cc_start: 0.8095 (t0) cc_final: 0.7115 (t0) REVERT: B 91 LYS cc_start: 0.9636 (ttmt) cc_final: 0.9391 (ttpp) REVERT: D 102 GLU cc_start: 0.8668 (mp0) cc_final: 0.8409 (mm-30) REVERT: E 59 GLU cc_start: 0.8248 (pm20) cc_final: 0.7852 (pm20) REVERT: E 120 MET cc_start: 0.8923 (OUTLIER) cc_final: 0.8699 (mtt) REVERT: F 63 GLU cc_start: 0.8526 (pt0) cc_final: 0.8269 (pt0) REVERT: G 90 ASP cc_start: 0.8382 (t70) cc_final: 0.8102 (t0) REVERT: H 68 GLU cc_start: 0.8626 (tp30) cc_final: 0.8304 (tp30) REVERT: H 90 GLU cc_start: 0.8849 (mp0) cc_final: 0.8471 (mp0) REVERT: H 113 LYS cc_start: 0.9312 (ttpp) cc_final: 0.9094 (ttmm) REVERT: K 24 TYR cc_start: 0.8852 (m-10) cc_final: 0.8425 (m-80) REVERT: K 43 ILE cc_start: 0.8653 (tp) cc_final: 0.8340 (mt) outliers start: 20 outliers final: 11 residues processed: 164 average time/residue: 0.6543 time to fit residues: 115.5477 Evaluate side-chains 160 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 148 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain K residue 13 ASN Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain L residue 64 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 20 optimal weight: 0.5980 chunk 89 optimal weight: 20.0000 chunk 27 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 92 optimal weight: 10.0000 chunk 73 optimal weight: 20.0000 chunk 113 optimal weight: 30.0000 chunk 86 optimal weight: 40.0000 chunk 122 optimal weight: 9.9990 chunk 28 optimal weight: 3.9990 chunk 128 optimal weight: 30.0000 overall best weight: 4.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN B 25 ASN C 73 ASN ** N 31 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 = 0.3599 r_free = 0.3599 target = 0.069010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.041847 restraints weight = 69059.759| |-----------------------------------------------------------------------------| r_work (start): 0.2743 rms_B_bonded: 3.81 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8975 moved from start: 0.7417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 15238 Z= 0.272 Angle : 0.734 10.403 21893 Z= 0.402 Chirality : 0.046 0.229 2535 Planarity : 0.005 0.069 1744 Dihedral : 29.278 82.931 4419 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.88 % Allowed : 29.89 % Favored : 68.23 % 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: 1.84 (0.25), residues: 1057 helix: 2.43 (0.21), residues: 617 sheet: 2.13 (0.99), residues: 25 loop : -0.77 (0.28), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 30 TYR 0.012 0.002 TYR F 51 PHE 0.010 0.001 PHE K 97 TRP 0.008 0.002 TRP M 25 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00573 / 0.27 (15218) covalent geometry : angle 0.72946 / 0.40 (21869) hydrogen bonds : bond 0.06518 / 4.34 ( 869) hydrogen bonds : angle 3.51584 / 2.52 ( 2207) metal coordination : bond 0.01497 / 0.69 ( 20) metal coordination : angle 2.55648 / 1.53 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4026.28 seconds wall clock time: 69 minutes 10.49 seconds (4150.49 seconds total)