Starting phenix.real_space_refine on Thu Aug 6 11:30:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dde_46771/08_2026/9dde_46771.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dde_46771/08_2026/9dde_46771.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9dde_46771/08_2026/9dde_46771.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dde_46771/08_2026/9dde_46771.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9dde_46771/08_2026/9dde_46771.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dde_46771/08_2026/9dde_46771.map" } resolution = 3.2 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= 0.006 sd= 0.059 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 324 5.49 5 S 34 5.16 5 C 8654 2.51 5 N 2852 2.21 5 O 3525 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 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: 15394 Number of models: 1 Model: "" Number of chains: 18 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: 663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 663 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 82} 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: "C" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 812 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 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: 647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 647 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} 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: "G" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 816 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 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: 3345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 3345 Classifications: {'DNA': 162} Link IDs: {'rna3p': 161} Chain: "J" Number of atoms: 3297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 3297 Classifications: {'DNA': 162} Link IDs: {'rna3p': 161} Chain: "K" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 783 Classifications: {'peptide': 102} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 5, 'TRANS': 96} Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 47 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "L" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 763 Classifications: {'peptide': 101} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 7, 'TRANS': 93} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 31 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: 305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 305 Classifications: {'peptide': 40} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 38} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "N" Number of atoms: 467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 467 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 3, 'TRANS': 70} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 130 Unresolved non-hydrogen angles: 159 Unresolved non-hydrogen dihedrals: 109 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'PHE:plan': 2, 'GLU:plan': 6, 'ASN:plan1': 2, 'ASP:plan': 2, 'ARG:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 77 Chain: "O" Number of atoms: 467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 467 Classifications: {'peptide': 71} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 1, 'TRANS': 69} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 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 12728 SG CYS K 18 110.369 47.497 86.380 1.00172.81 S ATOM 12749 SG CYS K 21 113.957 46.507 85.515 1.00171.27 S ATOM 12887 SG CYS K 39 112.069 48.574 83.128 1.00170.07 S ATOM 12909 SG CYS K 42 111.045 44.883 83.675 1.00170.96 S ATOM 12846 SG CYS K 34 98.527 51.073 90.704 1.00173.73 S ATOM 12996 SG CYS K 53 100.863 48.206 91.830 1.00177.96 S ATOM 13017 SG CYS K 56 98.621 49.902 94.368 1.00184.67 S ATOM 13653 SG CYS L 51 100.265 74.273 84.400 1.00185.19 S ATOM 13674 SG CYS L 54 101.442 77.195 86.194 1.00181.49 S ATOM 13815 SG CYS L 72 100.667 73.995 88.092 1.00169.07 S ATOM 13834 SG CYS L 75 97.777 76.217 86.748 1.00168.71 S ATOM 13769 SG CYS L 67 94.926 63.191 78.331 1.00151.96 S ATOM 13923 SG CYS L 87 95.103 66.989 77.587 1.00170.12 S ATOM 13943 SG CYS L 90 95.202 64.478 74.680 1.00157.27 S ATOM 14193 SG CYS M 27 29.418 51.535 66.943 1.00123.52 S ATOM 14212 SG CYS M 30 27.721 52.692 63.677 1.00112.94 S ATOM 14292 SG CYS M 41 29.720 49.538 63.755 1.00100.03 S ATOM 14312 SG CYS M 44 31.513 52.805 63.995 1.00 94.27 S Time building chain proxies: 3.02, per 1000 atoms: 0.20 Number of scatterers: 15394 At special positions: 0 Unit cell: (137.541, 124.545, 144.039, 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 34 16.00 P 324 15.00 O 3525 8.00 N 2852 7.00 C 8654 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: 1.33 Conformation dependent library (CDL) restraints added in 529.4 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 53 " pdb="ZN ZN K 402 " - pdb=" SG CYS K 56 " pdb="ZN ZN K 402 " - pdb=" SG CYS K 34 " 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 90 " pdb="ZN ZN L 402 " - pdb=" SG CYS L 87 " pdb="ZN ZN L 402 " - pdb=" SG CYS L 67 " pdb=" ZN M 301 " pdb="ZN ZN M 301 " - pdb=" SG CYS M 41 " pdb="ZN ZN M 301 " - pdb=" SG CYS M 44 " pdb="ZN ZN M 301 " - pdb=" SG CYS M 30 " pdb="ZN ZN M 301 " - pdb=" SG CYS M 27 " Number of angles added : 24 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2164 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 16 sheets defined 60.5% alpha, 5.8% beta 161 base pairs and 290 stacking pairs defined. Time for finding SS restraints: 2.34 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 removed outlier: 3.503A pdb=" N VAL A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 25 through 29 removed outlier: 3.892A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) 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 21 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 73 removed outlier: 3.645A 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 56 Processing helix chain 'E' and resid 63 through 77 removed outlier: 4.175A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.632A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 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 94 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.502A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 3.672A 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 90 through 97 Processing helix chain 'G' and resid 112 through 116 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 14 through 16 No H-bonds generated for 'chain 'K' and resid 14 through 16' Processing helix chain 'K' and resid 40 through 48 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 'O' and resid 38 through 51 removed outlier: 4.345A pdb=" N LEU O 42 " --> pdb=" O PRO O 38 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N SER O 50 " --> pdb=" O ALA O 46 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LYS O 51 " --> pdb=" O VAL O 47 " (cutoff:3.500A) Processing helix chain 'O' and resid 58 through 69 Processing helix chain 'O' and resid 75 through 89 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.873A 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: 7.482A 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: 6.852A 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: 6.861A 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: 7.295A 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: 9.330A pdb=" N LEU N 67 " --> pdb=" O GLN N 2 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N PHE N 4 " --> pdb=" O LEU N 67 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N LEU N 69 " --> pdb=" O PHE N 4 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LYS N 6 " --> pdb=" O LEU N 69 " (cutoff:3.500A) removed outlier: 8.301A pdb=" N LEU N 71 " --> pdb=" O LYS N 6 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'O' and resid 56 through 57 523 hydrogen bonds defined for protein. 1530 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 415 hydrogen bonds 830 hydrogen bond angles 0 basepair planarities 161 basepair parallelities 290 stacking parallelities Total time for adding SS restraints: 3.06 Time building geometry restraints manager: 1.74 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: 3440 1.33 - 1.46: 4869 1.46 - 1.58: 7316 1.58 - 1.70: 646 1.70 - 1.82: 46 Bond restraints: 16317 Sorted by residual: bond pdb=" C1' DC I 36 " pdb=" N1 DC I 36 " ideal model delta sigma weight residual 1.468 1.546 -0.078 1.40e-02 5.10e+03 3.10e+01 bond pdb=" C1' DC J 14 " pdb=" N1 DC J 14 " ideal model delta sigma weight residual 1.468 1.537 -0.069 1.40e-02 5.10e+03 2.46e+01 bond pdb=" N GLY M 49 " pdb=" CA GLY M 49 " ideal model delta sigma weight residual 1.444 1.477 -0.033 9.60e-03 1.09e+04 1.18e+01 bond pdb=" N ASN K 13 " pdb=" CA ASN K 13 " ideal model delta sigma weight residual 1.462 1.494 -0.032 9.50e-03 1.11e+04 1.15e+01 bond pdb=" C3' DC I 36 " pdb=" C2' DC I 36 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.09e+01 ... (remaining 16312 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.91: 22443 1.91 - 3.81: 977 3.81 - 5.72: 46 5.72 - 7.63: 15 7.63 - 9.54: 1 Bond angle restraints: 23482 Sorted by residual: angle pdb=" O4' DG J 120 " pdb=" C4' DG J 120 " pdb=" C3' DG J 120 " ideal model delta sigma weight residual 106.00 103.22 2.78 6.00e-01 2.78e+00 2.14e+01 angle pdb=" O4' DG I 76 " pdb=" C4' DG I 76 " pdb=" C3' DG I 76 " ideal model delta sigma weight residual 106.00 103.24 2.76 6.00e-01 2.78e+00 2.12e+01 angle pdb=" O4' DG I 75 " pdb=" C4' DG I 75 " pdb=" C3' DG I 75 " ideal model delta sigma weight residual 106.00 103.31 2.69 6.00e-01 2.78e+00 2.01e+01 angle pdb=" N3 DT I 78 " pdb=" C4 DT I 78 " pdb=" O4 DT I 78 " ideal model delta sigma weight residual 119.90 122.57 -2.67 6.00e-01 2.78e+00 1.98e+01 angle pdb=" O4' DC J 131 " pdb=" C4' DC J 131 " pdb=" C3' DC J 131 " ideal model delta sigma weight residual 106.00 103.36 2.64 6.00e-01 2.78e+00 1.93e+01 ... (remaining 23477 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.75: 6847 26.75 - 53.50: 1840 53.50 - 80.25: 274 80.25 - 107.00: 3 107.00 - 133.76: 2 Dihedral angle restraints: 8966 sinusoidal: 5630 harmonic: 3336 Sorted by residual: 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 86.24 133.76 1 3.50e+01 8.16e-04 1.33e+01 dihedral pdb=" CA LYS K 8 " pdb=" C LYS K 8 " pdb=" N ILE K 9 " pdb=" CA ILE K 9 " ideal model delta harmonic sigma weight residual 180.00 161.83 18.17 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" C4' DC I 128 " pdb=" C3' DC I 128 " pdb=" O3' DC I 128 " pdb=" P DT I 129 " ideal model delta sinusoidal sigma weight residual 220.00 91.73 128.27 1 3.50e+01 8.16e-04 1.27e+01 ... (remaining 8963 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 2681 0.111 - 0.222: 41 0.222 - 0.333: 0 0.333 - 0.443: 0 0.443 - 0.554: 6 Chirality restraints: 2728 Sorted by residual: chirality pdb=" P DC I 173 " pdb=" OP1 DC I 173 " pdb=" OP2 DC I 173 " pdb=" O5' DC I 173 " both_signs ideal model delta sigma weight residual True 2.34 -2.89 -0.55 2.00e-01 2.50e+01 7.68e+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 7.25e+00 chirality pdb=" P DG I 174 " pdb=" OP1 DG I 174 " pdb=" OP2 DG I 174 " pdb=" O5' DG I 174 " both_signs ideal model delta sigma weight residual True 2.34 -2.86 -0.53 2.00e-01 2.50e+01 6.89e+00 ... (remaining 2725 not shown) Planarity restraints: 1851 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP D 48 " -0.014 2.00e-02 2.50e+03 2.83e-02 8.00e+00 pdb=" C ASP D 48 " 0.049 2.00e-02 2.50e+03 pdb=" O ASP D 48 " -0.018 2.00e-02 2.50e+03 pdb=" N THR D 49 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 80 " 0.019 2.00e-02 2.50e+03 1.61e-02 5.16e+00 pdb=" CG TYR D 80 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TYR D 80 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR D 80 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR D 80 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR D 80 " 0.012 2.00e-02 2.50e+03 pdb=" CZ TYR D 80 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR D 80 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 23 " 0.193 9.50e-02 1.11e+02 8.64e-02 4.59e+00 pdb=" NE ARG B 23 " -0.012 2.00e-02 2.50e+03 pdb=" CZ ARG B 23 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG B 23 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG B 23 " 0.007 2.00e-02 2.50e+03 ... (remaining 1848 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2156 2.76 - 3.30: 13224 3.30 - 3.83: 28260 3.83 - 4.37: 32748 4.37 - 4.90: 48324 Nonbonded interactions: 124712 Sorted by model distance: nonbonded pdb=" OE2 GLU O 52 " pdb=" OG SER O 54 " model vdw 2.226 3.040 nonbonded pdb=" N GLN L 25 " pdb=" OE1 GLN L 25 " model vdw 2.229 3.120 nonbonded pdb=" O TYR C 39 " pdb=" OG SER D 75 " model vdw 2.239 3.040 nonbonded pdb=" OD2 ASP A 106 " pdb=" NH2 ARG A 131 " model vdw 2.248 3.120 nonbonded pdb=" O LEU L 80 " pdb=" NZ LYS L 85 " model vdw 2.297 3.120 ... (remaining 124707 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' and (resid 21 through 22 or (resid 23 and (name N or name CA or name \ C or name O or name CB )) or resid 24 through 101)) selection = (chain 'F' and resid 21 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 118)) } 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: 4.420 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: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 18.040 Find NCS groups from input model: 0.130 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: 0.000 Load rotamer database and sin/cos tables:1.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 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 0.078 16337 Z= 0.531 Angle : 0.793 9.537 23506 Z= 0.664 Chirality : 0.051 0.554 2728 Planarity : 0.005 0.086 1851 Dihedral : 26.365 133.756 6802 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.33 % Allowed : 14.32 % Favored : 85.35 % 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: 1.79 (0.25), residues: 1121 helix: 2.48 (0.20), residues: 658 sheet: 0.20 (0.85), residues: 35 loop : -0.86 (0.27), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 76 TYR 0.038 0.002 TYR D 80 PHE 0.013 0.001 PHE E 78 TRP 0.005 0.001 TRP M 25 HIS 0.009 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00611 / 0.53 (16317) covalent geometry : angle 0.78847 / 0.66 (23482) hydrogen bonds : bond 0.06812 / 4.61 ( 938) hydrogen bonds : angle 3.32878 / 2.32 ( 2360) metal coordination : bond 0.01036 / 0.46 ( 20) metal coordination : angle 2.63993 / 1.51 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 307 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 ASP cc_start: 0.8134 (m-30) cc_final: 0.7934 (m-30) REVERT: B 59 LYS cc_start: 0.8917 (tttp) cc_final: 0.8701 (ttmm) REVERT: F 67 ARG cc_start: 0.8501 (ttp80) cc_final: 0.8132 (ttm-80) REVERT: K 70 ARG cc_start: 0.8713 (mmt90) cc_final: 0.8464 (mmt-90) REVERT: K 74 THR cc_start: 0.8779 (p) cc_final: 0.8491 (t) REVERT: K 80 TYR cc_start: 0.8022 (m-80) cc_final: 0.7786 (m-10) REVERT: K 90 GLU cc_start: 0.9083 (tp30) cc_final: 0.8862 (tp30) REVERT: L 61 THR cc_start: 0.9312 (m) cc_final: 0.9015 (p) REVERT: L 71 PHE cc_start: 0.8741 (m-80) cc_final: 0.8198 (m-80) REVERT: M 61 LEU cc_start: 0.7939 (tp) cc_final: 0.7280 (pt) outliers start: 3 outliers final: 0 residues processed: 308 average time/residue: 0.1451 time to fit residues: 61.7301 Evaluate side-chains 247 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 247 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.0970 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 10.0000 chunk 55 optimal weight: 0.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 76 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.056992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.036150 restraints weight = 78408.051| |-----------------------------------------------------------------------------| r_work (start): 0.2737 rms_B_bonded: 3.55 r_work: 0.2573 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.2573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8917 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 16337 Z= 0.170 Angle : 0.654 9.163 23506 Z= 0.382 Chirality : 0.044 0.243 2728 Planarity : 0.005 0.059 1851 Dihedral : 28.827 127.523 4782 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.66 % Allowed : 18.76 % Favored : 79.58 % 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: 1.91 (0.25), residues: 1121 helix: 2.64 (0.20), residues: 664 sheet: -0.12 (0.87), residues: 35 loop : -0.94 (0.27), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 35 TYR 0.035 0.002 TYR D 80 PHE 0.020 0.002 PHE M 24 TRP 0.001 0.000 TRP L 17 HIS 0.004 0.001 HIS K 2 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.17 (16317) covalent geometry : angle 0.64682 / 0.38 (23482) hydrogen bonds : bond 0.05382 / 3.62 ( 938) hydrogen bonds : angle 3.09261 / 2.19 ( 2360) metal coordination : bond 0.01565 / 0.74 ( 20) metal coordination : angle 3.10313 / 1.77 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 252 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 ASP cc_start: 0.9143 (m-30) cc_final: 0.8793 (m-30) REVERT: B 88 TYR cc_start: 0.8934 (m-10) cc_final: 0.8683 (m-80) REVERT: C 90 ASP cc_start: 0.9114 (t0) cc_final: 0.8697 (t0) REVERT: H 73 GLU cc_start: 0.9243 (tp30) cc_final: 0.9008 (mm-30) REVERT: K 45 ARG cc_start: 0.9719 (mmt90) cc_final: 0.9369 (mmm160) REVERT: K 74 THR cc_start: 0.7383 (p) cc_final: 0.7175 (t) REVERT: L 66 GLU cc_start: 0.6389 (tm-30) cc_final: 0.5935 (pp20) REVERT: M 61 LEU cc_start: 0.8132 (tp) cc_final: 0.7642 (pt) outliers start: 15 outliers final: 8 residues processed: 259 average time/residue: 0.1242 time to fit residues: 45.4224 Evaluate side-chains 249 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 241 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain K residue 69 ILE Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain L residue 77 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 141 optimal weight: 5.9990 chunk 92 optimal weight: 9.9990 chunk 3 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 119 optimal weight: 0.9980 chunk 111 optimal weight: 6.9990 chunk 113 optimal weight: 10.0000 chunk 11 optimal weight: 3.9990 chunk 98 optimal weight: 10.0000 chunk 31 optimal weight: 1.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN E 125 GLN H 46 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.055633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.034966 restraints weight = 79529.124| |-----------------------------------------------------------------------------| r_work (start): 0.2681 rms_B_bonded: 3.59 r_work: 0.2513 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.2513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8962 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 16337 Z= 0.246 Angle : 0.686 9.210 23506 Z= 0.388 Chirality : 0.046 0.344 2728 Planarity : 0.005 0.053 1851 Dihedral : 29.155 123.132 4782 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.22 % Allowed : 19.64 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.78 (0.25), residues: 1121 helix: 2.50 (0.20), residues: 668 sheet: 0.26 (0.95), residues: 35 loop : -1.01 (0.27), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 35 TYR 0.023 0.002 TYR D 80 PHE 0.015 0.002 PHE K 38 TRP 0.002 0.000 TRP M 25 HIS 0.010 0.001 HIS L 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00496 / 0.25 (16317) covalent geometry : angle 0.67896 / 0.39 (23482) hydrogen bonds : bond 0.05855 / 3.92 ( 938) hydrogen bonds : angle 3.33184 / 2.37 ( 2360) metal coordination : bond 0.01851 / 0.94 ( 20) metal coordination : angle 3.15151 / 2.01 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 239 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 ASP cc_start: 0.9173 (m-30) cc_final: 0.8869 (m-30) REVERT: C 90 ASP cc_start: 0.9021 (t0) cc_final: 0.8695 (t0) REVERT: D 90 GLU cc_start: 0.8792 (mp0) cc_final: 0.8552 (mp0) REVERT: E 76 GLN cc_start: 0.9220 (tp-100) cc_final: 0.8785 (tp-100) REVERT: G 90 ASP cc_start: 0.8573 (t0) cc_final: 0.8295 (t70) REVERT: H 32 GLU cc_start: 0.9090 (mp0) cc_final: 0.8579 (mp0) REVERT: H 73 GLU cc_start: 0.9260 (tp30) cc_final: 0.8704 (mm-30) REVERT: H 76 ARG cc_start: 0.8913 (mtm180) cc_final: 0.8695 (mtm110) REVERT: H 87 THR cc_start: 0.9211 (OUTLIER) cc_final: 0.8769 (p) REVERT: H 98 LEU cc_start: 0.9444 (OUTLIER) cc_final: 0.9138 (mm) REVERT: K 74 THR cc_start: 0.7457 (p) cc_final: 0.7217 (t) REVERT: L 97 LYS cc_start: 0.8797 (mtmt) cc_final: 0.8485 (mtpt) REVERT: M 61 LEU cc_start: 0.8401 (tp) cc_final: 0.7922 (pt) REVERT: N 72 ARG cc_start: 0.8247 (ptp90) cc_final: 0.8008 (ptp90) outliers start: 20 outliers final: 15 residues processed: 247 average time/residue: 0.1356 time to fit residues: 47.3798 Evaluate side-chains 252 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 235 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain K residue 69 ILE Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain M residue 29 VAL Chi-restraints excluded: chain N residue 5 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 7 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 9 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 99 optimal weight: 10.0000 chunk 49 optimal weight: 0.6980 chunk 14 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 chunk 70 optimal weight: 3.9990 chunk 80 optimal weight: 10.0000 chunk 96 optimal weight: 10.0000 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 HIS D 106 HIS K 76 GLN N 68 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.056259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.035472 restraints weight = 79675.472| |-----------------------------------------------------------------------------| r_work (start): 0.2714 rms_B_bonded: 3.56 r_work: 0.2550 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.2550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8938 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 16337 Z= 0.149 Angle : 0.631 9.558 23506 Z= 0.363 Chirality : 0.043 0.380 2728 Planarity : 0.004 0.041 1851 Dihedral : 29.120 120.733 4782 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.22 % Allowed : 19.76 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.95 (0.25), residues: 1121 helix: 2.64 (0.20), residues: 660 sheet: 0.10 (0.94), residues: 35 loop : -0.84 (0.28), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG L 91 TYR 0.029 0.001 TYR D 80 PHE 0.024 0.002 PHE K 38 TRP 0.001 0.000 TRP L 17 HIS 0.004 0.001 HIS L 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.15 (16317) covalent geometry : angle 0.62183 / 0.36 (23482) hydrogen bonds : bond 0.04900 / 3.29 ( 938) hydrogen bonds : angle 3.04941 / 2.18 ( 2360) metal coordination : bond 0.01852 / 0.65 ( 20) metal coordination : angle 3.33177 / 2.17 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 251 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 ASP cc_start: 0.9139 (m-30) cc_final: 0.8810 (m-30) REVERT: D 90 GLU cc_start: 0.8810 (mp0) cc_final: 0.8583 (mp0) REVERT: E 76 GLN cc_start: 0.9196 (tp-100) cc_final: 0.8682 (tp-100) REVERT: F 24 ASP cc_start: 0.7190 (t0) cc_final: 0.6933 (t0) REVERT: F 63 GLU cc_start: 0.8897 (tm-30) cc_final: 0.8661 (tm-30) REVERT: G 17 ARG cc_start: 0.9053 (OUTLIER) cc_final: 0.8662 (mtt180) REVERT: G 90 ASP cc_start: 0.8461 (t0) cc_final: 0.8165 (t70) REVERT: H 31 LYS cc_start: 0.9485 (mttt) cc_final: 0.9281 (mptt) REVERT: H 98 LEU cc_start: 0.9425 (OUTLIER) cc_final: 0.9134 (mm) REVERT: K 61 HIS cc_start: 0.7527 (t-90) cc_final: 0.7241 (t-90) REVERT: K 74 THR cc_start: 0.7440 (p) cc_final: 0.7216 (t) REVERT: L 66 GLU cc_start: 0.6567 (tm-30) cc_final: 0.6347 (pp20) REVERT: M 61 LEU cc_start: 0.8430 (tp) cc_final: 0.7971 (pt) outliers start: 20 outliers final: 11 residues processed: 259 average time/residue: 0.1207 time to fit residues: 44.4546 Evaluate side-chains 253 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 240 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain G residue 17 ARG Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain K residue 69 ILE Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain N residue 5 VAL Chi-restraints excluded: chain N residue 70 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 103 optimal weight: 9.9990 chunk 110 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 92 optimal weight: 10.0000 chunk 15 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 97 optimal weight: 10.0000 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.055264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.034303 restraints weight = 79217.845| |-----------------------------------------------------------------------------| r_work (start): 0.2666 rms_B_bonded: 3.64 r_work: 0.2495 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.2495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8982 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 16337 Z= 0.240 Angle : 0.699 10.380 23506 Z= 0.387 Chirality : 0.045 0.237 2728 Planarity : 0.004 0.039 1851 Dihedral : 29.339 119.120 4782 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.33 % Allowed : 20.31 % Favored : 76.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.92 (0.25), residues: 1121 helix: 2.66 (0.20), residues: 656 sheet: -0.06 (0.93), residues: 36 loop : -0.89 (0.28), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG K 70 TYR 0.039 0.002 TYR D 80 PHE 0.011 0.002 PHE K 38 TRP 0.003 0.001 TRP M 25 HIS 0.007 0.001 HIS L 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00492 / 0.24 (16317) covalent geometry : angle 0.68467 / 0.39 (23482) hydrogen bonds : bond 0.05879 / 3.93 ( 938) hydrogen bonds : angle 3.24556 / 2.32 ( 2360) metal coordination : bond 0.01246 / 0.87 ( 20) metal coordination : angle 4.47934 / 2.84 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 235 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8996 (tp30) cc_final: 0.8756 (tp30) REVERT: A 106 ASP cc_start: 0.9145 (m-30) cc_final: 0.8828 (m-30) REVERT: B 63 GLU cc_start: 0.8903 (mt-10) cc_final: 0.8664 (mt-10) REVERT: B 88 TYR cc_start: 0.9097 (m-10) cc_final: 0.8623 (m-80) REVERT: D 90 GLU cc_start: 0.8871 (mp0) cc_final: 0.8611 (mp0) REVERT: E 59 GLU cc_start: 0.8854 (pm20) cc_final: 0.8589 (pm20) REVERT: E 76 GLN cc_start: 0.9199 (tp-100) cc_final: 0.8675 (tp-100) REVERT: F 24 ASP cc_start: 0.7493 (t0) cc_final: 0.7270 (t70) REVERT: G 17 ARG cc_start: 0.9164 (OUTLIER) cc_final: 0.8761 (mtm180) REVERT: H 31 LYS cc_start: 0.9493 (mttt) cc_final: 0.9274 (mptt) REVERT: H 87 THR cc_start: 0.9153 (OUTLIER) cc_final: 0.8756 (p) REVERT: H 98 LEU cc_start: 0.9418 (OUTLIER) cc_final: 0.9120 (mm) REVERT: K 74 THR cc_start: 0.7446 (p) cc_final: 0.7229 (t) REVERT: L 101 ARG cc_start: 0.8143 (tpp80) cc_final: 0.7868 (tpp80) REVERT: M 61 LEU cc_start: 0.8548 (tp) cc_final: 0.8105 (pt) outliers start: 30 outliers final: 19 residues processed: 245 average time/residue: 0.1313 time to fit residues: 45.2723 Evaluate side-chains 252 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 230 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain G residue 17 ARG Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain K residue 69 ILE Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain M residue 29 VAL Chi-restraints excluded: chain N residue 5 VAL Chi-restraints excluded: chain N residue 70 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 68 optimal weight: 0.9980 chunk 9 optimal weight: 5.9990 chunk 108 optimal weight: 7.9990 chunk 86 optimal weight: 10.0000 chunk 45 optimal weight: 1.9990 chunk 78 optimal weight: 10.0000 chunk 42 optimal weight: 1.9990 chunk 118 optimal weight: 9.9990 chunk 50 optimal weight: 0.3980 chunk 97 optimal weight: 9.9990 chunk 126 optimal weight: 0.9980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.055722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.034809 restraints weight = 78521.320| |-----------------------------------------------------------------------------| r_work (start): 0.2692 rms_B_bonded: 3.62 r_work: 0.2524 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.2524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8961 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 16337 Z= 0.161 Angle : 0.650 10.863 23506 Z= 0.366 Chirality : 0.043 0.226 2728 Planarity : 0.004 0.040 1851 Dihedral : 29.247 118.017 4782 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.11 % Allowed : 20.75 % Favored : 77.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.88 (0.25), residues: 1121 helix: 2.59 (0.20), residues: 660 sheet: -0.04 (0.92), residues: 36 loop : -0.87 (0.29), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 94 TYR 0.037 0.001 TYR D 80 PHE 0.015 0.001 PHE K 38 TRP 0.001 0.000 TRP M 25 HIS 0.002 0.001 HIS D 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.16 (16317) covalent geometry : angle 0.63429 / 0.36 (23482) hydrogen bonds : bond 0.04989 / 3.34 ( 938) hydrogen bonds : angle 3.04213 / 2.18 ( 2360) metal coordination : bond 0.01599 / 0.69 ( 20) metal coordination : angle 4.42751 / 2.76 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 244 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.9040 (tp30) cc_final: 0.8795 (tp30) REVERT: A 106 ASP cc_start: 0.9123 (m-30) cc_final: 0.8743 (m-30) REVERT: B 88 TYR cc_start: 0.8978 (m-10) cc_final: 0.8655 (m-80) REVERT: D 90 GLU cc_start: 0.8841 (mp0) cc_final: 0.8587 (mp0) REVERT: E 59 GLU cc_start: 0.8810 (pm20) cc_final: 0.8609 (pm20) REVERT: E 76 GLN cc_start: 0.9139 (tp-100) cc_final: 0.8608 (tp-100) REVERT: G 17 ARG cc_start: 0.9139 (OUTLIER) cc_final: 0.8687 (mtt180) REVERT: H 87 THR cc_start: 0.9053 (OUTLIER) cc_final: 0.8571 (p) REVERT: H 98 LEU cc_start: 0.9415 (OUTLIER) cc_final: 0.9112 (mm) REVERT: K 61 HIS cc_start: 0.7783 (t-90) cc_final: 0.7506 (t-90) REVERT: K 74 THR cc_start: 0.7332 (p) cc_final: 0.7069 (t) REVERT: L 101 ARG cc_start: 0.8137 (tpp80) cc_final: 0.7890 (tpp80) REVERT: M 47 ARG cc_start: 0.8362 (mmm-85) cc_final: 0.8071 (mmm160) REVERT: M 61 LEU cc_start: 0.8588 (tp) cc_final: 0.8164 (pt) outliers start: 19 outliers final: 11 residues processed: 248 average time/residue: 0.1256 time to fit residues: 43.8731 Evaluate side-chains 250 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 236 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain G residue 17 ARG Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain K residue 69 ILE Chi-restraints excluded: chain L residue 36 LEU Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain M residue 27 CYS Chi-restraints excluded: chain N residue 5 VAL Chi-restraints excluded: chain N residue 70 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 15 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 57 optimal weight: 0.5980 chunk 39 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 chunk 52 optimal weight: 0.9990 chunk 138 optimal weight: 6.9990 chunk 107 optimal weight: 5.9990 chunk 85 optimal weight: 10.0000 chunk 11 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 76 GLN K 89 ASN ** L 69 HIS ** 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 = 0.3390 r_free = 0.3390 target = 0.055913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.035159 restraints weight = 79399.772| |-----------------------------------------------------------------------------| r_work (start): 0.2712 rms_B_bonded: 3.63 r_work: 0.2547 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.2547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8945 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 16337 Z= 0.146 Angle : 0.644 9.603 23506 Z= 0.365 Chirality : 0.042 0.219 2728 Planarity : 0.004 0.046 1851 Dihedral : 29.126 115.667 4782 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.33 % Allowed : 22.20 % Favored : 75.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 1.93 (0.25), residues: 1121 helix: 2.62 (0.20), residues: 660 sheet: 0.20 (0.93), residues: 36 loop : -0.87 (0.29), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 45 TYR 0.035 0.001 TYR D 80 PHE 0.011 0.001 PHE K 38 TRP 0.001 0.000 TRP M 25 HIS 0.004 0.001 HIS K 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.15 (16317) covalent geometry : angle 0.63039 / 0.36 (23482) hydrogen bonds : bond 0.04643 / 3.11 ( 938) hydrogen bonds : angle 2.94589 / 2.10 ( 2360) metal coordination : bond 0.00969 / 0.64 ( 20) metal coordination : angle 4.10433 / 2.65 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 248 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.9073 (tp30) cc_final: 0.8809 (tp30) REVERT: A 106 ASP cc_start: 0.9090 (m-30) cc_final: 0.8739 (m-30) REVERT: D 90 GLU cc_start: 0.8848 (mp0) cc_final: 0.8575 (mp0) REVERT: E 59 GLU cc_start: 0.8765 (pm20) cc_final: 0.8539 (pm20) REVERT: E 76 GLN cc_start: 0.9118 (tp-100) cc_final: 0.8593 (tp-100) REVERT: G 17 ARG cc_start: 0.9130 (OUTLIER) cc_final: 0.8686 (mtt180) REVERT: H 87 THR cc_start: 0.8952 (OUTLIER) cc_final: 0.8615 (p) REVERT: H 98 LEU cc_start: 0.9398 (OUTLIER) cc_final: 0.9108 (mm) REVERT: K 74 THR cc_start: 0.7331 (p) cc_final: 0.7107 (t) REVERT: L 101 ARG cc_start: 0.8239 (tpp80) cc_final: 0.7403 (mmt-90) REVERT: M 61 LEU cc_start: 0.8579 (tp) cc_final: 0.8167 (pt) outliers start: 21 outliers final: 13 residues processed: 255 average time/residue: 0.1262 time to fit residues: 45.4914 Evaluate side-chains 252 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 236 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain G residue 17 ARG Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain K residue 69 ILE Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain L residue 92 LYS Chi-restraints excluded: chain M residue 27 CYS Chi-restraints excluded: chain N residue 5 VAL Chi-restraints excluded: chain N residue 70 VAL Chi-restraints excluded: chain O residue 98 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 43 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 9 optimal weight: 9.9990 chunk 44 optimal weight: 0.5980 chunk 89 optimal weight: 10.0000 chunk 117 optimal weight: 10.0000 chunk 21 optimal weight: 0.8980 chunk 45 optimal weight: 0.7980 chunk 36 optimal weight: 4.9990 chunk 137 optimal weight: 10.0000 chunk 125 optimal weight: 10.0000 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 GLN C 94 ASN ** L 69 HIS ** 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 = 0.3390 r_free = 0.3390 target = 0.055842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.035099 restraints weight = 80280.637| |-----------------------------------------------------------------------------| r_work (start): 0.2710 rms_B_bonded: 3.65 r_work: 0.2546 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.2546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8947 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 16337 Z= 0.153 Angle : 0.658 16.961 23506 Z= 0.367 Chirality : 0.042 0.219 2728 Planarity : 0.004 0.044 1851 Dihedral : 29.115 113.507 4782 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.78 % Allowed : 22.53 % Favored : 75.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 1.80 (0.25), residues: 1121 helix: 2.46 (0.20), residues: 670 sheet: 0.53 (0.96), residues: 35 loop : -0.93 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 45 TYR 0.031 0.001 TYR D 80 PHE 0.008 0.001 PHE K 97 TRP 0.000 0.000 TRP L 17 HIS 0.006 0.001 HIS K 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.15 (16317) covalent geometry : angle 0.64451 / 0.37 (23482) hydrogen bonds : bond 0.04711 / 3.16 ( 938) hydrogen bonds : angle 3.01181 / 2.16 ( 2360) metal coordination : bond 0.01111 / 0.69 ( 20) metal coordination : angle 4.24631 / 2.85 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 242 time to evaluate : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 ASP cc_start: 0.9036 (m-30) cc_final: 0.8722 (m-30) REVERT: D 76 ARG cc_start: 0.8994 (ttm-80) cc_final: 0.8793 (ttm110) REVERT: D 90 GLU cc_start: 0.8847 (mp0) cc_final: 0.8561 (mp0) REVERT: E 59 GLU cc_start: 0.8737 (pm20) cc_final: 0.8503 (pm20) REVERT: E 76 GLN cc_start: 0.9111 (tp-100) cc_final: 0.8576 (tp-100) REVERT: G 17 ARG cc_start: 0.9123 (OUTLIER) cc_final: 0.8697 (mtm180) REVERT: H 98 LEU cc_start: 0.9404 (OUTLIER) cc_final: 0.9097 (mm) REVERT: K 46 TYR cc_start: 0.8777 (t80) cc_final: 0.8368 (t80) REVERT: K 59 GLN cc_start: 0.8846 (tt0) cc_final: 0.8457 (tp40) REVERT: K 74 THR cc_start: 0.7232 (p) cc_final: 0.6991 (t) REVERT: L 97 LYS cc_start: 0.8583 (mtmt) cc_final: 0.8324 (mtmt) REVERT: L 101 ARG cc_start: 0.8114 (tpp80) cc_final: 0.7260 (mmt-90) REVERT: M 61 LEU cc_start: 0.8645 (tp) cc_final: 0.8264 (pt) outliers start: 16 outliers final: 14 residues processed: 245 average time/residue: 0.1300 time to fit residues: 44.5932 Evaluate side-chains 254 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 238 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain G residue 17 ARG Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain K residue 40 LYS Chi-restraints excluded: chain K residue 69 ILE Chi-restraints excluded: chain L residue 36 LEU Chi-restraints excluded: chain L residue 56 ASP Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain L residue 92 LYS Chi-restraints excluded: chain M residue 27 CYS Chi-restraints excluded: chain M residue 29 VAL Chi-restraints excluded: chain N residue 5 VAL Chi-restraints excluded: chain N residue 70 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 130 optimal weight: 7.9990 chunk 79 optimal weight: 9.9990 chunk 134 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 45 optimal weight: 0.4980 chunk 13 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 89 optimal weight: 10.0000 chunk 38 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 GLN C 104 GLN ** L 69 HIS ** 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 = 0.3400 r_free = 0.3400 target = 0.056069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.035653 restraints weight = 79934.376| |-----------------------------------------------------------------------------| r_work (start): 0.2723 rms_B_bonded: 3.62 r_work: 0.2558 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.2558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8935 moved from start: 0.2995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 16337 Z= 0.148 Angle : 0.646 14.294 23506 Z= 0.363 Chirality : 0.041 0.221 2728 Planarity : 0.004 0.044 1851 Dihedral : 29.069 110.932 4782 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.89 % Allowed : 23.75 % Favored : 74.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 1121 helix: 2.50 (0.20), residues: 668 sheet: 0.49 (0.96), residues: 35 loop : -0.91 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 70 TYR 0.044 0.001 TYR B 88 PHE 0.010 0.001 PHE K 97 TRP 0.001 0.000 TRP L 17 HIS 0.002 0.000 HIS K 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.15 (16317) covalent geometry : angle 0.63473 / 0.36 (23482) hydrogen bonds : bond 0.04448 / 2.98 ( 938) hydrogen bonds : angle 2.95103 / 2.11 ( 2360) metal coordination : bond 0.01060 / 0.66 ( 20) metal coordination : angle 3.79924 / 2.51 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 241 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 ASP cc_start: 0.9002 (m-30) cc_final: 0.8699 (m-30) REVERT: A 108 ASN cc_start: 0.9567 (t0) cc_final: 0.9259 (t0) REVERT: D 81 ASN cc_start: 0.9066 (m-40) cc_final: 0.8837 (m-40) REVERT: D 90 GLU cc_start: 0.8854 (mp0) cc_final: 0.8541 (mp0) REVERT: E 59 GLU cc_start: 0.8692 (pm20) cc_final: 0.8459 (pm20) REVERT: E 76 GLN cc_start: 0.9090 (tp-100) cc_final: 0.8559 (tp-100) REVERT: G 17 ARG cc_start: 0.9132 (OUTLIER) cc_final: 0.8698 (mtm180) REVERT: H 98 LEU cc_start: 0.9381 (OUTLIER) cc_final: 0.9077 (mm) REVERT: K 27 ASP cc_start: 0.7803 (p0) cc_final: 0.7547 (p0) REVERT: K 46 TYR cc_start: 0.8983 (t80) cc_final: 0.8635 (t80) REVERT: K 74 THR cc_start: 0.7322 (p) cc_final: 0.7082 (t) REVERT: L 101 ARG cc_start: 0.8241 (tpp80) cc_final: 0.7433 (mmt-90) REVERT: M 61 LEU cc_start: 0.8699 (tp) cc_final: 0.8325 (pt) REVERT: N 72 ARG cc_start: 0.8340 (ptp90) cc_final: 0.7924 (ptp90) outliers start: 17 outliers final: 13 residues processed: 246 average time/residue: 0.1198 time to fit residues: 41.6100 Evaluate side-chains 250 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 235 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain G residue 17 ARG Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain K residue 69 ILE Chi-restraints excluded: chain L residue 36 LEU Chi-restraints excluded: chain L residue 56 ASP Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain L residue 92 LYS Chi-restraints excluded: chain M residue 27 CYS Chi-restraints excluded: chain N residue 5 VAL Chi-restraints excluded: chain N residue 70 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 104 optimal weight: 50.0000 chunk 51 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 141 optimal weight: 10.0000 chunk 123 optimal weight: 6.9990 chunk 93 optimal weight: 10.0000 chunk 121 optimal weight: 7.9990 chunk 71 optimal weight: 0.8980 chunk 98 optimal weight: 10.0000 chunk 94 optimal weight: 10.0000 overall best weight: 3.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 93 GLN ** L 69 HIS ** 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 = 0.3346 r_free = 0.3346 target = 0.054362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.033445 restraints weight = 80047.387| |-----------------------------------------------------------------------------| r_work (start): 0.2644 rms_B_bonded: 3.61 r_work: 0.2477 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.2477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9002 moved from start: 0.3156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 16337 Z= 0.282 Angle : 0.774 14.722 23506 Z= 0.411 Chirality : 0.047 0.216 2728 Planarity : 0.005 0.055 1851 Dihedral : 29.449 109.248 4782 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.55 % Allowed : 23.97 % Favored : 74.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 1.60 (0.25), residues: 1121 helix: 2.27 (0.20), residues: 668 sheet: 0.42 (0.96), residues: 36 loop : -0.95 (0.30), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG M 47 TYR 0.048 0.002 TYR B 88 PHE 0.012 0.002 PHE G 25 TRP 0.001 0.000 TRP M 25 HIS 0.005 0.001 HIS D 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00589 / 0.28 (16317) covalent geometry : angle 0.75836 / 0.41 (23482) hydrogen bonds : bond 0.06641 / 4.43 ( 938) hydrogen bonds : angle 3.41311 / 2.44 ( 2360) metal coordination : bond 0.01446 / 0.95 ( 20) metal coordination : angle 4.82877 / 3.32 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 231 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 106 ASP cc_start: 0.9117 (m-30) cc_final: 0.8823 (m-30) REVERT: D 90 GLU cc_start: 0.8910 (mp0) cc_final: 0.8552 (mp0) REVERT: E 59 GLU cc_start: 0.8909 (pm20) cc_final: 0.8652 (pm20) REVERT: E 76 GLN cc_start: 0.9162 (tp-100) cc_final: 0.8610 (tp-100) REVERT: G 17 ARG cc_start: 0.9209 (OUTLIER) cc_final: 0.8799 (mtt180) REVERT: K 46 TYR cc_start: 0.8980 (t80) cc_final: 0.8636 (t80) REVERT: K 59 GLN cc_start: 0.8963 (tt0) cc_final: 0.8560 (tp40) REVERT: K 74 THR cc_start: 0.7303 (p) cc_final: 0.7050 (t) REVERT: L 97 LYS cc_start: 0.8577 (mtmt) cc_final: 0.8360 (mtmt) REVERT: L 101 ARG cc_start: 0.8158 (tpp80) cc_final: 0.7947 (tpp80) REVERT: M 61 LEU cc_start: 0.8662 (tp) cc_final: 0.8253 (pt) outliers start: 14 outliers final: 12 residues processed: 234 average time/residue: 0.1208 time to fit residues: 39.3072 Evaluate side-chains 240 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 227 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain G residue 17 ARG Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain K residue 69 ILE Chi-restraints excluded: chain L residue 36 LEU Chi-restraints excluded: chain L residue 56 ASP Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain L residue 92 LYS Chi-restraints excluded: chain M residue 29 VAL Chi-restraints excluded: chain N residue 5 VAL Chi-restraints excluded: chain N residue 70 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 74 optimal weight: 9.9990 chunk 27 optimal weight: 0.7980 chunk 94 optimal weight: 10.0000 chunk 51 optimal weight: 0.5980 chunk 35 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 89 optimal weight: 10.0000 chunk 56 optimal weight: 0.7980 chunk 91 optimal weight: 10.0000 chunk 112 optimal weight: 6.9990 chunk 66 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.055381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.034949 restraints weight = 78759.495| |-----------------------------------------------------------------------------| r_work (start): 0.2700 rms_B_bonded: 3.51 r_work: 0.2537 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.2537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8958 moved from start: 0.3177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16337 Z= 0.148 Angle : 0.669 14.981 23506 Z= 0.371 Chirality : 0.042 0.218 2728 Planarity : 0.004 0.042 1851 Dihedral : 29.226 108.541 4782 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.66 % Allowed : 24.20 % Favored : 74.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.79 (0.26), residues: 1121 helix: 2.47 (0.20), residues: 666 sheet: 0.36 (0.96), residues: 36 loop : -0.92 (0.30), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG K 70 TYR 0.033 0.001 TYR B 88 PHE 0.012 0.001 PHE K 97 TRP 0.002 0.000 TRP M 25 HIS 0.002 0.001 HIS L 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.15 (16317) covalent geometry : angle 0.65538 / 0.37 (23482) hydrogen bonds : bond 0.04792 / 3.20 ( 938) hydrogen bonds : angle 3.05229 / 2.18 ( 2360) metal coordination : bond 0.00957 / 0.59 ( 20) metal coordination : angle 4.23948 / 2.90 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3902.82 seconds wall clock time: 67 minutes 9.53 seconds (4029.53 seconds total)