Starting phenix.real_space_refine on Fri Jul 3 16:23:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dde_46771/07_2026/9dde_46771.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dde_46771/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9dde_46771/07_2026/9dde_46771.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dde_46771/07_2026/9dde_46771.map" model { file = "/net/cci-nas-00/data/ceres_data/9dde_46771/07_2026/9dde_46771.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dde_46771/07_2026/9dde_46771.cif" } 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-dev-6108/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: 3.42, per 1000 atoms: 0.22 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: 1.16 Conformation dependent library (CDL) restraints added in 473.6 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: 2.14 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: 2.80 Time building geometry restraints manager: 1.55 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: 22456 1.91 - 3.81: 964 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: 3.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 17.900 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.530 ------------------------------------------------------------------------------- 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 : 0.786 9.537 23506 Z= 0.659 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 0.78227 / 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 : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 0.1609 time to fit residues: 67.8480 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 : 0.430 ------------------------------------------------------------------------------- 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: 10.0000 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 10.0000 chunk 55 optimal weight: 0.9980 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 = 0.3406 r_free = 0.3406 target = 0.056988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.036178 restraints weight = 78080.518| |-----------------------------------------------------------------------------| r_work (start): 0.2735 rms_B_bonded: 3.57 r_work: 0.2571 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.2571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8917 moved from start: 0.1499 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= 0.175 Angle : 0.641 9.089 23506 Z= 0.378 Chirality : 0.043 0.238 2728 Planarity : 0.005 0.055 1851 Dihedral : 28.862 128.561 4782 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.55 % Allowed : 18.53 % Favored : 79.91 % 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: 1.90 (0.25), residues: 1121 helix: 2.63 (0.20), residues: 664 sheet: -0.16 (0.87), residues: 35 loop : -0.94 (0.27), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 35 TYR 0.035 0.002 TYR D 80 PHE 0.021 0.002 PHE M 24 TRP 0.001 0.000 TRP L 17 HIS 0.003 0.001 HIS K 2 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.17 (16317) covalent geometry : angle 0.63411 / 0.38 (23482) hydrogen bonds : bond 0.05329 / 3.58 ( 938) hydrogen bonds : angle 3.09768 / 2.19 ( 2360) metal coordination : bond 0.01679 / 0.81 ( 20) metal coordination : angle 3.06728 / 1.73 ( 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 266 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 252 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 ASP cc_start: 0.9098 (m-30) cc_final: 0.8885 (m-30) REVERT: B 88 TYR cc_start: 0.8934 (m-10) cc_final: 0.8709 (m-80) REVERT: C 90 ASP cc_start: 0.9101 (t0) cc_final: 0.8693 (t0) REVERT: H 73 GLU cc_start: 0.9238 (tp30) cc_final: 0.9001 (mm-30) REVERT: K 45 ARG cc_start: 0.9718 (mmt90) cc_final: 0.9374 (mmm160) REVERT: K 74 THR cc_start: 0.7429 (p) cc_final: 0.7218 (t) REVERT: L 66 GLU cc_start: 0.6434 (tm-30) cc_final: 0.5982 (pp20) REVERT: M 61 LEU cc_start: 0.8129 (tp) cc_final: 0.7637 (pt) outliers start: 14 outliers final: 7 residues processed: 259 average time/residue: 0.1398 time to fit residues: 50.9806 Evaluate side-chains 246 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 239 time to evaluate : 0.525 ------------------------------------------------------------------------------- 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 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: 6.9990 chunk 92 optimal weight: 10.0000 chunk 3 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 119 optimal weight: 8.9990 chunk 111 optimal weight: 6.9990 chunk 113 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 98 optimal weight: 10.0000 chunk 31 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN D 106 HIS E 125 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 = 0.3358 r_free = 0.3358 target = 0.055061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.034194 restraints weight = 79742.679| |-----------------------------------------------------------------------------| r_work (start): 0.2658 rms_B_bonded: 3.62 r_work: 0.2490 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.2490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8985 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 16337 Z= 0.269 Angle : 0.705 8.397 23506 Z= 0.397 Chirality : 0.047 0.363 2728 Planarity : 0.005 0.047 1851 Dihedral : 29.381 122.599 4782 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.77 % Allowed : 18.42 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.69 (0.25), residues: 1121 helix: 2.45 (0.20), residues: 662 sheet: -0.00 (0.94), residues: 36 loop : -1.01 (0.27), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG M 33 TYR 0.033 0.002 TYR D 80 PHE 0.012 0.002 PHE E 78 TRP 0.004 0.000 TRP M 25 HIS 0.013 0.001 HIS L 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00550 / 0.27 (16317) covalent geometry : angle 0.69673 / 0.40 (23482) hydrogen bonds : bond 0.06507 / 4.35 ( 938) hydrogen bonds : angle 3.43345 / 2.44 ( 2360) metal coordination : bond 0.02424 / 1.19 ( 20) metal coordination : angle 3.45005 / 2.34 ( 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 261 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 236 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.9014 (tp30) cc_final: 0.8759 (tp30) REVERT: B 63 GLU cc_start: 0.8960 (mt-10) cc_final: 0.8737 (mt-10) REVERT: B 88 TYR cc_start: 0.9038 (m-10) cc_final: 0.8727 (m-80) REVERT: C 90 ASP cc_start: 0.8939 (t0) cc_final: 0.8607 (t0) REVERT: E 59 GLU cc_start: 0.8908 (pm20) cc_final: 0.8643 (pm20) REVERT: E 76 GLN cc_start: 0.9221 (tp-100) cc_final: 0.8713 (tp-100) REVERT: G 17 ARG cc_start: 0.9156 (OUTLIER) cc_final: 0.8772 (mtt180) REVERT: H 32 GLU cc_start: 0.9095 (mp0) cc_final: 0.8660 (mp0) REVERT: H 73 GLU cc_start: 0.9279 (tp30) cc_final: 0.9047 (tp30) REVERT: H 98 LEU cc_start: 0.9450 (OUTLIER) cc_final: 0.9147 (mm) REVERT: K 74 THR cc_start: 0.7468 (p) cc_final: 0.7248 (t) REVERT: L 53 ILE cc_start: 0.8270 (mm) cc_final: 0.8004 (mm) REVERT: L 97 LYS cc_start: 0.8808 (mtmt) cc_final: 0.8517 (mtmt) REVERT: L 103 ASP cc_start: 0.8136 (t0) cc_final: 0.7915 (t0) REVERT: M 61 LEU cc_start: 0.8441 (tp) cc_final: 0.7970 (pt) outliers start: 25 outliers final: 17 residues processed: 246 average time/residue: 0.1501 time to fit residues: 51.7940 Evaluate side-chains 245 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 226 time to evaluate : 0.413 ------------------------------------------------------------------------------- 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 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 65 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 7 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 9 optimal weight: 8.9990 chunk 3 optimal weight: 1.9990 chunk 99 optimal weight: 9.9990 chunk 49 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 chunk 70 optimal weight: 4.9990 chunk 80 optimal weight: 9.9990 chunk 96 optimal weight: 10.0000 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 HIS K 76 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.056014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.035068 restraints weight = 79583.360| |-----------------------------------------------------------------------------| r_work (start): 0.2703 rms_B_bonded: 3.60 r_work: 0.2537 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.2537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8948 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 16337 Z= 0.148 Angle : 0.619 8.301 23506 Z= 0.360 Chirality : 0.043 0.224 2728 Planarity : 0.004 0.046 1851 Dihedral : 29.252 120.144 4782 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.22 % Allowed : 19.98 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.90 (0.25), residues: 1121 helix: 2.59 (0.20), residues: 660 sheet: -0.28 (0.93), residues: 35 loop : -0.81 (0.28), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 76 TYR 0.032 0.001 TYR D 80 PHE 0.012 0.001 PHE K 38 TRP 0.001 0.000 TRP M 25 HIS 0.003 0.001 HIS N 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.15 (16317) covalent geometry : angle 0.61083 / 0.36 (23482) hydrogen bonds : bond 0.04901 / 3.29 ( 938) hydrogen bonds : angle 3.01577 / 2.15 ( 2360) metal coordination : bond 0.01583 / 0.60 ( 20) metal coordination : angle 3.27490 / 2.09 ( 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 269 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 249 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.9027 (tp30) cc_final: 0.8775 (tp30) REVERT: B 88 TYR cc_start: 0.8934 (m-10) cc_final: 0.8618 (m-80) REVERT: C 90 ASP cc_start: 0.8998 (t0) cc_final: 0.8788 (t0) REVERT: E 59 GLU cc_start: 0.8801 (pm20) cc_final: 0.8563 (pm20) REVERT: E 76 GLN cc_start: 0.9161 (tp-100) cc_final: 0.8641 (tp-100) REVERT: F 24 ASP cc_start: 0.7388 (t0) cc_final: 0.7137 (t70) REVERT: F 63 GLU cc_start: 0.8938 (tm-30) cc_final: 0.8702 (tm-30) REVERT: H 31 LYS cc_start: 0.9493 (mttt) cc_final: 0.9289 (mptt) REVERT: H 73 GLU cc_start: 0.9185 (tp30) cc_final: 0.8978 (mm-30) REVERT: H 98 LEU cc_start: 0.9412 (OUTLIER) cc_final: 0.9090 (mm) REVERT: K 33 GLU cc_start: 0.6700 (mp0) cc_final: 0.6458 (mp0) REVERT: K 61 HIS cc_start: 0.7723 (t-90) cc_final: 0.7418 (t-90) REVERT: K 74 THR cc_start: 0.7470 (p) cc_final: 0.7249 (t) REVERT: L 66 GLU cc_start: 0.6853 (tm-30) cc_final: 0.6555 (pp20) REVERT: L 97 LYS cc_start: 0.8708 (mtmt) cc_final: 0.8395 (mtmt) REVERT: M 61 LEU cc_start: 0.8528 (tp) cc_final: 0.8097 (pt) outliers start: 20 outliers final: 11 residues processed: 257 average time/residue: 0.1450 time to fit residues: 52.4725 Evaluate side-chains 250 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 238 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain K residue 12 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 L residue 95 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: 10.0000 chunk 110 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 20 optimal weight: 0.0870 chunk 92 optimal weight: 10.0000 chunk 15 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 97 optimal weight: 9.9990 overall best weight: 1.3964 ------------------------------------------------------------------------------- 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 = 0.055794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.034892 restraints weight = 79849.131| |-----------------------------------------------------------------------------| r_work (start): 0.2694 rms_B_bonded: 3.65 r_work: 0.2525 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.2525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8958 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 16337 Z= 0.168 Angle : 0.629 10.489 23506 Z= 0.359 Chirality : 0.042 0.224 2728 Planarity : 0.004 0.037 1851 Dihedral : 29.277 117.910 4782 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.55 % Allowed : 19.87 % Favored : 77.58 % 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: 1.94 (0.25), residues: 1121 helix: 2.64 (0.20), residues: 660 sheet: -0.22 (0.95), residues: 35 loop : -0.84 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG K 70 TYR 0.035 0.001 TYR D 80 PHE 0.009 0.001 PHE E 78 TRP 0.001 0.000 TRP L 17 HIS 0.002 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.17 (16317) covalent geometry : angle 0.61623 / 0.36 (23482) hydrogen bonds : bond 0.05081 / 3.41 ( 938) hydrogen bonds : angle 3.04374 / 2.17 ( 2360) metal coordination : bond 0.01561 / 0.66 ( 20) metal coordination : angle 4.00311 / 2.46 ( 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: 23 poor density : 242 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.9089 (tp30) cc_final: 0.8806 (tp30) REVERT: B 27 GLN cc_start: 0.8595 (pm20) cc_final: 0.8333 (pm20) REVERT: C 90 ASP cc_start: 0.9039 (t0) cc_final: 0.8764 (t0) REVERT: E 59 GLU cc_start: 0.8809 (pm20) cc_final: 0.8567 (pm20) REVERT: E 76 GLN cc_start: 0.9166 (tp-100) cc_final: 0.8638 (tp-100) REVERT: F 24 ASP cc_start: 0.7435 (t0) cc_final: 0.7211 (t70) REVERT: F 63 GLU cc_start: 0.8972 (tm-30) cc_final: 0.8719 (tm-30) REVERT: G 17 ARG cc_start: 0.9117 (OUTLIER) cc_final: 0.8760 (mtm180) REVERT: G 90 ASP cc_start: 0.8712 (t0) cc_final: 0.8280 (t70) REVERT: H 31 LYS cc_start: 0.9483 (mttt) cc_final: 0.9278 (mptt) REVERT: H 87 THR cc_start: 0.9075 (OUTLIER) cc_final: 0.8715 (p) REVERT: H 98 LEU cc_start: 0.9420 (OUTLIER) cc_final: 0.9136 (mm) REVERT: K 61 HIS cc_start: 0.7729 (t-90) cc_final: 0.7403 (t-90) REVERT: K 74 THR cc_start: 0.7401 (p) cc_final: 0.7165 (t) REVERT: L 97 LYS cc_start: 0.8640 (mtmt) cc_final: 0.8354 (mtmt) REVERT: M 61 LEU cc_start: 0.8570 (tp) cc_final: 0.8138 (pt) outliers start: 23 outliers final: 15 residues processed: 251 average time/residue: 0.1353 time to fit residues: 48.4215 Evaluate side-chains 257 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 239 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 112 ILE 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 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 12 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 M residue 27 CYS 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: 3.9990 chunk 9 optimal weight: 6.9990 chunk 108 optimal weight: 5.9990 chunk 86 optimal weight: 10.0000 chunk 45 optimal weight: 1.9990 chunk 78 optimal weight: 10.0000 chunk 42 optimal weight: 0.6980 chunk 118 optimal weight: 9.9990 chunk 50 optimal weight: 0.9990 chunk 97 optimal weight: 9.9990 chunk 126 optimal weight: 0.2980 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 46 HIS 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 = 0.3376 r_free = 0.3376 target = 0.055606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.034698 restraints weight = 79353.842| |-----------------------------------------------------------------------------| r_work (start): 0.2688 rms_B_bonded: 3.65 r_work: 0.2520 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.2520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8962 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16337 Z= 0.176 Angle : 0.633 8.927 23506 Z= 0.359 Chirality : 0.042 0.224 2728 Planarity : 0.004 0.041 1851 Dihedral : 29.311 116.463 4782 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.44 % Allowed : 20.64 % Favored : 76.91 % 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: 2.63 (0.20), residues: 660 sheet: -0.11 (0.95), residues: 35 loop : -0.86 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG L 101 TYR 0.042 0.002 TYR B 88 PHE 0.013 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 0.00339 / 0.18 (16317) covalent geometry : angle 0.62013 / 0.36 (23482) hydrogen bonds : bond 0.05058 / 3.38 ( 938) hydrogen bonds : angle 3.05103 / 2.17 ( 2360) metal coordination : bond 0.01291 / 0.64 ( 20) metal coordination : angle 4.04888 / 2.55 ( 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: 22 poor density : 241 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 27 GLN cc_start: 0.8673 (pm20) cc_final: 0.8442 (pm20) REVERT: B 63 GLU cc_start: 0.8937 (mt-10) cc_final: 0.8736 (mt-10) REVERT: B 88 TYR cc_start: 0.9025 (m-80) cc_final: 0.8608 (m-80) REVERT: C 90 ASP cc_start: 0.9054 (t0) cc_final: 0.8689 (t0) REVERT: E 59 GLU cc_start: 0.8819 (pm20) cc_final: 0.8580 (pm20) REVERT: E 76 GLN cc_start: 0.9129 (tp-100) cc_final: 0.8596 (tp-100) REVERT: F 63 GLU cc_start: 0.8970 (tm-30) cc_final: 0.8729 (tm-30) REVERT: G 17 ARG cc_start: 0.9141 (OUTLIER) cc_final: 0.8798 (mtm180) REVERT: H 31 LYS cc_start: 0.9467 (mttt) cc_final: 0.9251 (mptt) REVERT: H 87 THR cc_start: 0.9088 (OUTLIER) cc_final: 0.8634 (p) REVERT: H 90 GLU cc_start: 0.9140 (mp0) cc_final: 0.8925 (mp0) REVERT: H 98 LEU cc_start: 0.9419 (OUTLIER) cc_final: 0.9131 (mm) REVERT: K 27 ASP cc_start: 0.7869 (p0) cc_final: 0.7617 (p0) REVERT: K 74 THR cc_start: 0.7444 (p) cc_final: 0.7216 (t) REVERT: L 101 ARG cc_start: 0.7963 (tpp80) cc_final: 0.7173 (mmt-90) REVERT: L 103 ASP cc_start: 0.8105 (t0) cc_final: 0.7877 (t0) REVERT: M 47 ARG cc_start: 0.8335 (mmm-85) cc_final: 0.8102 (mmm160) REVERT: M 61 LEU cc_start: 0.8573 (tp) cc_final: 0.8144 (pt) outliers start: 22 outliers final: 17 residues processed: 249 average time/residue: 0.1401 time to fit residues: 48.8303 Evaluate side-chains 256 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 236 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 81 ASP 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 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 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 12 LEU Chi-restraints excluded: chain K residue 69 ILE Chi-restraints excluded: chain L residue 36 LEU Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain M residue 27 CYS Chi-restraints excluded: chain M residue 29 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: 3.9990 chunk 64 optimal weight: 0.8980 chunk 57 optimal weight: 0.6980 chunk 39 optimal weight: 3.9990 chunk 6 optimal weight: 0.5980 chunk 52 optimal weight: 0.9980 chunk 138 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 85 optimal weight: 10.0000 chunk 11 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3391 r_free = 0.3391 target = 0.055984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.035050 restraints weight = 79740.544| |-----------------------------------------------------------------------------| r_work (start): 0.2711 rms_B_bonded: 3.67 r_work: 0.2542 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.2542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8947 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16337 Z= 0.145 Angle : 0.620 9.522 23506 Z= 0.354 Chirality : 0.041 0.218 2728 Planarity : 0.004 0.036 1851 Dihedral : 29.206 114.597 4782 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.44 % Allowed : 21.53 % Favored : 76.03 % 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: 1121 helix: 2.59 (0.20), residues: 660 sheet: 0.03 (0.97), residues: 35 loop : -0.87 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 70 TYR 0.031 0.001 TYR D 80 PHE 0.011 0.001 PHE K 38 TRP 0.002 0.000 TRP L 17 HIS 0.002 0.001 HIS D 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.15 (16317) covalent geometry : angle 0.60500 / 0.35 (23482) hydrogen bonds : bond 0.04632 / 3.11 ( 938) hydrogen bonds : angle 2.97661 / 2.12 ( 2360) metal coordination : bond 0.00958 / 0.54 ( 20) metal coordination : angle 4.29607 / 2.76 ( 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: 22 poor density : 247 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 GLU cc_start: 0.8736 (mp0) cc_final: 0.8491 (mp0) REVERT: B 27 GLN cc_start: 0.8701 (pm20) cc_final: 0.8441 (pm20) REVERT: C 90 ASP cc_start: 0.8961 (t0) cc_final: 0.8624 (t0) REVERT: E 59 GLU cc_start: 0.8775 (pm20) cc_final: 0.8529 (pm20) REVERT: E 76 GLN cc_start: 0.9102 (tp-100) cc_final: 0.8567 (tp-100) REVERT: F 63 GLU cc_start: 0.8917 (tm-30) cc_final: 0.8667 (tm-30) REVERT: G 17 ARG cc_start: 0.9109 (OUTLIER) cc_final: 0.8713 (mtm180) REVERT: H 31 LYS cc_start: 0.9470 (mttt) cc_final: 0.9241 (mptt) REVERT: H 87 THR cc_start: 0.9029 (OUTLIER) cc_final: 0.8545 (p) REVERT: H 98 LEU cc_start: 0.9396 (OUTLIER) cc_final: 0.9104 (mm) REVERT: K 74 THR cc_start: 0.7320 (p) cc_final: 0.7071 (t) REVERT: M 61 LEU cc_start: 0.8579 (tp) cc_final: 0.8165 (pt) outliers start: 22 outliers final: 16 residues processed: 254 average time/residue: 0.1498 time to fit residues: 53.5099 Evaluate side-chains 259 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 240 time to evaluate : 0.444 ------------------------------------------------------------------------------- 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 87 THR Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain G residue 17 ARG 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 12 LEU Chi-restraints excluded: chain K residue 69 ILE Chi-restraints excluded: chain K residue 71 SER 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 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: 1.9990 chunk 9 optimal weight: 7.9990 chunk 44 optimal weight: 0.8980 chunk 89 optimal weight: 10.0000 chunk 117 optimal weight: 7.9990 chunk 21 optimal weight: 0.9990 chunk 45 optimal weight: 0.1980 chunk 36 optimal weight: 4.9990 chunk 137 optimal weight: 8.9990 chunk 125 optimal weight: 8.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- 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 = 0.3387 r_free = 0.3387 target = 0.055803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.035049 restraints weight = 80326.952| |-----------------------------------------------------------------------------| r_work (start): 0.2701 rms_B_bonded: 3.62 r_work: 0.2535 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.2535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8947 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16337 Z= 0.160 Angle : 0.644 16.321 23506 Z= 0.361 Chirality : 0.042 0.213 2728 Planarity : 0.004 0.038 1851 Dihedral : 29.206 112.565 4782 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.11 % Allowed : 22.97 % Favored : 74.92 % 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: 1.77 (0.25), residues: 1121 helix: 2.45 (0.20), residues: 668 sheet: 0.05 (0.99), residues: 35 loop : -0.93 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 70 TYR 0.057 0.002 TYR B 88 PHE 0.009 0.001 PHE K 97 TRP 0.001 0.000 TRP L 17 HIS 0.006 0.001 HIS K 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.16 (16317) covalent geometry : angle 0.62836 / 0.36 (23482) hydrogen bonds : bond 0.04792 / 3.21 ( 938) hydrogen bonds : angle 3.02678 / 2.17 ( 2360) metal coordination : bond 0.00799 / 0.56 ( 20) metal coordination : angle 4.41088 / 2.95 ( 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 255 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 236 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 27 GLN cc_start: 0.8679 (pm20) cc_final: 0.8467 (pm20) REVERT: C 90 ASP cc_start: 0.8981 (t0) cc_final: 0.8655 (t0) REVERT: E 59 GLU cc_start: 0.8770 (pm20) cc_final: 0.8519 (pm20) REVERT: E 76 GLN cc_start: 0.9100 (tp-100) cc_final: 0.8564 (tp-100) REVERT: G 17 ARG cc_start: 0.9143 (OUTLIER) cc_final: 0.8753 (mtm180) REVERT: H 31 LYS cc_start: 0.9461 (mttt) cc_final: 0.9228 (mptt) REVERT: H 87 THR cc_start: 0.8994 (OUTLIER) cc_final: 0.8626 (p) REVERT: K 59 GLN cc_start: 0.8974 (tt0) cc_final: 0.8354 (tp40) REVERT: K 74 THR cc_start: 0.7372 (p) cc_final: 0.7115 (t) REVERT: L 101 ARG cc_start: 0.8049 (tpp80) cc_final: 0.7289 (mmt-90) REVERT: M 61 LEU cc_start: 0.8643 (tp) cc_final: 0.8263 (pt) outliers start: 19 outliers final: 14 residues processed: 244 average time/residue: 0.1507 time to fit residues: 51.5355 Evaluate side-chains 251 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 235 time to evaluate : 0.433 ------------------------------------------------------------------------------- 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 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 12 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 130 optimal weight: 8.9990 chunk 79 optimal weight: 10.0000 chunk 134 optimal weight: 8.9990 chunk 30 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 7 optimal weight: 0.2980 chunk 10 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 chunk 89 optimal weight: 10.0000 chunk 38 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 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 = 0.3398 r_free = 0.3398 target = 0.056013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.035645 restraints weight = 80352.415| |-----------------------------------------------------------------------------| r_work (start): 0.2728 rms_B_bonded: 3.67 r_work: 0.2565 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.2565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8938 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16337 Z= 0.143 Angle : 0.637 13.698 23506 Z= 0.359 Chirality : 0.041 0.211 2728 Planarity : 0.004 0.036 1851 Dihedral : 29.134 110.206 4782 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.89 % Allowed : 22.75 % Favored : 75.36 % 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: 1.81 (0.25), residues: 1121 helix: 2.52 (0.20), residues: 660 sheet: 0.13 (0.99), residues: 35 loop : -0.90 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 76 TYR 0.038 0.001 TYR B 88 PHE 0.011 0.001 PHE K 97 TRP 0.001 0.000 TRP L 17 HIS 0.003 0.000 HIS K 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.14 (16317) covalent geometry : angle 0.62117 / 0.36 (23482) hydrogen bonds : bond 0.04419 / 2.97 ( 938) hydrogen bonds : angle 2.97061 / 2.12 ( 2360) metal coordination : bond 0.00613 / 0.44 ( 20) metal coordination : angle 4.50496 / 2.93 ( 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 262 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 245 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 GLU cc_start: 0.8740 (mp0) cc_final: 0.8431 (mp0) REVERT: C 90 ASP cc_start: 0.8891 (t0) cc_final: 0.8561 (t0) REVERT: D 81 ASN cc_start: 0.9019 (m-40) cc_final: 0.8795 (m-40) REVERT: E 59 GLU cc_start: 0.8744 (pm20) cc_final: 0.8499 (pm20) REVERT: E 76 GLN cc_start: 0.9072 (tp-100) cc_final: 0.8538 (tp-100) REVERT: H 31 LYS cc_start: 0.9449 (mttt) cc_final: 0.9244 (mptt) REVERT: H 87 THR cc_start: 0.8913 (OUTLIER) cc_final: 0.8575 (p) REVERT: H 98 LEU cc_start: 0.9385 (OUTLIER) cc_final: 0.9089 (mm) REVERT: K 46 TYR cc_start: 0.8989 (t80) cc_final: 0.8779 (t80) REVERT: K 74 THR cc_start: 0.7332 (p) cc_final: 0.7114 (t) REVERT: M 61 LEU cc_start: 0.8701 (tp) cc_final: 0.8323 (pt) outliers start: 17 outliers final: 15 residues processed: 250 average time/residue: 0.1471 time to fit residues: 51.8398 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 : 0.429 ------------------------------------------------------------------------------- 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 36 ILE Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 99 LEU 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 12 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 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 104 optimal weight: 50.0000 chunk 51 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 141 optimal weight: 8.9990 chunk 123 optimal weight: 6.9990 chunk 93 optimal weight: 9.9990 chunk 121 optimal weight: 8.9990 chunk 71 optimal weight: 0.6980 chunk 98 optimal weight: 10.0000 chunk 94 optimal weight: 10.0000 overall best weight: 3.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 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 = 0.3352 r_free = 0.3352 target = 0.054583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.034043 restraints weight = 80060.010| |-----------------------------------------------------------------------------| r_work (start): 0.2655 rms_B_bonded: 3.61 r_work: 0.2488 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.2488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8989 moved from start: 0.3104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 16337 Z= 0.286 Angle : 0.736 14.600 23506 Z= 0.399 Chirality : 0.045 0.205 2728 Planarity : 0.005 0.040 1851 Dihedral : 29.432 108.734 4782 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.66 % Allowed : 24.08 % Favored : 74.25 % 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: 1.72 (0.26), residues: 1121 helix: 2.40 (0.20), residues: 663 sheet: 0.09 (0.98), residues: 36 loop : -0.88 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 76 TYR 0.058 0.002 TYR D 80 PHE 0.013 0.002 PHE K 97 TRP 0.001 0.000 TRP L 17 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00598 / 0.29 (16317) covalent geometry : angle 0.72246 / 0.40 (23482) hydrogen bonds : bond 0.06150 / 4.11 ( 938) hydrogen bonds : angle 3.34761 / 2.39 ( 2360) metal coordination : bond 0.01250 / 0.88 ( 20) metal coordination : angle 4.52367 / 3.08 ( 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 241 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 226 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 90 ASP cc_start: 0.9005 (t0) cc_final: 0.8725 (t0) REVERT: E 59 GLU cc_start: 0.8905 (pm20) cc_final: 0.8669 (pm20) REVERT: E 76 GLN cc_start: 0.9150 (tp-100) cc_final: 0.8588 (tp-100) REVERT: G 17 ARG cc_start: 0.9195 (OUTLIER) cc_final: 0.8885 (mtm180) REVERT: H 31 LYS cc_start: 0.9461 (mttt) cc_final: 0.9234 (mptt) REVERT: H 87 THR cc_start: 0.9043 (OUTLIER) cc_final: 0.8767 (p) REVERT: K 74 THR cc_start: 0.7414 (p) cc_final: 0.7129 (t) REVERT: L 101 ARG cc_start: 0.8012 (tpp80) cc_final: 0.7221 (mmt-90) REVERT: M 61 LEU cc_start: 0.8687 (tp) cc_final: 0.8289 (pt) REVERT: N 72 ARG cc_start: 0.8133 (ptp90) cc_final: 0.7618 (ptp90) outliers start: 15 outliers final: 13 residues processed: 232 average time/residue: 0.1544 time to fit residues: 49.9996 Evaluate side-chains 238 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 223 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 36 ILE 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 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 12 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 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: 10.0000 chunk 27 optimal weight: 0.9980 chunk 94 optimal weight: 10.0000 chunk 51 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 chunk 89 optimal weight: 10.0000 chunk 56 optimal weight: 0.8980 chunk 91 optimal weight: 10.0000 chunk 112 optimal weight: 8.9990 chunk 66 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.055464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.035004 restraints weight = 79567.998| |-----------------------------------------------------------------------------| r_work (start): 0.2702 rms_B_bonded: 3.61 r_work: 0.2538 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.2538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8956 moved from start: 0.3147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16337 Z= 0.148 Angle : 0.655 14.963 23506 Z= 0.366 Chirality : 0.042 0.209 2728 Planarity : 0.004 0.038 1851 Dihedral : 29.276 107.932 4782 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.89 % Allowed : 24.08 % Favored : 74.03 % 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: 1.80 (0.26), residues: 1121 helix: 2.47 (0.20), residues: 661 sheet: -0.05 (0.95), residues: 36 loop : -0.80 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG K 70 TYR 0.056 0.001 TYR B 88 PHE 0.014 0.001 PHE K 97 TRP 0.002 0.000 TRP M 25 HIS 0.004 0.001 HIS D 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.15 (16317) covalent geometry : angle 0.64132 / 0.36 (23482) hydrogen bonds : bond 0.04775 / 3.20 ( 938) hydrogen bonds : angle 3.05556 / 2.18 ( 2360) metal coordination : bond 0.00855 / 0.49 ( 20) metal coordination : angle 4.27964 / 2.85 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4355.30 seconds wall clock time: 75 minutes 5.95 seconds (4505.95 seconds total)