Starting phenix.real_space_refine on Fri Jul 3 08:04:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dgg_46823/07_2026/9dgg_46823.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dgg_46823/07_2026/9dgg_46823.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9dgg_46823/07_2026/9dgg_46823.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dgg_46823/07_2026/9dgg_46823.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9dgg_46823/07_2026/9dgg_46823.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dgg_46823/07_2026/9dgg_46823.map" } resolution = 2.98 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= 0.009 sd= 0.052 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 4 6.06 5 P 286 5.49 5 S 30 5.16 5 C 7498 2.51 5 N 2473 2.21 5 O 3048 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 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: 13339 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 796 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 93} 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: "B" Number of atoms: 650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 650 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 80} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 811 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "D" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 718 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "E" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 779 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 91} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 647 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 81} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "G" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 815 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: "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: 2948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2948 Classifications: {'DNA': 143} Link IDs: {'rna3p': 142} Chain: "J" Number of atoms: 2915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2915 Classifications: {'DNA': 143} Link IDs: {'rna3p': 142} Chain: "K" Number of atoms: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 773 Classifications: {'peptide': 101} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 5, 'TRANS': 95} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 49 Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 3, 'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "L" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 757 Classifications: {'peptide': 101} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 7, 'TRANS': 93} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 21 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 11922 SG CYS K 18 25.021 51.829 54.507 1.00135.22 S ATOM 11943 SG CYS K 21 21.745 50.037 54.263 1.00124.42 S ATOM 12081 SG CYS K 39 23.963 49.309 57.216 1.00130.53 S ATOM 12103 SG CYS K 42 24.962 48.085 53.730 1.00120.87 S ATOM 12040 SG CYS K 34 36.111 58.907 54.236 1.00114.18 S ATOM 12184 SG CYS K 53 33.577 58.092 51.442 1.00122.85 S ATOM 12205 SG CYS K 56 34.973 61.605 51.773 1.00126.03 S ATOM 12839 SG CYS L 51 36.841 63.352 77.033 1.00131.51 S ATOM 12860 SG CYS L 54 35.221 66.064 79.034 1.00126.05 S ATOM 13004 SG CYS L 72 35.238 66.138 75.239 1.00129.09 S ATOM 13023 SG CYS L 75 38.438 66.933 77.192 1.00119.18 S ATOM 12958 SG CYS L 67 41.328 54.065 69.566 1.00118.73 S ATOM 13112 SG CYS L 87 42.526 55.196 73.032 1.00136.41 S ATOM 13132 SG CYS L 90 42.913 51.478 71.966 1.00125.62 S Time building chain proxies: 2.94, per 1000 atoms: 0.22 Number of scatterers: 13339 At special positions: 0 Unit cell: (110.696, 116.176, 124.944, 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 4 29.99 S 30 16.00 P 286 15.00 O 3048 8.00 N 2473 7.00 C 7498 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: 1.04 Conformation dependent library (CDL) restraints added in 449.7 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 56 " pdb="ZN ZN K 402 " - pdb=" SG CYS K 53 " pdb="ZN ZN K 402 " - pdb=" SG CYS K 34 " pdb=" ZN L 401 " pdb="ZN ZN L 401 " - pdb=" SG CYS L 72 " 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 75 " pdb=" ZN L 402 " pdb="ZN ZN L 402 " - pdb=" ND1 HIS L 69 " pdb="ZN ZN L 402 " - pdb=" SG CYS L 67 " pdb="ZN ZN L 402 " - pdb=" SG CYS L 87 " pdb="ZN ZN L 402 " - pdb=" SG CYS L 90 " Number of angles added : 18 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1814 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 13 sheets defined 66.1% alpha, 4.3% beta 141 base pairs and 254 stacking pairs defined. Time for finding SS restraints: 1.98 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 Processing helix chain 'B' and resid 82 through 93 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 Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 101 through 120 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.529A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 72 removed outlier: 4.487A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (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 12 through 17 Processing helix chain 'K' and resid 40 through 48 removed outlier: 3.769A pdb=" N GLU K 48 " --> pdb=" O VAL K 44 " (cutoff:3.500A) Processing helix chain 'K' and resid 64 through 67 Processing helix chain 'K' and resid 72 through 83 Processing helix chain 'K' and resid 85 through 99 Processing helix chain 'L' and resid 21 through 25 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 sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.859A 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: 7.374A 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: 6.878A 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: 6.664A 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: 7.548A 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 72 473 hydrogen bonds defined for protein. 1377 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 362 hydrogen bonds 720 hydrogen bond angles 0 basepair planarities 141 basepair parallelities 254 stacking parallelities Total time for adding SS restraints: 2.20 Time building geometry restraints manager: 1.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3279 1.34 - 1.46: 4148 1.46 - 1.58: 6115 1.58 - 1.70: 570 1.70 - 1.82: 44 Bond restraints: 14156 Sorted by residual: bond pdb=" C3' DC I 128 " pdb=" C2' DC I 128 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.17e+01 bond pdb=" C3' DC J 94 " pdb=" C2' DC J 94 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.09e+01 bond pdb=" C3' DG J 54 " pdb=" C2' DG J 54 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.01e+01 bond pdb=" C3' DG I 115 " pdb=" C2' DG I 115 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.84e+00 bond pdb=" C3' DC J 164 " pdb=" C2' DC J 164 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.38e+00 ... (remaining 14151 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 19243 1.66 - 3.31: 1070 3.31 - 4.97: 51 4.97 - 6.63: 10 6.63 - 8.28: 5 Bond angle restraints: 20379 Sorted by residual: angle pdb=" N ASN G 73 " pdb=" CA ASN G 73 " pdb=" C ASN G 73 " ideal model delta sigma weight residual 114.39 107.00 7.39 1.45e+00 4.76e-01 2.60e+01 angle pdb=" O4' DG J 120 " pdb=" C4' DG J 120 " pdb=" C3' DG J 120 " ideal model delta sigma weight residual 106.00 103.27 2.73 6.00e-01 2.78e+00 2.07e+01 angle pdb=" N3 DT J 55 " pdb=" C4 DT J 55 " pdb=" O4 DT J 55 " ideal model delta sigma weight residual 119.90 122.51 -2.61 6.00e-01 2.78e+00 1.90e+01 angle pdb=" N3 DT J 162 " pdb=" C4 DT J 162 " pdb=" O4 DT J 162 " ideal model delta sigma weight residual 119.90 122.51 -2.61 6.00e-01 2.78e+00 1.89e+01 angle pdb=" N3 DT I 103 " pdb=" C4 DT I 103 " pdb=" O4 DT I 103 " ideal model delta sigma weight residual 119.90 122.50 -2.60 6.00e-01 2.78e+00 1.88e+01 ... (remaining 20374 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.97: 5863 26.97 - 53.94: 1631 53.94 - 80.91: 286 80.91 - 107.89: 2 107.89 - 134.86: 2 Dihedral angle restraints: 7784 sinusoidal: 4984 harmonic: 2800 Sorted by residual: 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 85.14 134.86 1 3.50e+01 8.16e-04 1.34e+01 dihedral pdb=" C4' DC I 36 " pdb=" C3' DC I 36 " pdb=" O3' DC I 36 " pdb=" P DT I 37 " ideal model delta sinusoidal sigma weight residual 220.00 87.44 132.56 1 3.50e+01 8.16e-04 1.31e+01 dihedral pdb=" CG ARG B 95 " pdb=" CD ARG B 95 " pdb=" NE ARG B 95 " pdb=" CZ ARG B 95 " ideal model delta sinusoidal sigma weight residual -90.00 -42.02 -47.98 2 1.50e+01 4.44e-03 1.18e+01 ... (remaining 7781 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.109: 2304 0.109 - 0.218: 43 0.218 - 0.327: 1 0.327 - 0.436: 0 0.436 - 0.545: 2 Chirality restraints: 2350 Sorted by residual: chirality pdb=" P DG J 152 " pdb=" OP1 DG J 152 " pdb=" OP2 DG J 152 " pdb=" O5' DG J 152 " both_signs ideal model delta sigma weight residual True 2.34 -2.88 -0.55 2.00e-01 2.50e+01 7.43e+00 chirality pdb=" P DC I 36 " pdb=" OP1 DC I 36 " pdb=" OP2 DC I 36 " pdb=" O5' DC I 36 " both_signs ideal model delta sigma weight residual True 2.34 -2.86 -0.52 2.00e-01 2.50e+01 6.87e+00 chirality pdb=" CA ILE B 29 " pdb=" N ILE B 29 " pdb=" C ILE B 29 " pdb=" CB ILE B 29 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.40e+00 ... (remaining 2347 not shown) Planarity restraints: 1587 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU D 99 " 0.035 5.00e-02 4.00e+02 5.27e-02 4.44e+00 pdb=" N PRO D 100 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO D 100 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO D 100 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR L 22 " -0.011 2.00e-02 2.50e+03 1.41e-02 3.96e+00 pdb=" CG TYR L 22 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR L 22 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR L 22 " -0.011 2.00e-02 2.50e+03 pdb=" CE1 TYR L 22 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR L 22 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR L 22 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR L 22 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU H 99 " -0.030 5.00e-02 4.00e+02 4.50e-02 3.24e+00 pdb=" N PRO H 100 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO H 100 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO H 100 " -0.025 5.00e-02 4.00e+02 ... (remaining 1584 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2206 2.77 - 3.31: 12147 3.31 - 3.84: 26790 3.84 - 4.37: 30203 4.37 - 4.90: 44284 Nonbonded interactions: 115630 Sorted by model distance: nonbonded pdb=" OD1 ASP L 103 " pdb=" N PHE L 106 " model vdw 2.243 3.120 nonbonded pdb=" OG SER A 57 " pdb=" OE1 GLU A 59 " model vdw 2.262 3.040 nonbonded pdb=" OH TYR A 99 " pdb=" OE1 GLU A 133 " model vdw 2.279 3.040 nonbonded pdb=" OH TYR E 99 " pdb=" OE1 GLU E 133 " model vdw 2.300 3.040 nonbonded pdb=" NH2 ARG K 93 " pdb=" OG1 THR L 27 " model vdw 2.302 3.120 ... (remaining 115625 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 20 through 21 and (name N or name CA or name C or name O \ or name CB )) or resid 22 or (resid 23 through 24 and (name N or name CA or name \ C or name O or name CB )) or resid 25 through 101)) selection = (chain 'F' and resid 20 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: 1.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 15.430 Find NCS groups from input model: 0.140 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:6.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 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 0.040 14172 Z= 0.501 Angle : 0.772 8.282 20397 Z= 0.652 Chirality : 0.048 0.545 2350 Planarity : 0.005 0.060 1587 Dihedral : 27.077 134.857 5970 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.26 % Allowed : 17.67 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.29 (0.27), residues: 939 helix: 2.30 (0.20), residues: 617 sheet: None (None), residues: 0 loop : -0.01 (0.33), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 95 TYR 0.034 0.002 TYR L 22 PHE 0.022 0.002 PHE K 87 TRP 0.004 0.001 TRP L 17 HIS 0.005 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00563 / 0.50 (14156) covalent geometry : angle 0.76987 / 0.65 (20379) hydrogen bonds : bond 0.06112 / 4.22 ( 835) hydrogen bonds : angle 2.98110 / 2.15 ( 2097) metal coordination : bond 0.00733 / 0.53 ( 16) metal coordination : angle 2.14623 / 1.30 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 310 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 24 GLN cc_start: 0.9253 (mm-40) cc_final: 0.9038 (mm110) REVERT: C 104 GLN cc_start: 0.8957 (mm110) cc_final: 0.8754 (mm110) REVERT: D 39 TYR cc_start: 0.8605 (t80) cc_final: 0.8307 (t80) REVERT: D 42 LEU cc_start: 0.9575 (tp) cc_final: 0.9338 (tp) REVERT: D 112 THR cc_start: 0.9565 (m) cc_final: 0.9360 (p) REVERT: E 58 THR cc_start: 0.9595 (p) cc_final: 0.9306 (t) REVERT: F 88 TYR cc_start: 0.9249 (m-10) cc_final: 0.9017 (m-80) REVERT: G 62 ILE cc_start: 0.9698 (mm) cc_final: 0.9452 (tt) REVERT: G 90 ASP cc_start: 0.8474 (t70) cc_final: 0.8077 (t0) REVERT: H 80 TYR cc_start: 0.9196 (m-10) cc_final: 0.8521 (m-10) REVERT: H 102 GLU cc_start: 0.8715 (mm-30) cc_final: 0.8306 (mm-30) REVERT: K 10 THR cc_start: 0.8704 (p) cc_final: 0.8501 (m) REVERT: K 74 THR cc_start: 0.9531 (m) cc_final: 0.8959 (p) REVERT: L 65 LYS cc_start: 0.8894 (mttt) cc_final: 0.7712 (mttm) REVERT: L 86 GLU cc_start: 0.8809 (pt0) cc_final: 0.8606 (pp20) REVERT: L 101 ARG cc_start: 0.8138 (mmt-90) cc_final: 0.7875 (mmt-90) REVERT: L 107 ASP cc_start: 0.9149 (m-30) cc_final: 0.8723 (m-30) outliers start: 2 outliers final: 0 residues processed: 310 average time/residue: 0.6026 time to fit residues: 202.4752 Evaluate side-chains 237 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 237 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 20.0000 chunk 113 optimal weight: 4.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 117 optimal weight: 5.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN F 93 GLN G 73 ASN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 76 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.051944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.037346 restraints weight = 61406.788| |-----------------------------------------------------------------------------| r_work (start): 0.2745 rms_B_bonded: 2.22 r_work: 0.2584 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8872 moved from start: 0.1501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14172 Z= 0.164 Angle : 0.633 8.246 20397 Z= 0.373 Chirality : 0.043 0.249 2350 Planarity : 0.005 0.041 1587 Dihedral : 29.722 130.862 4181 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 3.97 % Allowed : 26.12 % Favored : 69.91 % 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: 2.29 (0.27), residues: 939 helix: 2.38 (0.21), residues: 613 sheet: None (None), residues: 0 loop : -0.16 (0.32), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 70 TYR 0.011 0.001 TYR K 24 PHE 0.009 0.001 PHE L 71 TRP 0.004 0.002 TRP L 17 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.16 (14156) covalent geometry : angle 0.62993 / 0.37 (20379) hydrogen bonds : bond 0.04438 / 2.99 ( 835) hydrogen bonds : angle 2.96336 / 2.15 ( 2097) metal coordination : bond 0.01502 / 0.96 ( 16) metal coordination : angle 2.08855 / 1.18 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 249 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.9252 (tt0) cc_final: 0.9025 (tt0) REVERT: A 76 GLN cc_start: 0.9051 (mm-40) cc_final: 0.8789 (pt0) REVERT: C 39 TYR cc_start: 0.9384 (m-80) cc_final: 0.9183 (m-80) REVERT: C 72 ASP cc_start: 0.9402 (t0) cc_final: 0.9181 (m-30) REVERT: C 76 THR cc_start: 0.9441 (p) cc_final: 0.9215 (t) REVERT: C 104 GLN cc_start: 0.8967 (mm110) cc_final: 0.8610 (mm110) REVERT: D 39 TYR cc_start: 0.8698 (t80) cc_final: 0.8424 (t80) REVERT: D 42 LEU cc_start: 0.9361 (tp) cc_final: 0.9112 (tp) REVERT: D 65 ASP cc_start: 0.9160 (t0) cc_final: 0.8917 (t0) REVERT: D 102 GLU cc_start: 0.9150 (tp30) cc_final: 0.8778 (tp30) REVERT: D 112 THR cc_start: 0.9632 (m) cc_final: 0.9359 (p) REVERT: E 58 THR cc_start: 0.9476 (p) cc_final: 0.9236 (t) REVERT: E 59 GLU cc_start: 0.8507 (pm20) cc_final: 0.8271 (pm20) REVERT: E 94 GLU cc_start: 0.9048 (mm-30) cc_final: 0.8738 (mm-30) REVERT: E 125 GLN cc_start: 0.9262 (mt0) cc_final: 0.9026 (mt0) REVERT: F 85 ASP cc_start: 0.9379 (m-30) cc_final: 0.9135 (m-30) REVERT: F 88 TYR cc_start: 0.9213 (m-10) cc_final: 0.8796 (m-80) REVERT: G 41 GLU cc_start: 0.8648 (tm-30) cc_final: 0.8372 (tm-30) REVERT: G 62 ILE cc_start: 0.9524 (mm) cc_final: 0.9290 (tt) REVERT: G 90 ASP cc_start: 0.8137 (t70) cc_final: 0.7905 (t0) REVERT: H 65 ASP cc_start: 0.9369 (t0) cc_final: 0.9138 (t0) REVERT: K 27 ASP cc_start: 0.8917 (t0) cc_final: 0.8635 (t0) REVERT: K 72 ASP cc_start: 0.9060 (t0) cc_final: 0.8711 (t0) REVERT: K 91 MET cc_start: 0.8783 (tpt) cc_final: 0.7411 (tpp) REVERT: L 23 GLU cc_start: 0.9462 (mt-10) cc_final: 0.9052 (pt0) REVERT: L 65 LYS cc_start: 0.8544 (mttt) cc_final: 0.8323 (mttm) REVERT: L 70 ARG cc_start: 0.9563 (mmt-90) cc_final: 0.9190 (mmt-90) REVERT: L 81 ARG cc_start: 0.9459 (OUTLIER) cc_final: 0.8806 (ttm-80) REVERT: L 86 GLU cc_start: 0.8987 (pt0) cc_final: 0.8634 (pp20) REVERT: L 101 ARG cc_start: 0.8477 (mmt-90) cc_final: 0.7595 (mmt180) REVERT: L 103 ASP cc_start: 0.8941 (t0) cc_final: 0.8391 (t0) REVERT: L 107 ASP cc_start: 0.9465 (m-30) cc_final: 0.9029 (m-30) outliers start: 31 outliers final: 11 residues processed: 263 average time/residue: 0.5824 time to fit residues: 166.1197 Evaluate side-chains 238 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 226 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain K residue 71 SER Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain L residue 81 ARG Chi-restraints excluded: chain L residue 84 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 84 optimal weight: 20.0000 chunk 50 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 110 optimal weight: 9.9990 chunk 83 optimal weight: 20.0000 chunk 109 optimal weight: 7.9990 chunk 38 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 111 optimal weight: 0.2980 chunk 91 optimal weight: 10.0000 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN F 93 GLN ** H 81 ASN ** 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 = 0.3250 r_free = 0.3250 target = 0.051399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.036783 restraints weight = 60814.352| |-----------------------------------------------------------------------------| r_work (start): 0.2725 rms_B_bonded: 2.32 r_work: 0.2549 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8919 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14172 Z= 0.142 Angle : 0.619 9.579 20397 Z= 0.361 Chirality : 0.042 0.225 2350 Planarity : 0.005 0.050 1587 Dihedral : 29.817 127.727 4181 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.07 % Allowed : 28.04 % Favored : 68.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.27 (0.27), residues: 939 helix: 2.38 (0.20), residues: 613 sheet: None (None), residues: 0 loop : -0.19 (0.31), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 95 TYR 0.009 0.001 TYR D 34 PHE 0.007 0.001 PHE A 67 TRP 0.005 0.002 TRP L 17 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.14 (14156) covalent geometry : angle 0.61496 / 0.36 (20379) hydrogen bonds : bond 0.03973 / 2.67 ( 835) hydrogen bonds : angle 2.94003 / 2.12 ( 2097) metal coordination : bond 0.00984 / 0.59 ( 16) metal coordination : angle 2.51724 / 1.71 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 251 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.9262 (tt0) cc_final: 0.9029 (tt0) REVERT: A 76 GLN cc_start: 0.9042 (mm-40) cc_final: 0.8827 (pt0) REVERT: B 84 MET cc_start: 0.9260 (mmm) cc_final: 0.8997 (mmm) REVERT: C 72 ASP cc_start: 0.9377 (t0) cc_final: 0.9132 (m-30) REVERT: C 76 THR cc_start: 0.9465 (p) cc_final: 0.9262 (t) REVERT: C 91 GLU cc_start: 0.9195 (tt0) cc_final: 0.8609 (tp30) REVERT: C 104 GLN cc_start: 0.8990 (mm110) cc_final: 0.8622 (mm110) REVERT: D 39 TYR cc_start: 0.8779 (t80) cc_final: 0.8482 (t80) REVERT: D 42 LEU cc_start: 0.9407 (tp) cc_final: 0.9154 (tp) REVERT: D 65 ASP cc_start: 0.9310 (t0) cc_final: 0.8972 (t0) REVERT: D 68 GLU cc_start: 0.9250 (mt-10) cc_final: 0.8938 (tm-30) REVERT: D 102 GLU cc_start: 0.9086 (tp30) cc_final: 0.8647 (tp30) REVERT: D 112 THR cc_start: 0.9663 (m) cc_final: 0.9388 (p) REVERT: E 58 THR cc_start: 0.9561 (p) cc_final: 0.9357 (t) REVERT: E 59 GLU cc_start: 0.8759 (pm20) cc_final: 0.8423 (pm20) REVERT: E 94 GLU cc_start: 0.9086 (mm-30) cc_final: 0.8799 (mm-30) REVERT: E 125 GLN cc_start: 0.9318 (mt0) cc_final: 0.9062 (mt0) REVERT: F 85 ASP cc_start: 0.9350 (m-30) cc_final: 0.9104 (m-30) REVERT: F 88 TYR cc_start: 0.9274 (m-10) cc_final: 0.8909 (m-80) REVERT: G 41 GLU cc_start: 0.8557 (tm-30) cc_final: 0.8344 (tm-30) REVERT: G 62 ILE cc_start: 0.9565 (mm) cc_final: 0.9318 (tt) REVERT: G 95 LYS cc_start: 0.9524 (ttmt) cc_final: 0.9251 (tppp) REVERT: H 65 ASP cc_start: 0.9471 (t0) cc_final: 0.9196 (t0) REVERT: K 27 ASP cc_start: 0.9019 (t0) cc_final: 0.8733 (t0) REVERT: K 72 ASP cc_start: 0.9119 (t0) cc_final: 0.8823 (t0) REVERT: L 23 GLU cc_start: 0.9380 (mt-10) cc_final: 0.9055 (pt0) REVERT: L 65 LYS cc_start: 0.8617 (mttt) cc_final: 0.8265 (mttm) REVERT: L 70 ARG cc_start: 0.9546 (mmt-90) cc_final: 0.9322 (mmt-90) REVERT: L 74 ASP cc_start: 0.9649 (m-30) cc_final: 0.9230 (p0) REVERT: L 86 GLU cc_start: 0.9123 (pt0) cc_final: 0.8714 (pp20) REVERT: L 101 ARG cc_start: 0.8491 (mmt-90) cc_final: 0.7776 (mmt180) REVERT: L 103 ASP cc_start: 0.8833 (t0) cc_final: 0.8341 (t0) REVERT: L 107 ASP cc_start: 0.9456 (m-30) cc_final: 0.9021 (m-30) outliers start: 24 outliers final: 12 residues processed: 259 average time/residue: 0.5539 time to fit residues: 155.9032 Evaluate side-chains 243 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 231 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain H residue 30 ARG Chi-restraints excluded: chain K residue 31 ILE Chi-restraints excluded: chain K residue 37 SER Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 40 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 103 optimal weight: 10.0000 chunk 111 optimal weight: 7.9990 chunk 96 optimal weight: 20.0000 chunk 16 optimal weight: 4.9990 chunk 53 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 39 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 57 optimal weight: 4.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN A 113 HIS C 38 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.049819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2702 r_free = 0.2702 target = 0.034777 restraints weight = 60901.648| |-----------------------------------------------------------------------------| r_work (start): 0.2658 rms_B_bonded: 2.30 r_work: 0.2484 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9008 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 14172 Z= 0.230 Angle : 0.661 8.612 20397 Z= 0.372 Chirality : 0.043 0.229 2350 Planarity : 0.005 0.042 1587 Dihedral : 30.196 125.506 4181 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.33 % Allowed : 28.17 % Favored : 68.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.33 (0.27), residues: 939 helix: 2.44 (0.21), residues: 613 sheet: None (None), residues: 0 loop : -0.20 (0.32), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 76 TYR 0.017 0.002 TYR C 39 PHE 0.011 0.002 PHE K 87 TRP 0.006 0.002 TRP L 17 HIS 0.006 0.001 HIS K 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.23 (14156) covalent geometry : angle 0.65767 / 0.37 (20379) hydrogen bonds : bond 0.04433 / 3.00 ( 835) hydrogen bonds : angle 3.08813 / 2.22 ( 2097) metal coordination : bond 0.02368 / 1.59 ( 16) metal coordination : angle 2.28795 / 1.61 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 229 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8649 (pm20) cc_final: 0.8371 (pm20) REVERT: A 73 GLU cc_start: 0.9327 (tt0) cc_final: 0.9095 (tt0) REVERT: A 76 GLN cc_start: 0.9203 (mm-40) cc_final: 0.8923 (pt0) REVERT: A 87 SER cc_start: 0.9513 (OUTLIER) cc_final: 0.9302 (p) REVERT: C 91 GLU cc_start: 0.9236 (tt0) cc_final: 0.8676 (tp30) REVERT: C 104 GLN cc_start: 0.9003 (mm110) cc_final: 0.8570 (mm110) REVERT: D 42 LEU cc_start: 0.9471 (tp) cc_final: 0.9215 (tp) REVERT: D 65 ASP cc_start: 0.9391 (t0) cc_final: 0.9048 (t0) REVERT: D 68 GLU cc_start: 0.9274 (mt-10) cc_final: 0.9006 (tm-30) REVERT: D 102 GLU cc_start: 0.9140 (tp30) cc_final: 0.8732 (tp30) REVERT: D 112 THR cc_start: 0.9689 (m) cc_final: 0.9420 (p) REVERT: E 58 THR cc_start: 0.9645 (p) cc_final: 0.9414 (t) REVERT: E 59 GLU cc_start: 0.8912 (pm20) cc_final: 0.8517 (pm20) REVERT: E 73 GLU cc_start: 0.9012 (tt0) cc_final: 0.8728 (tt0) REVERT: E 94 GLU cc_start: 0.9133 (mm-30) cc_final: 0.8817 (mm-30) REVERT: E 125 GLN cc_start: 0.9350 (mt0) cc_final: 0.9114 (mt0) REVERT: F 85 ASP cc_start: 0.9351 (m-30) cc_final: 0.9082 (m-30) REVERT: F 88 TYR cc_start: 0.9351 (m-10) cc_final: 0.9084 (m-80) REVERT: G 41 GLU cc_start: 0.8681 (tm-30) cc_final: 0.8467 (tm-30) REVERT: G 62 ILE cc_start: 0.9648 (mm) cc_final: 0.9430 (tt) REVERT: G 90 ASP cc_start: 0.8750 (t0) cc_final: 0.8242 (t0) REVERT: G 95 LYS cc_start: 0.9523 (ttmt) cc_final: 0.9267 (tppp) REVERT: H 65 ASP cc_start: 0.9497 (t0) cc_final: 0.9184 (t0) REVERT: H 80 TYR cc_start: 0.9224 (m-10) cc_final: 0.8675 (m-10) REVERT: H 102 GLU cc_start: 0.9088 (mm-30) cc_final: 0.8440 (mm-30) REVERT: K 17 MET cc_start: 0.9093 (mmm) cc_final: 0.8845 (mmm) REVERT: K 27 ASP cc_start: 0.9008 (t0) cc_final: 0.8718 (t0) REVERT: K 72 ASP cc_start: 0.9074 (t0) cc_final: 0.8715 (t0) REVERT: L 65 LYS cc_start: 0.8823 (mttt) cc_final: 0.7858 (mttm) REVERT: L 81 ARG cc_start: 0.9441 (OUTLIER) cc_final: 0.8888 (ttm-80) REVERT: L 101 ARG cc_start: 0.8730 (mmt-90) cc_final: 0.7935 (mmt-90) REVERT: L 103 ASP cc_start: 0.8874 (t0) cc_final: 0.8318 (t0) REVERT: L 107 ASP cc_start: 0.9427 (m-30) cc_final: 0.8985 (m-30) outliers start: 26 outliers final: 13 residues processed: 243 average time/residue: 0.5751 time to fit residues: 151.3790 Evaluate side-chains 228 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 213 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain K residue 31 ILE Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 66 GLU Chi-restraints excluded: chain L residue 81 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 52 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 89 optimal weight: 20.0000 chunk 90 optimal weight: 10.0000 chunk 43 optimal weight: 3.9990 chunk 85 optimal weight: 30.0000 chunk 22 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 92 optimal weight: 9.9990 chunk 1 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 ASN ** 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 = 0.3215 r_free = 0.3215 target = 0.049948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.034889 restraints weight = 60826.880| |-----------------------------------------------------------------------------| r_work (start): 0.2666 rms_B_bonded: 2.30 r_work: 0.2491 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8995 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 14172 Z= 0.171 Angle : 0.645 13.133 20397 Z= 0.366 Chirality : 0.043 0.231 2350 Planarity : 0.005 0.042 1587 Dihedral : 30.222 123.874 4181 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.97 % Allowed : 28.30 % Favored : 67.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.37 (0.27), residues: 939 helix: 2.49 (0.21), residues: 613 sheet: None (None), residues: 0 loop : -0.23 (0.31), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 70 TYR 0.010 0.001 TYR D 80 PHE 0.007 0.001 PHE A 67 TRP 0.007 0.002 TRP L 17 HIS 0.005 0.001 HIS K 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.17 (14156) covalent geometry : angle 0.64266 / 0.37 (20379) hydrogen bonds : bond 0.03826 / 2.57 ( 835) hydrogen bonds : angle 2.99970 / 2.17 ( 2097) metal coordination : bond 0.01833 / 1.30 ( 16) metal coordination : angle 1.98095 / 1.37 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 240 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8694 (pm20) cc_final: 0.8289 (pm20) REVERT: A 64 LYS cc_start: 0.9402 (OUTLIER) cc_final: 0.9183 (mmmm) REVERT: A 73 GLU cc_start: 0.9327 (tt0) cc_final: 0.9099 (tt0) REVERT: A 76 GLN cc_start: 0.9201 (mm-40) cc_final: 0.8952 (pt0) REVERT: A 87 SER cc_start: 0.9497 (OUTLIER) cc_final: 0.9294 (p) REVERT: A 125 GLN cc_start: 0.9417 (mt0) cc_final: 0.9215 (mt0) REVERT: C 91 GLU cc_start: 0.9228 (tt0) cc_final: 0.8678 (tp30) REVERT: C 104 GLN cc_start: 0.8971 (mm110) cc_final: 0.8546 (mm110) REVERT: C 116 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8239 (mm) REVERT: D 42 LEU cc_start: 0.9444 (tp) cc_final: 0.9192 (tp) REVERT: D 65 ASP cc_start: 0.9411 (t0) cc_final: 0.9070 (t0) REVERT: D 68 GLU cc_start: 0.9265 (mt-10) cc_final: 0.9010 (tm-30) REVERT: D 112 THR cc_start: 0.9682 (m) cc_final: 0.9407 (p) REVERT: E 58 THR cc_start: 0.9623 (p) cc_final: 0.9420 (t) REVERT: E 59 GLU cc_start: 0.8920 (pm20) cc_final: 0.8482 (pm20) REVERT: E 73 GLU cc_start: 0.9002 (tt0) cc_final: 0.8716 (tt0) REVERT: E 94 GLU cc_start: 0.9120 (mm-30) cc_final: 0.8774 (mm-30) REVERT: E 125 GLN cc_start: 0.9345 (mt0) cc_final: 0.9124 (mt0) REVERT: F 85 ASP cc_start: 0.9308 (m-30) cc_final: 0.9075 (m-30) REVERT: F 88 TYR cc_start: 0.9349 (m-10) cc_final: 0.9127 (m-80) REVERT: F 92 ARG cc_start: 0.9456 (OUTLIER) cc_final: 0.9108 (mmm-85) REVERT: G 41 GLU cc_start: 0.8697 (tm-30) cc_final: 0.8448 (tm-30) REVERT: G 62 ILE cc_start: 0.9608 (mm) cc_final: 0.9397 (tt) REVERT: G 90 ASP cc_start: 0.8562 (t0) cc_final: 0.7775 (t0) REVERT: G 95 LYS cc_start: 0.9524 (ttmt) cc_final: 0.9264 (tppp) REVERT: H 65 ASP cc_start: 0.9513 (t0) cc_final: 0.9186 (t0) REVERT: H 80 TYR cc_start: 0.9223 (m-10) cc_final: 0.8691 (m-10) REVERT: H 102 GLU cc_start: 0.9084 (mm-30) cc_final: 0.8482 (mm-30) REVERT: K 27 ASP cc_start: 0.9045 (t0) cc_final: 0.8732 (t0) REVERT: K 72 ASP cc_start: 0.9182 (t0) cc_final: 0.8776 (t0) REVERT: L 86 GLU cc_start: 0.8009 (pp20) cc_final: 0.7802 (pp20) REVERT: L 103 ASP cc_start: 0.8779 (t0) cc_final: 0.8236 (t0) REVERT: L 107 ASP cc_start: 0.9423 (m-30) cc_final: 0.8962 (m-30) outliers start: 31 outliers final: 13 residues processed: 255 average time/residue: 0.5389 time to fit residues: 149.4811 Evaluate side-chains 240 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 223 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain K residue 31 ILE Chi-restraints excluded: chain K residue 42 CYS Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 40 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 84 optimal weight: 20.0000 chunk 74 optimal weight: 20.0000 chunk 27 optimal weight: 0.7980 chunk 20 optimal weight: 6.9990 chunk 59 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 89 optimal weight: 20.0000 chunk 36 optimal weight: 10.0000 chunk 4 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 ASN ** 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 = 0.3228 r_free = 0.3228 target = 0.050401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.035408 restraints weight = 60541.459| |-----------------------------------------------------------------------------| r_work (start): 0.2683 rms_B_bonded: 2.28 r_work: 0.2509 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8980 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14172 Z= 0.145 Angle : 0.640 13.489 20397 Z= 0.359 Chirality : 0.042 0.226 2350 Planarity : 0.004 0.035 1587 Dihedral : 30.168 122.631 4181 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.94 % Allowed : 29.71 % Favored : 67.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.33 (0.27), residues: 939 helix: 2.44 (0.21), residues: 619 sheet: None (None), residues: 0 loop : -0.24 (0.31), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG L 70 TYR 0.010 0.001 TYR D 80 PHE 0.008 0.001 PHE A 67 TRP 0.008 0.002 TRP L 17 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.14 (14156) covalent geometry : angle 0.63576 / 0.36 (20379) hydrogen bonds : bond 0.03719 / 2.51 ( 835) hydrogen bonds : angle 2.96039 / 2.14 ( 2097) metal coordination : bond 0.00975 / 0.55 ( 16) metal coordination : angle 2.50282 / 1.70 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 236 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8676 (pm20) cc_final: 0.8232 (pm20) REVERT: A 64 LYS cc_start: 0.9377 (OUTLIER) cc_final: 0.9160 (mmmm) REVERT: A 73 GLU cc_start: 0.9301 (tt0) cc_final: 0.9069 (tt0) REVERT: A 76 GLN cc_start: 0.9218 (mm-40) cc_final: 0.8962 (pt0) REVERT: A 125 GLN cc_start: 0.9430 (mt0) cc_final: 0.9182 (mt0) REVERT: C 91 GLU cc_start: 0.9237 (tt0) cc_final: 0.8662 (tp30) REVERT: C 104 GLN cc_start: 0.8953 (mm110) cc_final: 0.8511 (mm110) REVERT: C 116 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8219 (mm) REVERT: D 42 LEU cc_start: 0.9422 (tp) cc_final: 0.9172 (tp) REVERT: D 65 ASP cc_start: 0.9414 (t0) cc_final: 0.9069 (t0) REVERT: D 68 GLU cc_start: 0.9259 (mt-10) cc_final: 0.8998 (tm-30) REVERT: D 102 GLU cc_start: 0.8988 (tp30) cc_final: 0.8405 (tp30) REVERT: D 112 THR cc_start: 0.9670 (m) cc_final: 0.9401 (p) REVERT: E 59 GLU cc_start: 0.8887 (pm20) cc_final: 0.8431 (pm20) REVERT: E 73 GLU cc_start: 0.9011 (tt0) cc_final: 0.8717 (tt0) REVERT: E 94 GLU cc_start: 0.9107 (mm-30) cc_final: 0.8734 (mm-30) REVERT: E 125 GLN cc_start: 0.9350 (mt0) cc_final: 0.9109 (mt0) REVERT: F 88 TYR cc_start: 0.9342 (m-10) cc_final: 0.9135 (m-80) REVERT: F 92 ARG cc_start: 0.9418 (OUTLIER) cc_final: 0.8999 (mmm-85) REVERT: G 41 GLU cc_start: 0.8705 (tm-30) cc_final: 0.8425 (tm-30) REVERT: G 62 ILE cc_start: 0.9586 (mm) cc_final: 0.9345 (tt) REVERT: G 90 ASP cc_start: 0.8619 (t0) cc_final: 0.8068 (t0) REVERT: G 92 GLU cc_start: 0.9097 (mt-10) cc_final: 0.8885 (mt-10) REVERT: G 95 LYS cc_start: 0.9525 (ttmt) cc_final: 0.9251 (tppp) REVERT: H 65 ASP cc_start: 0.9516 (t0) cc_final: 0.9186 (t0) REVERT: H 80 TYR cc_start: 0.9224 (m-10) cc_final: 0.8712 (m-10) REVERT: K 27 ASP cc_start: 0.9110 (t0) cc_final: 0.8770 (t0) REVERT: K 72 ASP cc_start: 0.9193 (t0) cc_final: 0.8752 (t0) REVERT: L 101 ARG cc_start: 0.8760 (mmt-90) cc_final: 0.8152 (mmt-90) REVERT: L 103 ASP cc_start: 0.8764 (t0) cc_final: 0.8219 (t0) REVERT: L 107 ASP cc_start: 0.9413 (m-30) cc_final: 0.8943 (m-30) outliers start: 23 outliers final: 14 residues processed: 248 average time/residue: 0.5792 time to fit residues: 155.6612 Evaluate side-chains 239 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 222 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain K residue 31 ILE Chi-restraints excluded: chain K residue 42 CYS Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 84 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 92 optimal weight: 10.0000 chunk 66 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 61 optimal weight: 0.7980 chunk 106 optimal weight: 5.9990 chunk 68 optimal weight: 5.9990 chunk 70 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 15 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.049849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.034869 restraints weight = 60733.012| |-----------------------------------------------------------------------------| r_work (start): 0.2671 rms_B_bonded: 2.29 r_work: 0.2496 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9000 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14172 Z= 0.167 Angle : 0.656 11.990 20397 Z= 0.364 Chirality : 0.042 0.227 2350 Planarity : 0.004 0.047 1587 Dihedral : 30.223 121.757 4181 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.94 % Allowed : 30.73 % Favored : 66.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.43 (0.27), residues: 939 helix: 2.55 (0.21), residues: 613 sheet: None (None), residues: 0 loop : -0.23 (0.32), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 76 TYR 0.011 0.001 TYR L 114 PHE 0.009 0.001 PHE A 67 TRP 0.007 0.002 TRP L 17 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.17 (14156) covalent geometry : angle 0.65236 / 0.36 (20379) hydrogen bonds : bond 0.03791 / 2.58 ( 835) hydrogen bonds : angle 2.97772 / 2.15 ( 2097) metal coordination : bond 0.01337 / 0.86 ( 16) metal coordination : angle 2.36079 / 1.72 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 226 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8666 (pm20) cc_final: 0.8259 (pm20) REVERT: A 64 LYS cc_start: 0.9390 (OUTLIER) cc_final: 0.9186 (mmmm) REVERT: A 73 GLU cc_start: 0.9304 (tt0) cc_final: 0.9093 (tt0) REVERT: A 76 GLN cc_start: 0.9192 (mm-40) cc_final: 0.8892 (pt0) REVERT: A 87 SER cc_start: 0.9494 (OUTLIER) cc_final: 0.9290 (p) REVERT: A 125 GLN cc_start: 0.9438 (mt0) cc_final: 0.9178 (mt0) REVERT: C 62 ILE cc_start: 0.9636 (mt) cc_final: 0.9390 (tt) REVERT: C 91 GLU cc_start: 0.9244 (tt0) cc_final: 0.8681 (tp30) REVERT: C 104 GLN cc_start: 0.8945 (mm110) cc_final: 0.8549 (mm110) REVERT: C 116 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8241 (mm) REVERT: D 42 LEU cc_start: 0.9441 (tp) cc_final: 0.9186 (tp) REVERT: D 65 ASP cc_start: 0.9428 (t0) cc_final: 0.9092 (t0) REVERT: D 68 GLU cc_start: 0.9272 (mt-10) cc_final: 0.9043 (tm-30) REVERT: D 73 GLU cc_start: 0.9304 (tp30) cc_final: 0.9043 (mm-30) REVERT: D 102 GLU cc_start: 0.8972 (tp30) cc_final: 0.8564 (tp30) REVERT: D 112 THR cc_start: 0.9682 (m) cc_final: 0.9416 (p) REVERT: E 59 GLU cc_start: 0.8885 (pm20) cc_final: 0.8431 (pm20) REVERT: E 73 GLU cc_start: 0.9036 (tt0) cc_final: 0.8732 (tt0) REVERT: E 94 GLU cc_start: 0.9121 (mm-30) cc_final: 0.8737 (mm-30) REVERT: E 125 GLN cc_start: 0.9396 (mt0) cc_final: 0.9177 (mt0) REVERT: F 88 TYR cc_start: 0.9340 (m-10) cc_final: 0.9112 (m-80) REVERT: F 92 ARG cc_start: 0.9423 (OUTLIER) cc_final: 0.8916 (mmm-85) REVERT: G 41 GLU cc_start: 0.8766 (tm-30) cc_final: 0.8432 (tm-30) REVERT: G 62 ILE cc_start: 0.9606 (mm) cc_final: 0.9378 (tt) REVERT: G 90 ASP cc_start: 0.8541 (t0) cc_final: 0.7765 (t0) REVERT: G 95 LYS cc_start: 0.9532 (ttmt) cc_final: 0.9257 (tppp) REVERT: H 31 LYS cc_start: 0.8491 (mmtt) cc_final: 0.8280 (mmpt) REVERT: H 65 ASP cc_start: 0.9520 (t0) cc_final: 0.9185 (t0) REVERT: H 80 TYR cc_start: 0.9222 (m-10) cc_final: 0.8686 (m-10) REVERT: H 102 GLU cc_start: 0.8994 (mm-30) cc_final: 0.8442 (mm-30) REVERT: K 27 ASP cc_start: 0.9135 (t0) cc_final: 0.8905 (p0) REVERT: K 72 ASP cc_start: 0.9132 (t0) cc_final: 0.8685 (t0) REVERT: L 101 ARG cc_start: 0.8802 (mmt-90) cc_final: 0.8358 (mmt-90) REVERT: L 103 ASP cc_start: 0.8776 (t0) cc_final: 0.8294 (t0) REVERT: L 107 ASP cc_start: 0.9404 (m-30) cc_final: 0.8946 (m-30) outliers start: 23 outliers final: 14 residues processed: 237 average time/residue: 0.5787 time to fit residues: 148.8602 Evaluate side-chains 236 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 218 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain K residue 42 CYS Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 84 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 9 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 chunk 111 optimal weight: 0.0970 chunk 44 optimal weight: 2.9990 chunk 78 optimal weight: 10.0000 chunk 60 optimal weight: 0.9990 chunk 88 optimal weight: 20.0000 chunk 5 optimal weight: 1.9990 chunk 74 optimal weight: 20.0000 chunk 65 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 15 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.049764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.034834 restraints weight = 61115.538| |-----------------------------------------------------------------------------| r_work (start): 0.2665 rms_B_bonded: 2.28 r_work: 0.2491 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8929 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14172 Z= 0.179 Angle : 0.681 13.251 20397 Z= 0.370 Chirality : 0.042 0.229 2350 Planarity : 0.004 0.038 1587 Dihedral : 30.292 121.099 4181 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.33 % Allowed : 31.11 % Favored : 65.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.45 (0.27), residues: 939 helix: 2.61 (0.21), residues: 607 sheet: None (None), residues: 0 loop : -0.27 (0.32), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG L 70 TYR 0.015 0.001 TYR D 34 PHE 0.008 0.001 PHE A 67 TRP 0.005 0.002 TRP L 17 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.18 (14156) covalent geometry : angle 0.67786 / 0.37 (20379) hydrogen bonds : bond 0.03828 / 2.60 ( 835) hydrogen bonds : angle 3.00185 / 2.17 ( 2097) metal coordination : bond 0.01398 / 1.03 ( 16) metal coordination : angle 2.27506 / 1.62 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 226 time to evaluate : 0.273 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8596 (pm20) cc_final: 0.8176 (pm20) REVERT: A 76 GLN cc_start: 0.9219 (mm-40) cc_final: 0.8954 (tt0) REVERT: C 91 GLU cc_start: 0.9226 (tt0) cc_final: 0.8620 (tp30) REVERT: C 104 GLN cc_start: 0.8904 (mm110) cc_final: 0.8531 (mm110) REVERT: C 116 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8147 (mm) REVERT: D 42 LEU cc_start: 0.9321 (tp) cc_final: 0.9069 (tp) REVERT: D 65 ASP cc_start: 0.9423 (t0) cc_final: 0.9045 (OUTLIER) REVERT: D 68 GLU cc_start: 0.9234 (mt-10) cc_final: 0.8955 (tm-30) REVERT: D 73 GLU cc_start: 0.9342 (tp30) cc_final: 0.9062 (tp30) REVERT: D 112 THR cc_start: 0.9643 (m) cc_final: 0.9375 (p) REVERT: E 59 GLU cc_start: 0.8820 (pm20) cc_final: 0.8348 (pm20) REVERT: E 73 GLU cc_start: 0.8982 (tt0) cc_final: 0.8676 (tt0) REVERT: E 94 GLU cc_start: 0.9071 (mm-30) cc_final: 0.8686 (mm-30) REVERT: E 125 GLN cc_start: 0.9370 (mt0) cc_final: 0.9140 (mt0) REVERT: F 88 TYR cc_start: 0.9276 (m-10) cc_final: 0.9045 (m-80) REVERT: F 92 ARG cc_start: 0.9398 (OUTLIER) cc_final: 0.8833 (mmm-85) REVERT: G 41 GLU cc_start: 0.8750 (tm-30) cc_final: 0.8372 (tm-30) REVERT: G 90 ASP cc_start: 0.8416 (t0) cc_final: 0.7837 (t0) REVERT: G 92 GLU cc_start: 0.9141 (mt-10) cc_final: 0.8925 (mt-10) REVERT: G 95 LYS cc_start: 0.9517 (ttmt) cc_final: 0.9265 (tppp) REVERT: H 65 ASP cc_start: 0.9522 (t0) cc_final: 0.9165 (t0) REVERT: H 80 TYR cc_start: 0.9189 (m-10) cc_final: 0.8728 (m-10) REVERT: H 102 GLU cc_start: 0.9029 (mm-30) cc_final: 0.8496 (mm-30) REVERT: K 27 ASP cc_start: 0.9164 (t0) cc_final: 0.8920 (p0) REVERT: K 72 ASP cc_start: 0.9207 (t0) cc_final: 0.8666 (t0) REVERT: L 41 SER cc_start: 0.9051 (OUTLIER) cc_final: 0.8802 (p) REVERT: L 101 ARG cc_start: 0.8774 (mmt-90) cc_final: 0.8222 (mmt-90) REVERT: L 103 ASP cc_start: 0.8859 (t0) cc_final: 0.8377 (t0) REVERT: L 106 PHE cc_start: 0.9510 (OUTLIER) cc_final: 0.9123 (t80) REVERT: L 107 ASP cc_start: 0.9448 (m-30) cc_final: 0.9004 (m-30) outliers start: 26 outliers final: 18 residues processed: 240 average time/residue: 0.5702 time to fit residues: 148.1522 Evaluate side-chains 242 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 221 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain K residue 12 LEU Chi-restraints excluded: chain K residue 42 CYS Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 41 SER Chi-restraints excluded: chain L residue 84 ASN Chi-restraints excluded: chain L residue 106 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 12 optimal weight: 1.9990 chunk 84 optimal weight: 20.0000 chunk 33 optimal weight: 0.9990 chunk 73 optimal weight: 30.0000 chunk 59 optimal weight: 0.9990 chunk 43 optimal weight: 5.9990 chunk 49 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 115 optimal weight: 6.9990 chunk 100 optimal weight: 9.9990 chunk 112 optimal weight: 0.7980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 15 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.050250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.035433 restraints weight = 61329.330| |-----------------------------------------------------------------------------| r_work (start): 0.2684 rms_B_bonded: 2.28 r_work: 0.2508 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8924 moved from start: 0.2815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14172 Z= 0.146 Angle : 0.668 13.371 20397 Z= 0.366 Chirality : 0.042 0.225 2350 Planarity : 0.004 0.037 1587 Dihedral : 30.247 120.513 4181 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.43 % Allowed : 31.75 % Favored : 65.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.39 (0.27), residues: 939 helix: 2.55 (0.21), residues: 610 sheet: None (None), residues: 0 loop : -0.29 (0.31), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG L 70 TYR 0.014 0.001 TYR D 34 PHE 0.009 0.001 PHE A 67 TRP 0.004 0.002 TRP L 17 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.15 (14156) covalent geometry : angle 0.66472 / 0.37 (20379) hydrogen bonds : bond 0.03671 / 2.49 ( 835) hydrogen bonds : angle 2.97935 / 2.15 ( 2097) metal coordination : bond 0.00841 / 0.64 ( 16) metal coordination : angle 2.38698 / 1.76 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 227 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8612 (pm20) cc_final: 0.8197 (pm20) REVERT: A 76 GLN cc_start: 0.9204 (mm-40) cc_final: 0.8940 (tt0) REVERT: C 62 ILE cc_start: 0.9541 (mt) cc_final: 0.9280 (tt) REVERT: C 91 GLU cc_start: 0.9225 (tt0) cc_final: 0.8574 (tp30) REVERT: C 104 GLN cc_start: 0.8890 (mm110) cc_final: 0.8508 (mm110) REVERT: C 116 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8130 (mm) REVERT: D 42 LEU cc_start: 0.9317 (tp) cc_final: 0.9063 (tp) REVERT: D 65 ASP cc_start: 0.9414 (t0) cc_final: 0.9063 (OUTLIER) REVERT: D 68 GLU cc_start: 0.9203 (mt-10) cc_final: 0.8942 (tm-30) REVERT: D 73 GLU cc_start: 0.9347 (tp30) cc_final: 0.9103 (mm-30) REVERT: D 112 THR cc_start: 0.9638 (m) cc_final: 0.9384 (p) REVERT: E 59 GLU cc_start: 0.8837 (pm20) cc_final: 0.8367 (pm20) REVERT: E 73 GLU cc_start: 0.8985 (tt0) cc_final: 0.8772 (tt0) REVERT: E 94 GLU cc_start: 0.9072 (mm-30) cc_final: 0.8685 (mm-30) REVERT: E 125 GLN cc_start: 0.9370 (mt0) cc_final: 0.9142 (mt0) REVERT: F 87 VAL cc_start: 0.9498 (p) cc_final: 0.9297 (m) REVERT: F 88 TYR cc_start: 0.9277 (m-10) cc_final: 0.9065 (m-80) REVERT: G 41 GLU cc_start: 0.8735 (tm-30) cc_final: 0.8354 (tm-30) REVERT: G 90 ASP cc_start: 0.8402 (t0) cc_final: 0.7660 (t0) REVERT: G 95 LYS cc_start: 0.9519 (ttmt) cc_final: 0.9257 (tppp) REVERT: H 31 LYS cc_start: 0.8349 (mmtt) cc_final: 0.8134 (mmpt) REVERT: H 32 GLU cc_start: 0.8431 (mm-30) cc_final: 0.8172 (tt0) REVERT: H 65 ASP cc_start: 0.9526 (t0) cc_final: 0.9164 (t0) REVERT: H 80 TYR cc_start: 0.9147 (m-10) cc_final: 0.8716 (m-10) REVERT: H 102 GLU cc_start: 0.9030 (mm-30) cc_final: 0.8488 (mm-30) REVERT: K 27 ASP cc_start: 0.9179 (t0) cc_final: 0.8929 (p0) REVERT: K 72 ASP cc_start: 0.9238 (t0) cc_final: 0.8647 (t0) REVERT: K 91 MET cc_start: 0.9330 (mmm) cc_final: 0.8968 (tmm) REVERT: L 41 SER cc_start: 0.9015 (OUTLIER) cc_final: 0.8757 (p) REVERT: L 86 GLU cc_start: 0.7921 (pp20) cc_final: 0.7622 (pp20) REVERT: L 103 ASP cc_start: 0.8855 (t0) cc_final: 0.8355 (t0) REVERT: L 106 PHE cc_start: 0.9496 (OUTLIER) cc_final: 0.9118 (t80) REVERT: L 107 ASP cc_start: 0.9442 (m-30) cc_final: 0.8997 (m-30) outliers start: 19 outliers final: 15 residues processed: 240 average time/residue: 0.5970 time to fit residues: 155.4456 Evaluate side-chains 236 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 219 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain K residue 42 CYS Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 41 SER Chi-restraints excluded: chain L residue 106 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 85 optimal weight: 30.0000 chunk 34 optimal weight: 3.9990 chunk 78 optimal weight: 10.0000 chunk 82 optimal weight: 20.0000 chunk 77 optimal weight: 10.0000 chunk 99 optimal weight: 30.0000 chunk 0 optimal weight: 10.0000 chunk 16 optimal weight: 0.6980 chunk 56 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 15 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.049855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.034950 restraints weight = 61545.921| |-----------------------------------------------------------------------------| r_work (start): 0.2673 rms_B_bonded: 2.31 r_work: 0.2498 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8928 moved from start: 0.2947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14172 Z= 0.169 Angle : 0.690 13.742 20397 Z= 0.372 Chirality : 0.042 0.224 2350 Planarity : 0.004 0.048 1587 Dihedral : 30.292 119.976 4181 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.56 % Allowed : 32.39 % Favored : 65.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.43 (0.27), residues: 939 helix: 2.60 (0.21), residues: 607 sheet: None (None), residues: 0 loop : -0.29 (0.31), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG L 70 TYR 0.010 0.001 TYR D 39 PHE 0.008 0.001 PHE A 67 TRP 0.005 0.002 TRP L 17 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.17 (14156) covalent geometry : angle 0.68698 / 0.37 (20379) hydrogen bonds : bond 0.03799 / 2.58 ( 835) hydrogen bonds : angle 3.00119 / 2.16 ( 2097) metal coordination : bond 0.01204 / 0.93 ( 16) metal coordination : angle 2.38355 / 1.75 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 222 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8607 (pm20) cc_final: 0.8189 (pm20) REVERT: A 76 GLN cc_start: 0.9220 (mm-40) cc_final: 0.8940 (tt0) REVERT: C 59 THR cc_start: 0.9549 (m) cc_final: 0.9210 (t) REVERT: C 62 ILE cc_start: 0.9531 (mt) cc_final: 0.9307 (tt) REVERT: C 91 GLU cc_start: 0.9234 (tt0) cc_final: 0.8600 (tp30) REVERT: C 104 GLN cc_start: 0.8886 (mm110) cc_final: 0.8501 (mm110) REVERT: C 116 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8149 (mm) REVERT: D 42 LEU cc_start: 0.9314 (tp) cc_final: 0.9057 (tp) REVERT: D 65 ASP cc_start: 0.9422 (t0) cc_final: 0.9062 (OUTLIER) REVERT: D 68 GLU cc_start: 0.9217 (mt-10) cc_final: 0.8945 (tm-30) REVERT: D 73 GLU cc_start: 0.9366 (tp30) cc_final: 0.9135 (mm-30) REVERT: D 112 THR cc_start: 0.9639 (m) cc_final: 0.9388 (p) REVERT: E 59 GLU cc_start: 0.8848 (pm20) cc_final: 0.8376 (pm20) REVERT: E 73 GLU cc_start: 0.8981 (tt0) cc_final: 0.8766 (tt0) REVERT: E 94 GLU cc_start: 0.9075 (mm-30) cc_final: 0.8688 (mm-30) REVERT: E 125 GLN cc_start: 0.9373 (mt0) cc_final: 0.9145 (mt0) REVERT: G 41 GLU cc_start: 0.8731 (tm-30) cc_final: 0.8346 (tm-30) REVERT: G 90 ASP cc_start: 0.8436 (t0) cc_final: 0.7881 (t0) REVERT: G 95 LYS cc_start: 0.9513 (ttmt) cc_final: 0.9264 (tppp) REVERT: H 31 LYS cc_start: 0.8360 (mmtt) cc_final: 0.8137 (mmpt) REVERT: H 32 GLU cc_start: 0.8444 (mm-30) cc_final: 0.8139 (tt0) REVERT: H 65 ASP cc_start: 0.9530 (t0) cc_final: 0.9164 (t0) REVERT: H 80 TYR cc_start: 0.9148 (m-10) cc_final: 0.8761 (m-10) REVERT: H 102 GLU cc_start: 0.9045 (mm-30) cc_final: 0.8511 (mm-30) REVERT: K 27 ASP cc_start: 0.9181 (t0) cc_final: 0.8932 (p0) REVERT: K 72 ASP cc_start: 0.9233 (t0) cc_final: 0.8651 (t0) REVERT: K 91 MET cc_start: 0.9327 (mmm) cc_final: 0.8960 (tmm) REVERT: L 41 SER cc_start: 0.9009 (OUTLIER) cc_final: 0.8745 (p) REVERT: L 86 GLU cc_start: 0.7990 (pp20) cc_final: 0.7696 (pp20) REVERT: L 101 ARG cc_start: 0.8966 (mmt90) cc_final: 0.8479 (mmt180) REVERT: L 103 ASP cc_start: 0.8854 (t0) cc_final: 0.8376 (t0) REVERT: L 106 PHE cc_start: 0.9507 (OUTLIER) cc_final: 0.9161 (t80) REVERT: L 107 ASP cc_start: 0.9439 (m-30) cc_final: 0.9000 (m-30) outliers start: 20 outliers final: 16 residues processed: 234 average time/residue: 0.6163 time to fit residues: 156.4465 Evaluate side-chains 235 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 217 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain K residue 42 CYS Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 41 SER Chi-restraints excluded: chain L residue 106 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 66 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 77 optimal weight: 10.0000 chunk 89 optimal weight: 20.0000 chunk 115 optimal weight: 9.9990 chunk 112 optimal weight: 0.0370 chunk 73 optimal weight: 30.0000 chunk 35 optimal weight: 0.7980 chunk 116 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 3 optimal weight: 0.7980 overall best weight: 1.5262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 44 GLN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 15 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.050138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.035354 restraints weight = 61406.484| |-----------------------------------------------------------------------------| r_work (start): 0.2680 rms_B_bonded: 2.28 r_work: 0.2508 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8926 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14172 Z= 0.158 Angle : 0.690 14.023 20397 Z= 0.371 Chirality : 0.042 0.224 2350 Planarity : 0.005 0.058 1587 Dihedral : 30.280 119.464 4181 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.30 % Allowed : 32.65 % Favored : 65.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.39 (0.27), residues: 939 helix: 2.57 (0.21), residues: 607 sheet: None (None), residues: 0 loop : -0.30 (0.32), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG L 70 TYR 0.030 0.002 TYR F 88 PHE 0.007 0.001 PHE A 67 TRP 0.005 0.002 TRP L 17 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.16 (14156) covalent geometry : angle 0.68682 / 0.37 (20379) hydrogen bonds : bond 0.03700 / 2.51 ( 835) hydrogen bonds : angle 3.00385 / 2.16 ( 2097) metal coordination : bond 0.01149 / 0.90 ( 16) metal coordination : angle 2.40241 / 1.73 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4289.27 seconds wall clock time: 73 minutes 40.76 seconds (4420.76 seconds total)