Starting phenix.real_space_refine on Thu Aug 6 02:25:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dgg_46823/08_2026/9dgg_46823.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dgg_46823/08_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9dgg_46823/08_2026/9dgg_46823.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dgg_46823/08_2026/9dgg_46823.map" model { file = "/net/cci-nas-00/data/ceres_data/9dgg_46823/08_2026/9dgg_46823.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dgg_46823/08_2026/9dgg_46823.cif" } 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-2.2rc3-6140/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: 2.68, per 1000 atoms: 0.20 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: 1.00 Conformation dependent library (CDL) restraints added in 354.4 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K 401 " pdb="ZN ZN K 401 " - pdb=" SG CYS K 21 " pdb="ZN ZN K 401 " - pdb=" SG CYS K 39 " pdb="ZN ZN K 401 " - pdb=" SG CYS K 18 " pdb="ZN ZN K 401 " - pdb=" SG CYS K 42 " pdb=" ZN K 402 " pdb="ZN ZN K 402 " - pdb=" ND1 HIS K 36 " pdb="ZN ZN K 402 " - pdb=" SG CYS K 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: 1.73 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: 2.09 Time building geometry restraints manager: 1.30 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: 19227 1.66 - 3.31: 1086 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: 1.000 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: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.700 Find NCS groups from input model: 0.100 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: 0.000 Load rotamer database and sin/cos tables:8.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.890 ------------------------------------------------------------------------------- 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= 0.502 Angle : 0.779 8.282 20397 Z= 0.657 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 0.77630 / 0.66 (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 : 0.309 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: 0.9037 (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: 0.8384 (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: 0.8522 (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: 0.5662 time to fit residues: 190.3795 Evaluate side-chains 239 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 239 time to evaluate : 0.261 ------------------------------------------------------------------------------- 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: 5.9990 chunk 33 optimal weight: 1.9990 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: 1.9990 ------------------------------------------------------------------------------- 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 = 0.3272 r_free = 0.3272 target = 0.051324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.036506 restraints weight = 61218.380| |-----------------------------------------------------------------------------| r_work (start): 0.2727 rms_B_bonded: 2.21 r_work: 0.2565 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8897 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 14172 Z= 0.188 Angle : 0.662 9.057 20397 Z= 0.384 Chirality : 0.044 0.263 2350 Planarity : 0.005 0.042 1587 Dihedral : 29.690 130.403 4181 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.84 % Allowed : 26.25 % 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: 2.39 (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 0.008 0.001 ARG L 70 TYR 0.015 0.001 TYR K 24 PHE 0.008 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 0.00365 / 0.19 (14156) covalent geometry : angle 0.65885 / 0.38 (20379) hydrogen bonds : bond 0.04516 / 3.04 ( 835) hydrogen bonds : angle 2.99613 / 2.18 ( 2097) metal coordination : bond 0.01885 / 1.22 ( 16) metal coordination : angle 2.18695 / 1.28 ( 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 274 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 244 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.9269 (tt0) cc_final: 0.9044 (tt0) REVERT: A 76 GLN cc_start: 0.9082 (mm-40) cc_final: 0.8809 (pt0) REVERT: A 129 ARG cc_start: 0.9080 (OUTLIER) cc_final: 0.8617 (tpt-90) REVERT: C 39 TYR cc_start: 0.9404 (m-80) cc_final: 0.9196 (m-80) REVERT: C 72 ASP cc_start: 0.9401 (t0) cc_final: 0.9196 (m-30) REVERT: C 76 THR cc_start: 0.9476 (p) cc_final: 0.9263 (t) REVERT: C 104 GLN cc_start: 0.8996 (mm110) cc_final: 0.8680 (mm110) REVERT: D 42 LEU cc_start: 0.9390 (tp) cc_final: 0.9135 (tp) REVERT: D 65 ASP cc_start: 0.9175 (t0) cc_final: 0.8917 (t0) REVERT: D 73 GLU cc_start: 0.8912 (mm-30) cc_final: 0.8689 (mm-30) REVERT: D 102 GLU cc_start: 0.9171 (tp30) cc_final: 0.8661 (tp30) REVERT: D 112 THR cc_start: 0.9656 (m) cc_final: 0.9368 (p) REVERT: E 58 THR cc_start: 0.9496 (p) cc_final: 0.9245 (t) REVERT: E 59 GLU cc_start: 0.8565 (pm20) cc_final: 0.8336 (pm20) REVERT: E 94 GLU cc_start: 0.9061 (mm-30) cc_final: 0.8774 (mm-30) REVERT: E 125 GLN cc_start: 0.9277 (mt0) cc_final: 0.9042 (mt0) REVERT: F 85 ASP cc_start: 0.9378 (m-30) cc_final: 0.9131 (m-30) REVERT: F 88 TYR cc_start: 0.9217 (m-10) cc_final: 0.8782 (m-80) REVERT: G 41 GLU cc_start: 0.8682 (tm-30) cc_final: 0.8390 (tm-30) REVERT: G 62 ILE cc_start: 0.9556 (mm) cc_final: 0.9312 (tt) REVERT: G 90 ASP cc_start: 0.8197 (t70) cc_final: 0.7686 (t0) REVERT: H 65 ASP cc_start: 0.9372 (t0) cc_final: 0.9162 (t0) REVERT: H 102 GLU cc_start: 0.9185 (mm-30) cc_final: 0.8599 (mm-30) REVERT: K 27 ASP cc_start: 0.8953 (t0) cc_final: 0.8683 (t0) REVERT: K 72 ASP cc_start: 0.9056 (t0) cc_final: 0.8736 (t0) REVERT: K 91 MET cc_start: 0.8761 (tpt) cc_final: 0.8297 (tmm) REVERT: L 23 GLU cc_start: 0.9437 (mt-10) cc_final: 0.9025 (pt0) REVERT: L 65 LYS cc_start: 0.8594 (mttt) cc_final: 0.8074 (mttm) REVERT: L 70 ARG cc_start: 0.9556 (mmt-90) cc_final: 0.9305 (mmt-90) REVERT: L 81 ARG cc_start: 0.9486 (OUTLIER) cc_final: 0.8827 (ttm-80) REVERT: L 86 GLU cc_start: 0.9013 (pt0) cc_final: 0.8656 (pp20) REVERT: L 101 ARG cc_start: 0.8474 (mmt-90) cc_final: 0.7577 (mmt-90) REVERT: L 103 ASP cc_start: 0.8938 (t0) cc_final: 0.8478 (t0) REVERT: L 107 ASP cc_start: 0.9463 (m-30) cc_final: 0.9028 (m-30) outliers start: 30 outliers final: 13 residues processed: 258 average time/residue: 0.6013 time to fit residues: 168.3925 Evaluate side-chains 238 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 223 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 129 ARG 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 G residue 79 ILE Chi-restraints excluded: chain K residue 71 SER Chi-restraints excluded: chain L residue 39 VAL 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: 1.9990 chunk 34 optimal weight: 0.9980 chunk 110 optimal weight: 0.4980 chunk 83 optimal weight: 20.0000 chunk 109 optimal weight: 4.9990 chunk 38 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 111 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 = 0.3243 r_free = 0.3243 target = 0.051055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.036247 restraints weight = 61191.975| |-----------------------------------------------------------------------------| r_work (start): 0.2713 rms_B_bonded: 2.36 r_work: 0.2540 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8928 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 0.039 14172 Z= 0.144 Angle : 0.630 10.185 20397 Z= 0.364 Chirality : 0.043 0.243 2350 Planarity : 0.004 0.037 1587 Dihedral : 29.803 127.353 4181 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.46 % Allowed : 27.14 % Favored : 69.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.32 (0.27), residues: 939 helix: 2.42 (0.21), residues: 613 sheet: None (None), residues: 0 loop : -0.19 (0.31), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 70 TYR 0.010 0.001 TYR D 34 PHE 0.009 0.001 PHE D 67 TRP 0.006 0.002 TRP L 17 HIS 0.005 0.001 HIS K 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.14 (14156) covalent geometry : angle 0.62572 / 0.36 (20379) hydrogen bonds : bond 0.03931 / 2.64 ( 835) hydrogen bonds : angle 2.95651 / 2.13 ( 2097) metal coordination : bond 0.01116 / 0.70 ( 16) metal coordination : angle 2.42123 / 1.70 ( 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 279 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 252 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8210 (pm20) cc_final: 0.7997 (pm20) REVERT: A 73 GLU cc_start: 0.9267 (tt0) cc_final: 0.9031 (tt0) REVERT: A 76 GLN cc_start: 0.9085 (mm-40) cc_final: 0.8867 (pt0) REVERT: B 84 MET cc_start: 0.9261 (mmm) cc_final: 0.9006 (mmm) REVERT: C 72 ASP cc_start: 0.9398 (t0) cc_final: 0.9127 (m-30) REVERT: C 91 GLU cc_start: 0.9200 (tt0) cc_final: 0.8638 (tp30) REVERT: C 104 GLN cc_start: 0.9003 (mm110) cc_final: 0.8638 (mm110) REVERT: D 42 LEU cc_start: 0.9415 (tp) cc_final: 0.9155 (tp) REVERT: D 65 ASP cc_start: 0.9307 (t0) cc_final: 0.9004 (t0) REVERT: D 73 GLU cc_start: 0.8983 (OUTLIER) cc_final: 0.8769 (mm-30) REVERT: D 102 GLU cc_start: 0.9089 (tp30) cc_final: 0.8701 (tp30) REVERT: D 112 THR cc_start: 0.9663 (m) cc_final: 0.9384 (p) REVERT: E 58 THR cc_start: 0.9563 (p) cc_final: 0.9353 (t) REVERT: E 59 GLU cc_start: 0.8783 (pm20) cc_final: 0.8430 (pm20) REVERT: E 94 GLU cc_start: 0.9077 (mm-30) cc_final: 0.8800 (mm-30) REVERT: E 125 GLN cc_start: 0.9316 (mt0) cc_final: 0.9063 (mt0) REVERT: F 85 ASP cc_start: 0.9383 (m-30) cc_final: 0.9125 (m-30) REVERT: G 41 GLU cc_start: 0.8585 (tm-30) cc_final: 0.8370 (tm-30) REVERT: G 62 ILE cc_start: 0.9571 (mm) cc_final: 0.9330 (tt) REVERT: G 95 LYS cc_start: 0.9471 (ttmt) cc_final: 0.9259 (tppp) REVERT: H 65 ASP cc_start: 0.9476 (t0) cc_final: 0.9209 (t0) REVERT: H 80 TYR cc_start: 0.9181 (m-10) cc_final: 0.8605 (m-10) REVERT: H 102 GLU cc_start: 0.9160 (mm-30) cc_final: 0.8656 (mm-30) REVERT: K 27 ASP cc_start: 0.9034 (t0) cc_final: 0.8726 (t0) REVERT: K 72 ASP cc_start: 0.9164 (t0) cc_final: 0.8841 (t0) REVERT: K 86 LEU cc_start: 0.9173 (tm) cc_final: 0.8970 (tm) REVERT: L 57 MET cc_start: 0.7881 (tmm) cc_final: 0.7672 (tmm) REVERT: L 65 LYS cc_start: 0.8662 (mttt) cc_final: 0.8370 (mttm) REVERT: L 70 ARG cc_start: 0.9542 (mmt-90) cc_final: 0.9290 (mmt-90) REVERT: L 74 ASP cc_start: 0.9648 (m-30) cc_final: 0.9232 (p0) REVERT: L 86 GLU cc_start: 0.9128 (pt0) cc_final: 0.8721 (pp20) REVERT: L 101 ARG cc_start: 0.8518 (mmt-90) cc_final: 0.7770 (mmt180) REVERT: L 103 ASP cc_start: 0.8842 (t0) cc_final: 0.8307 (t0) REVERT: L 107 ASP cc_start: 0.9465 (m-30) cc_final: 0.9026 (m-30) outliers start: 27 outliers final: 15 residues processed: 264 average time/residue: 0.6119 time to fit residues: 175.2688 Evaluate side-chains 249 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 233 time to evaluate : 0.390 ------------------------------------------------------------------------------- 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 D residue 44 GLN Chi-restraints excluded: chain D residue 73 GLU 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 H residue 53 SER 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 K residue 91 MET 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: 0.0070 chunk 111 optimal weight: 6.9990 chunk 96 optimal weight: 20.0000 chunk 16 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 32 optimal weight: 7.9990 chunk 27 optimal weight: 0.5980 chunk 39 optimal weight: 6.9990 chunk 25 optimal weight: 0.9990 chunk 57 optimal weight: 4.9990 overall best weight: 1.7204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN A 113 HIS ** C 38 ASN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.050690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.035725 restraints weight = 60935.394| |-----------------------------------------------------------------------------| r_work (start): 0.2695 rms_B_bonded: 2.28 r_work: 0.2523 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8973 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14172 Z= 0.166 Angle : 0.634 9.241 20397 Z= 0.363 Chirality : 0.043 0.244 2350 Planarity : 0.004 0.046 1587 Dihedral : 29.941 125.508 4181 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.59 % Allowed : 28.43 % Favored : 67.99 % 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: 2.36 (0.27), residues: 939 helix: 2.46 (0.21), residues: 613 sheet: None (None), residues: 0 loop : -0.17 (0.32), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 30 TYR 0.039 0.002 TYR F 88 PHE 0.010 0.001 PHE K 87 TRP 0.005 0.002 TRP L 17 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.17 (14156) covalent geometry : angle 0.63117 / 0.36 (20379) hydrogen bonds : bond 0.03933 / 2.65 ( 835) hydrogen bonds : angle 3.04210 / 2.19 ( 2097) metal coordination : bond 0.01532 / 0.98 ( 16) metal coordination : angle 2.25850 / 1.55 ( 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 268 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 240 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.9321 (tt0) cc_final: 0.9100 (tt0) REVERT: A 76 GLN cc_start: 0.9152 (mm-40) cc_final: 0.8901 (pt0) REVERT: A 87 SER cc_start: 0.9453 (p) cc_final: 0.9232 (p) REVERT: C 91 GLU cc_start: 0.9220 (tt0) cc_final: 0.8633 (tp30) REVERT: C 104 GLN cc_start: 0.8963 (mm110) cc_final: 0.8509 (mm110) REVERT: D 42 LEU cc_start: 0.9450 (tp) cc_final: 0.9194 (tp) REVERT: D 65 ASP cc_start: 0.9373 (t0) cc_final: 0.9026 (t0) REVERT: D 68 GLU cc_start: 0.9211 (mt-10) cc_final: 0.8993 (tm-30) REVERT: D 102 GLU cc_start: 0.9098 (tp30) cc_final: 0.8619 (tp30) REVERT: D 112 THR cc_start: 0.9670 (m) cc_final: 0.9398 (p) REVERT: E 58 THR cc_start: 0.9609 (p) cc_final: 0.9393 (t) REVERT: E 59 GLU cc_start: 0.8860 (pm20) cc_final: 0.8450 (pm20) REVERT: E 94 GLU cc_start: 0.9112 (mm-30) cc_final: 0.8767 (mm-30) REVERT: E 125 GLN cc_start: 0.9339 (mt0) cc_final: 0.9079 (mt0) REVERT: F 85 ASP cc_start: 0.9338 (m-30) cc_final: 0.9094 (m-30) REVERT: G 41 GLU cc_start: 0.8606 (tm-30) cc_final: 0.8392 (tm-30) REVERT: G 62 ILE cc_start: 0.9607 (mm) cc_final: 0.9359 (tt) REVERT: G 90 ASP cc_start: 0.8441 (t0) cc_final: 0.7993 (t0) REVERT: G 95 LYS cc_start: 0.9518 (ttmt) cc_final: 0.9229 (tppp) REVERT: H 65 ASP cc_start: 0.9495 (t0) cc_final: 0.9177 (t0) REVERT: H 76 ARG cc_start: 0.9015 (ttm-80) cc_final: 0.8811 (ttm-80) REVERT: H 80 TYR cc_start: 0.9043 (m-10) cc_final: 0.8698 (m-10) REVERT: H 102 GLU cc_start: 0.9147 (mm-30) cc_final: 0.8671 (mm-30) REVERT: K 17 MET cc_start: 0.9053 (mmm) cc_final: 0.8761 (mmm) REVERT: K 27 ASP cc_start: 0.8985 (t0) cc_final: 0.8678 (t0) REVERT: K 72 ASP cc_start: 0.9119 (t0) cc_final: 0.8770 (t0) REVERT: L 65 LYS cc_start: 0.8808 (mttt) cc_final: 0.8125 (mttm) REVERT: L 74 ASP cc_start: 0.9642 (m-30) cc_final: 0.9243 (p0) REVERT: L 81 ARG cc_start: 0.9395 (OUTLIER) cc_final: 0.8811 (ttm-80) REVERT: L 101 ARG cc_start: 0.8664 (mmt-90) cc_final: 0.7908 (mmt-90) REVERT: L 103 ASP cc_start: 0.8833 (t0) cc_final: 0.8300 (t0) REVERT: L 107 ASP cc_start: 0.9430 (m-30) cc_final: 0.8978 (m-30) outliers start: 28 outliers final: 13 residues processed: 252 average time/residue: 0.6422 time to fit residues: 175.3153 Evaluate side-chains 242 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 228 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 49 LEU Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain H residue 53 SER 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: 1.9990 chunk 49 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 89 optimal weight: 20.0000 chunk 90 optimal weight: 10.0000 chunk 43 optimal weight: 4.9990 chunk 85 optimal weight: 30.0000 chunk 22 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 chunk 92 optimal weight: 10.0000 chunk 1 optimal weight: 5.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.049428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2688 r_free = 0.2688 target = 0.034371 restraints weight = 61219.207| |-----------------------------------------------------------------------------| r_work (start): 0.2645 rms_B_bonded: 2.28 r_work: 0.2470 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9007 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 14172 Z= 0.241 Angle : 0.690 10.038 20397 Z= 0.381 Chirality : 0.044 0.250 2350 Planarity : 0.005 0.042 1587 Dihedral : 30.227 123.880 4181 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.46 % Allowed : 28.30 % Favored : 68.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.43 (0.27), residues: 939 helix: 2.53 (0.21), residues: 613 sheet: None (None), residues: 0 loop : -0.18 (0.32), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 70 TYR 0.034 0.002 TYR F 88 PHE 0.008 0.001 PHE K 97 TRP 0.007 0.002 TRP L 17 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00490 / 0.24 (14156) covalent geometry : angle 0.68651 / 0.38 (20379) hydrogen bonds : bond 0.04285 / 2.91 ( 835) hydrogen bonds : angle 3.10298 / 2.24 ( 2097) metal coordination : bond 0.02982 / 2.18 ( 16) metal coordination : angle 2.35115 / 1.60 ( 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 257 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 230 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8697 (pm20) cc_final: 0.8479 (pm20) REVERT: A 73 GLU cc_start: 0.9317 (tt0) cc_final: 0.9091 (tt0) REVERT: A 76 GLN cc_start: 0.9215 (mm-40) cc_final: 0.8928 (pt0) REVERT: A 129 ARG cc_start: 0.9349 (OUTLIER) cc_final: 0.8858 (tpt90) REVERT: C 72 ASP cc_start: 0.9239 (m-30) cc_final: 0.9007 (m-30) REVERT: C 91 GLU cc_start: 0.9251 (tt0) cc_final: 0.8690 (tp30) REVERT: C 104 GLN cc_start: 0.8991 (mm110) cc_final: 0.8575 (mm110) REVERT: C 116 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8222 (mm) REVERT: D 42 LEU cc_start: 0.9456 (tp) cc_final: 0.9206 (tp) REVERT: D 65 ASP cc_start: 0.9424 (t0) cc_final: 0.9063 (t0) REVERT: D 102 GLU cc_start: 0.9157 (tp30) cc_final: 0.8760 (tp30) REVERT: D 112 THR cc_start: 0.9689 (m) cc_final: 0.9413 (p) REVERT: E 58 THR cc_start: 0.9656 (p) cc_final: 0.9428 (t) REVERT: E 59 GLU cc_start: 0.8935 (pm20) cc_final: 0.8501 (pm20) REVERT: E 73 GLU cc_start: 0.9017 (tt0) cc_final: 0.8519 (tt0) REVERT: E 94 GLU cc_start: 0.9118 (mm-30) cc_final: 0.8752 (mm-30) REVERT: E 125 GLN cc_start: 0.9349 (mt0) cc_final: 0.9131 (mt0) REVERT: F 73 THR cc_start: 0.9687 (OUTLIER) cc_final: 0.9269 (p) REVERT: F 85 ASP cc_start: 0.9381 (m-30) cc_final: 0.9097 (m-30) REVERT: F 88 TYR cc_start: 0.9285 (m-80) cc_final: 0.9080 (m-80) REVERT: F 92 ARG cc_start: 0.9471 (OUTLIER) cc_final: 0.9128 (mmm-85) REVERT: G 41 GLU cc_start: 0.8677 (tm-30) cc_final: 0.8370 (tm-30) REVERT: G 62 ILE cc_start: 0.9628 (mm) cc_final: 0.9419 (tt) REVERT: G 90 ASP cc_start: 0.8562 (t0) cc_final: 0.8228 (t0) REVERT: G 95 LYS cc_start: 0.9523 (ttmt) cc_final: 0.9256 (tppp) REVERT: H 65 ASP cc_start: 0.9526 (t0) cc_final: 0.9191 (t0) REVERT: H 80 TYR cc_start: 0.9020 (m-10) cc_final: 0.8790 (m-10) REVERT: H 102 GLU cc_start: 0.9204 (mm-30) cc_final: 0.8693 (mm-30) REVERT: K 17 MET cc_start: 0.9095 (mmm) cc_final: 0.8817 (mmm) REVERT: K 27 ASP cc_start: 0.9029 (t0) cc_final: 0.8699 (t0) REVERT: K 72 ASP cc_start: 0.9210 (t0) cc_final: 0.8780 (t0) REVERT: L 65 LYS cc_start: 0.8846 (mttt) cc_final: 0.7890 (mttm) REVERT: L 70 ARG cc_start: 0.9427 (mmt-90) cc_final: 0.9127 (mmt-90) REVERT: L 86 GLU cc_start: 0.8058 (pp20) cc_final: 0.7802 (pp20) REVERT: L 101 ARG cc_start: 0.8683 (mmt-90) cc_final: 0.8005 (mmt-90) REVERT: L 103 ASP cc_start: 0.8802 (t0) cc_final: 0.8162 (t0) REVERT: L 107 ASP cc_start: 0.9436 (m-30) cc_final: 0.8978 (m-30) outliers start: 27 outliers final: 17 residues processed: 247 average time/residue: 0.6480 time to fit residues: 173.4279 Evaluate side-chains 234 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 213 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ARG 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 116 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 73 THR 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 H residue 99 LEU 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 66 GLU Chi-restraints excluded: chain L residue 84 ASN 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: 0.9990 chunk 20 optimal weight: 5.9990 chunk 59 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 89 optimal weight: 20.0000 chunk 36 optimal weight: 8.9990 chunk 4 optimal weight: 3.9990 chunk 103 optimal weight: 8.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- 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 = 0.3211 r_free = 0.3211 target = 0.049786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.034823 restraints weight = 60526.288| |-----------------------------------------------------------------------------| r_work (start): 0.2667 rms_B_bonded: 2.26 r_work: 0.2494 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9000 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 14172 Z= 0.165 Angle : 0.672 13.594 20397 Z= 0.375 Chirality : 0.044 0.277 2350 Planarity : 0.004 0.039 1587 Dihedral : 30.191 122.579 4181 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.84 % Allowed : 29.19 % Favored : 66.97 % 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: 2.41 (0.27), residues: 939 helix: 2.53 (0.21), residues: 613 sheet: None (None), residues: 0 loop : -0.24 (0.31), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 76 TYR 0.027 0.001 TYR F 88 PHE 0.008 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 0.00330 / 0.16 (14156) covalent geometry : angle 0.66969 / 0.38 (20379) hydrogen bonds : bond 0.03823 / 2.56 ( 835) hydrogen bonds : angle 3.01700 / 2.17 ( 2097) metal coordination : bond 0.01261 / 0.72 ( 16) metal coordination : angle 2.14974 / 1.48 ( 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 264 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 234 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8706 (pm20) cc_final: 0.8428 (pm20) REVERT: A 73 GLU cc_start: 0.9311 (tt0) cc_final: 0.9084 (tt0) REVERT: A 76 GLN cc_start: 0.9208 (mm-40) cc_final: 0.8913 (pt0) REVERT: A 129 ARG cc_start: 0.9354 (OUTLIER) cc_final: 0.8590 (tpt-90) REVERT: C 24 GLN cc_start: 0.9324 (mm-40) cc_final: 0.9082 (mm-40) REVERT: C 91 GLU cc_start: 0.9230 (tt0) cc_final: 0.8663 (tp30) REVERT: C 104 GLN cc_start: 0.8981 (mm110) cc_final: 0.8562 (mm110) REVERT: C 116 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8287 (mm) REVERT: D 42 LEU cc_start: 0.9442 (tp) cc_final: 0.9185 (tp) REVERT: D 65 ASP cc_start: 0.9410 (t0) cc_final: 0.9081 (t0) REVERT: D 102 GLU cc_start: 0.9054 (tp30) cc_final: 0.8536 (tp30) REVERT: D 112 THR cc_start: 0.9683 (m) cc_final: 0.9411 (p) REVERT: E 58 THR cc_start: 0.9651 (p) cc_final: 0.9436 (t) REVERT: E 59 GLU cc_start: 0.8927 (pm20) cc_final: 0.8471 (pm20) REVERT: E 73 GLU cc_start: 0.9006 (tt0) cc_final: 0.8463 (tt0) REVERT: E 94 GLU cc_start: 0.9097 (mm-30) cc_final: 0.8698 (mm-30) REVERT: E 125 GLN cc_start: 0.9354 (mt0) cc_final: 0.9111 (mt0) REVERT: F 85 ASP cc_start: 0.9333 (m-30) cc_final: 0.9114 (m-30) REVERT: F 88 TYR cc_start: 0.9293 (m-80) cc_final: 0.9014 (m-80) REVERT: F 92 ARG cc_start: 0.9429 (OUTLIER) cc_final: 0.8951 (mmm-85) REVERT: G 41 GLU cc_start: 0.8744 (tm-30) cc_final: 0.8449 (tm-30) REVERT: G 62 ILE cc_start: 0.9607 (mm) cc_final: 0.9363 (tt) REVERT: G 95 LYS cc_start: 0.9520 (ttmt) cc_final: 0.9246 (tppp) REVERT: H 65 ASP cc_start: 0.9513 (t0) cc_final: 0.9181 (t0) REVERT: H 80 TYR cc_start: 0.9110 (m-10) cc_final: 0.8721 (m-10) REVERT: H 102 GLU cc_start: 0.9156 (mm-30) cc_final: 0.8692 (mm-30) REVERT: K 27 ASP cc_start: 0.9072 (t0) cc_final: 0.8758 (t0) REVERT: K 72 ASP cc_start: 0.9197 (t0) cc_final: 0.8785 (t0) REVERT: L 65 LYS cc_start: 0.8806 (mttt) cc_final: 0.7804 (mttm) REVERT: L 81 ARG cc_start: 0.9462 (OUTLIER) cc_final: 0.9139 (ttm-80) REVERT: L 101 ARG cc_start: 0.8657 (mmt-90) cc_final: 0.7959 (mmt-90) REVERT: L 103 ASP cc_start: 0.8840 (t0) cc_final: 0.8294 (t0) REVERT: L 107 ASP cc_start: 0.9403 (m-30) cc_final: 0.8940 (m-30) outliers start: 30 outliers final: 17 residues processed: 252 average time/residue: 0.6519 time to fit residues: 177.8325 Evaluate side-chains 240 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 219 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 129 ARG 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 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 H residue 53 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 81 ARG 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: 1.9990 chunk 61 optimal weight: 0.7980 chunk 106 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 70 optimal weight: 0.5980 chunk 4 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 44 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 = 0.3220 r_free = 0.3220 target = 0.050029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.035049 restraints weight = 60663.658| |-----------------------------------------------------------------------------| r_work (start): 0.2677 rms_B_bonded: 2.29 r_work: 0.2501 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8986 moved from start: 0.2612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 14172 Z= 0.149 Angle : 0.664 12.272 20397 Z= 0.367 Chirality : 0.043 0.244 2350 Planarity : 0.005 0.046 1587 Dihedral : 30.139 121.566 4181 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.56 % Allowed : 30.47 % Favored : 66.97 % 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: 2.42 (0.27), residues: 939 helix: 2.60 (0.21), residues: 607 sheet: None (None), residues: 0 loop : -0.31 (0.31), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 76 TYR 0.023 0.001 TYR F 88 PHE 0.008 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 0.00289 / 0.15 (14156) covalent geometry : angle 0.66098 / 0.37 (20379) hydrogen bonds : bond 0.03721 / 2.53 ( 835) hydrogen bonds : angle 2.97632 / 2.15 ( 2097) metal coordination : bond 0.01006 / 0.73 ( 16) metal coordination : angle 2.17172 / 1.56 ( 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 257 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 237 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8726 (pm20) cc_final: 0.8401 (pm20) REVERT: A 73 GLU cc_start: 0.9300 (tt0) cc_final: 0.9090 (tt0) REVERT: A 76 GLN cc_start: 0.9183 (mm-40) cc_final: 0.8857 (pt0) REVERT: A 129 ARG cc_start: 0.9359 (OUTLIER) cc_final: 0.8599 (tpt-90) REVERT: C 24 GLN cc_start: 0.9313 (mm-40) cc_final: 0.9106 (mm-40) REVERT: C 91 GLU cc_start: 0.9236 (tt0) cc_final: 0.8655 (tp30) REVERT: C 104 GLN cc_start: 0.8965 (mm110) cc_final: 0.8535 (mm110) REVERT: D 42 LEU cc_start: 0.9416 (tp) cc_final: 0.9162 (tp) REVERT: D 65 ASP cc_start: 0.9410 (t0) cc_final: 0.9068 (OUTLIER) REVERT: D 112 THR cc_start: 0.9675 (m) cc_final: 0.9407 (p) REVERT: E 59 GLU cc_start: 0.8899 (pm20) cc_final: 0.8431 (pm20) REVERT: E 125 GLN cc_start: 0.9353 (mt0) cc_final: 0.9109 (mt0) REVERT: F 88 TYR cc_start: 0.9319 (m-80) cc_final: 0.9046 (m-80) REVERT: F 92 ARG cc_start: 0.9419 (OUTLIER) cc_final: 0.8917 (mmm-85) REVERT: G 41 GLU cc_start: 0.8726 (tm-30) cc_final: 0.8403 (tm-30) REVERT: G 62 ILE cc_start: 0.9588 (mm) cc_final: 0.9346 (tt) REVERT: G 90 ASP cc_start: 0.8622 (t0) cc_final: 0.8033 (t0) REVERT: G 95 LYS cc_start: 0.9521 (ttmt) cc_final: 0.9237 (tppp) REVERT: H 65 ASP cc_start: 0.9522 (t0) cc_final: 0.9183 (t0) REVERT: H 80 TYR cc_start: 0.9110 (m-10) cc_final: 0.8706 (m-10) REVERT: H 102 GLU cc_start: 0.9157 (mm-30) cc_final: 0.8713 (mm-30) REVERT: K 27 ASP cc_start: 0.9124 (t0) cc_final: 0.8776 (t0) REVERT: K 72 ASP cc_start: 0.9170 (t0) cc_final: 0.8735 (t0) REVERT: L 103 ASP cc_start: 0.8754 (t0) cc_final: 0.8233 (t0) REVERT: L 107 ASP cc_start: 0.9410 (m-30) cc_final: 0.8929 (m-30) outliers start: 20 outliers final: 15 residues processed: 248 average time/residue: 0.6257 time to fit residues: 168.4870 Evaluate side-chains 234 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 218 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain C residue 16 THR 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 9 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 chunk 111 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 78 optimal weight: 10.0000 chunk 60 optimal weight: 1.9990 chunk 88 optimal weight: 20.0000 chunk 5 optimal weight: 0.9990 chunk 74 optimal weight: 20.0000 chunk 65 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 75 HIS ** 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 = 0.3203 r_free = 0.3203 target = 0.049395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2693 r_free = 0.2693 target = 0.034483 restraints weight = 60992.789| |-----------------------------------------------------------------------------| r_work (start): 0.2645 rms_B_bonded: 2.31 r_work: 0.2470 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8942 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 14172 Z= 0.223 Angle : 0.725 13.249 20397 Z= 0.389 Chirality : 0.044 0.248 2350 Planarity : 0.005 0.049 1587 Dihedral : 30.328 121.140 4181 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.82 % Allowed : 31.75 % Favored : 65.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.36 (0.27), residues: 939 helix: 2.55 (0.21), residues: 607 sheet: None (None), residues: 0 loop : -0.33 (0.32), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 70 TYR 0.022 0.002 TYR F 88 PHE 0.008 0.001 PHE A 67 TRP 0.007 0.003 TRP L 17 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.22 (14156) covalent geometry : angle 0.72049 / 0.39 (20379) hydrogen bonds : bond 0.04256 / 2.89 ( 835) hydrogen bonds : angle 3.10115 / 2.24 ( 2097) metal coordination : bond 0.02123 / 1.62 ( 16) metal coordination : angle 2.67290 / 1.93 ( 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 239 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 217 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8698 (pm20) cc_final: 0.8309 (pm20) REVERT: A 76 GLN cc_start: 0.9213 (mm-40) cc_final: 0.8938 (tt0) REVERT: A 129 ARG cc_start: 0.9376 (OUTLIER) cc_final: 0.8889 (tpt90) REVERT: C 91 GLU cc_start: 0.9219 (tt0) cc_final: 0.8609 (tp30) REVERT: C 104 GLN cc_start: 0.8916 (mm110) cc_final: 0.8545 (mm110) REVERT: C 116 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8190 (mm) REVERT: D 42 LEU cc_start: 0.9328 (tp) cc_final: 0.9078 (tp) REVERT: D 65 ASP cc_start: 0.9443 (t0) cc_final: 0.9092 (t0) REVERT: D 112 THR cc_start: 0.9611 (m) cc_final: 0.9341 (p) REVERT: E 59 GLU cc_start: 0.8853 (pm20) cc_final: 0.8381 (pm20) REVERT: E 73 GLU cc_start: 0.8961 (tt0) cc_final: 0.8712 (tt0) REVERT: E 94 GLU cc_start: 0.9069 (mm-30) cc_final: 0.8661 (mm-30) REVERT: E 125 GLN cc_start: 0.9297 (mt0) cc_final: 0.9025 (mt0) REVERT: F 88 TYR cc_start: 0.9326 (m-10) cc_final: 0.9081 (m-80) REVERT: F 92 ARG cc_start: 0.9394 (OUTLIER) cc_final: 0.8850 (mmm-85) REVERT: G 41 GLU cc_start: 0.8743 (tm-30) cc_final: 0.8351 (tm-30) REVERT: G 90 ASP cc_start: 0.8440 (t0) cc_final: 0.7673 (t0) REVERT: G 95 LYS cc_start: 0.9530 (ttmt) cc_final: 0.9278 (tppp) REVERT: H 32 GLU cc_start: 0.8412 (mt-10) cc_final: 0.8087 (tt0) REVERT: H 65 ASP cc_start: 0.9531 (t0) cc_final: 0.9180 (t0) REVERT: H 80 TYR cc_start: 0.9137 (m-10) cc_final: 0.8767 (m-10) REVERT: H 102 GLU cc_start: 0.9205 (mm-30) cc_final: 0.8743 (mm-30) REVERT: K 27 ASP cc_start: 0.9110 (t0) cc_final: 0.8890 (p0) REVERT: K 72 ASP cc_start: 0.9235 (t0) cc_final: 0.8690 (t0) REVERT: L 86 GLU cc_start: 0.7994 (pp20) cc_final: 0.7748 (pp20) REVERT: L 101 ARG cc_start: 0.8803 (mmt-90) cc_final: 0.7933 (mmt-90) REVERT: L 103 ASP cc_start: 0.8905 (t0) cc_final: 0.8362 (t0) REVERT: L 106 PHE cc_start: 0.9513 (OUTLIER) cc_final: 0.9134 (t80) REVERT: L 107 ASP cc_start: 0.9454 (m-30) cc_final: 0.8988 (m-30) outliers start: 22 outliers final: 17 residues processed: 230 average time/residue: 0.6500 time to fit residues: 162.0039 Evaluate side-chains 232 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 211 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain B residue 96 THR 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 35 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 106 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 12 optimal weight: 0.9990 chunk 84 optimal weight: 20.0000 chunk 33 optimal weight: 1.9990 chunk 73 optimal weight: 20.0000 chunk 59 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 41 optimal weight: 0.8980 chunk 115 optimal weight: 20.0000 chunk 100 optimal weight: 6.9990 chunk 112 optimal weight: 0.6980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3222 r_free = 0.3222 target = 0.049761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.034876 restraints weight = 61186.613| |-----------------------------------------------------------------------------| r_work (start): 0.2671 rms_B_bonded: 2.30 r_work: 0.2496 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8929 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 14172 Z= 0.151 Angle : 0.693 13.495 20397 Z= 0.375 Chirality : 0.043 0.246 2350 Planarity : 0.004 0.047 1587 Dihedral : 30.240 120.458 4181 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.20 % Allowed : 31.37 % Favored : 65.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.35 (0.27), residues: 939 helix: 2.55 (0.21), residues: 607 sheet: None (None), residues: 0 loop : -0.36 (0.31), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG L 70 TYR 0.022 0.001 TYR F 88 PHE 0.008 0.001 PHE A 67 TRP 0.005 0.002 TRP L 17 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.15 (14156) covalent geometry : angle 0.68954 / 0.38 (20379) hydrogen bonds : bond 0.03727 / 2.53 ( 835) hydrogen bonds : angle 3.02989 / 2.17 ( 2097) metal coordination : bond 0.01165 / 0.89 ( 16) metal coordination : angle 2.47634 / 1.84 ( 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 252 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 227 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8673 (pm20) cc_final: 0.8303 (pm20) REVERT: A 76 GLN cc_start: 0.9221 (mm-40) cc_final: 0.8933 (tt0) REVERT: A 129 ARG cc_start: 0.9376 (OUTLIER) cc_final: 0.8621 (tpt-90) REVERT: C 59 THR cc_start: 0.9535 (m) cc_final: 0.9290 (t) REVERT: C 91 GLU cc_start: 0.9208 (tt0) cc_final: 0.8555 (tp30) REVERT: C 104 GLN cc_start: 0.8897 (mm110) cc_final: 0.8517 (mm110) REVERT: C 116 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.8189 (mm) REVERT: D 42 LEU cc_start: 0.9310 (tp) cc_final: 0.9051 (tp) REVERT: D 65 ASP cc_start: 0.9422 (t0) cc_final: 0.9056 (OUTLIER) REVERT: D 99 LEU cc_start: 0.9265 (mt) cc_final: 0.9048 (mp) REVERT: D 102 GLU cc_start: 0.9006 (tp30) cc_final: 0.8599 (tp30) REVERT: D 112 THR cc_start: 0.9595 (m) cc_final: 0.9342 (p) REVERT: E 59 GLU cc_start: 0.8858 (pm20) cc_final: 0.8389 (pm20) REVERT: E 73 GLU cc_start: 0.8953 (tt0) cc_final: 0.8708 (tt0) REVERT: E 125 GLN cc_start: 0.9366 (mt0) cc_final: 0.9137 (mt0) REVERT: F 88 TYR cc_start: 0.9230 (m-10) cc_final: 0.8982 (m-80) REVERT: F 92 ARG cc_start: 0.9376 (OUTLIER) cc_final: 0.8788 (mmm-85) REVERT: G 41 GLU cc_start: 0.8685 (tm-30) cc_final: 0.8353 (tm-30) REVERT: G 90 ASP cc_start: 0.8469 (t0) cc_final: 0.7947 (t0) REVERT: G 95 LYS cc_start: 0.9519 (ttmt) cc_final: 0.9266 (tppp) REVERT: H 32 GLU cc_start: 0.8403 (mt-10) cc_final: 0.8093 (tt0) REVERT: H 65 ASP cc_start: 0.9534 (t0) cc_final: 0.9173 (t0) REVERT: H 73 GLU cc_start: 0.9248 (tp30) cc_final: 0.9040 (tp30) REVERT: H 80 TYR cc_start: 0.9094 (m-10) cc_final: 0.8733 (m-10) REVERT: K 27 ASP cc_start: 0.9123 (t0) cc_final: 0.8898 (p0) REVERT: K 72 ASP cc_start: 0.9175 (t0) cc_final: 0.8621 (t0) REVERT: L 41 SER cc_start: 0.9042 (OUTLIER) cc_final: 0.8786 (p) REVERT: L 101 ARG cc_start: 0.8802 (mmt-90) cc_final: 0.8193 (mmt-90) REVERT: L 103 ASP cc_start: 0.8880 (t0) cc_final: 0.8338 (t0) REVERT: L 106 PHE cc_start: 0.9486 (OUTLIER) cc_final: 0.9097 (t80) REVERT: L 107 ASP cc_start: 0.9446 (m-30) cc_final: 0.9056 (m-30) outliers start: 25 outliers final: 19 residues processed: 242 average time/residue: 0.6532 time to fit residues: 170.9095 Evaluate side-chains 242 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 219 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 129 ARG 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 E residue 130 ILE 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 H residue 99 LEU Chi-restraints excluded: chain K residue 37 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 85 optimal weight: 30.0000 chunk 34 optimal weight: 0.0060 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: 1.9990 chunk 56 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 overall best weight: 1.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 75 HIS ** 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 = 0.3223 r_free = 0.3223 target = 0.049835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.034947 restraints weight = 61237.371| |-----------------------------------------------------------------------------| r_work (start): 0.2671 rms_B_bonded: 2.31 r_work: 0.2498 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8930 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 0.089 14172 Z= 0.159 Angle : 0.699 13.800 20397 Z= 0.381 Chirality : 0.043 0.240 2350 Planarity : 0.005 0.051 1587 Dihedral : 30.186 119.929 4181 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.82 % Allowed : 32.39 % Favored : 64.79 % 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: 2.36 (0.27), residues: 939 helix: 2.50 (0.21), residues: 613 sheet: None (None), residues: 0 loop : -0.29 (0.32), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG L 70 TYR 0.022 0.001 TYR F 88 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 0.00321 / 0.16 (14156) covalent geometry : angle 0.69534 / 0.38 (20379) hydrogen bonds : bond 0.03761 / 2.57 ( 835) hydrogen bonds : angle 3.04460 / 2.18 ( 2097) metal coordination : bond 0.01317 / 1.03 ( 16) metal coordination : angle 2.42268 / 1.79 ( 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 245 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 223 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8669 (pm20) cc_final: 0.8297 (pm20) REVERT: A 76 GLN cc_start: 0.9223 (mm-40) cc_final: 0.8930 (tt0) REVERT: A 129 ARG cc_start: 0.9357 (OUTLIER) cc_final: 0.8622 (tpt-90) REVERT: C 91 GLU cc_start: 0.9187 (tt0) cc_final: 0.8568 (tp30) REVERT: C 104 GLN cc_start: 0.8898 (mm110) cc_final: 0.8510 (mm110) REVERT: C 116 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.8146 (mm) REVERT: D 42 LEU cc_start: 0.9315 (tp) cc_final: 0.9057 (tp) REVERT: D 65 ASP cc_start: 0.9427 (t0) cc_final: 0.9089 (OUTLIER) REVERT: D 99 LEU cc_start: 0.9253 (mt) cc_final: 0.9036 (mp) REVERT: D 102 GLU cc_start: 0.9004 (tp30) cc_final: 0.8604 (tp30) REVERT: D 112 THR cc_start: 0.9606 (m) cc_final: 0.9359 (p) REVERT: E 59 GLU cc_start: 0.8885 (pm20) cc_final: 0.8409 (pm20) REVERT: E 73 GLU cc_start: 0.8956 (tt0) cc_final: 0.8707 (tt0) REVERT: E 125 GLN cc_start: 0.9370 (mt0) cc_final: 0.9153 (mt0) REVERT: F 88 TYR cc_start: 0.9234 (m-10) cc_final: 0.8961 (m-80) REVERT: F 92 ARG cc_start: 0.9386 (OUTLIER) cc_final: 0.8809 (mmm-85) REVERT: G 41 GLU cc_start: 0.8682 (tm-30) cc_final: 0.8349 (tm-30) REVERT: G 90 ASP cc_start: 0.8458 (t0) cc_final: 0.7879 (t0) REVERT: G 95 LYS cc_start: 0.9524 (ttmt) cc_final: 0.9270 (tppp) REVERT: H 65 ASP cc_start: 0.9537 (t0) cc_final: 0.9176 (t0) REVERT: H 80 TYR cc_start: 0.9089 (m-10) cc_final: 0.8690 (m-10) REVERT: K 27 ASP cc_start: 0.9130 (t0) cc_final: 0.8913 (p0) REVERT: K 72 ASP cc_start: 0.9152 (t0) cc_final: 0.8578 (t0) REVERT: L 48 GLU cc_start: 0.9145 (mp0) cc_final: 0.8905 (pm20) REVERT: L 86 GLU cc_start: 0.7982 (pp20) cc_final: 0.6802 (pp20) REVERT: L 91 ARG cc_start: 0.8806 (tpp-160) cc_final: 0.7976 (mmp80) REVERT: L 101 ARG cc_start: 0.8824 (mmt-90) cc_final: 0.8197 (mmt-90) REVERT: L 103 ASP cc_start: 0.8857 (t0) cc_final: 0.8236 (t0) REVERT: L 107 ASP cc_start: 0.9423 (m-30) cc_final: 0.9017 (m-30) outliers start: 22 outliers final: 18 residues processed: 236 average time/residue: 0.6489 time to fit residues: 166.1149 Evaluate side-chains 239 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 219 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 129 ARG 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 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 H residue 99 LEU Chi-restraints excluded: chain K residue 12 LEU Chi-restraints excluded: chain K residue 37 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 66 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 77 optimal weight: 10.0000 chunk 89 optimal weight: 20.0000 chunk 115 optimal weight: 4.9990 chunk 112 optimal weight: 8.9990 chunk 73 optimal weight: 20.0000 chunk 35 optimal weight: 0.9980 chunk 116 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 3 optimal weight: 0.7980 overall best weight: 2.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 75 HIS ** 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 = 0.3239 r_free = 0.3239 target = 0.049559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.034927 restraints weight = 62105.380| |-----------------------------------------------------------------------------| r_work (start): 0.2700 rms_B_bonded: 2.18 r_work: 0.2538 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9035 moved from start: 0.3036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 14172 Z= 0.207 Angle : 0.736 14.720 20397 Z= 0.390 Chirality : 0.044 0.296 2350 Planarity : 0.005 0.052 1587 Dihedral : 30.267 119.762 4181 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.56 % Allowed : 32.14 % Favored : 65.30 % 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: 2.53 (0.21), residues: 613 sheet: None (None), residues: 0 loop : -0.29 (0.32), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG L 70 TYR 0.020 0.002 TYR F 88 PHE 0.008 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 0.00425 / 0.21 (14156) covalent geometry : angle 0.73203 / 0.39 (20379) hydrogen bonds : bond 0.04103 / 2.79 ( 835) hydrogen bonds : angle 3.07348 / 2.20 ( 2097) metal coordination : bond 0.01967 / 1.52 ( 16) metal coordination : angle 2.59380 / 1.89 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4486.60 seconds wall clock time: 77 minutes 10.15 seconds (4630.15 seconds total)