Starting phenix.real_space_refine on Sat Aug 23 15:35:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u5h_41922/08_2025/8u5h_41922.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u5h_41922/08_2025/8u5h_41922.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8u5h_41922/08_2025/8u5h_41922.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u5h_41922/08_2025/8u5h_41922.map" model { file = "/net/cci-nas-00/data/ceres_data/8u5h_41922/08_2025/8u5h_41922.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u5h_41922/08_2025/8u5h_41922.cif" } resolution = 3.23 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= 0.004 sd= 2.051 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: 5 Type Number sf(0) Gaussians P 314 5.49 5 S 15 5.16 5 C 7463 2.51 5 N 2514 2.21 5 O 3130 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13436 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 281 Classifications: {'peptide': 41} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 3, 'TRANS': 37} Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2, 'ARG:plan': 3, 'GLU:plan': 1, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 47 Chain: "B" Number of atoms: 163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 163 Classifications: {'peptide': 23} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 2, 'TRANS': 20} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "C" Number of atoms: 3200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 3200 Classifications: {'DNA': 157} Link IDs: {'rna3p': 156} Chain: "D" Number of atoms: 488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 488 Classifications: {'peptide': 66} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 3, 'TRANS': 62} Chain breaks: 2 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 31 Chain: "H" Number of atoms: 3237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 3237 Classifications: {'DNA': 157} Link IDs: {'rna3p': 156} Chain: "I" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 807 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 94} 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: "J" Number of atoms: 676 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 84, 667 Classifications: {'peptide': 84} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 82} 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 Conformer: "B" Number of residues, atoms: 84, 667 Classifications: {'peptide': 84} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 82} 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 bond proxies already assigned to first conformer: 664 Chain: "K" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 824 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 104} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 10 Chain: "M" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 731 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 92} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "O" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 816 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 94} 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: "Q" 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: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "R" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 825 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 102} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "S" Number of atoms: 741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 741 Classifications: {'peptide': 96} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 93} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ALYS J 20 " occ=0.77 ... (16 atoms not shown) pdb=" NZ BLYS J 20 " occ=0.23 Time building chain proxies: 2.72, per 1000 atoms: 0.20 Number of scatterers: 13436 At special positions: 0 Unit cell: (90.1331, 127.174, 122.235, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 15 16.00 P 314 15.00 O 3130 8.00 N 2514 7.00 C 7463 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.90 Conformation dependent library (CDL) restraints added in 420.2 milliseconds Enol-peptide restraints added in 1.4 microseconds 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1694 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 10 sheets defined 64.7% alpha, 4.1% beta 153 base pairs and 259 stacking pairs defined. Time for finding SS restraints: 2.08 Creating SS restraints... Processing helix chain 'A' and resid 199 through 210 Processing helix chain 'B' and resid 173 through 177 removed outlier: 3.589A pdb=" N GLU B 177 " --> pdb=" O LEU B 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 35 removed outlier: 3.606A pdb=" N ILE D 30 " --> pdb=" O VAL D 26 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLN D 31 " --> pdb=" O LYS D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 39 No H-bonds generated for 'chain 'D' and resid 37 through 39' Processing helix chain 'D' and resid 56 through 60 Processing helix chain 'I' and resid 44 through 57 removed outlier: 4.226A pdb=" N LEU I 48 " --> pdb=" O GLY I 44 " (cutoff:3.500A) Processing helix chain 'I' and resid 63 through 79 removed outlier: 3.854A pdb=" N ASP I 77 " --> pdb=" O GLU I 73 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N PHE I 78 " --> pdb=" O ILE I 74 " (cutoff:3.500A) Processing helix chain 'I' and resid 85 through 114 removed outlier: 3.638A pdb=" N MET I 90 " --> pdb=" O ARG I 86 " (cutoff:3.500A) Processing helix chain 'I' and resid 120 through 131 Processing helix chain 'J' and resid 25 through 29 Processing helix chain 'J' and resid 30 through 42 Processing helix chain 'J' and resid 49 through 76 removed outlier: 4.043A pdb=" N GLU J 53 " --> pdb=" O LEU J 49 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ARG J 55 " --> pdb=" O TYR J 51 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASP J 68 " --> pdb=" O ASN J 64 " (cutoff:3.500A) Processing helix chain 'J' and resid 82 through 94 Processing helix chain 'K' and resid 16 through 22 Processing helix chain 'K' and resid 26 through 37 Processing helix chain 'K' and resid 45 through 73 removed outlier: 4.247A pdb=" N VAL K 49 " --> pdb=" O ALA K 45 " (cutoff:3.500A) Processing helix chain 'K' and resid 79 through 88 removed outlier: 3.722A pdb=" N LEU K 83 " --> pdb=" O ILE K 79 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLN K 84 " --> pdb=" O PRO K 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 90 through 97 Processing helix chain 'M' and resid 34 through 46 Processing helix chain 'M' and resid 52 through 81 removed outlier: 3.853A pdb=" N ASN M 81 " --> pdb=" O LEU M 77 " (cutoff:3.500A) Processing helix chain 'M' and resid 87 through 99 Processing helix chain 'M' and resid 101 through 119 removed outlier: 3.887A pdb=" N SER M 109 " --> pdb=" O LYS M 105 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TYR M 118 " --> pdb=" O ALA M 114 " (cutoff:3.500A) Processing helix chain 'O' and resid 45 through 57 removed outlier: 3.577A pdb=" N ARG O 49 " --> pdb=" O THR O 45 " (cutoff:3.500A) Processing helix chain 'O' and resid 63 through 76 Processing helix chain 'O' and resid 85 through 114 Processing helix chain 'O' and resid 120 through 132 removed outlier: 3.507A pdb=" N ILE O 124 " --> pdb=" O MET O 120 " (cutoff:3.500A) Processing helix chain 'Q' and resid 25 through 29 removed outlier: 3.507A pdb=" N ILE Q 29 " --> pdb=" O ILE Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 30 through 42 Processing helix chain 'Q' and resid 49 through 76 removed outlier: 3.580A pdb=" N GLU Q 53 " --> pdb=" O LEU Q 49 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ARG Q 55 " --> pdb=" O TYR Q 51 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASP Q 68 " --> pdb=" O ASN Q 64 " (cutoff:3.500A) Processing helix chain 'Q' and resid 82 through 93 Processing helix chain 'R' and resid 16 through 22 Processing helix chain 'R' and resid 26 through 37 Processing helix chain 'R' and resid 45 through 73 removed outlier: 4.346A pdb=" N VAL R 49 " --> pdb=" O ALA R 45 " (cutoff:3.500A) Processing helix chain 'R' and resid 79 through 89 Processing helix chain 'R' and resid 90 through 97 Processing helix chain 'S' and resid 34 through 46 Processing helix chain 'S' and resid 52 through 81 removed outlier: 4.154A pdb=" N ASN S 81 " --> pdb=" O LEU S 77 " (cutoff:3.500A) Processing helix chain 'S' and resid 87 through 99 Processing helix chain 'S' and resid 101 through 121 removed outlier: 3.578A pdb=" N LYS S 105 " --> pdb=" O GLY S 101 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 13 through 16 removed outlier: 3.759A pdb=" N LEU D 15 " --> pdb=" O ILE D 3 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'I' and resid 83 through 84 removed outlier: 6.851A pdb=" N ARG I 83 " --> pdb=" O VAL J 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'I' and resid 118 through 119 Processing sheet with id=AA4, first strand: chain 'J' and resid 96 through 98 removed outlier: 6.848A pdb=" N THR J 96 " --> pdb=" O THR R 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'K' and resid 42 through 43 removed outlier: 7.109A pdb=" N ARG K 42 " --> pdb=" O ILE M 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'K' and resid 77 through 78 Processing sheet with id=AA7, first strand: chain 'K' and resid 100 through 102 Processing sheet with id=AA8, first strand: chain 'O' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'R' and resid 42 through 43 removed outlier: 7.880A pdb=" N ARG R 42 " --> pdb=" O ILE S 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'R' and resid 77 through 78 424 hydrogen bonds defined for protein. 1251 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 385 hydrogen bonds 750 hydrogen bond angles 0 basepair planarities 153 basepair parallelities 259 stacking parallelities Total time for adding SS restraints: 2.69 Time building geometry restraints manager: 1.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2494 1.33 - 1.45: 4642 1.45 - 1.57: 6525 1.57 - 1.69: 626 1.69 - 1.81: 26 Bond restraints: 14313 Sorted by residual: bond pdb=" P DC H 48 " pdb=" OP2 DC H 48 " ideal model delta sigma weight residual 1.480 1.521 -0.041 2.00e-02 2.50e+03 4.13e+00 bond pdb=" P DT C 214 " pdb=" OP2 DT C 214 " ideal model delta sigma weight residual 1.480 1.520 -0.040 2.00e-02 2.50e+03 4.00e+00 bond pdb=" P DA C 220 " pdb=" OP2 DA C 220 " ideal model delta sigma weight residual 1.480 1.519 -0.039 2.00e-02 2.50e+03 3.82e+00 bond pdb=" P DC H 114 " pdb=" OP2 DC H 114 " ideal model delta sigma weight residual 1.480 1.519 -0.039 2.00e-02 2.50e+03 3.80e+00 bond pdb=" P DT C 170 " pdb=" OP2 DT C 170 " ideal model delta sigma weight residual 1.480 1.518 -0.038 2.00e-02 2.50e+03 3.67e+00 ... (remaining 14308 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 19968 1.81 - 3.62: 629 3.62 - 5.43: 65 5.43 - 7.24: 32 7.24 - 9.05: 5 Bond angle restraints: 20699 Sorted by residual: angle pdb=" O3' DT C 214 " pdb=" P DC C 215 " pdb=" O5' DC C 215 " ideal model delta sigma weight residual 104.00 99.13 4.87 1.50e+00 4.44e-01 1.05e+01 angle pdb=" C3' DG H 135 " pdb=" O3' DG H 135 " pdb=" P DG H 136 " ideal model delta sigma weight residual 120.20 124.81 -4.61 1.50e+00 4.44e-01 9.44e+00 angle pdb=" C GLY K 37 " pdb=" N ASN K 38 " pdb=" CA ASN K 38 " ideal model delta sigma weight residual 121.54 127.40 -5.86 1.91e+00 2.74e-01 9.41e+00 angle pdb=" O3' DT H 49 " pdb=" P DT H 50 " pdb=" O5' DT H 50 " ideal model delta sigma weight residual 104.00 99.49 4.51 1.50e+00 4.44e-01 9.05e+00 angle pdb=" O3' DG C 205 " pdb=" P DT C 206 " pdb=" O5' DT C 206 " ideal model delta sigma weight residual 104.00 99.77 4.23 1.50e+00 4.44e-01 7.94e+00 ... (remaining 20694 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.81: 6275 35.81 - 71.62: 1468 71.62 - 107.43: 29 107.43 - 143.24: 6 143.24 - 179.05: 21 Dihedral angle restraints: 7799 sinusoidal: 5181 harmonic: 2618 Sorted by residual: dihedral pdb=" C4' DA H 5 " pdb=" C3' DA H 5 " pdb=" O3' DA H 5 " pdb=" P DT H 6 " ideal model delta sinusoidal sigma weight residual 220.00 40.95 179.05 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DC C 224 " pdb=" C3' DC C 224 " pdb=" O3' DC C 224 " pdb=" P DT C 225 " ideal model delta sinusoidal sigma weight residual -140.00 37.49 -177.49 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DA C 309 " pdb=" C3' DA C 309 " pdb=" O3' DA C 309 " pdb=" P DT C 310 " ideal model delta sinusoidal sigma weight residual -140.00 34.44 -174.44 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 7796 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.122: 2337 0.122 - 0.243: 11 0.243 - 0.365: 0 0.365 - 0.486: 0 0.486 - 0.608: 19 Chirality restraints: 2367 Sorted by residual: chirality pdb=" P DG H 136 " pdb=" OP1 DG H 136 " pdb=" OP2 DG H 136 " pdb=" O5' DG H 136 " both_signs ideal model delta sigma weight residual True 2.35 -2.95 -0.61 2.00e-01 2.50e+01 9.24e+00 chirality pdb=" P DC C 221 " pdb=" OP1 DC C 221 " pdb=" OP2 DC C 221 " pdb=" O5' DC C 221 " both_signs ideal model delta sigma weight residual True 2.35 -2.93 -0.59 2.00e-01 2.50e+01 8.60e+00 chirality pdb=" P DC H 48 " pdb=" OP1 DC H 48 " pdb=" OP2 DC H 48 " pdb=" O5' DC H 48 " both_signs ideal model delta sigma weight residual True 2.35 -2.93 -0.58 2.00e-01 2.50e+01 8.40e+00 ... (remaining 2364 not shown) Planarity restraints: 1540 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG I 42 " 0.036 5.00e-02 4.00e+02 5.41e-02 4.69e+00 pdb=" N PRO I 43 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO I 43 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO I 43 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DG C 202 " 0.001 2.00e-02 2.50e+03 1.17e-02 4.09e+00 pdb=" N9 DG C 202 " 0.008 2.00e-02 2.50e+03 pdb=" C8 DG C 202 " -0.001 2.00e-02 2.50e+03 pdb=" N7 DG C 202 " 0.000 2.00e-02 2.50e+03 pdb=" C5 DG C 202 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DG C 202 " -0.013 2.00e-02 2.50e+03 pdb=" O6 DG C 202 " 0.012 2.00e-02 2.50e+03 pdb=" N1 DG C 202 " 0.004 2.00e-02 2.50e+03 pdb=" C2 DG C 202 " -0.030 2.00e-02 2.50e+03 pdb=" N2 DG C 202 " 0.019 2.00e-02 2.50e+03 pdb=" N3 DG C 202 " 0.000 2.00e-02 2.50e+03 pdb=" C4 DG C 202 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE R 79 " -0.032 5.00e-02 4.00e+02 4.79e-02 3.68e+00 pdb=" N PRO R 80 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO R 80 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO R 80 " -0.027 5.00e-02 4.00e+02 ... (remaining 1537 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1301 2.74 - 3.28: 12529 3.28 - 3.82: 27024 3.82 - 4.36: 30349 4.36 - 4.90: 44242 Nonbonded interactions: 115445 Sorted by model distance: nonbonded pdb=" N2 DG C 262 " pdb=" O2 DC H 53 " model vdw 2.200 2.496 nonbonded pdb=" N2 DG C 181 " pdb=" O2 DC H 134 " model vdw 2.201 2.496 nonbonded pdb=" OG SER I 57 " pdb=" OE1 GLU I 59 " model vdw 2.209 3.040 nonbonded pdb=" OP2 DG C 187 " pdb=" OG SER S 53 " model vdw 2.225 3.040 nonbonded pdb=" O2 DC C 180 " pdb=" N2 DG H 135 " model vdw 2.227 2.496 ... (remaining 115440 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 'I' selection = (chain 'O' and resid 38 through 135) } ncs_group { reference = (chain 'J' and ((resid 21 through 23 and (name N or name CA or name C or name O \ or name CB )) or resid 24 through 102)) selection = (chain 'Q' and resid 21 through 102) } ncs_group { reference = (chain 'K' and resid 12 through 119) selection = (chain 'R' and ((resid 12 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 56 or (resid 57 and (name N or name CA or name \ C or name O or name CB )) or resid 58 through 61 or (resid 62 and (name N or na \ me CA or name C or name O or name CB )) or resid 63 through 93 or (resid 94 and \ (name N or name CA or name C or name O or name CB )) or resid 95 through 119)) } ncs_group { reference = chain 'M' selection = (chain 'S' and (resid 28 through 105 or (resid 106 through 107 and (name N or na \ me CA or name C or name O or name CB )) or resid 108 through 122)) } 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=0.23 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: 0.370 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 13.130 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 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 : 0.005 0.045 14313 Z= 0.202 Angle : 0.710 9.048 20699 Z= 0.390 Chirality : 0.060 0.608 2367 Planarity : 0.004 0.054 1540 Dihedral : 30.149 179.048 6105 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 0.85 % Allowed : 30.31 % Favored : 68.84 % 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 aren not related in a simple way. whole: 0.94 (0.28), residues: 879 helix: 1.55 (0.22), residues: 553 sheet: 1.21 (1.16), residues: 21 loop : -1.17 (0.33), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG J 95 TYR 0.020 0.002 TYR J 88 PHE 0.009 0.001 PHE J 100 TRP 0.007 0.001 TRP A 176 HIS 0.004 0.001 HIS S 79 Details of bonding type rmsd covalent geometry : bond 0.00456 (14313) covalent geometry : angle 0.70969 (20699) hydrogen bonds : bond 0.13680 ( 809) hydrogen bonds : angle 5.46606 ( 2001) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 138 time to evaluate : 0.284 Fit side-chains REVERT: I 59 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.7419 (pm20) REVERT: M 61 SER cc_start: 0.9096 (m) cc_final: 0.8864 (m) REVERT: Q 91 LYS cc_start: 0.8994 (ttpt) cc_final: 0.8785 (ttmm) outliers start: 6 outliers final: 2 residues processed: 140 average time/residue: 0.1291 time to fit residues: 24.4269 Evaluate side-chains 140 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 137 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 59 GLU Chi-restraints excluded: chain J residue 62 LEU Chi-restraints excluded: chain M residue 44 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 108 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 113 optimal weight: 0.9990 chunk 53 optimal weight: 0.0980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 0.4980 chunk 100 optimal weight: 0.9990 overall best weight: 0.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 84 GLN ** M 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 108 ASN Q 25 ASN Q 93 GLN ** R 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.180206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.120920 restraints weight = 38461.677| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.48 r_work: 0.3105 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3111 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3111 r_free = 0.3111 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3111 r_free = 0.3111 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3111 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.1008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14313 Z= 0.165 Angle : 0.613 8.053 20699 Z= 0.356 Chirality : 0.036 0.144 2367 Planarity : 0.004 0.052 1540 Dihedral : 32.468 178.905 4442 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 3.54 % Allowed : 27.90 % Favored : 68.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.33 (0.29), residues: 879 helix: 1.84 (0.22), residues: 574 sheet: 0.74 (1.22), residues: 21 loop : -1.14 (0.34), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 95 TYR 0.017 0.001 TYR J 88 PHE 0.010 0.001 PHE J 100 TRP 0.005 0.001 TRP A 176 HIS 0.004 0.001 HIS S 106 Details of bonding type rmsd covalent geometry : bond 0.00378 (14313) covalent geometry : angle 0.61288 (20699) hydrogen bonds : bond 0.05502 ( 809) hydrogen bonds : angle 3.19687 ( 2001) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 168 time to evaluate : 0.329 Fit side-chains REVERT: J 78 ARG cc_start: 0.8826 (ptp90) cc_final: 0.8247 (ptt-90) REVERT: K 25 PHE cc_start: 0.8800 (OUTLIER) cc_final: 0.7564 (t80) REVERT: M 44 GLN cc_start: 0.8669 (tt0) cc_final: 0.8157 (tt0) REVERT: M 61 SER cc_start: 0.8989 (m) cc_final: 0.8748 (m) REVERT: O 73 GLU cc_start: 0.9217 (tm-30) cc_final: 0.8801 (tt0) REVERT: Q 91 LYS cc_start: 0.8981 (ttpt) cc_final: 0.8734 (ttmm) REVERT: R 89 ASN cc_start: 0.8612 (m-40) cc_final: 0.8126 (m-40) REVERT: S 118 TYR cc_start: 0.8233 (t80) cc_final: 0.7997 (t80) outliers start: 25 outliers final: 9 residues processed: 182 average time/residue: 0.1329 time to fit residues: 32.5200 Evaluate side-chains 158 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 148 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 70 LEU Chi-restraints excluded: chain J residue 43 VAL Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain J residue 84 MET Chi-restraints excluded: chain K residue 25 PHE Chi-restraints excluded: chain K residue 110 ASN Chi-restraints excluded: chain M residue 90 GLU Chi-restraints excluded: chain Q residue 82 THR Chi-restraints excluded: chain S residue 36 ILE Chi-restraints excluded: chain S residue 98 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 56 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 26 optimal weight: 20.0000 chunk 112 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 chunk 55 optimal weight: 0.5980 chunk 4 optimal weight: 0.0570 chunk 42 optimal weight: 0.0570 chunk 46 optimal weight: 3.9990 chunk 84 optimal weight: 7.9990 chunk 53 optimal weight: 1.9990 overall best weight: 0.9420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 25 ASN ** R 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.179462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.119982 restraints weight = 42683.759| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 2.72 r_work: 0.3073 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3072 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3072 r_free = 0.3072 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3072 r_free = 0.3072 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3072 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.1223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14313 Z= 0.169 Angle : 0.607 8.559 20699 Z= 0.352 Chirality : 0.037 0.178 2367 Planarity : 0.004 0.054 1540 Dihedral : 32.429 178.647 4434 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 3.54 % Allowed : 28.33 % Favored : 68.13 % 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 aren not related in a simple way. whole: 1.41 (0.28), residues: 879 helix: 1.91 (0.22), residues: 576 sheet: 0.51 (1.20), residues: 21 loop : -1.14 (0.34), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 95 TYR 0.016 0.001 TYR M 118 PHE 0.009 0.001 PHE J 100 TRP 0.004 0.001 TRP A 176 HIS 0.005 0.001 HIS Q 75 Details of bonding type rmsd covalent geometry : bond 0.00390 (14313) covalent geometry : angle 0.60715 (20699) hydrogen bonds : bond 0.05324 ( 809) hydrogen bonds : angle 3.08345 ( 2001) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 154 time to evaluate : 0.210 Fit side-chains revert: symmetry clash REVERT: D 1 MET cc_start: 0.7023 (mtt) cc_final: 0.4651 (tmm) REVERT: K 25 PHE cc_start: 0.8863 (OUTLIER) cc_final: 0.7567 (t80) REVERT: M 44 GLN cc_start: 0.8642 (tt0) cc_final: 0.8138 (tt0) REVERT: M 61 SER cc_start: 0.8966 (m) cc_final: 0.8729 (m) REVERT: O 59 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.7676 (pm20) REVERT: O 73 GLU cc_start: 0.9223 (tm-30) cc_final: 0.8692 (tt0) REVERT: R 89 ASN cc_start: 0.8615 (m-40) cc_final: 0.8285 (m-40) REVERT: S 90 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7580 (tp30) REVERT: S 96 ARG cc_start: 0.8408 (ttm-80) cc_final: 0.8085 (ttm170) outliers start: 25 outliers final: 12 residues processed: 168 average time/residue: 0.1172 time to fit residues: 26.5631 Evaluate side-chains 162 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 147 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 65 LEU Chi-restraints excluded: chain I residue 70 LEU Chi-restraints excluded: chain I residue 118 THR Chi-restraints excluded: chain J residue 43 VAL Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain J residue 84 MET Chi-restraints excluded: chain K residue 25 PHE Chi-restraints excluded: chain K residue 110 ASN Chi-restraints excluded: chain M residue 52 SER Chi-restraints excluded: chain O residue 59 GLU Chi-restraints excluded: chain R residue 20 ARG Chi-restraints excluded: chain R residue 83 LEU Chi-restraints excluded: chain S residue 36 ILE Chi-restraints excluded: chain S residue 90 GLU Chi-restraints excluded: chain S residue 98 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 49 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 30 optimal weight: 7.9990 chunk 7 optimal weight: 10.0000 chunk 113 optimal weight: 4.9990 chunk 92 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 27 optimal weight: 20.0000 chunk 99 optimal weight: 0.8980 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 2 GLN I 76 GLN ** M 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 25 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 = 0.4033 r_free = 0.4033 target = 0.171814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.111347 restraints weight = 32735.963| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 2.46 r_work: 0.2959 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2962 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2962 r_free = 0.2962 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2962 r_free = 0.2962 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2962 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 14313 Z= 0.287 Angle : 0.694 12.279 20699 Z= 0.393 Chirality : 0.041 0.200 2367 Planarity : 0.005 0.054 1540 Dihedral : 32.753 178.031 4434 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 4.96 % Allowed : 28.33 % Favored : 66.71 % 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 aren not related in a simple way. whole: 1.07 (0.28), residues: 879 helix: 1.64 (0.21), residues: 576 sheet: -0.03 (1.15), residues: 21 loop : -1.20 (0.34), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J 95 TYR 0.031 0.003 TYR Q 88 PHE 0.008 0.002 PHE A 190 TRP 0.013 0.002 TRP A 176 HIS 0.006 0.002 HIS S 106 Details of bonding type rmsd covalent geometry : bond 0.00676 (14313) covalent geometry : angle 0.69441 (20699) hydrogen bonds : bond 0.06196 ( 809) hydrogen bonds : angle 3.31321 ( 2001) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 151 time to evaluate : 0.319 Fit side-chains revert: symmetry clash REVERT: D 6 LYS cc_start: 0.9127 (mmtm) cc_final: 0.7040 (tppt) REVERT: I 59 GLU cc_start: 0.8597 (pm20) cc_final: 0.8087 (pm20) REVERT: K 42 ARG cc_start: 0.7717 (OUTLIER) cc_final: 0.6989 (ptm160) REVERT: K 73 ASN cc_start: 0.8610 (t0) cc_final: 0.8407 (t0) REVERT: O 51 ILE cc_start: 0.8608 (OUTLIER) cc_final: 0.7993 (mt) REVERT: O 59 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.7785 (pm20) REVERT: Q 25 ASN cc_start: 0.9130 (t0) cc_final: 0.8871 (t0) REVERT: R 83 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8769 (mp) outliers start: 35 outliers final: 18 residues processed: 176 average time/residue: 0.1294 time to fit residues: 30.5048 Evaluate side-chains 163 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 141 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain I residue 65 LEU Chi-restraints excluded: chain I residue 70 LEU Chi-restraints excluded: chain I residue 107 THR Chi-restraints excluded: chain I residue 118 THR Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain J residue 84 MET Chi-restraints excluded: chain K residue 42 ARG Chi-restraints excluded: chain K residue 110 ASN Chi-restraints excluded: chain K residue 114 VAL Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain M residue 52 SER Chi-restraints excluded: chain M residue 90 GLU Chi-restraints excluded: chain O residue 51 ILE Chi-restraints excluded: chain O residue 59 GLU Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 83 LEU Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain S residue 36 ILE Chi-restraints excluded: chain S residue 84 SER Chi-restraints excluded: chain S residue 98 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 60 optimal weight: 0.8980 chunk 67 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 30 optimal weight: 7.9990 chunk 44 optimal weight: 0.8980 chunk 96 optimal weight: 4.9990 chunk 2 optimal weight: 9.9990 chunk 62 optimal weight: 0.7980 chunk 59 optimal weight: 6.9990 chunk 63 optimal weight: 0.6980 chunk 93 optimal weight: 0.3980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 76 GLN M 46 HIS ** M 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 125 GLN Q 25 ASN Q 93 GLN ** R 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 79 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.177525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.120134 restraints weight = 51330.462| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 2.97 r_work: 0.3008 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3015 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3015 r_free = 0.3015 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3015 r_free = 0.3015 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3015 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14313 Z= 0.162 Angle : 0.610 9.965 20699 Z= 0.352 Chirality : 0.036 0.200 2367 Planarity : 0.004 0.058 1540 Dihedral : 32.469 179.569 4434 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 4.67 % Allowed : 27.62 % Favored : 67.71 % 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 aren not related in a simple way. whole: 1.44 (0.28), residues: 879 helix: 1.97 (0.22), residues: 577 sheet: -0.16 (1.13), residues: 21 loop : -1.15 (0.34), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG M 83 TYR 0.012 0.001 TYR M 118 PHE 0.010 0.001 PHE A 190 TRP 0.004 0.001 TRP A 176 HIS 0.005 0.001 HIS S 79 Details of bonding type rmsd covalent geometry : bond 0.00370 (14313) covalent geometry : angle 0.60954 (20699) hydrogen bonds : bond 0.05231 ( 809) hydrogen bonds : angle 2.93719 ( 2001) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 158 time to evaluate : 0.409 Fit side-chains revert: symmetry clash REVERT: D 6 LYS cc_start: 0.9080 (mmtm) cc_final: 0.7502 (tppt) REVERT: K 25 PHE cc_start: 0.8980 (OUTLIER) cc_final: 0.7741 (t80) REVERT: K 73 ASN cc_start: 0.8621 (t0) cc_final: 0.8364 (t0) REVERT: M 44 GLN cc_start: 0.8524 (tt0) cc_final: 0.8078 (tt0) REVERT: M 98 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8139 (mm) REVERT: O 51 ILE cc_start: 0.8642 (OUTLIER) cc_final: 0.8034 (mt) REVERT: O 59 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.7973 (pm20) REVERT: O 81 ASP cc_start: 0.8257 (t0) cc_final: 0.7786 (t0) REVERT: Q 25 ASN cc_start: 0.9228 (OUTLIER) cc_final: 0.8857 (t0) REVERT: R 89 ASN cc_start: 0.8535 (m-40) cc_final: 0.8193 (m-40) outliers start: 33 outliers final: 15 residues processed: 181 average time/residue: 0.1223 time to fit residues: 30.0454 Evaluate side-chains 165 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 145 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain I residue 65 LEU Chi-restraints excluded: chain I residue 70 LEU Chi-restraints excluded: chain I residue 76 GLN Chi-restraints excluded: chain I residue 107 THR Chi-restraints excluded: chain J residue 43 VAL Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain J residue 84 MET Chi-restraints excluded: chain K residue 25 PHE Chi-restraints excluded: chain K residue 85 LEU Chi-restraints excluded: chain M residue 52 SER Chi-restraints excluded: chain M residue 98 LEU Chi-restraints excluded: chain O residue 51 ILE Chi-restraints excluded: chain O residue 59 GLU Chi-restraints excluded: chain Q residue 25 ASN Chi-restraints excluded: chain R residue 19 SER Chi-restraints excluded: chain R residue 83 LEU Chi-restraints excluded: chain S residue 36 ILE Chi-restraints excluded: chain S residue 84 SER Chi-restraints excluded: chain S residue 98 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 111 optimal weight: 0.9990 chunk 26 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 17 optimal weight: 8.9990 chunk 24 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 chunk 35 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.6980 chunk 60 optimal weight: 3.9990 chunk 82 optimal weight: 0.3980 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 76 GLN M 46 HIS ** M 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 79 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.174432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.115272 restraints weight = 42791.150| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.61 r_work: 0.2990 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2989 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2989 r_free = 0.2989 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2989 r_free = 0.2989 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.2989 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 14313 Z= 0.208 Angle : 0.636 10.904 20699 Z= 0.364 Chirality : 0.038 0.214 2367 Planarity : 0.004 0.055 1540 Dihedral : 32.574 178.236 4434 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 5.24 % Allowed : 28.05 % Favored : 66.71 % 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 aren not related in a simple way. whole: 1.35 (0.28), residues: 879 helix: 1.90 (0.22), residues: 579 sheet: -0.15 (1.12), residues: 21 loop : -1.21 (0.34), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG M 83 TYR 0.026 0.002 TYR Q 88 PHE 0.009 0.001 PHE A 190 TRP 0.008 0.001 TRP A 176 HIS 0.005 0.001 HIS M 46 Details of bonding type rmsd covalent geometry : bond 0.00488 (14313) covalent geometry : angle 0.63566 (20699) hydrogen bonds : bond 0.05470 ( 809) hydrogen bonds : angle 3.05090 ( 2001) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 152 time to evaluate : 0.327 Fit side-chains revert: symmetry clash REVERT: D 1 MET cc_start: 0.6886 (mtt) cc_final: 0.4998 (tmm) REVERT: K 25 PHE cc_start: 0.9028 (OUTLIER) cc_final: 0.7688 (t80) REVERT: K 73 ASN cc_start: 0.8654 (t0) cc_final: 0.8400 (t0) REVERT: M 44 GLN cc_start: 0.8528 (tt0) cc_final: 0.8067 (tt0) REVERT: M 98 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8084 (mm) REVERT: O 51 ILE cc_start: 0.8621 (OUTLIER) cc_final: 0.8022 (mt) REVERT: O 59 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.7930 (pm20) REVERT: O 81 ASP cc_start: 0.8281 (t0) cc_final: 0.7774 (t0) REVERT: Q 25 ASN cc_start: 0.9140 (t0) cc_final: 0.8920 (t0) REVERT: Q 27 GLN cc_start: 0.9346 (mm110) cc_final: 0.9040 (mm-40) REVERT: Q 97 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8697 (tp) outliers start: 37 outliers final: 22 residues processed: 179 average time/residue: 0.1178 time to fit residues: 28.5991 Evaluate side-chains 172 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 145 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 TRP Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain I residue 65 LEU Chi-restraints excluded: chain I residue 70 LEU Chi-restraints excluded: chain I residue 76 GLN Chi-restraints excluded: chain I residue 107 THR Chi-restraints excluded: chain I residue 118 THR Chi-restraints excluded: chain J residue 43 VAL Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain J residue 84 MET Chi-restraints excluded: chain K residue 25 PHE Chi-restraints excluded: chain K residue 110 ASN Chi-restraints excluded: chain K residue 114 VAL Chi-restraints excluded: chain M residue 52 SER Chi-restraints excluded: chain M residue 98 LEU Chi-restraints excluded: chain O residue 51 ILE Chi-restraints excluded: chain O residue 59 GLU Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain Q residue 97 LEU Chi-restraints excluded: chain R residue 19 SER Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 83 LEU Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain S residue 36 ILE Chi-restraints excluded: chain S residue 84 SER Chi-restraints excluded: chain S residue 98 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 72 optimal weight: 0.9990 chunk 28 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 31 optimal weight: 7.9990 chunk 76 optimal weight: 2.9990 chunk 5 optimal weight: 20.0000 chunk 57 optimal weight: 0.8980 chunk 19 optimal weight: 10.0000 chunk 16 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 76 GLN M 46 HIS ** M 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 25 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 = 0.4052 r_free = 0.4052 target = 0.174235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.114454 restraints weight = 37443.959| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.56 r_work: 0.2997 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2996 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2996 r_free = 0.2996 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2996 r_free = 0.2996 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.2996 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 14313 Z= 0.203 Angle : 0.636 10.305 20699 Z= 0.363 Chirality : 0.038 0.217 2367 Planarity : 0.004 0.055 1540 Dihedral : 32.581 177.716 4434 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 5.10 % Allowed : 27.76 % Favored : 67.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.34 (0.28), residues: 879 helix: 1.89 (0.22), residues: 580 sheet: -0.51 (1.09), residues: 22 loop : -1.20 (0.34), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG M 83 TYR 0.027 0.002 TYR Q 88 PHE 0.010 0.001 PHE J 100 TRP 0.007 0.001 TRP A 176 HIS 0.004 0.001 HIS Q 75 Details of bonding type rmsd covalent geometry : bond 0.00477 (14313) covalent geometry : angle 0.63572 (20699) hydrogen bonds : bond 0.05427 ( 809) hydrogen bonds : angle 3.02933 ( 2001) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 146 time to evaluate : 0.365 Fit side-chains revert: symmetry clash REVERT: D 1 MET cc_start: 0.6555 (mtt) cc_final: 0.4650 (tmm) REVERT: D 6 LYS cc_start: 0.9016 (mmtm) cc_final: 0.7092 (tppt) REVERT: K 25 PHE cc_start: 0.9021 (OUTLIER) cc_final: 0.7750 (t80) REVERT: K 73 ASN cc_start: 0.8609 (t0) cc_final: 0.8389 (t0) REVERT: M 44 GLN cc_start: 0.8508 (tt0) cc_final: 0.8046 (tt0) REVERT: M 98 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8109 (mm) REVERT: O 51 ILE cc_start: 0.8633 (OUTLIER) cc_final: 0.8043 (mt) REVERT: O 59 GLU cc_start: 0.8475 (OUTLIER) cc_final: 0.7932 (pm20) REVERT: O 73 GLU cc_start: 0.9314 (tm-30) cc_final: 0.8995 (tt0) REVERT: O 81 ASP cc_start: 0.8279 (t0) cc_final: 0.7777 (t0) REVERT: Q 25 ASN cc_start: 0.9104 (t0) cc_final: 0.8886 (t0) REVERT: Q 27 GLN cc_start: 0.9370 (mm110) cc_final: 0.9072 (mm-40) REVERT: S 61 SER cc_start: 0.9304 (OUTLIER) cc_final: 0.8844 (m) outliers start: 36 outliers final: 27 residues processed: 172 average time/residue: 0.1436 time to fit residues: 33.3747 Evaluate side-chains 172 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 140 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 TRP Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain I residue 65 LEU Chi-restraints excluded: chain I residue 70 LEU Chi-restraints excluded: chain I residue 71 VAL Chi-restraints excluded: chain I residue 76 GLN Chi-restraints excluded: chain I residue 107 THR Chi-restraints excluded: chain I residue 118 THR Chi-restraints excluded: chain J residue 43 VAL Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain J residue 84 MET Chi-restraints excluded: chain K residue 25 PHE Chi-restraints excluded: chain K residue 85 LEU Chi-restraints excluded: chain K residue 110 ASN Chi-restraints excluded: chain K residue 114 VAL Chi-restraints excluded: chain M residue 52 SER Chi-restraints excluded: chain M residue 98 LEU Chi-restraints excluded: chain M residue 103 LEU Chi-restraints excluded: chain O residue 51 ILE Chi-restraints excluded: chain O residue 59 GLU Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain Q residue 82 THR Chi-restraints excluded: chain R residue 19 SER Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 83 LEU Chi-restraints excluded: chain S residue 36 ILE Chi-restraints excluded: chain S residue 43 LYS Chi-restraints excluded: chain S residue 61 SER Chi-restraints excluded: chain S residue 84 SER Chi-restraints excluded: chain S residue 98 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 54 optimal weight: 0.6980 chunk 105 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 19 optimal weight: 10.0000 chunk 111 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 79 optimal weight: 5.9990 chunk 59 optimal weight: 9.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 46 HIS ** M 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.175761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.115778 restraints weight = 31321.664| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 2.33 r_work: 0.3043 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3043 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3043 r_free = 0.3043 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3043 r_free = 0.3043 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3043 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 14313 Z= 0.173 Angle : 0.618 10.748 20699 Z= 0.354 Chirality : 0.037 0.224 2367 Planarity : 0.004 0.057 1540 Dihedral : 32.536 177.874 4434 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 4.39 % Allowed : 28.90 % Favored : 66.71 % 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 aren not related in a simple way. whole: 1.47 (0.29), residues: 879 helix: 1.99 (0.22), residues: 580 sheet: -0.45 (1.10), residues: 22 loop : -1.14 (0.34), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG M 83 TYR 0.020 0.002 TYR S 118 PHE 0.009 0.001 PHE J 100 TRP 0.006 0.001 TRP A 176 HIS 0.005 0.001 HIS Q 75 Details of bonding type rmsd covalent geometry : bond 0.00400 (14313) covalent geometry : angle 0.61775 (20699) hydrogen bonds : bond 0.05230 ( 809) hydrogen bonds : angle 2.95426 ( 2001) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 146 time to evaluate : 0.264 Fit side-chains REVERT: D 1 MET cc_start: 0.6475 (mtt) cc_final: 0.4214 (tmm) REVERT: I 58 THR cc_start: 0.8926 (t) cc_final: 0.8616 (t) REVERT: I 59 GLU cc_start: 0.8282 (pm20) cc_final: 0.7926 (pm20) REVERT: K 25 PHE cc_start: 0.8987 (OUTLIER) cc_final: 0.7744 (t80) REVERT: M 44 GLN cc_start: 0.8495 (tt0) cc_final: 0.7955 (tt0) REVERT: M 98 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8124 (mm) REVERT: O 51 ILE cc_start: 0.8631 (OUTLIER) cc_final: 0.8051 (mt) REVERT: O 59 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.7968 (pm20) REVERT: O 73 GLU cc_start: 0.9286 (tm-30) cc_final: 0.9031 (tt0) REVERT: O 81 ASP cc_start: 0.8217 (t0) cc_final: 0.7718 (t0) REVERT: Q 27 GLN cc_start: 0.9360 (mm110) cc_final: 0.9065 (mm-40) outliers start: 31 outliers final: 21 residues processed: 168 average time/residue: 0.1267 time to fit residues: 29.0120 Evaluate side-chains 165 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 140 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 TRP Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain I residue 65 LEU Chi-restraints excluded: chain I residue 70 LEU Chi-restraints excluded: chain I residue 71 VAL Chi-restraints excluded: chain I residue 107 THR Chi-restraints excluded: chain J residue 43 VAL Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain J residue 84 MET Chi-restraints excluded: chain K residue 25 PHE Chi-restraints excluded: chain K residue 110 ASN Chi-restraints excluded: chain M residue 52 SER Chi-restraints excluded: chain M residue 98 LEU Chi-restraints excluded: chain M residue 103 LEU Chi-restraints excluded: chain O residue 51 ILE Chi-restraints excluded: chain O residue 59 GLU Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain Q residue 82 THR Chi-restraints excluded: chain R residue 20 ARG Chi-restraints excluded: chain R residue 83 LEU Chi-restraints excluded: chain S residue 36 ILE Chi-restraints excluded: chain S residue 84 SER Chi-restraints excluded: chain S residue 98 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 102 optimal weight: 0.7980 chunk 24 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 9 optimal weight: 6.9990 chunk 29 optimal weight: 8.9990 chunk 85 optimal weight: 0.9980 chunk 75 optimal weight: 3.9990 chunk 21 optimal weight: 0.0970 chunk 98 optimal weight: 4.9990 chunk 40 optimal weight: 6.9990 chunk 96 optimal weight: 9.9990 overall best weight: 1.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 76 GLN M 46 HIS ** M 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 25 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 = 0.4048 r_free = 0.4048 target = 0.174079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.114792 restraints weight = 33959.018| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.46 r_work: 0.3007 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3003 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3003 r_free = 0.3003 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3003 r_free = 0.3003 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3003 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 14313 Z= 0.206 Angle : 0.638 10.519 20699 Z= 0.365 Chirality : 0.038 0.223 2367 Planarity : 0.004 0.056 1540 Dihedral : 32.585 177.418 4434 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 4.11 % Allowed : 28.90 % Favored : 67.00 % 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 aren not related in a simple way. whole: 1.42 (0.28), residues: 879 helix: 1.94 (0.22), residues: 579 sheet: 0.05 (1.13), residues: 22 loop : -1.18 (0.34), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG M 83 TYR 0.027 0.002 TYR Q 88 PHE 0.009 0.002 PHE J 100 TRP 0.006 0.001 TRP A 176 HIS 0.005 0.001 HIS Q 75 Details of bonding type rmsd covalent geometry : bond 0.00485 (14313) covalent geometry : angle 0.63829 (20699) hydrogen bonds : bond 0.05415 ( 809) hydrogen bonds : angle 3.00848 ( 2001) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 141 time to evaluate : 0.361 Fit side-chains REVERT: D 1 MET cc_start: 0.5699 (mtt) cc_final: 0.5333 (mtt) REVERT: D 6 LYS cc_start: 0.8868 (mmtm) cc_final: 0.6866 (tppt) REVERT: I 58 THR cc_start: 0.8908 (t) cc_final: 0.8620 (t) REVERT: K 25 PHE cc_start: 0.9018 (OUTLIER) cc_final: 0.7748 (t80) REVERT: M 98 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8089 (mm) REVERT: O 51 ILE cc_start: 0.8620 (OUTLIER) cc_final: 0.8029 (mt) REVERT: O 59 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.7917 (pm20) REVERT: O 63 ARG cc_start: 0.8506 (OUTLIER) cc_final: 0.7722 (mmt-90) REVERT: O 73 GLU cc_start: 0.9275 (tm-30) cc_final: 0.8969 (tt0) REVERT: O 81 ASP cc_start: 0.8384 (t0) cc_final: 0.7949 (t0) REVERT: Q 97 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8709 (tp) REVERT: R 76 THR cc_start: 0.9159 (p) cc_final: 0.8931 (t) REVERT: S 61 SER cc_start: 0.9299 (OUTLIER) cc_final: 0.8834 (m) outliers start: 29 outliers final: 19 residues processed: 163 average time/residue: 0.1430 time to fit residues: 31.1610 Evaluate side-chains 164 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 138 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 TRP Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain I residue 65 LEU Chi-restraints excluded: chain I residue 70 LEU Chi-restraints excluded: chain I residue 71 VAL Chi-restraints excluded: chain I residue 107 THR Chi-restraints excluded: chain J residue 43 VAL Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain J residue 84 MET Chi-restraints excluded: chain K residue 25 PHE Chi-restraints excluded: chain K residue 110 ASN Chi-restraints excluded: chain M residue 52 SER Chi-restraints excluded: chain M residue 98 LEU Chi-restraints excluded: chain M residue 103 LEU Chi-restraints excluded: chain O residue 51 ILE Chi-restraints excluded: chain O residue 59 GLU Chi-restraints excluded: chain O residue 63 ARG Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain Q residue 97 LEU Chi-restraints excluded: chain R residue 20 ARG Chi-restraints excluded: chain R residue 83 LEU Chi-restraints excluded: chain S residue 36 ILE Chi-restraints excluded: chain S residue 61 SER Chi-restraints excluded: chain S residue 84 SER Chi-restraints excluded: chain S residue 98 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 72 optimal weight: 0.2980 chunk 98 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 chunk 82 optimal weight: 0.7980 chunk 26 optimal weight: 20.0000 chunk 0 optimal weight: 0.7980 chunk 18 optimal weight: 7.9990 chunk 57 optimal weight: 0.7980 chunk 100 optimal weight: 0.6980 chunk 70 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 76 GLN M 46 HIS ** M 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 25 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 = 0.4086 r_free = 0.4086 target = 0.177837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.120429 restraints weight = 47524.774| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 2.89 r_work: 0.3043 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3038 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3038 r_free = 0.3038 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3038 r_free = 0.3038 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3038 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 14313 Z= 0.160 Angle : 0.612 9.895 20699 Z= 0.352 Chirality : 0.037 0.223 2367 Planarity : 0.004 0.060 1540 Dihedral : 32.470 177.762 4434 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 3.12 % Allowed : 29.89 % Favored : 67.00 % 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 aren not related in a simple way. whole: 1.64 (0.29), residues: 879 helix: 2.10 (0.22), residues: 579 sheet: 0.40 (1.14), residues: 22 loop : -1.10 (0.35), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG M 83 TYR 0.014 0.001 TYR Q 88 PHE 0.010 0.001 PHE J 100 TRP 0.004 0.001 TRP A 176 HIS 0.005 0.001 HIS Q 75 Details of bonding type rmsd covalent geometry : bond 0.00367 (14313) covalent geometry : angle 0.61204 (20699) hydrogen bonds : bond 0.05110 ( 809) hydrogen bonds : angle 2.85555 ( 2001) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 150 time to evaluate : 0.351 Fit side-chains REVERT: D 1 MET cc_start: 0.5870 (mtt) cc_final: 0.5441 (mtt) REVERT: K 25 PHE cc_start: 0.8914 (OUTLIER) cc_final: 0.7663 (t80) REVERT: K 74 LYS cc_start: 0.8921 (ptpp) cc_final: 0.8559 (ttpt) REVERT: M 44 GLN cc_start: 0.8510 (tt0) cc_final: 0.7910 (tt0) REVERT: M 98 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8065 (mm) REVERT: O 51 ILE cc_start: 0.8630 (OUTLIER) cc_final: 0.8032 (mt) REVERT: O 59 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.8009 (pm20) REVERT: O 73 GLU cc_start: 0.9276 (tm-30) cc_final: 0.8940 (tt0) REVERT: O 81 ASP cc_start: 0.8286 (t0) cc_final: 0.7800 (t0) REVERT: Q 27 GLN cc_start: 0.9348 (mm110) cc_final: 0.9071 (mm-40) REVERT: Q 97 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8699 (tp) outliers start: 22 outliers final: 16 residues processed: 167 average time/residue: 0.1337 time to fit residues: 30.2430 Evaluate side-chains 165 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 144 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 TRP Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain I residue 65 LEU Chi-restraints excluded: chain I residue 70 LEU Chi-restraints excluded: chain I residue 71 VAL Chi-restraints excluded: chain I residue 107 THR Chi-restraints excluded: chain J residue 43 VAL Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain J residue 84 MET Chi-restraints excluded: chain K residue 25 PHE Chi-restraints excluded: chain K residue 114 VAL Chi-restraints excluded: chain M residue 52 SER Chi-restraints excluded: chain M residue 98 LEU Chi-restraints excluded: chain O residue 51 ILE Chi-restraints excluded: chain O residue 59 GLU Chi-restraints excluded: chain Q residue 97 LEU Chi-restraints excluded: chain R residue 20 ARG Chi-restraints excluded: chain R residue 83 LEU Chi-restraints excluded: chain S residue 36 ILE Chi-restraints excluded: chain S residue 84 SER Chi-restraints excluded: chain S residue 98 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 89 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 41 optimal weight: 8.9990 chunk 11 optimal weight: 6.9990 chunk 88 optimal weight: 0.0980 chunk 78 optimal weight: 5.9990 chunk 100 optimal weight: 1.9990 chunk 19 optimal weight: 10.0000 chunk 70 optimal weight: 5.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 46 HIS ** M 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 25 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.177303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.118679 restraints weight = 38164.894| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 2.38 r_work: 0.3065 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3061 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3061 r_free = 0.3061 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3061 r_free = 0.3061 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3061 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 14313 Z= 0.167 Angle : 0.612 9.755 20699 Z= 0.352 Chirality : 0.037 0.228 2367 Planarity : 0.004 0.058 1540 Dihedral : 32.435 177.604 4434 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 3.54 % Allowed : 29.32 % Favored : 67.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.66 (0.29), residues: 879 helix: 2.11 (0.22), residues: 579 sheet: 0.44 (1.22), residues: 22 loop : -1.08 (0.35), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG I 131 TYR 0.020 0.002 TYR Q 88 PHE 0.009 0.001 PHE J 100 TRP 0.005 0.001 TRP A 176 HIS 0.005 0.001 HIS Q 75 Details of bonding type rmsd covalent geometry : bond 0.00386 (14313) covalent geometry : angle 0.61245 (20699) hydrogen bonds : bond 0.05136 ( 809) hydrogen bonds : angle 2.87407 ( 2001) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2980.31 seconds wall clock time: 51 minutes 29.10 seconds (3089.10 seconds total)