Starting phenix.real_space_refine on Thu Jul 31 02:44:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u5h_41922/07_2025/8u5h_41922.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u5h_41922/07_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_41922/07_2025/8u5h_41922.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u5h_41922/07_2025/8u5h_41922.map" model { file = "/net/cci-nas-00/data/ceres_data/8u5h_41922/07_2025/8u5h_41922.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u5h_41922/07_2025/8u5h_41922.cif" } resolution = 3.23 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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, 'GLU:plan': 1, 'ARG:plan': 3, 'TRP:plan': 2, 'ASP: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: {'GLN:plan1': 1, 'GLU:plan': 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: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} 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: 8.54, per 1000 atoms: 0.64 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: 3.42 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 6.97 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: 6.46 Time building geometry restraints manager: 4.06 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.540 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 39.240 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.890 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.007 0.001 TRP A 176 HIS 0.004 0.001 HIS S 79 PHE 0.009 0.001 PHE J 100 TYR 0.020 0.002 TYR J 88 ARG 0.009 0.000 ARG J 95 Details of bonding type rmsd hydrogen bonds : bond 0.13680 ( 809) hydrogen bonds : angle 5.46606 ( 2001) covalent geometry : bond 0.00456 (14313) covalent geometry : angle 0.70969 (20699) *********************** 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 : 1.059 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: 0.3467 time to fit residues: 64.8675 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 : 1.019 ------------------------------------------------------------------------------- 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 97 optimal weight: 2.9990 chunk 87 optimal weight: 0.5980 chunk 48 optimal weight: 3.9990 chunk 29 optimal weight: 8.9990 chunk 58 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 chunk 67 optimal weight: 6.9990 chunk 104 optimal weight: 0.5980 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4084 r_free = 0.4084 target = 0.176702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.116434 restraints weight = 40089.557| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 2.60 r_work: 0.3031 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3027 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3027 r_free = 0.3027 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3027 r_free = 0.3027 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3027 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.1044 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= 0.205 Angle : 0.638 8.770 20699 Z= 0.369 Chirality : 0.038 0.156 2367 Planarity : 0.004 0.051 1540 Dihedral : 32.582 179.403 4442 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 3.82 % Allowed : 27.90 % Favored : 68.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.28), residues: 879 helix: 1.71 (0.22), residues: 576 sheet: 0.59 (1.19), residues: 21 loop : -1.22 (0.34), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 176 HIS 0.005 0.001 HIS S 106 PHE 0.010 0.001 PHE J 100 TYR 0.022 0.002 TYR J 88 ARG 0.007 0.001 ARG J 95 Details of bonding type rmsd hydrogen bonds : bond 0.05724 ( 809) hydrogen bonds : angle 3.28339 ( 2001) covalent geometry : bond 0.00481 (14313) covalent geometry : angle 0.63844 (20699) *********************** 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 189 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 162 time to evaluate : 1.083 Fit side-chains REVERT: D 12 THR cc_start: 0.2578 (OUTLIER) cc_final: 0.2322 (t) REVERT: J 78 ARG cc_start: 0.8893 (ptp90) cc_final: 0.8247 (ptt-90) REVERT: K 73 ASN cc_start: 0.8523 (t0) cc_final: 0.8304 (t0) REVERT: M 44 GLN cc_start: 0.8718 (tt0) cc_final: 0.8306 (tt0) REVERT: M 61 SER cc_start: 0.9012 (m) cc_final: 0.8765 (m) REVERT: O 81 ASP cc_start: 0.8093 (t0) cc_final: 0.7807 (t0) REVERT: R 89 ASN cc_start: 0.8698 (m-40) cc_final: 0.8078 (m-40) REVERT: S 37 TYR cc_start: 0.9326 (m-80) cc_final: 0.9081 (m-80) REVERT: S 118 TYR cc_start: 0.8477 (t80) cc_final: 0.8260 (t80) outliers start: 27 outliers final: 13 residues processed: 176 average time/residue: 0.3400 time to fit residues: 80.0636 Evaluate side-chains 158 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 144 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 12 THR 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 110 ASN Chi-restraints excluded: chain M residue 90 GLU Chi-restraints excluded: chain Q residue 82 THR 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 43 LYS 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 24 optimal weight: 9.9990 chunk 56 optimal weight: 0.7980 chunk 92 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 4 optimal weight: 0.0060 chunk 112 optimal weight: 0.5980 chunk 2 optimal weight: 0.0570 chunk 32 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 chunk 70 optimal weight: 10.0000 chunk 48 optimal weight: 1.9990 overall best weight: 0.6916 ------------------------------------------------------------------------------- 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 = 0.4108 r_free = 0.4108 target = 0.179121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.118798 restraints weight = 38106.607| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 2.46 r_work: 0.3084 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3083 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3083 r_free = 0.3083 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3083 r_free = 0.3083 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3083 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.1234 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= 0.162 Angle : 0.609 8.888 20699 Z= 0.352 Chirality : 0.037 0.173 2367 Planarity : 0.004 0.055 1540 Dihedral : 32.506 179.033 4434 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 3.26 % Allowed : 29.18 % Favored : 67.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.28), residues: 879 helix: 1.93 (0.22), residues: 574 sheet: 0.38 (1.19), residues: 21 loop : -1.14 (0.34), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 176 HIS 0.003 0.001 HIS J 75 PHE 0.007 0.001 PHE J 100 TYR 0.012 0.001 TYR K 39 ARG 0.007 0.000 ARG J 95 Details of bonding type rmsd hydrogen bonds : bond 0.05340 ( 809) hydrogen bonds : angle 3.07062 ( 2001) covalent geometry : bond 0.00372 (14313) covalent geometry : angle 0.60914 (20699) *********************** 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: 23 poor density : 156 time to evaluate : 1.053 Fit side-chains revert: symmetry clash REVERT: D 1 MET cc_start: 0.6790 (mtt) cc_final: 0.4599 (tmm) REVERT: K 25 PHE cc_start: 0.8909 (OUTLIER) cc_final: 0.7759 (t80) REVERT: K 73 ASN cc_start: 0.8583 (t0) cc_final: 0.8338 (t0) REVERT: M 44 GLN cc_start: 0.8654 (tt0) cc_final: 0.8150 (tt0) REVERT: O 59 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.7792 (pm20) REVERT: O 73 GLU cc_start: 0.9223 (tm-30) cc_final: 0.8670 (tt0) REVERT: R 89 ASN cc_start: 0.8578 (m-40) cc_final: 0.7907 (m-40) REVERT: S 65 ASP cc_start: 0.8902 (t0) cc_final: 0.8697 (t0) REVERT: S 77 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8955 (tt) outliers start: 23 outliers final: 10 residues processed: 170 average time/residue: 0.3351 time to fit residues: 76.3727 Evaluate side-chains 161 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 148 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 65 LEU 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 52 SER Chi-restraints excluded: chain O residue 59 GLU Chi-restraints excluded: chain R residue 20 ARG Chi-restraints excluded: chain S residue 36 ILE Chi-restraints excluded: chain S residue 77 LEU 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 87 optimal weight: 0.9980 chunk 105 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 31 optimal weight: 7.9990 chunk 57 optimal weight: 0.8980 chunk 38 optimal weight: 5.9990 chunk 34 optimal weight: 6.9990 chunk 52 optimal weight: 0.9990 chunk 96 optimal weight: 9.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 2 GLN I 125 GLN ** J 93 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.178746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.119121 restraints weight = 28553.000| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 2.20 r_work: 0.3101 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3100 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3100 r_free = 0.3100 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3100 r_free = 0.3100 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3100 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.1460 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= 0.166 Angle : 0.606 10.356 20699 Z= 0.350 Chirality : 0.037 0.188 2367 Planarity : 0.004 0.056 1540 Dihedral : 32.471 179.299 4434 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 4.39 % Allowed : 28.33 % Favored : 67.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.29), residues: 879 helix: 2.06 (0.22), residues: 570 sheet: 0.47 (1.16), residues: 21 loop : -0.96 (0.34), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 176 HIS 0.003 0.001 HIS J 75 PHE 0.008 0.001 PHE J 100 TYR 0.016 0.002 TYR Q 88 ARG 0.007 0.000 ARG J 95 Details of bonding type rmsd hydrogen bonds : bond 0.05283 ( 809) hydrogen bonds : angle 2.98908 ( 2001) covalent geometry : bond 0.00384 (14313) covalent geometry : angle 0.60637 (20699) *********************** 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 191 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 160 time to evaluate : 1.039 Fit side-chains REVERT: D 1 MET cc_start: 0.6717 (mtt) cc_final: 0.4459 (tmm) REVERT: D 6 LYS cc_start: 0.9097 (mmtm) cc_final: 0.7433 (tppt) REVERT: K 25 PHE cc_start: 0.8874 (OUTLIER) cc_final: 0.7755 (t80) REVERT: M 44 GLN cc_start: 0.8639 (tt0) cc_final: 0.8120 (tt0) REVERT: O 51 ILE cc_start: 0.8584 (OUTLIER) cc_final: 0.8023 (mt) REVERT: O 59 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.7838 (pm20) REVERT: O 81 ASP cc_start: 0.8046 (t0) cc_final: 0.7541 (t0) REVERT: R 89 ASN cc_start: 0.8497 (m-40) cc_final: 0.8128 (m-40) REVERT: S 65 ASP cc_start: 0.8899 (t0) cc_final: 0.8640 (t0) REVERT: S 96 ARG cc_start: 0.8393 (ttm-80) cc_final: 0.8186 (ttm-80) outliers start: 31 outliers final: 13 residues processed: 178 average time/residue: 0.3304 time to fit residues: 79.2267 Evaluate side-chains 169 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 153 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 65 LEU 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 85 LEU Chi-restraints excluded: chain K residue 114 VAL Chi-restraints excluded: chain M residue 52 SER 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 20 ARG Chi-restraints excluded: chain R residue 83 LEU Chi-restraints excluded: chain S residue 36 ILE 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 33 optimal weight: 4.9990 chunk 62 optimal weight: 0.8980 chunk 78 optimal weight: 0.7980 chunk 69 optimal weight: 0.4980 chunk 1 optimal weight: 7.9990 chunk 84 optimal weight: 6.9990 chunk 64 optimal weight: 4.9990 chunk 87 optimal weight: 0.9980 chunk 10 optimal weight: 5.9990 chunk 6 optimal weight: 20.0000 chunk 105 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 76 GLN I 125 GLN ** J 93 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** S 79 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.179787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.120410 restraints weight = 29203.363| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 2.32 r_work: 0.3110 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3106 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3106 r_free = 0.3106 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3106 r_free = 0.3106 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3106 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.1715 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= 0.163 Angle : 0.607 10.897 20699 Z= 0.350 Chirality : 0.036 0.207 2367 Planarity : 0.004 0.057 1540 Dihedral : 32.412 179.502 4434 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 4.53 % Allowed : 27.90 % Favored : 67.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.29), residues: 879 helix: 2.14 (0.22), residues: 571 sheet: 0.32 (1.03), residues: 21 loop : -0.94 (0.34), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 176 HIS 0.006 0.001 HIS S 79 PHE 0.010 0.001 PHE J 100 TYR 0.015 0.001 TYR J 88 ARG 0.008 0.000 ARG J 95 Details of bonding type rmsd hydrogen bonds : bond 0.05197 ( 809) hydrogen bonds : angle 2.93379 ( 2001) covalent geometry : bond 0.00374 (14313) covalent geometry : angle 0.60653 (20699) *********************** 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 187 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 155 time to evaluate : 1.128 Fit side-chains REVERT: D 4 PHE cc_start: 0.7965 (OUTLIER) cc_final: 0.7435 (m-80) REVERT: D 6 LYS cc_start: 0.9057 (mmtm) cc_final: 0.7319 (tppt) REVERT: I 59 GLU cc_start: 0.8420 (pm20) cc_final: 0.8189 (pm20) REVERT: K 25 PHE cc_start: 0.8842 (OUTLIER) cc_final: 0.7669 (t80) REVERT: K 73 ASN cc_start: 0.8542 (t0) cc_final: 0.8284 (t0) REVERT: M 44 GLN cc_start: 0.8585 (tt0) cc_final: 0.8069 (tt0) REVERT: M 98 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8181 (mt) REVERT: O 51 ILE cc_start: 0.8580 (OUTLIER) cc_final: 0.8013 (mt) REVERT: O 56 LYS cc_start: 0.8214 (ttpt) cc_final: 0.7608 (ttpp) REVERT: O 59 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.7940 (pm20) REVERT: O 81 ASP cc_start: 0.8063 (t0) cc_final: 0.7543 (t0) REVERT: Q 91 LYS cc_start: 0.8991 (ttpt) cc_final: 0.8723 (ttmm) REVERT: R 89 ASN cc_start: 0.8437 (m-40) cc_final: 0.8154 (m-40) REVERT: S 65 ASP cc_start: 0.8811 (t0) cc_final: 0.8518 (t0) outliers start: 32 outliers final: 15 residues processed: 176 average time/residue: 0.4044 time to fit residues: 95.5845 Evaluate side-chains 169 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 149 time to evaluate : 1.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 4 PHE 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 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 105 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 28 optimal weight: 10.0000 chunk 38 optimal weight: 5.9990 chunk 75 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 S 79 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.171611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.110365 restraints weight = 36851.899| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 2.65 r_work: 0.2946 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2947 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2947 r_free = 0.2947 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2947 r_free = 0.2947 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.2947 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 14313 Z= 0.274 Angle : 0.687 10.981 20699 Z= 0.390 Chirality : 0.041 0.214 2367 Planarity : 0.005 0.052 1540 Dihedral : 32.708 177.481 4434 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 12.49 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.28), residues: 879 helix: 1.73 (0.22), residues: 578 sheet: 0.17 (1.11), residues: 22 loop : -1.19 (0.34), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 176 HIS 0.006 0.002 HIS M 46 PHE 0.017 0.002 PHE I 78 TYR 0.035 0.002 TYR Q 88 ARG 0.008 0.001 ARG J 95 Details of bonding type rmsd hydrogen bonds : bond 0.06049 ( 809) hydrogen bonds : angle 3.28179 ( 2001) covalent geometry : bond 0.00647 (14313) covalent geometry : angle 0.68698 (20699) *********************** 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 188 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 152 time to evaluate : 1.084 Fit side-chains REVERT: I 57 SER cc_start: 0.9460 (t) cc_final: 0.9167 (p) REVERT: I 134 ARG cc_start: 0.7955 (OUTLIER) cc_final: 0.7695 (ttm-80) REVERT: K 25 PHE cc_start: 0.9071 (OUTLIER) cc_final: 0.7758 (t80) REVERT: K 42 ARG cc_start: 0.7748 (OUTLIER) cc_final: 0.7020 (ptm160) REVERT: K 73 ASN cc_start: 0.8530 (t0) cc_final: 0.8307 (t0) REVERT: M 98 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8139 (mm) REVERT: M 117 LYS cc_start: 0.8384 (OUTLIER) cc_final: 0.8124 (tttp) REVERT: O 51 ILE cc_start: 0.8634 (OUTLIER) cc_final: 0.8024 (mt) REVERT: O 59 GLU cc_start: 0.8423 (OUTLIER) cc_final: 0.7916 (pm20) REVERT: O 81 ASP cc_start: 0.8224 (t0) cc_final: 0.7670 (t0) REVERT: Q 97 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8714 (tp) REVERT: R 76 THR cc_start: 0.9112 (p) cc_final: 0.8858 (t) REVERT: S 65 ASP cc_start: 0.8994 (t0) cc_final: 0.8741 (t0) REVERT: S 90 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7658 (mm-30) outliers start: 36 outliers final: 15 residues processed: 180 average time/residue: 0.3344 time to fit residues: 81.1993 Evaluate side-chains 166 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 142 time to evaluate : 1.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 TRP 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 117 VAL Chi-restraints excluded: chain I residue 134 ARG 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 42 ARG 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 117 LYS 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 83 LEU Chi-restraints excluded: chain S residue 36 ILE Chi-restraints excluded: chain S residue 84 SER Chi-restraints excluded: chain S residue 90 GLU 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 77 optimal weight: 0.8980 chunk 30 optimal weight: 7.9990 chunk 52 optimal weight: 0.5980 chunk 108 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 chunk 65 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 39 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 chunk 105 optimal weight: 0.9980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 76 GLN M 44 GLN M 46 HIS ** M 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 125 GLN ** Q 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.175985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.117963 restraints weight = 41666.416| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 2.56 r_work: 0.3025 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3028 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3028 r_free = 0.3028 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3028 r_free = 0.3028 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3028 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.2093 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= 0.174 Angle : 0.622 10.614 20699 Z= 0.357 Chirality : 0.037 0.216 2367 Planarity : 0.004 0.058 1540 Dihedral : 32.502 178.364 4434 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 4.11 % Allowed : 28.33 % Favored : 67.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.28), residues: 879 helix: 1.95 (0.22), residues: 578 sheet: -0.16 (1.02), residues: 22 loop : -1.17 (0.34), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 176 HIS 0.005 0.001 HIS M 46 PHE 0.010 0.001 PHE A 190 TYR 0.020 0.002 TYR Q 88 ARG 0.007 0.000 ARG M 83 Details of bonding type rmsd hydrogen bonds : bond 0.05247 ( 809) hydrogen bonds : angle 2.95492 ( 2001) covalent geometry : bond 0.00405 (14313) covalent geometry : angle 0.62199 (20699) *********************** 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 177 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 148 time to evaluate : 1.117 Fit side-chains REVERT: I 134 ARG cc_start: 0.7823 (OUTLIER) cc_final: 0.7603 (ttm-80) REVERT: K 25 PHE cc_start: 0.8973 (OUTLIER) cc_final: 0.7709 (t80) REVERT: K 73 ASN cc_start: 0.8545 (t0) cc_final: 0.8332 (t0) REVERT: M 44 GLN cc_start: 0.8489 (tt0) cc_final: 0.8092 (tt0) REVERT: M 98 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8036 (mm) REVERT: O 51 ILE cc_start: 0.8601 (OUTLIER) cc_final: 0.8001 (mt) REVERT: O 59 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.7933 (pm20) REVERT: O 81 ASP cc_start: 0.8221 (t0) cc_final: 0.7688 (t0) REVERT: S 65 ASP cc_start: 0.8912 (t0) cc_final: 0.8654 (t0) outliers start: 29 outliers final: 16 residues processed: 169 average time/residue: 0.3455 time to fit residues: 78.7571 Evaluate side-chains 161 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 140 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 TRP Chi-restraints excluded: chain I residue 65 LEU Chi-restraints excluded: chain I residue 70 LEU Chi-restraints excluded: chain I residue 115 LYS Chi-restraints excluded: chain I residue 117 VAL Chi-restraints excluded: chain I residue 134 ARG 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 114 VAL 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 9 optimal weight: 6.9990 chunk 70 optimal weight: 10.0000 chunk 105 optimal weight: 0.9990 chunk 63 optimal weight: 3.9990 chunk 87 optimal weight: 0.0870 chunk 88 optimal weight: 0.0000 chunk 93 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 27 optimal weight: 20.0000 chunk 96 optimal weight: 9.9990 chunk 50 optimal weight: 1.9990 overall best weight: 1.4168 ------------------------------------------------------------------------------- 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 = 0.4061 r_free = 0.4061 target = 0.175189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.117077 restraints weight = 42305.495| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 2.58 r_work: 0.3010 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3009 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3009 r_free = 0.3009 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3009 r_free = 0.3009 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3009 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.2172 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= 0.187 Angle : 0.624 10.260 20699 Z= 0.358 Chirality : 0.038 0.223 2367 Planarity : 0.004 0.058 1540 Dihedral : 32.532 177.830 4434 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 3.82 % Allowed : 28.61 % Favored : 67.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.29), residues: 879 helix: 1.96 (0.22), residues: 580 sheet: -0.29 (1.14), residues: 22 loop : -1.14 (0.34), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 176 HIS 0.004 0.001 HIS J 75 PHE 0.009 0.001 PHE A 190 TYR 0.022 0.002 TYR Q 88 ARG 0.007 0.000 ARG M 83 Details of bonding type rmsd hydrogen bonds : bond 0.05322 ( 809) hydrogen bonds : angle 2.99172 ( 2001) covalent geometry : bond 0.00438 (14313) covalent geometry : angle 0.62416 (20699) *********************** 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 166 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 139 time to evaluate : 0.986 Fit side-chains REVERT: I 134 ARG cc_start: 0.7831 (OUTLIER) cc_final: 0.7608 (ttm-80) REVERT: K 25 PHE cc_start: 0.9012 (OUTLIER) cc_final: 0.7696 (t80) REVERT: K 73 ASN cc_start: 0.8577 (t0) cc_final: 0.8354 (t0) REVERT: M 44 GLN cc_start: 0.8480 (tt0) cc_final: 0.8089 (tt0) REVERT: M 98 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8070 (mm) REVERT: O 51 ILE cc_start: 0.8613 (OUTLIER) cc_final: 0.8029 (mt) REVERT: O 59 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.7919 (pm20) REVERT: O 63 ARG cc_start: 0.8514 (OUTLIER) cc_final: 0.7679 (mmt-90) REVERT: O 81 ASP cc_start: 0.8211 (t0) cc_final: 0.7678 (t0) REVERT: R 76 THR cc_start: 0.9090 (p) cc_final: 0.8888 (t) REVERT: S 65 ASP cc_start: 0.8932 (t0) cc_final: 0.8661 (t0) outliers start: 27 outliers final: 18 residues processed: 159 average time/residue: 0.3614 time to fit residues: 76.6191 Evaluate side-chains 162 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 138 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 TRP 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 115 LYS Chi-restraints excluded: chain I residue 134 ARG 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 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 63 ARG Chi-restraints excluded: chain O residue 65 LEU 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 108 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 40 optimal weight: 7.9990 chunk 90 optimal weight: 2.9990 chunk 27 optimal weight: 20.0000 chunk 39 optimal weight: 5.9990 chunk 52 optimal weight: 0.7980 chunk 15 optimal weight: 4.9990 chunk 56 optimal weight: 0.8980 chunk 86 optimal weight: 0.5980 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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 = 0.4059 r_free = 0.4059 target = 0.175181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.116925 restraints weight = 43651.825| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 2.63 r_work: 0.3005 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3005 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3005 r_free = 0.3005 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3005 r_free = 0.3005 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3005 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2254 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= 0.189 Angle : 0.626 9.876 20699 Z= 0.358 Chirality : 0.038 0.226 2367 Planarity : 0.004 0.058 1540 Dihedral : 32.533 177.577 4434 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 3.97 % Allowed : 28.33 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.29), residues: 879 helix: 1.99 (0.22), residues: 579 sheet: -0.12 (1.22), residues: 22 loop : -1.13 (0.34), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 176 HIS 0.004 0.001 HIS Q 75 PHE 0.009 0.001 PHE A 190 TYR 0.025 0.002 TYR Q 88 ARG 0.007 0.000 ARG M 83 Details of bonding type rmsd hydrogen bonds : bond 0.05312 ( 809) hydrogen bonds : angle 2.97301 ( 2001) covalent geometry : bond 0.00442 (14313) covalent geometry : angle 0.62573 (20699) *********************** 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 168 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 140 time to evaluate : 1.016 Fit side-chains REVERT: I 58 THR cc_start: 0.8988 (t) cc_final: 0.8782 (t) REVERT: K 25 PHE cc_start: 0.9007 (OUTLIER) cc_final: 0.7672 (t80) REVERT: K 42 ARG cc_start: 0.7646 (OUTLIER) cc_final: 0.6926 (ptm160) REVERT: M 44 GLN cc_start: 0.8440 (tt0) cc_final: 0.8116 (tt0) REVERT: M 98 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8071 (mm) REVERT: O 51 ILE cc_start: 0.8611 (OUTLIER) cc_final: 0.8023 (mt) REVERT: O 59 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.7929 (pm20) REVERT: O 63 ARG cc_start: 0.8513 (OUTLIER) cc_final: 0.7737 (mmt-90) REVERT: O 74 ILE cc_start: 0.9013 (tt) cc_final: 0.8565 (mt) REVERT: O 81 ASP cc_start: 0.8234 (t0) cc_final: 0.7708 (t0) REVERT: S 65 ASP cc_start: 0.8929 (t0) cc_final: 0.8660 (t0) outliers start: 28 outliers final: 17 residues processed: 161 average time/residue: 0.3637 time to fit residues: 77.2225 Evaluate side-chains 157 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 134 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 TRP 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 115 LYS 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 42 ARG Chi-restraints excluded: chain K residue 85 LEU Chi-restraints excluded: chain K residue 114 VAL 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 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 95 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 chunk 99 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 78 optimal weight: 6.9990 chunk 89 optimal weight: 0.7980 chunk 8 optimal weight: 7.9990 chunk 69 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 76 GLN I 125 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.173833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.113768 restraints weight = 32556.587| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 2.32 r_work: 0.3019 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3016 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3016 r_free = 0.3016 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3016 r_free = 0.3016 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3016 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 14313 Z= 0.206 Angle : 0.638 9.854 20699 Z= 0.366 Chirality : 0.038 0.227 2367 Planarity : 0.004 0.057 1540 Dihedral : 32.590 177.237 4434 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 3.97 % Allowed : 27.90 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.29), residues: 879 helix: 1.95 (0.22), residues: 579 sheet: -0.22 (1.21), residues: 22 loop : -1.12 (0.35), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 176 HIS 0.004 0.001 HIS Q 75 PHE 0.008 0.001 PHE A 190 TYR 0.029 0.002 TYR Q 88 ARG 0.007 0.000 ARG M 83 Details of bonding type rmsd hydrogen bonds : bond 0.05439 ( 809) hydrogen bonds : angle 3.03887 ( 2001) covalent geometry : bond 0.00486 (14313) covalent geometry : angle 0.63752 (20699) ********************** 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 168 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 140 time to evaluate : 1.056 Fit side-chains REVERT: I 58 THR cc_start: 0.8935 (t) cc_final: 0.8686 (t) REVERT: K 25 PHE cc_start: 0.9029 (OUTLIER) cc_final: 0.7712 (t80) REVERT: K 42 ARG cc_start: 0.7660 (OUTLIER) cc_final: 0.6938 (ptm160) REVERT: K 74 LYS cc_start: 0.8909 (ptpp) cc_final: 0.8538 (ttpt) REVERT: M 98 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8089 (mm) REVERT: O 51 ILE cc_start: 0.8611 (OUTLIER) cc_final: 0.8030 (mt) REVERT: O 59 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.7931 (pm20) REVERT: O 63 ARG cc_start: 0.8512 (OUTLIER) cc_final: 0.7709 (mmt-90) REVERT: O 74 ILE cc_start: 0.9003 (tt) cc_final: 0.8688 (mt) REVERT: O 81 ASP cc_start: 0.8224 (t0) cc_final: 0.7700 (t0) REVERT: Q 97 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8688 (tp) REVERT: S 65 ASP cc_start: 0.8909 (t0) cc_final: 0.8643 (t0) outliers start: 28 outliers final: 19 residues processed: 160 average time/residue: 0.3864 time to fit residues: 81.7535 Evaluate side-chains 160 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 134 time to evaluate : 1.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 TRP 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 115 LYS 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 27 VAL Chi-restraints excluded: chain K residue 42 ARG 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 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 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 77 optimal weight: 4.9990 chunk 113 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 21 optimal weight: 0.0170 chunk 109 optimal weight: 0.7980 chunk 99 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 16 optimal weight: 6.9990 chunk 37 optimal weight: 5.9990 chunk 47 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 overall best weight: 0.9020 ------------------------------------------------------------------------------- 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** Q 27 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.176947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.119522 restraints weight = 43239.189| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 2.67 r_work: 0.3042 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3045 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3045 r_free = 0.3045 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 = 0.3045 r_free = 0.3045 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3045 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.2448 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 : 0.615 9.355 20699 Z= 0.354 Chirality : 0.037 0.231 2367 Planarity : 0.004 0.060 1540 Dihedral : 32.459 177.357 4434 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 3.40 % Allowed : 28.75 % Favored : 67.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.29), residues: 879 helix: 2.09 (0.22), residues: 579 sheet: -0.22 (1.20), residues: 22 loop : -1.03 (0.35), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 176 HIS 0.003 0.001 HIS J 75 PHE 0.010 0.001 PHE A 190 TYR 0.017 0.002 TYR Q 88 ARG 0.008 0.000 ARG M 83 Details of bonding type rmsd hydrogen bonds : bond 0.05126 ( 809) hydrogen bonds : angle 2.88965 ( 2001) covalent geometry : bond 0.00385 (14313) covalent geometry : angle 0.61544 (20699) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8104.61 seconds wall clock time: 144 minutes 20.45 seconds (8660.45 seconds total)