Starting phenix.real_space_refine on Thu May 15 10:22:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u5h_41922/05_2025/8u5h_41922.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u5h_41922/05_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_41922/05_2025/8u5h_41922.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u5h_41922/05_2025/8u5h_41922.map" model { file = "/net/cci-nas-00/data/ceres_data/8u5h_41922/05_2025/8u5h_41922.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u5h_41922/05_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-5687/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: 7.76, per 1000 atoms: 0.58 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: 3.11 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: 6.87 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: 5.44 Time building geometry restraints manager: 3.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2494 1.33 - 1.45: 4642 1.45 - 1.57: 6525 1.57 - 1.69: 626 1.69 - 1.81: 26 Bond restraints: 14313 Sorted by residual: bond pdb=" P DC H 48 " pdb=" OP2 DC H 48 " ideal model delta sigma weight residual 1.480 1.521 -0.041 2.00e-02 2.50e+03 4.13e+00 bond pdb=" P DT C 214 " pdb=" OP2 DT C 214 " ideal model delta sigma weight residual 1.480 1.520 -0.040 2.00e-02 2.50e+03 4.00e+00 bond pdb=" P DA C 220 " pdb=" OP2 DA C 220 " ideal model delta sigma weight residual 1.480 1.519 -0.039 2.00e-02 2.50e+03 3.82e+00 bond pdb=" P DC H 114 " pdb=" OP2 DC H 114 " ideal model delta sigma weight residual 1.480 1.519 -0.039 2.00e-02 2.50e+03 3.80e+00 bond pdb=" P DT C 170 " pdb=" OP2 DT C 170 " ideal model delta sigma weight residual 1.480 1.518 -0.038 2.00e-02 2.50e+03 3.67e+00 ... (remaining 14308 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 19968 1.81 - 3.62: 629 3.62 - 5.43: 65 5.43 - 7.24: 32 7.24 - 9.05: 5 Bond angle restraints: 20699 Sorted by residual: angle pdb=" O3' DT C 214 " pdb=" P DC C 215 " pdb=" O5' DC C 215 " ideal model delta sigma weight residual 104.00 99.13 4.87 1.50e+00 4.44e-01 1.05e+01 angle pdb=" C3' DG H 135 " pdb=" O3' DG H 135 " pdb=" P DG H 136 " ideal model delta sigma weight residual 120.20 124.81 -4.61 1.50e+00 4.44e-01 9.44e+00 angle pdb=" C GLY K 37 " pdb=" N ASN K 38 " pdb=" CA ASN K 38 " ideal model delta sigma weight residual 121.54 127.40 -5.86 1.91e+00 2.74e-01 9.41e+00 angle pdb=" O3' DT H 49 " pdb=" P DT H 50 " pdb=" O5' DT H 50 " ideal model delta sigma weight residual 104.00 99.49 4.51 1.50e+00 4.44e-01 9.05e+00 angle pdb=" O3' DG C 205 " pdb=" P DT C 206 " pdb=" O5' DT C 206 " ideal model delta sigma weight residual 104.00 99.77 4.23 1.50e+00 4.44e-01 7.94e+00 ... (remaining 20694 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.81: 6275 35.81 - 71.62: 1468 71.62 - 107.43: 29 107.43 - 143.24: 6 143.24 - 179.05: 21 Dihedral angle restraints: 7799 sinusoidal: 5181 harmonic: 2618 Sorted by residual: dihedral pdb=" C4' DA H 5 " pdb=" C3' DA H 5 " pdb=" O3' DA H 5 " pdb=" P DT H 6 " ideal model delta sinusoidal sigma weight residual 220.00 40.95 179.05 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DC C 224 " pdb=" C3' DC C 224 " pdb=" O3' DC C 224 " pdb=" P DT C 225 " ideal model delta sinusoidal sigma weight residual -140.00 37.49 -177.49 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DA C 309 " pdb=" C3' DA C 309 " pdb=" O3' DA C 309 " pdb=" P DT C 310 " ideal model delta sinusoidal sigma weight residual -140.00 34.44 -174.44 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 7796 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.122: 2337 0.122 - 0.243: 11 0.243 - 0.365: 0 0.365 - 0.486: 0 0.486 - 0.608: 19 Chirality restraints: 2367 Sorted by residual: chirality pdb=" P DG H 136 " pdb=" OP1 DG H 136 " pdb=" OP2 DG H 136 " pdb=" O5' DG H 136 " both_signs ideal model delta sigma weight residual True 2.35 -2.95 -0.61 2.00e-01 2.50e+01 9.24e+00 chirality pdb=" P DC C 221 " pdb=" OP1 DC C 221 " pdb=" OP2 DC C 221 " pdb=" O5' DC C 221 " both_signs ideal model delta sigma weight residual True 2.35 -2.93 -0.59 2.00e-01 2.50e+01 8.60e+00 chirality pdb=" P DC H 48 " pdb=" OP1 DC H 48 " pdb=" OP2 DC H 48 " pdb=" O5' DC H 48 " both_signs ideal model delta sigma weight residual True 2.35 -2.93 -0.58 2.00e-01 2.50e+01 8.40e+00 ... (remaining 2364 not shown) Planarity restraints: 1540 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG I 42 " 0.036 5.00e-02 4.00e+02 5.41e-02 4.69e+00 pdb=" N PRO I 43 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO I 43 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO I 43 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DG C 202 " 0.001 2.00e-02 2.50e+03 1.17e-02 4.09e+00 pdb=" N9 DG C 202 " 0.008 2.00e-02 2.50e+03 pdb=" C8 DG C 202 " -0.001 2.00e-02 2.50e+03 pdb=" N7 DG C 202 " 0.000 2.00e-02 2.50e+03 pdb=" C5 DG C 202 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DG C 202 " -0.013 2.00e-02 2.50e+03 pdb=" O6 DG C 202 " 0.012 2.00e-02 2.50e+03 pdb=" N1 DG C 202 " 0.004 2.00e-02 2.50e+03 pdb=" C2 DG C 202 " -0.030 2.00e-02 2.50e+03 pdb=" N2 DG C 202 " 0.019 2.00e-02 2.50e+03 pdb=" N3 DG C 202 " 0.000 2.00e-02 2.50e+03 pdb=" C4 DG C 202 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE R 79 " -0.032 5.00e-02 4.00e+02 4.79e-02 3.68e+00 pdb=" N PRO R 80 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO R 80 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO R 80 " -0.027 5.00e-02 4.00e+02 ... (remaining 1537 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1301 2.74 - 3.28: 12529 3.28 - 3.82: 27024 3.82 - 4.36: 30349 4.36 - 4.90: 44242 Nonbonded interactions: 115445 Sorted by model distance: nonbonded pdb=" N2 DG C 262 " pdb=" O2 DC H 53 " model vdw 2.200 2.496 nonbonded pdb=" N2 DG C 181 " pdb=" O2 DC H 134 " model vdw 2.201 2.496 nonbonded pdb=" OG SER I 57 " pdb=" OE1 GLU I 59 " model vdw 2.209 3.040 nonbonded pdb=" OP2 DG C 187 " pdb=" OG SER S 53 " model vdw 2.225 3.040 nonbonded pdb=" O2 DC C 180 " pdb=" N2 DG H 135 " model vdw 2.227 2.496 ... (remaining 115440 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'I' selection = (chain 'O' and resid 38 through 135) } ncs_group { reference = (chain 'J' and ((resid 21 through 23 and (name N or name CA or name C or name O \ or name CB )) or resid 24 through 102)) selection = (chain 'Q' and resid 21 through 102) } ncs_group { reference = (chain 'K' and resid 12 through 119) selection = (chain 'R' and ((resid 12 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 56 or (resid 57 and (name N or name CA or name \ C or name O or name CB )) or resid 58 through 61 or (resid 62 and (name N or na \ me CA or name C or name O or name CB )) or resid 63 through 93 or (resid 94 and \ (name N or name CA or name C or name O or name CB )) or resid 95 through 119)) } ncs_group { reference = chain 'M' selection = (chain 'S' and (resid 28 through 105 or (resid 106 through 107 and (name N or na \ me CA or name C or name O or name CB )) or resid 108 through 122)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.23 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 36.450 Find NCS groups from input model: 0.330 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: 0.000 Load rotamer database and sin/cos tables:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.440 ------------------------------------------------------------------------------- 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 : 0.916 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: 0.3357 time to fit residues: 62.5636 Evaluate side-chains 140 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 137 time to evaluate : 0.913 ------------------------------------------------------------------------------- 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: 0.9980 chunk 67 optimal weight: 6.9990 chunk 104 optimal weight: 0.5980 overall best weight: 1.4384 ------------------------------------------------------------------------------- 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 = 0.4088 r_free = 0.4088 target = 0.177109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.116791 restraints weight = 40147.804| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.63 r_work: 0.3039 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3041 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3041 r_free = 0.3041 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3041 r_free = 0.3041 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3041 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.1002 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= 0.194 Angle : 0.632 8.701 20699 Z= 0.365 Chirality : 0.038 0.152 2367 Planarity : 0.004 0.052 1540 Dihedral : 32.558 179.151 4442 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 3.40 % Allowed : 28.33 % 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: 1.21 (0.28), residues: 879 helix: 1.75 (0.22), residues: 575 sheet: 0.58 (1.19), residues: 21 loop : -1.18 (0.34), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 176 HIS 0.004 0.001 HIS S 106 PHE 0.011 0.001 PHE J 100 TYR 0.021 0.002 TYR J 88 ARG 0.007 0.001 ARG J 95 Details of bonding type rmsd hydrogen bonds : bond 0.05670 ( 809) hydrogen bonds : angle 3.26763 ( 2001) covalent geometry : bond 0.00452 (14313) covalent geometry : angle 0.63207 (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 185 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 161 time to evaluate : 0.908 Fit side-chains REVERT: J 78 ARG cc_start: 0.8868 (ptp90) cc_final: 0.8224 (ptt-90) REVERT: K 73 ASN cc_start: 0.8503 (t0) cc_final: 0.8274 (t0) REVERT: M 44 GLN cc_start: 0.8645 (tt0) cc_final: 0.8138 (tt0) REVERT: M 61 SER cc_start: 0.8993 (m) cc_final: 0.8732 (m) REVERT: O 73 GLU cc_start: 0.9243 (tm-30) cc_final: 0.8697 (tt0) REVERT: O 81 ASP cc_start: 0.8107 (t0) cc_final: 0.7820 (t0) REVERT: Q 91 LYS cc_start: 0.9003 (ttpt) cc_final: 0.8702 (ttmm) REVERT: R 89 ASN cc_start: 0.8693 (m-40) cc_final: 0.8060 (m-40) REVERT: S 37 TYR cc_start: 0.9314 (m-80) cc_final: 0.9070 (m-80) REVERT: S 65 ASP cc_start: 0.8952 (t0) cc_final: 0.8732 (t0) REVERT: S 118 TYR cc_start: 0.8398 (t80) cc_final: 0.8167 (t80) outliers start: 24 outliers final: 12 residues processed: 173 average time/residue: 0.3415 time to fit residues: 78.4145 Evaluate side-chains 155 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 143 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 70 LEU Chi-restraints excluded: chain J residue 43 VAL Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain J residue 84 MET Chi-restraints excluded: chain K residue 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 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: 10.0000 chunk 56 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 4 optimal weight: 0.0000 chunk 112 optimal weight: 0.6980 chunk 2 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 chunk 70 optimal weight: 9.9990 chunk 48 optimal weight: 2.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- 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** ** J 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 25 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.176554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.116132 restraints weight = 38068.776| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 2.48 r_work: 0.3029 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3030 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3030 r_free = 0.3030 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3030 r_free = 0.3030 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3030 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.1356 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= 0.195 Angle : 0.627 9.517 20699 Z= 0.361 Chirality : 0.038 0.185 2367 Planarity : 0.004 0.055 1540 Dihedral : 32.566 179.835 4434 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 3.68 % Allowed : 29.04 % 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: 1.35 (0.28), residues: 879 helix: 1.87 (0.22), residues: 576 sheet: 0.58 (1.22), residues: 21 loop : -1.16 (0.34), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 176 HIS 0.003 0.001 HIS S 106 PHE 0.009 0.001 PHE J 100 TYR 0.020 0.002 TYR J 88 ARG 0.008 0.000 ARG J 95 Details of bonding type rmsd hydrogen bonds : bond 0.05540 ( 809) hydrogen bonds : angle 3.13550 ( 2001) covalent geometry : bond 0.00458 (14313) covalent geometry : angle 0.62692 (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 176 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 150 time to evaluate : 1.031 Fit side-chains REVERT: D 6 LYS cc_start: 0.9153 (mmtm) cc_final: 0.7295 (tppt) REVERT: K 25 PHE cc_start: 0.8966 (OUTLIER) cc_final: 0.7781 (t80) REVERT: K 73 ASN cc_start: 0.8556 (t0) cc_final: 0.8304 (t0) REVERT: M 44 GLN cc_start: 0.8678 (tt0) cc_final: 0.8315 (tt0) REVERT: O 59 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.7832 (pm20) REVERT: O 81 ASP cc_start: 0.8226 (t0) cc_final: 0.7799 (t0) REVERT: S 65 ASP cc_start: 0.8934 (t0) cc_final: 0.8683 (t0) outliers start: 26 outliers final: 14 residues processed: 165 average time/residue: 0.3217 time to fit residues: 71.6775 Evaluate side-chains 158 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 142 time to evaluate : 0.903 ------------------------------------------------------------------------------- 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 K residue 114 VAL Chi-restraints excluded: chain M residue 52 SER 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 76 THR Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain S residue 36 ILE 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: 0.6980 chunk 105 optimal weight: 1.9990 chunk 46 optimal weight: 0.4980 chunk 56 optimal weight: 0.9980 chunk 100 optimal weight: 3.9990 chunk 31 optimal weight: 7.9990 chunk 57 optimal weight: 0.6980 chunk 38 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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** 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.178012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.117105 restraints weight = 28556.445| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 2.26 r_work: 0.3077 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3081 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3081 r_free = 0.3081 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3081 r_free = 0.3081 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3081 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.1573 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= 0.167 Angle : 0.609 11.154 20699 Z= 0.351 Chirality : 0.037 0.188 2367 Planarity : 0.004 0.057 1540 Dihedral : 32.481 179.749 4434 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 4.25 % Allowed : 27.76 % Favored : 67.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.53 (0.29), residues: 879 helix: 2.03 (0.22), residues: 576 sheet: 0.47 (1.19), residues: 21 loop : -1.13 (0.34), residues: 282 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 0.008 0.001 PHE A 190 TYR 0.017 0.002 TYR Q 88 ARG 0.006 0.000 ARG M 83 Details of bonding type rmsd hydrogen bonds : bond 0.05276 ( 809) hydrogen bonds : angle 2.98309 ( 2001) covalent geometry : bond 0.00387 (14313) covalent geometry : angle 0.60932 (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 184 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 154 time to evaluate : 0.916 Fit side-chains REVERT: K 25 PHE cc_start: 0.8937 (OUTLIER) cc_final: 0.7718 (t80) REVERT: K 73 ASN cc_start: 0.8608 (t0) cc_final: 0.8373 (t0) REVERT: M 44 GLN cc_start: 0.8611 (tt0) cc_final: 0.8197 (tt0) REVERT: O 51 ILE cc_start: 0.8545 (OUTLIER) cc_final: 0.7944 (mt) REVERT: O 59 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.7872 (pm20) REVERT: O 81 ASP cc_start: 0.8142 (t0) cc_final: 0.7705 (t0) REVERT: R 89 ASN cc_start: 0.8500 (m-40) cc_final: 0.8126 (m-40) REVERT: S 65 ASP cc_start: 0.8844 (t0) cc_final: 0.8548 (t0) outliers start: 30 outliers final: 12 residues processed: 173 average time/residue: 0.3049 time to fit residues: 71.5685 Evaluate side-chains 161 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 146 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain I residue 65 LEU Chi-restraints excluded: chain I residue 70 LEU Chi-restraints excluded: chain I residue 76 GLN Chi-restraints excluded: chain 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 O residue 51 ILE Chi-restraints excluded: chain O residue 59 GLU Chi-restraints excluded: chain R residue 20 ARG Chi-restraints excluded: chain R residue 83 LEU Chi-restraints excluded: chain S residue 36 ILE Chi-restraints excluded: chain S residue 84 SER Chi-restraints excluded: chain S residue 98 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 33 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 78 optimal weight: 0.7980 chunk 69 optimal weight: 0.0770 chunk 1 optimal weight: 3.9990 chunk 84 optimal weight: 6.9990 chunk 64 optimal weight: 4.9990 chunk 87 optimal weight: 0.7980 chunk 10 optimal weight: 5.9990 chunk 6 optimal weight: 20.0000 chunk 105 optimal weight: 0.9980 overall best weight: 1.3340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 125 GLN ** 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 = 0.4084 r_free = 0.4084 target = 0.177067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.115919 restraints weight = 29074.016| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.22 r_work: 0.3068 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3070 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3070 r_free = 0.3070 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3070 r_free = 0.3070 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3070 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.1700 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= 0.183 Angle : 0.617 10.234 20699 Z= 0.355 Chirality : 0.037 0.200 2367 Planarity : 0.004 0.057 1540 Dihedral : 32.485 179.588 4434 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % 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: 1.54 (0.28), residues: 879 helix: 2.02 (0.22), residues: 579 sheet: 0.06 (1.14), residues: 21 loop : -1.08 (0.34), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 176 HIS 0.007 0.001 HIS M 46 PHE 0.009 0.001 PHE J 100 TYR 0.019 0.002 TYR Q 88 ARG 0.007 0.000 ARG J 95 Details of bonding type rmsd hydrogen bonds : bond 0.05304 ( 809) hydrogen bonds : angle 2.99379 ( 2001) covalent geometry : bond 0.00428 (14313) covalent geometry : angle 0.61701 (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 188 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 152 time to evaluate : 1.028 Fit side-chains REVERT: D 6 LYS cc_start: 0.9084 (mmtm) cc_final: 0.7159 (tppt) REVERT: K 25 PHE cc_start: 0.8952 (OUTLIER) cc_final: 0.7713 (t80) REVERT: K 42 ARG cc_start: 0.7654 (OUTLIER) cc_final: 0.6928 (ptm160) REVERT: M 44 GLN cc_start: 0.8565 (tt0) cc_final: 0.8165 (tt0) REVERT: M 98 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8135 (mm) REVERT: O 51 ILE cc_start: 0.8583 (OUTLIER) cc_final: 0.7952 (mt) REVERT: O 59 GLU cc_start: 0.8474 (OUTLIER) cc_final: 0.7902 (pm20) REVERT: O 81 ASP cc_start: 0.8098 (t0) cc_final: 0.7595 (t0) REVERT: Q 25 ASN cc_start: 0.9092 (OUTLIER) cc_final: 0.8831 (t0) REVERT: S 65 ASP cc_start: 0.8856 (t0) cc_final: 0.8579 (t0) REVERT: S 90 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7451 (mm-30) outliers start: 36 outliers final: 16 residues processed: 179 average time/residue: 0.3231 time to fit residues: 77.8868 Evaluate side-chains 169 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 146 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 65 LEU Chi-restraints excluded: chain I residue 70 LEU Chi-restraints excluded: chain I residue 76 GLN Chi-restraints excluded: chain I residue 117 VAL 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 110 ASN Chi-restraints excluded: chain K residue 114 VAL Chi-restraints excluded: chain M residue 52 SER Chi-restraints excluded: chain M residue 98 LEU Chi-restraints excluded: chain O residue 51 ILE Chi-restraints excluded: chain O residue 59 GLU Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain Q residue 25 ASN 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 90 GLU 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: 3.9990 chunk 1 optimal weight: 4.9990 chunk 28 optimal weight: 10.0000 chunk 38 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 114 optimal weight: 5.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 76 GLN I 125 GLN ** M 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 93 GLN S 79 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.170929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.109464 restraints weight = 36760.948| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 2.53 r_work: 0.2942 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2942 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2942 r_free = 0.2942 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2942 r_free = 0.2942 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.2942 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 14313 Z= 0.275 Angle : 0.688 10.858 20699 Z= 0.391 Chirality : 0.041 0.212 2367 Planarity : 0.005 0.053 1540 Dihedral : 32.738 176.917 4434 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 5.10 % Allowed : 27.05 % 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: 1.06 (0.28), residues: 879 helix: 1.64 (0.22), residues: 578 sheet: -0.47 (1.09), residues: 22 loop : -1.21 (0.34), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 176 HIS 0.006 0.002 HIS S 106 PHE 0.010 0.002 PHE I 67 TYR 0.036 0.002 TYR Q 88 ARG 0.006 0.001 ARG M 83 Details of bonding type rmsd hydrogen bonds : bond 0.06085 ( 809) hydrogen bonds : angle 3.30573 ( 2001) covalent geometry : bond 0.00647 (14313) covalent geometry : angle 0.68843 (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 185 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 149 time to evaluate : 0.943 Fit side-chains REVERT: D 1 MET cc_start: 0.5248 (mtt) cc_final: 0.4942 (mtt) REVERT: I 57 SER cc_start: 0.9430 (t) cc_final: 0.9224 (p) REVERT: K 25 PHE cc_start: 0.9061 (OUTLIER) cc_final: 0.7677 (t80) REVERT: K 42 ARG cc_start: 0.7775 (OUTLIER) cc_final: 0.7020 (ptm160) REVERT: M 98 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8148 (mm) REVERT: O 51 ILE cc_start: 0.8633 (OUTLIER) cc_final: 0.8037 (mt) REVERT: O 59 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.7901 (pm20) REVERT: O 63 ARG cc_start: 0.8561 (OUTLIER) cc_final: 0.7764 (mmt-90) REVERT: O 81 ASP cc_start: 0.8279 (t0) cc_final: 0.7826 (t0) REVERT: Q 97 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.8707 (tp) REVERT: R 76 THR cc_start: 0.9107 (OUTLIER) cc_final: 0.8839 (t) REVERT: S 65 ASP cc_start: 0.8994 (t0) cc_final: 0.8759 (t0) outliers start: 36 outliers final: 15 residues processed: 177 average time/residue: 0.3353 time to fit residues: 79.2814 Evaluate side-chains 167 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 144 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain I residue 65 LEU Chi-restraints excluded: chain I residue 70 LEU Chi-restraints excluded: chain I residue 71 VAL Chi-restraints excluded: chain I residue 117 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 110 ASN Chi-restraints excluded: chain K residue 114 VAL Chi-restraints excluded: chain M residue 52 SER Chi-restraints excluded: chain M residue 98 LEU Chi-restraints excluded: chain M residue 103 LEU Chi-restraints excluded: chain O residue 51 ILE Chi-restraints excluded: chain O residue 59 GLU Chi-restraints excluded: chain O residue 63 ARG Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain Q residue 97 LEU Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 83 LEU Chi-restraints excluded: chain S residue 36 ILE Chi-restraints excluded: chain S residue 84 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 77 optimal weight: 2.9990 chunk 30 optimal weight: 7.9990 chunk 52 optimal weight: 0.6980 chunk 108 optimal weight: 3.9990 chunk 96 optimal weight: 0.5980 chunk 65 optimal weight: 6.9990 chunk 5 optimal weight: 0.0270 chunk 78 optimal weight: 0.9990 chunk 39 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 chunk 105 optimal weight: 0.8980 overall best weight: 0.6440 ------------------------------------------------------------------------------- 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 93 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.177938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.120136 restraints weight = 41876.391| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 2.57 r_work: 0.3068 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3071 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3071 r_free = 0.3071 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3071 r_free = 0.3071 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3071 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 14313 Z= 0.160 Angle : 0.616 10.713 20699 Z= 0.354 Chirality : 0.037 0.216 2367 Planarity : 0.004 0.060 1540 Dihedral : 32.443 178.610 4434 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 3.54 % Allowed : 28.61 % 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: 1.42 (0.28), residues: 879 helix: 1.96 (0.22), residues: 578 sheet: -0.34 (1.07), residues: 21 loop : -1.19 (0.34), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 176 HIS 0.006 0.001 HIS Q 75 PHE 0.012 0.001 PHE J 100 TYR 0.015 0.001 TYR S 118 ARG 0.008 0.000 ARG M 83 Details of bonding type rmsd hydrogen bonds : bond 0.05128 ( 809) hydrogen bonds : angle 2.91009 ( 2001) covalent geometry : bond 0.00368 (14313) covalent geometry : angle 0.61620 (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 187 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 162 time to evaluate : 0.987 Fit side-chains REVERT: D 6 LYS cc_start: 0.8732 (mmtm) cc_final: 0.7214 (tppt) REVERT: K 25 PHE cc_start: 0.8909 (OUTLIER) cc_final: 0.7656 (t80) REVERT: M 44 GLN cc_start: 0.8648 (tt0) cc_final: 0.7741 (tt0) REVERT: M 98 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.8049 (mm) REVERT: O 51 ILE cc_start: 0.8576 (OUTLIER) cc_final: 0.7966 (mt) REVERT: O 59 GLU cc_start: 0.8518 (OUTLIER) cc_final: 0.7948 (pm20) REVERT: O 74 ILE cc_start: 0.8814 (tt) cc_final: 0.8567 (mt) REVERT: O 81 ASP cc_start: 0.8210 (t0) cc_final: 0.7707 (t0) REVERT: S 65 ASP cc_start: 0.8865 (t0) cc_final: 0.8613 (t0) outliers start: 25 outliers final: 14 residues processed: 180 average time/residue: 0.3265 time to fit residues: 78.6859 Evaluate side-chains 161 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 143 time to evaluate : 0.976 ------------------------------------------------------------------------------- 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 117 VAL Chi-restraints excluded: chain J residue 43 VAL Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain J residue 84 MET Chi-restraints excluded: chain K residue 25 PHE Chi-restraints excluded: chain K residue 114 VAL Chi-restraints excluded: chain M residue 46 HIS 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 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: 9.9990 chunk 105 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 87 optimal weight: 0.0870 chunk 88 optimal weight: 0.1980 chunk 93 optimal weight: 0.0980 chunk 15 optimal weight: 4.9990 chunk 27 optimal weight: 20.0000 chunk 96 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 overall best weight: 0.6762 ------------------------------------------------------------------------------- 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 75 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.178323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.120380 restraints weight = 42446.285| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 2.64 r_work: 0.3063 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3064 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3064 r_free = 0.3064 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3064 r_free = 0.3064 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3064 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.2292 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= 0.159 Angle : 0.610 8.573 20699 Z= 0.351 Chirality : 0.037 0.257 2367 Planarity : 0.004 0.058 1540 Dihedral : 32.477 178.411 4434 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 3.26 % Allowed : 29.46 % 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: 1.63 (0.29), residues: 879 helix: 2.07 (0.22), residues: 573 sheet: -0.17 (1.07), residues: 22 loop : -0.91 (0.35), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 176 HIS 0.011 0.001 HIS M 46 PHE 0.008 0.001 PHE J 100 TYR 0.017 0.001 TYR J 88 ARG 0.007 0.000 ARG M 83 Details of bonding type rmsd hydrogen bonds : bond 0.05088 ( 809) hydrogen bonds : angle 2.88463 ( 2001) covalent geometry : bond 0.00365 (14313) covalent geometry : angle 0.61018 (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 173 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 150 time to evaluate : 0.980 Fit side-chains REVERT: D 6 LYS cc_start: 0.8965 (mmtm) cc_final: 0.7314 (tppt) REVERT: K 25 PHE cc_start: 0.8907 (OUTLIER) cc_final: 0.7660 (t80) REVERT: K 56 GLU cc_start: 0.8320 (tt0) cc_final: 0.7999 (tt0) REVERT: K 74 LYS cc_start: 0.8902 (ptpp) cc_final: 0.8535 (ttpt) REVERT: M 44 GLN cc_start: 0.8772 (tt0) cc_final: 0.7986 (tt0) REVERT: M 98 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8062 (mm) REVERT: O 51 ILE cc_start: 0.8609 (OUTLIER) cc_final: 0.8026 (mt) REVERT: O 59 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.8008 (pm20) REVERT: O 81 ASP cc_start: 0.8200 (t0) cc_final: 0.7697 (t0) REVERT: S 65 ASP cc_start: 0.8875 (t0) cc_final: 0.8595 (t0) outliers start: 23 outliers final: 14 residues processed: 166 average time/residue: 0.3189 time to fit residues: 70.8325 Evaluate side-chains 161 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 143 time to evaluate : 0.883 ------------------------------------------------------------------------------- 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 117 VAL Chi-restraints excluded: chain J residue 43 VAL Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain J residue 84 MET Chi-restraints excluded: chain K residue 25 PHE Chi-restraints excluded: chain K residue 110 ASN Chi-restraints excluded: chain K residue 114 VAL Chi-restraints excluded: chain M residue 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 20 ARG Chi-restraints excluded: chain R residue 83 LEU Chi-restraints excluded: chain S residue 36 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 108 optimal weight: 3.9990 chunk 72 optimal weight: 0.8980 chunk 57 optimal weight: 0.7980 chunk 40 optimal weight: 7.9990 chunk 90 optimal weight: 3.9990 chunk 27 optimal weight: 20.0000 chunk 39 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 56 optimal weight: 0.6980 chunk 86 optimal weight: 3.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 125 GLN M 46 HIS M 81 ASN ** 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 = 0.4056 r_free = 0.4056 target = 0.175082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.116275 restraints weight = 43620.822| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.62 r_work: 0.3001 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3003 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3003 r_free = 0.3003 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3003 r_free = 0.3003 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3003 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 14313 Z= 0.200 Angle : 0.632 9.283 20699 Z= 0.361 Chirality : 0.038 0.219 2367 Planarity : 0.004 0.056 1540 Dihedral : 32.548 177.302 4434 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 3.12 % Allowed : 29.89 % Favored : 67.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.93 (0.22), residues: 580 sheet: 0.62 (1.15), residues: 22 loop : -1.08 (0.35), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 176 HIS 0.004 0.001 HIS Q 75 PHE 0.009 0.001 PHE D 4 TYR 0.026 0.002 TYR Q 88 ARG 0.007 0.001 ARG I 131 Details of bonding type rmsd hydrogen bonds : bond 0.05379 ( 809) hydrogen bonds : angle 2.99657 ( 2001) covalent geometry : bond 0.00469 (14313) covalent geometry : angle 0.63212 (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 167 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 145 time to evaluate : 0.980 Fit side-chains REVERT: K 25 PHE cc_start: 0.9007 (OUTLIER) cc_final: 0.7678 (t80) REVERT: K 74 LYS cc_start: 0.8914 (ptpp) cc_final: 0.8557 (ttpt) REVERT: M 98 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8074 (mm) REVERT: O 51 ILE cc_start: 0.8629 (OUTLIER) cc_final: 0.8027 (mt) REVERT: O 59 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.7967 (pm20) REVERT: O 81 ASP cc_start: 0.8261 (t0) cc_final: 0.7738 (t0) REVERT: R 76 THR cc_start: 0.9147 (p) cc_final: 0.8940 (t) REVERT: S 65 ASP cc_start: 0.8933 (t0) cc_final: 0.8633 (t0) outliers start: 22 outliers final: 14 residues processed: 160 average time/residue: 0.3359 time to fit residues: 71.9196 Evaluate side-chains 160 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 142 time to evaluate : 1.031 ------------------------------------------------------------------------------- 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 117 VAL Chi-restraints excluded: chain J residue 43 VAL Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain J residue 84 MET Chi-restraints excluded: chain K residue 25 PHE Chi-restraints excluded: chain K residue 114 VAL Chi-restraints excluded: chain M residue 98 LEU Chi-restraints excluded: chain M residue 103 LEU Chi-restraints excluded: chain O residue 51 ILE Chi-restraints excluded: chain O residue 59 GLU Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain Q residue 82 THR Chi-restraints excluded: chain R residue 83 LEU Chi-restraints excluded: chain S residue 36 ILE 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: 1.9990 chunk 78 optimal weight: 0.8980 chunk 89 optimal weight: 0.9980 chunk 8 optimal weight: 7.9990 chunk 69 optimal weight: 6.9990 chunk 49 optimal weight: 0.9980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 125 GLN M 46 HIS ** 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 = 0.4062 r_free = 0.4062 target = 0.175663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.116136 restraints weight = 32639.461| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 2.37 r_work: 0.3035 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3037 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3037 r_free = 0.3037 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3037 r_free = 0.3037 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3037 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.2409 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= 0.187 Angle : 0.628 8.669 20699 Z= 0.360 Chirality : 0.038 0.220 2367 Planarity : 0.004 0.057 1540 Dihedral : 32.525 177.139 4434 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 3.26 % Allowed : 29.46 % 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: 1.49 (0.29), residues: 879 helix: 1.94 (0.22), residues: 580 sheet: 1.00 (1.20), residues: 21 loop : -1.09 (0.35), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 176 HIS 0.004 0.001 HIS Q 75 PHE 0.007 0.001 PHE J 61 TYR 0.023 0.002 TYR S 118 ARG 0.009 0.001 ARG Q 95 Details of bonding type rmsd hydrogen bonds : bond 0.05312 ( 809) hydrogen bonds : angle 2.97371 ( 2001) covalent geometry : bond 0.00439 (14313) covalent geometry : angle 0.62813 (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 165 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 142 time to evaluate : 1.015 Fit side-chains REVERT: K 25 PHE cc_start: 0.8982 (OUTLIER) cc_final: 0.7753 (t80) REVERT: K 56 GLU cc_start: 0.8348 (tt0) cc_final: 0.8010 (tt0) REVERT: K 74 LYS cc_start: 0.8895 (ptpp) cc_final: 0.8531 (ttpt) REVERT: M 44 GLN cc_start: 0.8684 (tt0) cc_final: 0.8224 (tt0) REVERT: M 98 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8113 (mm) REVERT: O 51 ILE cc_start: 0.8646 (OUTLIER) cc_final: 0.8076 (mt) REVERT: O 59 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.7976 (pm20) REVERT: O 81 ASP cc_start: 0.8192 (t0) cc_final: 0.7675 (t0) REVERT: R 76 THR cc_start: 0.8999 (p) cc_final: 0.8792 (t) REVERT: S 65 ASP cc_start: 0.8899 (t0) cc_final: 0.8619 (t0) outliers start: 23 outliers final: 16 residues processed: 157 average time/residue: 0.3285 time to fit residues: 68.9857 Evaluate side-chains 156 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 136 time to evaluate : 0.906 ------------------------------------------------------------------------------- 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 J residue 43 VAL Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain J residue 84 MET Chi-restraints excluded: chain K residue 25 PHE Chi-restraints excluded: chain K residue 110 ASN Chi-restraints excluded: chain K residue 114 VAL Chi-restraints excluded: chain M residue 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 77 optimal weight: 0.8980 chunk 113 optimal weight: 0.9990 chunk 46 optimal weight: 4.9990 chunk 21 optimal weight: 8.9990 chunk 109 optimal weight: 0.6980 chunk 99 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 chunk 37 optimal weight: 5.9990 chunk 47 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 125 GLN M 46 HIS ** 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 = 0.4076 r_free = 0.4076 target = 0.176893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.118829 restraints weight = 43206.691| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 2.66 r_work: 0.3036 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3036 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3036 r_free = 0.3036 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3036 r_free = 0.3036 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3036 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.2443 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= 0.166 Angle : 0.616 7.637 20699 Z= 0.355 Chirality : 0.037 0.222 2367 Planarity : 0.004 0.059 1540 Dihedral : 32.482 177.299 4434 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.83 % Allowed : 29.75 % Favored : 67.42 % 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: 1.62 (0.29), residues: 879 helix: 2.05 (0.22), residues: 579 sheet: 0.99 (1.25), residues: 22 loop : -1.05 (0.35), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 176 HIS 0.005 0.001 HIS Q 75 PHE 0.007 0.001 PHE A 190 TYR 0.018 0.002 TYR K 39 ARG 0.007 0.001 ARG Q 95 Details of bonding type rmsd hydrogen bonds : bond 0.05156 ( 809) hydrogen bonds : angle 2.90691 ( 2001) covalent geometry : bond 0.00385 (14313) covalent geometry : angle 0.61577 (20699) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7202.53 seconds wall clock time: 124 minutes 40.74 seconds (7480.74 seconds total)