Starting phenix.real_space_refine on Wed Mar 4 09:35:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6t90_10406/03_2026/6t90_10406.cif Found real_map, /net/cci-nas-00/data/ceres_data/6t90_10406/03_2026/6t90_10406.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6t90_10406/03_2026/6t90_10406.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6t90_10406/03_2026/6t90_10406.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6t90_10406/03_2026/6t90_10406.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6t90_10406/03_2026/6t90_10406.map" } resolution = 3.05 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 sd= 0.050 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 280 5.49 5 S 22 5.16 5 C 7345 2.51 5 N 2431 2.21 5 O 2953 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13031 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 773 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 3, 'TRANS': 90} Chain: "B" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "C" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 837 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 4, 'TRANS': 104} Chain: "D" Number of atoms: 725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 725 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "E" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 783 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "F" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 646 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "G" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 840 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "H" Number of atoms: 725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 725 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 2870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 2870 Classifications: {'DNA': 141} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 140} Chain: "J" Number of atoms: 2905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 2905 Classifications: {'DNA': 141} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 140} Chain: "K" Number of atoms: 593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 593 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "L" Number of atoms: 636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 636 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 5, 'TRANS': 68} Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 10 Unusual residues: {'PTD': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'PTD:plan-1': 2, 'PTD:plan-2': 2} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PTD': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'PTD:plan-1': 1, 'PTD:plan-2': 1} Unresolved non-hydrogen planarities: 2 Chain: "D" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PTD': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'PTD:plan-1': 1, 'PTD:plan-2': 1} Unresolved non-hydrogen planarities: 2 Chain: "E" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 10 Unusual residues: {'PTD': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'PTD:plan-1': 2, 'PTD:plan-2': 2} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PTD': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'PTD:plan-1': 1, 'PTD:plan-2': 1} Unresolved non-hydrogen planarities: 2 Chain: "H" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PTD': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'PTD:plan-1': 1, 'PTD:plan-2': 1} Unresolved non-hydrogen planarities: 2 Chain: "K" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PTD': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'PTD:plan-1': 1, 'PTD:plan-2': 1} Unresolved non-hydrogen planarities: 2 Time building chain proxies: 2.49, per 1000 atoms: 0.19 Number of scatterers: 13031 At special positions: 0 Unit cell: (97.18, 117.82, 141.04, 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 22 16.00 P 280 15.00 O 2953 8.00 N 2431 7.00 C 7345 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=18, symmetry=0 Number of additional bonds: simple=18, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.91 Conformation dependent library (CDL) restraints added in 474.8 milliseconds 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1688 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 10 sheets defined 74.6% alpha, 2.2% beta 141 base pairs and 258 stacking pairs defined. Time for finding SS restraints: 1.96 Creating SS restraints... Processing helix chain 'A' and resid 45 through 58 Processing helix chain 'A' and resid 64 through 80 removed outlier: 3.521A pdb=" N PHE A 79 " --> pdb=" O ILE A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 115 Processing helix chain 'A' and resid 121 through 133 Processing helix chain 'B' and resid 25 through 30 removed outlier: 3.825A pdb=" N GLN B 28 " --> pdb=" O ASP B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 42 Processing helix chain 'B' and resid 50 through 77 Processing helix chain 'B' and resid 83 through 93 Processing helix chain 'C' and resid 17 through 22 Processing helix chain 'C' and resid 28 through 38 removed outlier: 3.959A pdb=" N GLY C 38 " --> pdb=" O LEU C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 74 removed outlier: 4.324A pdb=" N VAL C 50 " --> pdb=" O ALA C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 90 Processing helix chain 'C' and resid 91 through 98 Processing helix chain 'C' and resid 113 through 117 Processing helix chain 'D' and resid 38 through 50 removed outlier: 3.517A pdb=" N GLN D 48 " --> pdb=" O LYS D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 85 Processing helix chain 'D' and resid 91 through 103 Processing helix chain 'D' and resid 104 through 124 Processing helix chain 'E' and resid 45 through 58 Processing helix chain 'E' and resid 64 through 80 removed outlier: 3.551A pdb=" N ASP E 78 " --> pdb=" O GLU E 74 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE E 79 " --> pdb=" O ILE E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 115 Processing helix chain 'E' and resid 121 through 133 Processing helix chain 'F' and resid 25 through 30 removed outlier: 3.746A pdb=" N GLN F 28 " --> pdb=" O ASP F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 31 through 42 Processing helix chain 'F' and resid 50 through 77 Processing helix chain 'F' and resid 83 through 93 Processing helix chain 'G' and resid 17 through 22 Processing helix chain 'G' and resid 28 through 37 Processing helix chain 'G' and resid 47 through 74 Processing helix chain 'G' and resid 80 through 90 Processing helix chain 'G' and resid 91 through 98 Processing helix chain 'G' and resid 113 through 117 Processing helix chain 'H' and resid 38 through 50 Processing helix chain 'H' and resid 56 through 85 Processing helix chain 'H' and resid 91 through 103 Processing helix chain 'H' and resid 104 through 124 removed outlier: 4.071A pdb=" N LYS H 109 " --> pdb=" O GLY H 105 " (cutoff:3.500A) Processing helix chain 'K' and resid 139 through 160 Processing helix chain 'K' and resid 163 through 176 Processing helix chain 'K' and resid 180 through 189 Processing helix chain 'K' and resid 193 through 210 Proline residue: K 202 - end of helix Processing helix chain 'L' and resid 46 through 63 removed outlier: 3.630A pdb=" N GLY L 54 " --> pdb=" O VAL L 50 " (cutoff:3.500A) Processing helix chain 'L' and resid 67 through 81 Processing helix chain 'L' and resid 83 through 105 Proline residue: L 89 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.816A pdb=" N ARG A 84 " --> pdb=" O VAL B 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 119 through 120 Processing sheet with id=AA3, first strand: chain 'B' and resid 98 through 99 Processing sheet with id=AA4, first strand: chain 'C' and resid 43 through 44 removed outlier: 7.026A pdb=" N ARG C 43 " --> pdb=" O ILE D 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 78 through 79 Processing sheet with id=AA6, first strand: chain 'C' and resid 102 through 103 removed outlier: 6.655A pdb=" N THR C 102 " --> pdb=" O TYR F 99 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 84 through 85 removed outlier: 6.846A pdb=" N ARG E 84 " --> pdb=" O VAL F 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 119 through 120 Processing sheet with id=AA9, first strand: chain 'G' and resid 43 through 44 removed outlier: 7.125A pdb=" N ARG G 43 " --> pdb=" O ILE H 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 78 through 79 495 hydrogen bonds defined for protein. 1461 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 355 hydrogen bonds 710 hydrogen bond angles 0 basepair planarities 141 basepair parallelities 258 stacking parallelities Total time for adding SS restraints: 2.15 Time building geometry restraints manager: 1.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2245 1.32 - 1.45: 5458 1.45 - 1.58: 5540 1.58 - 1.71: 547 1.71 - 1.84: 34 Bond restraints: 13824 Sorted by residual: bond pdb=" CD ARG B 93 " pdb=" NE ARG B 93 " ideal model delta sigma weight residual 1.458 1.330 0.128 1.40e-02 5.10e+03 8.37e+01 bond pdb=" CD ARG B 36 " pdb=" NE ARG B 36 " ideal model delta sigma weight residual 1.458 1.359 0.099 1.40e-02 5.10e+03 5.02e+01 bond pdb=" CD ARG B 79 " pdb=" NE ARG B 79 " ideal model delta sigma weight residual 1.458 1.360 0.098 1.40e-02 5.10e+03 4.91e+01 bond pdb=" CD ARG F 40 " pdb=" NE ARG F 40 " ideal model delta sigma weight residual 1.458 1.360 0.098 1.40e-02 5.10e+03 4.86e+01 bond pdb=" CB HIS G 83 " pdb=" CG HIS G 83 " ideal model delta sigma weight residual 1.497 1.400 0.097 1.40e-02 5.10e+03 4.82e+01 ... (remaining 13819 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.11: 17059 2.11 - 4.23: 2384 4.23 - 6.34: 355 6.34 - 8.46: 29 8.46 - 10.57: 5 Bond angle restraints: 19832 Sorted by residual: angle pdb=" N LEU D 107 " pdb=" CA LEU D 107 " pdb=" C LEU D 107 " ideal model delta sigma weight residual 111.36 103.05 8.31 1.09e+00 8.42e-01 5.81e+01 angle pdb=" N LYS A 65 " pdb=" CA LYS A 65 " pdb=" C LYS A 65 " ideal model delta sigma weight residual 111.36 119.62 -8.26 1.09e+00 8.42e-01 5.74e+01 angle pdb=" N GLY L 54 " pdb=" CA GLY L 54 " pdb=" C GLY L 54 " ideal model delta sigma weight residual 112.49 103.43 9.06 1.21e+00 6.83e-01 5.61e+01 angle pdb=" N LYS E 65 " pdb=" CA LYS E 65 " pdb=" C LYS E 65 " ideal model delta sigma weight residual 111.36 119.51 -8.15 1.09e+00 8.42e-01 5.59e+01 angle pdb=" N LYS C 16 " pdb=" CA LYS C 16 " pdb=" C LYS C 16 " ideal model delta sigma weight residual 111.71 120.24 -8.53 1.15e+00 7.56e-01 5.50e+01 ... (remaining 19827 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.28: 6426 33.28 - 66.56: 1201 66.56 - 99.84: 12 99.84 - 133.13: 0 133.13 - 166.41: 2 Dihedral angle restraints: 7641 sinusoidal: 5027 harmonic: 2614 Sorted by residual: dihedral pdb=" C4' DT I 89 " pdb=" C3' DT I 89 " pdb=" O3' DT I 89 " pdb=" P DA I 90 " ideal model delta sinusoidal sigma weight residual 220.00 53.59 166.41 1 3.50e+01 8.16e-04 1.55e+01 dihedral pdb=" C4' DG I 4 " pdb=" C3' DG I 4 " pdb=" O3' DG I 4 " pdb=" P DA I 5 " ideal model delta sinusoidal sigma weight residual 220.00 57.11 162.89 1 3.50e+01 8.16e-04 1.53e+01 dihedral pdb=" CA PRO H 104 " pdb=" C PRO H 104 " pdb=" N GLY H 105 " pdb=" CA GLY H 105 " ideal model delta harmonic sigma weight residual 180.00 163.70 16.30 0 5.00e+00 4.00e-02 1.06e+01 ... (remaining 7638 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1228 0.070 - 0.139: 713 0.139 - 0.209: 247 0.209 - 0.279: 47 0.279 - 0.349: 5 Chirality restraints: 2240 Sorted by residual: chirality pdb=" CA ASN L 68 " pdb=" N ASN L 68 " pdb=" C ASN L 68 " pdb=" CB ASN L 68 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.04e+00 chirality pdb=" CA SER L 52 " pdb=" N SER L 52 " pdb=" C SER L 52 " pdb=" CB SER L 52 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.52e+00 chirality pdb=" CA LYS F 32 " pdb=" N LYS F 32 " pdb=" C LYS F 32 " pdb=" CB LYS F 32 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.16e+00 ... (remaining 2237 not shown) Planarity restraints: 1530 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY B 103 " 0.030 2.00e-02 2.50e+03 6.16e-02 3.80e+01 pdb=" C GLY B 103 " -0.107 2.00e-02 2.50e+03 pdb=" O GLY B 103 " 0.039 2.00e-02 2.50e+03 pdb=" OXT GLY B 103 " 0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY F 103 " -0.025 2.00e-02 2.50e+03 4.95e-02 2.45e+01 pdb=" C GLY F 103 " 0.086 2.00e-02 2.50e+03 pdb=" O GLY F 103 " -0.030 2.00e-02 2.50e+03 pdb=" OXT GLY F 103 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP K 207 " -0.047 2.00e-02 2.50e+03 2.27e-02 1.29e+01 pdb=" CG TRP K 207 " 0.010 2.00e-02 2.50e+03 pdb=" CD1 TRP K 207 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP K 207 " 0.021 2.00e-02 2.50e+03 pdb=" NE1 TRP K 207 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP K 207 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP K 207 " 0.028 2.00e-02 2.50e+03 pdb=" CZ2 TRP K 207 " -0.024 2.00e-02 2.50e+03 pdb=" CZ3 TRP K 207 " 0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP K 207 " -0.023 2.00e-02 2.50e+03 ... (remaining 1527 not shown) Histogram of nonbonded interaction distances: 2.46 - 2.95: 5241 2.95 - 3.44: 11069 3.44 - 3.92: 24541 3.92 - 4.41: 29390 4.41 - 4.90: 37969 Nonbonded interactions: 108210 Sorted by model distance: nonbonded pdb=" OG1 THR F 83 " pdb=" N ALA F 84 " model vdw 2.459 3.120 nonbonded pdb=" OG1 THR B 83 " pdb=" N ALA B 84 " model vdw 2.469 3.120 nonbonded pdb=" OP1 DA J 139 " pdb=" NH2 ARG L 53 " model vdw 2.471 3.120 nonbonded pdb=" CB GLU E 98 " pdb=" OE1 GLU E 98 " model vdw 2.479 2.752 nonbonded pdb=" O ALA C 11 " pdb=" CG ARG C 12 " model vdw 2.493 3.440 ... (remaining 108205 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'E' and resid 41 through 202) } ncs_group { reference = (chain 'B' and resid 23 through 103) selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 10 through 201) selection = (chain 'G' and (resid 10 through 117 or resid 201)) } ncs_group { reference = chain 'D' selection = chain 'H' } 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=0.00 max=1.00 mean=0.96 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.170 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: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.550 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 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 : 0.023 0.178 13842 Z= 1.287 Angle : 1.522 10.572 19832 Z= 1.013 Chirality : 0.093 0.349 2240 Planarity : 0.008 0.062 1530 Dihedral : 24.655 166.407 5953 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 0.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.24), residues: 883 helix: 0.80 (0.18), residues: 647 sheet: None (None), residues: 0 loop : 0.72 (0.33), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 37 TYR 0.047 0.008 TYR B 52 PHE 0.030 0.005 PHE L 90 TRP 0.047 0.010 TRP K 207 HIS 0.008 0.002 HIS G 32 Details of bonding type rmsd covalent geometry : bond 0.02194 (13824) covalent geometry : angle 1.52209 (19832) hydrogen bonds : bond 0.16252 ( 850) hydrogen bonds : angle 5.39970 ( 2171) Misc. bond : bond 0.16611 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 223 time to evaluate : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 36 GLU cc_start: 0.8885 (mt-10) cc_final: 0.8602 (pp20) REVERT: G 39 ASN cc_start: 0.7242 (m-40) cc_final: 0.6613 (m110) REVERT: K 163 THR cc_start: 0.7350 (p) cc_final: 0.7105 (p) outliers start: 0 outliers final: 0 residues processed: 223 average time/residue: 0.1480 time to fit residues: 43.8052 Evaluate side-chains 156 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 108 optimal weight: 10.0000 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 113 optimal weight: 6.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 0.9980 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN C 39 ASN C 74 ASN D 110 HIS G 32 HIS G 39 ASN H 85 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.098490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.062205 restraints weight = 37969.577| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 2.22 r_work: 0.2871 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.2866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13842 Z= 0.182 Angle : 0.628 11.680 19832 Z= 0.369 Chirality : 0.036 0.146 2240 Planarity : 0.005 0.039 1530 Dihedral : 28.435 178.812 4128 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.19 % Allowed : 5.68 % Favored : 93.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.01 (0.27), residues: 883 helix: 2.53 (0.19), residues: 672 sheet: None (None), residues: 0 loop : 0.25 (0.36), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 201 TYR 0.018 0.002 TYR H 41 PHE 0.019 0.002 PHE K 187 TRP 0.010 0.002 TRP L 51 HIS 0.004 0.001 HIS G 83 Details of bonding type rmsd covalent geometry : bond 0.00395 (13824) covalent geometry : angle 0.62822 (19832) hydrogen bonds : bond 0.05866 ( 850) hydrogen bonds : angle 3.14557 ( 2171) Misc. bond : bond 0.00104 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 221 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 60 GLU cc_start: 0.8669 (pm20) cc_final: 0.8439 (pm20) REVERT: E 124 ASP cc_start: 0.9069 (m-30) cc_final: 0.8867 (m-30) REVERT: F 26 ASN cc_start: 0.8747 (m-40) cc_final: 0.8477 (m-40) REVERT: H 94 GLU cc_start: 0.8880 (mp0) cc_final: 0.8634 (mp0) outliers start: 9 outliers final: 4 residues processed: 225 average time/residue: 0.1263 time to fit residues: 39.0234 Evaluate side-chains 180 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 176 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain E residue 77 GLN Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain K residue 153 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 63 optimal weight: 7.9990 chunk 60 optimal weight: 5.9990 chunk 68 optimal weight: 5.9990 chunk 84 optimal weight: 20.0000 chunk 102 optimal weight: 10.0000 chunk 81 optimal weight: 8.9990 chunk 47 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 chunk 64 optimal weight: 3.9990 chunk 80 optimal weight: 6.9990 chunk 74 optimal weight: 8.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 GLN C 25 GLN E 69 GLN ** H 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.095972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.058524 restraints weight = 37538.702| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 2.28 r_work: 0.2756 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.3373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 13842 Z= 0.274 Angle : 0.625 9.036 19832 Z= 0.364 Chirality : 0.038 0.157 2240 Planarity : 0.004 0.039 1530 Dihedral : 28.927 176.237 4128 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Rotamer: Outliers : 2.51 % Allowed : 8.06 % Favored : 89.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.99 (0.27), residues: 883 helix: 2.68 (0.20), residues: 665 sheet: None (None), residues: 0 loop : -0.30 (0.35), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 87 TYR 0.013 0.002 TYR H 84 PHE 0.026 0.002 PHE L 90 TRP 0.008 0.002 TRP L 51 HIS 0.004 0.001 HIS G 83 Details of bonding type rmsd covalent geometry : bond 0.00628 (13824) covalent geometry : angle 0.62484 (19832) hydrogen bonds : bond 0.05584 ( 850) hydrogen bonds : angle 3.29846 ( 2171) Misc. bond : bond 0.00038 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 178 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.8647 (pm20) cc_final: 0.8348 (pm20) REVERT: C 39 ASN cc_start: 0.8950 (OUTLIER) cc_final: 0.8322 (m-40) REVERT: C 93 GLU cc_start: 0.8935 (mp0) cc_final: 0.8698 (mp0) REVERT: D 106 GLU cc_start: 0.7990 (mm-30) cc_final: 0.7467 (mm-30) REVERT: F 26 ASN cc_start: 0.8803 (m-40) cc_final: 0.8421 (m-40) REVERT: G 111 ASN cc_start: 0.8121 (m-40) cc_final: 0.7854 (m110) REVERT: K 164 GLN cc_start: 0.4229 (OUTLIER) cc_final: 0.3999 (pt0) outliers start: 19 outliers final: 10 residues processed: 188 average time/residue: 0.1131 time to fit residues: 29.9390 Evaluate side-chains 176 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 164 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain C residue 39 ASN Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 77 GLN Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain H residue 40 ILE Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain K residue 147 GLU Chi-restraints excluded: chain K residue 153 LEU Chi-restraints excluded: chain K residue 164 GLN Chi-restraints excluded: chain L residue 105 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 79 optimal weight: 6.9990 chunk 15 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 84 optimal weight: 20.0000 chunk 92 optimal weight: 6.9990 chunk 22 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 102 optimal weight: 9.9990 chunk 10 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 GLN D 85 ASN E 69 GLN ** H 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.096995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.061532 restraints weight = 37204.288| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 2.22 r_work: 0.2816 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.3841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13842 Z= 0.189 Angle : 0.561 9.154 19832 Z= 0.335 Chirality : 0.034 0.131 2240 Planarity : 0.004 0.054 1530 Dihedral : 28.733 174.999 4128 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 2.38 % Allowed : 9.51 % Favored : 88.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.18 (0.28), residues: 883 helix: 2.84 (0.20), residues: 666 sheet: None (None), residues: 0 loop : -0.36 (0.37), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 93 TYR 0.011 0.001 TYR H 41 PHE 0.021 0.002 PHE K 187 TRP 0.007 0.002 TRP L 79 HIS 0.002 0.001 HIS L 101 Details of bonding type rmsd covalent geometry : bond 0.00421 (13824) covalent geometry : angle 0.56128 (19832) hydrogen bonds : bond 0.04644 ( 850) hydrogen bonds : angle 3.07645 ( 2171) Misc. bond : bond 0.00016 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 185 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 SER cc_start: 0.8538 (m) cc_final: 0.8049 (t) REVERT: A 60 GLU cc_start: 0.8578 (pm20) cc_final: 0.7405 (pm20) REVERT: C 91 ASP cc_start: 0.8409 (t0) cc_final: 0.8155 (t0) REVERT: C 93 GLU cc_start: 0.9001 (mp0) cc_final: 0.8490 (mp0) REVERT: D 77 GLU cc_start: 0.9137 (tp30) cc_final: 0.8843 (tp30) REVERT: D 106 GLU cc_start: 0.7764 (mm-30) cc_final: 0.7356 (mm-30) REVERT: G 111 ASN cc_start: 0.8026 (m-40) cc_final: 0.7737 (p0) outliers start: 18 outliers final: 10 residues processed: 190 average time/residue: 0.1197 time to fit residues: 31.8177 Evaluate side-chains 177 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 167 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 77 GLN Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain H residue 40 ILE Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain L residue 45 MET Chi-restraints excluded: chain L residue 105 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 31 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 18 optimal weight: 0.3980 chunk 65 optimal weight: 6.9990 chunk 7 optimal weight: 6.9990 chunk 104 optimal weight: 6.9990 chunk 101 optimal weight: 30.0000 chunk 43 optimal weight: 6.9990 chunk 102 optimal weight: 8.9990 chunk 55 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 overall best weight: 2.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN E 69 GLN H 110 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.096385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.060886 restraints weight = 37361.933| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 2.22 r_work: 0.2793 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.4057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 13842 Z= 0.203 Angle : 0.584 13.512 19832 Z= 0.341 Chirality : 0.034 0.139 2240 Planarity : 0.004 0.042 1530 Dihedral : 28.828 170.478 4128 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 2.51 % Allowed : 10.83 % Favored : 86.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.10 (0.28), residues: 883 helix: 2.80 (0.20), residues: 666 sheet: None (None), residues: 0 loop : -0.42 (0.37), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 87 TYR 0.014 0.001 TYR H 84 PHE 0.032 0.002 PHE K 187 TRP 0.006 0.001 TRP L 51 HIS 0.003 0.001 HIS B 76 Details of bonding type rmsd covalent geometry : bond 0.00457 (13824) covalent geometry : angle 0.58411 (19832) hydrogen bonds : bond 0.04820 ( 850) hydrogen bonds : angle 3.14094 ( 2171) Misc. bond : bond 0.00022 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 163 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 SER cc_start: 0.8573 (m) cc_final: 0.8072 (t) REVERT: A 60 GLU cc_start: 0.8573 (pm20) cc_final: 0.7494 (pm20) REVERT: C 39 ASN cc_start: 0.9057 (m-40) cc_final: 0.8542 (t0) REVERT: C 91 ASP cc_start: 0.8528 (t0) cc_final: 0.8139 (t0) REVERT: C 93 GLU cc_start: 0.9049 (mp0) cc_final: 0.8544 (mp0) REVERT: D 94 GLU cc_start: 0.9248 (OUTLIER) cc_final: 0.8664 (mp0) REVERT: D 106 GLU cc_start: 0.7943 (mm-30) cc_final: 0.7394 (mm-30) REVERT: G 111 ASN cc_start: 0.8082 (m-40) cc_final: 0.7829 (p0) outliers start: 19 outliers final: 14 residues processed: 170 average time/residue: 0.1079 time to fit residues: 26.3922 Evaluate side-chains 175 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 160 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLN Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain C residue 65 GLU Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 77 GLN Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 103 ILE Chi-restraints excluded: chain H residue 40 ILE Chi-restraints excluded: chain H residue 72 GLU Chi-restraints excluded: chain K residue 182 THR Chi-restraints excluded: chain L residue 105 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 9 optimal weight: 0.0370 chunk 97 optimal weight: 8.9990 chunk 10 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 13 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 74 optimal weight: 7.9990 chunk 78 optimal weight: 7.9990 chunk 60 optimal weight: 8.9990 chunk 94 optimal weight: 5.9990 chunk 77 optimal weight: 6.9990 overall best weight: 1.9864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.097231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.060322 restraints weight = 37307.020| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 2.26 r_work: 0.2808 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.4243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13842 Z= 0.176 Angle : 0.565 12.444 19832 Z= 0.333 Chirality : 0.033 0.141 2240 Planarity : 0.004 0.044 1530 Dihedral : 28.727 170.296 4128 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 2.25 % Allowed : 11.62 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.24 (0.28), residues: 883 helix: 2.92 (0.20), residues: 666 sheet: None (None), residues: 0 loop : -0.45 (0.38), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 87 TYR 0.018 0.001 TYR H 84 PHE 0.034 0.002 PHE K 187 TRP 0.009 0.002 TRP L 51 HIS 0.002 0.001 HIS B 76 Details of bonding type rmsd covalent geometry : bond 0.00390 (13824) covalent geometry : angle 0.56536 (19832) hydrogen bonds : bond 0.04463 ( 850) hydrogen bonds : angle 3.03520 ( 2171) Misc. bond : bond 0.00007 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 168 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 SER cc_start: 0.8558 (m) cc_final: 0.8059 (t) REVERT: A 60 GLU cc_start: 0.8568 (pm20) cc_final: 0.7551 (pm20) REVERT: C 91 ASP cc_start: 0.8525 (t0) cc_final: 0.8320 (t0) REVERT: D 77 GLU cc_start: 0.9137 (tp30) cc_final: 0.8777 (tp30) REVERT: D 94 GLU cc_start: 0.9253 (OUTLIER) cc_final: 0.8685 (mp0) REVERT: E 60 GLU cc_start: 0.8561 (pm20) cc_final: 0.7834 (pm20) REVERT: G 20 SER cc_start: 0.9629 (t) cc_final: 0.9255 (p) REVERT: G 91 ASP cc_start: 0.8734 (t0) cc_final: 0.8396 (t70) REVERT: G 111 ASN cc_start: 0.8065 (m-40) cc_final: 0.7847 (p0) outliers start: 17 outliers final: 12 residues processed: 175 average time/residue: 0.1137 time to fit residues: 28.4898 Evaluate side-chains 175 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 162 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain C residue 65 GLU Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain E residue 77 GLN Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain H residue 40 ILE Chi-restraints excluded: chain H residue 72 GLU Chi-restraints excluded: chain K residue 182 THR Chi-restraints excluded: chain L residue 45 MET Chi-restraints excluded: chain L residue 105 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 52 optimal weight: 4.9990 chunk 75 optimal weight: 8.9990 chunk 48 optimal weight: 0.8980 chunk 37 optimal weight: 8.9990 chunk 7 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 8 optimal weight: 0.9990 chunk 103 optimal weight: 6.9990 chunk 65 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 78 optimal weight: 6.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 94 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.096402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.058587 restraints weight = 37207.908| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 2.29 r_work: 0.2772 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.4331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 13842 Z= 0.215 Angle : 0.588 13.045 19832 Z= 0.343 Chirality : 0.034 0.150 2240 Planarity : 0.004 0.041 1530 Dihedral : 28.866 169.079 4128 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.64 % Allowed : 11.36 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.14 (0.28), residues: 883 helix: 2.87 (0.20), residues: 667 sheet: None (None), residues: 0 loop : -0.57 (0.38), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 87 TYR 0.016 0.001 TYR H 84 PHE 0.035 0.002 PHE K 187 TRP 0.006 0.002 TRP L 79 HIS 0.003 0.001 HIS B 76 Details of bonding type rmsd covalent geometry : bond 0.00487 (13824) covalent geometry : angle 0.58758 (19832) hydrogen bonds : bond 0.04876 ( 850) hydrogen bonds : angle 3.17148 ( 2171) Misc. bond : bond 0.00017 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 166 time to evaluate : 0.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 SER cc_start: 0.8644 (m) cc_final: 0.8134 (t) REVERT: A 60 GLU cc_start: 0.8549 (pm20) cc_final: 0.7570 (pm20) REVERT: C 39 ASN cc_start: 0.9108 (t0) cc_final: 0.8740 (t0) REVERT: C 91 ASP cc_start: 0.8591 (t0) cc_final: 0.8367 (t0) REVERT: D 77 GLU cc_start: 0.9138 (tp30) cc_final: 0.8902 (tp30) REVERT: D 94 GLU cc_start: 0.9277 (OUTLIER) cc_final: 0.8694 (mp0) REVERT: D 106 GLU cc_start: 0.8001 (mm-30) cc_final: 0.7672 (mm-30) REVERT: G 20 SER cc_start: 0.9634 (t) cc_final: 0.9262 (p) REVERT: G 91 ASP cc_start: 0.8828 (t0) cc_final: 0.8466 (t70) REVERT: G 111 ASN cc_start: 0.8068 (m-40) cc_final: 0.7851 (p0) REVERT: K 145 GLU cc_start: 0.8958 (tt0) cc_final: 0.8757 (tm-30) outliers start: 20 outliers final: 13 residues processed: 174 average time/residue: 0.1122 time to fit residues: 28.0142 Evaluate side-chains 175 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 161 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain C residue 65 GLU Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain E residue 77 GLN Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain H residue 40 ILE Chi-restraints excluded: chain H residue 72 GLU Chi-restraints excluded: chain K residue 182 THR Chi-restraints excluded: chain L residue 45 MET Chi-restraints excluded: chain L residue 92 ASP Chi-restraints excluded: chain L residue 105 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 93 optimal weight: 7.9990 chunk 48 optimal weight: 4.9990 chunk 53 optimal weight: 7.9990 chunk 41 optimal weight: 0.0370 chunk 100 optimal weight: 2.9990 chunk 9 optimal weight: 8.9990 chunk 11 optimal weight: 4.9990 chunk 75 optimal weight: 8.9990 chunk 5 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 overall best weight: 2.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.097117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.059396 restraints weight = 37055.727| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 2.26 r_work: 0.2795 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.4479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13842 Z= 0.185 Angle : 0.579 13.001 19832 Z= 0.338 Chirality : 0.033 0.149 2240 Planarity : 0.004 0.043 1530 Dihedral : 28.758 168.380 4128 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.25 % Allowed : 12.68 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.16 (0.28), residues: 883 helix: 2.86 (0.20), residues: 669 sheet: None (None), residues: 0 loop : -0.53 (0.39), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 87 TYR 0.018 0.001 TYR H 84 PHE 0.036 0.002 PHE K 187 TRP 0.010 0.001 TRP L 51 HIS 0.002 0.001 HIS F 76 Details of bonding type rmsd covalent geometry : bond 0.00414 (13824) covalent geometry : angle 0.57919 (19832) hydrogen bonds : bond 0.04489 ( 850) hydrogen bonds : angle 3.07959 ( 2171) Misc. bond : bond 0.00008 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 165 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 SER cc_start: 0.8614 (m) cc_final: 0.8097 (t) REVERT: A 60 GLU cc_start: 0.8540 (pm20) cc_final: 0.7558 (pm20) REVERT: C 91 ASP cc_start: 0.8572 (t0) cc_final: 0.8344 (t0) REVERT: D 77 GLU cc_start: 0.9159 (tp30) cc_final: 0.8946 (tp30) REVERT: D 94 GLU cc_start: 0.9262 (OUTLIER) cc_final: 0.8704 (mp0) REVERT: D 106 GLU cc_start: 0.7912 (mm-30) cc_final: 0.7505 (mm-30) REVERT: G 20 SER cc_start: 0.9644 (t) cc_final: 0.9290 (p) REVERT: G 91 ASP cc_start: 0.8829 (t0) cc_final: 0.8447 (t70) outliers start: 17 outliers final: 13 residues processed: 173 average time/residue: 0.1059 time to fit residues: 26.3020 Evaluate side-chains 175 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 161 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain C residue 65 GLU Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 77 GLN Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain H residue 40 ILE Chi-restraints excluded: chain H residue 72 GLU Chi-restraints excluded: chain K residue 182 THR Chi-restraints excluded: chain L residue 45 MET Chi-restraints excluded: chain L residue 105 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 58 optimal weight: 1.9990 chunk 75 optimal weight: 8.9990 chunk 103 optimal weight: 10.0000 chunk 73 optimal weight: 10.0000 chunk 30 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 10 optimal weight: 2.9990 chunk 91 optimal weight: 7.9990 chunk 78 optimal weight: 7.9990 chunk 31 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.097104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.059257 restraints weight = 37702.607| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 2.29 r_work: 0.2791 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.4588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13842 Z= 0.193 Angle : 0.593 13.094 19832 Z= 0.345 Chirality : 0.034 0.159 2240 Planarity : 0.004 0.066 1530 Dihedral : 28.798 167.266 4128 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.38 % Allowed : 13.21 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.03 (0.28), residues: 883 helix: 2.79 (0.20), residues: 666 sheet: None (None), residues: 0 loop : -0.61 (0.38), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG K 157 TYR 0.018 0.001 TYR H 84 PHE 0.042 0.002 PHE K 187 TRP 0.012 0.002 TRP L 51 HIS 0.003 0.001 HIS F 76 Details of bonding type rmsd covalent geometry : bond 0.00433 (13824) covalent geometry : angle 0.59348 (19832) hydrogen bonds : bond 0.04590 ( 850) hydrogen bonds : angle 3.11615 ( 2171) Misc. bond : bond 0.00011 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 164 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 SER cc_start: 0.8629 (m) cc_final: 0.8118 (t) REVERT: A 60 GLU cc_start: 0.8543 (pm20) cc_final: 0.7591 (pm20) REVERT: C 39 ASN cc_start: 0.8813 (t0) cc_final: 0.8361 (t0) REVERT: C 91 ASP cc_start: 0.8575 (t0) cc_final: 0.8344 (t0) REVERT: D 77 GLU cc_start: 0.9160 (tp30) cc_final: 0.8950 (tp30) REVERT: D 94 GLU cc_start: 0.9257 (OUTLIER) cc_final: 0.8700 (mp0) REVERT: D 106 GLU cc_start: 0.7959 (mm-30) cc_final: 0.7547 (mm-30) REVERT: G 20 SER cc_start: 0.9657 (t) cc_final: 0.9300 (p) REVERT: G 91 ASP cc_start: 0.8826 (t0) cc_final: 0.8433 (t70) REVERT: H 122 TYR cc_start: 0.9283 (t80) cc_final: 0.9016 (t80) REVERT: K 145 GLU cc_start: 0.9125 (tm-30) cc_final: 0.8843 (pp20) outliers start: 18 outliers final: 14 residues processed: 172 average time/residue: 0.1118 time to fit residues: 27.5434 Evaluate side-chains 174 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 159 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain C residue 65 GLU Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 77 GLN Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 103 ILE Chi-restraints excluded: chain H residue 40 ILE Chi-restraints excluded: chain H residue 72 GLU Chi-restraints excluded: chain K residue 182 THR Chi-restraints excluded: chain L residue 45 MET Chi-restraints excluded: chain L residue 105 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 107 optimal weight: 9.9990 chunk 19 optimal weight: 4.9990 chunk 101 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 65 optimal weight: 10.0000 chunk 85 optimal weight: 40.0000 chunk 78 optimal weight: 7.9990 chunk 108 optimal weight: 50.0000 chunk 47 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.096855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.058874 restraints weight = 37466.774| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 2.29 r_work: 0.2789 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.4665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 13842 Z= 0.201 Angle : 0.611 12.728 19832 Z= 0.352 Chirality : 0.035 0.184 2240 Planarity : 0.004 0.058 1530 Dihedral : 28.818 166.720 4128 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.11 % Allowed : 14.13 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.94 (0.28), residues: 883 helix: 2.73 (0.20), residues: 667 sheet: None (None), residues: 0 loop : -0.67 (0.38), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG K 201 TYR 0.017 0.001 TYR H 84 PHE 0.035 0.002 PHE K 187 TRP 0.016 0.002 TRP L 79 HIS 0.003 0.001 HIS F 76 Details of bonding type rmsd covalent geometry : bond 0.00455 (13824) covalent geometry : angle 0.61084 (19832) hydrogen bonds : bond 0.04593 ( 850) hydrogen bonds : angle 3.16436 ( 2171) Misc. bond : bond 0.00010 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 164 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 SER cc_start: 0.8620 (m) cc_final: 0.8102 (t) REVERT: A 60 GLU cc_start: 0.8528 (pm20) cc_final: 0.7568 (pm20) REVERT: C 39 ASN cc_start: 0.8808 (t0) cc_final: 0.8451 (t0) REVERT: C 91 ASP cc_start: 0.8605 (t0) cc_final: 0.8373 (t0) REVERT: D 77 GLU cc_start: 0.9153 (tp30) cc_final: 0.8946 (tp30) REVERT: D 94 GLU cc_start: 0.9267 (OUTLIER) cc_final: 0.8709 (mp0) REVERT: D 106 GLU cc_start: 0.7997 (mm-30) cc_final: 0.7582 (mm-30) REVERT: E 58 SER cc_start: 0.9070 (t) cc_final: 0.8745 (t) REVERT: G 20 SER cc_start: 0.9665 (t) cc_final: 0.9313 (p) REVERT: G 91 ASP cc_start: 0.8819 (t0) cc_final: 0.8424 (t70) REVERT: H 122 TYR cc_start: 0.9281 (t80) cc_final: 0.9013 (t80) REVERT: K 145 GLU cc_start: 0.9054 (tm-30) cc_final: 0.8766 (pp20) outliers start: 16 outliers final: 14 residues processed: 171 average time/residue: 0.1185 time to fit residues: 28.9615 Evaluate side-chains 176 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 161 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain C residue 65 GLU Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 77 GLN Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 103 ILE Chi-restraints excluded: chain H residue 40 ILE Chi-restraints excluded: chain H residue 72 GLU Chi-restraints excluded: chain K residue 182 THR Chi-restraints excluded: chain K residue 205 GLN Chi-restraints excluded: chain L residue 105 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 61 optimal weight: 1.9990 chunk 73 optimal weight: 10.0000 chunk 53 optimal weight: 7.9990 chunk 97 optimal weight: 8.9990 chunk 7 optimal weight: 7.9990 chunk 83 optimal weight: 10.0000 chunk 100 optimal weight: 9.9990 chunk 49 optimal weight: 0.9990 chunk 86 optimal weight: 50.0000 chunk 56 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.095826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.057740 restraints weight = 37485.208| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 2.29 r_work: 0.2750 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.4692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 13842 Z= 0.264 Angle : 0.636 12.103 19832 Z= 0.367 Chirality : 0.037 0.168 2240 Planarity : 0.004 0.040 1530 Dihedral : 29.050 167.411 4128 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.11 % Allowed : 14.53 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.71 (0.28), residues: 883 helix: 2.61 (0.20), residues: 665 sheet: None (None), residues: 0 loop : -0.89 (0.37), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 100 TYR 0.030 0.002 TYR K 162 PHE 0.035 0.002 PHE K 187 TRP 0.009 0.002 TRP L 79 HIS 0.003 0.001 HIS F 76 Details of bonding type rmsd covalent geometry : bond 0.00607 (13824) covalent geometry : angle 0.63610 (19832) hydrogen bonds : bond 0.05114 ( 850) hydrogen bonds : angle 3.34486 ( 2171) Misc. bond : bond 0.00015 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3190.97 seconds wall clock time: 54 minutes 58.12 seconds (3298.12 seconds total)