Starting phenix.real_space_refine on Sat Sep 12 00:33:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6t90_10406/09_2026/6t90_10406.cif Found real_map, /net/cci-nas-00/data/ceres_data/6t90_10406/09_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_10406/09_2026/6t90_10406.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6t90_10406/09_2026/6t90_10406.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6t90_10406/09_2026/6t90_10406.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6t90_10406/09_2026/6t90_10406.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6t90_10406/09_2026/6t90_10406.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6t90_10406/09_2026/6t90_10406.cif" } 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-2.2.1-6174/lib/python3.11/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: 2.35, per 1000 atoms: 0.18 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: 1.08 Conformation dependent library (CDL) restraints added in 387.9 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: 1.61 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: 1.89 Time building geometry restraints manager: 1.47 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=" C5 DA I 49 " pdb=" C4 DA I 49 " ideal model delta sigma weight residual 1.383 1.334 0.049 7.00e-03 2.04e+04 4.91e+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 ... (remaining 13819 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.21: 17067 2.21 - 4.43: 2400 4.43 - 6.64: 334 6.64 - 8.86: 28 8.86 - 11.07: 3 Bond angle restraints: 19832 Sorted by residual: angle pdb=" C3' DT I 89 " pdb=" O3' DT I 89 " pdb=" P DA I 90 " ideal model delta sigma weight residual 119.70 130.77 -11.07 1.20e+00 6.94e-01 8.51e+01 angle pdb=" C3' DG I 4 " pdb=" O3' DG I 4 " pdb=" P DA I 5 " ideal model delta sigma weight residual 119.70 129.89 -10.19 1.20e+00 6.94e-01 7.21e+01 angle pdb=" O2 DC I 111 " pdb=" C2 DC I 111 " pdb=" N3 DC I 111 " ideal model delta sigma weight residual 121.90 116.44 5.46 7.00e-01 2.04e+00 6.08e+01 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 ... (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: 1207 0.070 - 0.140: 723 0.140 - 0.209: 254 0.209 - 0.279: 50 0.279 - 0.349: 6 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: 1.380 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: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 11.910 Find NCS groups from input model: 0.130 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 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= 1.498 Angle : 1.568 11.072 19832 Z= 1.244 Chirality : 0.094 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/Z covalent geometry : bond 0.02175 / 1.37 (13824) covalent geometry : angle 1.56773 / 1.24 (19832) hydrogen bonds : bond 0.16252 / 10.49 ( 850) hydrogen bonds : angle 5.39970 / 3.90 ( 2171) Misc. bond : bond 0.16611 / 10.61 ( 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 : 0.381 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: 0.7133 (p) outliers start: 0 outliers final: 0 residues processed: 223 average time/residue: 0.1381 time to fit residues: 41.5817 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 : 0.349 ------------------------------------------------------------------------------- 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: 10.0000 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... A 77 GLN B 76 HIS C 74 ASN D 110 HIS G 32 HIS H 85 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.098986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.062227 restraints weight = 37260.861| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 2.24 r_work: 0.2850 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13842 Z= 0.201 Angle : 0.761 8.869 19832 Z= 0.447 Chirality : 0.050 0.264 2240 Planarity : 0.005 0.050 1530 Dihedral : 28.682 175.345 4128 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.45 % Allowed : 6.08 % Favored : 92.47 % 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: 2.58 (0.26), residues: 883 helix: 2.22 (0.19), residues: 668 sheet: None (None), residues: 0 loop : 0.15 (0.35), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 87 TYR 0.018 0.002 TYR L 110 PHE 0.023 0.002 PHE K 187 TRP 0.011 0.002 TRP L 51 HIS 0.008 0.001 HIS L 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.20 (13824) covalent geometry : angle 0.76085 / 0.45 (19832) hydrogen bonds : bond 0.07969 / 5.34 ( 850) hydrogen bonds : angle 3.50033 / 2.51 ( 2171) Misc. bond : bond 0.00704 / 0.41 ( 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 232 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 221 time to evaluate : 0.339 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: symmetry clash REVERT: A 59 THR cc_start: 0.9196 (p) cc_final: 0.8795 (t) REVERT: A 60 GLU cc_start: 0.8357 (pm20) cc_final: 0.7656 (pm20) REVERT: D 36 GLU cc_start: 0.9110 (mt-10) cc_final: 0.8899 (pp20) REVERT: F 26 ASN cc_start: 0.8751 (m-40) cc_final: 0.8124 (m-40) outliers start: 11 outliers final: 8 residues processed: 227 average time/residue: 0.1246 time to fit residues: 39.5098 Evaluate side-chains 193 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 185 time to evaluate : 0.357 ------------------------------------------------------------------------------- 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 77 GLN Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain K residue 153 LEU Chi-restraints excluded: chain K residue 164 GLN Chi-restraints excluded: chain L residue 98 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 63 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 68 optimal weight: 6.9990 chunk 84 optimal weight: 50.0000 chunk 102 optimal weight: 7.9990 chunk 81 optimal weight: 30.0000 chunk 47 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 64 optimal weight: 6.9990 chunk 80 optimal weight: 20.0000 chunk 74 optimal weight: 20.0000 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 69 GLN F 28 GLN G 74 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.097012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.061979 restraints weight = 37639.444| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 2.21 r_work: 0.2829 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 13842 Z= 0.204 Angle : 0.691 10.016 19832 Z= 0.405 Chirality : 0.043 0.232 2240 Planarity : 0.005 0.040 1530 Dihedral : 28.890 179.209 4128 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 2.64 % Allowed : 8.06 % Favored : 89.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.84 (0.27), residues: 883 helix: 2.52 (0.20), residues: 666 sheet: None (None), residues: 0 loop : -0.18 (0.35), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 157 TYR 0.027 0.002 TYR H 122 PHE 0.026 0.002 PHE K 187 TRP 0.009 0.002 TRP L 51 HIS 0.004 0.001 HIS L 67 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.20 (13824) covalent geometry : angle 0.69074 / 0.40 (19832) hydrogen bonds : bond 0.06596 / 4.41 ( 850) hydrogen bonds : angle 3.33701 / 2.40 ( 2171) Misc. bond : bond 0.00281 / 0.19 ( 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 214 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 194 time to evaluate : 0.301 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: symmetry clash REVERT: D 36 GLU cc_start: 0.9144 (mt-10) cc_final: 0.8939 (pp20) REVERT: D 106 GLU cc_start: 0.7814 (mm-30) cc_final: 0.7456 (mm-30) REVERT: E 60 GLU cc_start: 0.8742 (pm20) cc_final: 0.8439 (pm20) REVERT: F 26 ASN cc_start: 0.8769 (m-40) cc_final: 0.8523 (m-40) REVERT: G 91 ASP cc_start: 0.8712 (t0) cc_final: 0.8363 (t70) REVERT: K 191 GLN cc_start: 0.9139 (mp10) cc_final: 0.8929 (mp10) outliers start: 20 outliers final: 10 residues processed: 204 average time/residue: 0.1164 time to fit residues: 33.3815 Evaluate side-chains 187 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 177 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain D residue 72 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 77 THR Chi-restraints excluded: chain K residue 153 LEU Chi-restraints excluded: chain K residue 164 GLN Chi-restraints excluded: chain K residue 182 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 79 optimal weight: 20.0000 chunk 15 optimal weight: 6.9990 chunk 24 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 chunk 84 optimal weight: 50.0000 chunk 92 optimal weight: 20.0000 chunk 22 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 102 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 126 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.095899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.061008 restraints weight = 37999.087| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 2.11 r_work: 0.2817 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.3176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 13842 Z= 0.212 Angle : 0.672 8.339 19832 Z= 0.392 Chirality : 0.042 0.191 2240 Planarity : 0.004 0.039 1530 Dihedral : 29.117 178.325 4128 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 2.25 % Allowed : 9.78 % Favored : 87.98 % 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: 2.84 (0.28), residues: 883 helix: 2.59 (0.20), residues: 665 sheet: None (None), residues: 0 loop : -0.41 (0.36), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 87 TYR 0.019 0.002 TYR L 110 PHE 0.032 0.002 PHE L 90 TRP 0.006 0.002 TRP L 51 HIS 0.005 0.001 HIS F 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.21 (13824) covalent geometry : angle 0.67194 / 0.39 (19832) hydrogen bonds : bond 0.05982 / 4.01 ( 850) hydrogen bonds : angle 3.29679 / 2.38 ( 2171) Misc. bond : bond 0.00289 / 0.16 ( 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 190 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 173 time to evaluate : 0.269 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: A 58 SER cc_start: 0.8407 (t) cc_final: 0.8061 (t) REVERT: D 94 GLU cc_start: 0.9297 (OUTLIER) cc_final: 0.8641 (mp0) REVERT: D 106 GLU cc_start: 0.7787 (mm-30) cc_final: 0.7490 (mm-30) REVERT: E 60 GLU cc_start: 0.8692 (pm20) cc_final: 0.8429 (pm20) REVERT: F 26 ASN cc_start: 0.8725 (m-40) cc_final: 0.8390 (m-40) REVERT: G 91 ASP cc_start: 0.8777 (t0) cc_final: 0.8411 (t70) outliers start: 17 outliers final: 11 residues processed: 182 average time/residue: 0.1142 time to fit residues: 29.6843 Evaluate side-chains 177 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 165 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 61 LEU 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 77 THR Chi-restraints excluded: chain K residue 153 LEU Chi-restraints excluded: chain K residue 164 GLN Chi-restraints excluded: chain K residue 182 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 31 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 18 optimal weight: 0.9980 chunk 65 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 chunk 104 optimal weight: 4.9990 chunk 101 optimal weight: 7.9990 chunk 43 optimal weight: 9.9990 chunk 102 optimal weight: 7.9990 chunk 55 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 126 GLN G 74 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.095320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.060160 restraints weight = 38177.368| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 2.15 r_work: 0.2800 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.3460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 13842 Z= 0.216 Angle : 0.660 9.806 19832 Z= 0.384 Chirality : 0.041 0.211 2240 Planarity : 0.004 0.043 1530 Dihedral : 29.280 175.170 4128 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 2.38 % Allowed : 10.17 % Favored : 87.45 % 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: 2.88 (0.28), residues: 883 helix: 2.65 (0.20), residues: 665 sheet: None (None), residues: 0 loop : -0.51 (0.36), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 157 TYR 0.020 0.002 TYR L 110 PHE 0.022 0.002 PHE L 90 TRP 0.012 0.003 TRP L 51 HIS 0.005 0.001 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.22 (13824) covalent geometry : angle 0.66035 / 0.38 (19832) hydrogen bonds : bond 0.05806 / 3.88 ( 850) hydrogen bonds : angle 3.30643 / 2.37 ( 2171) Misc. bond : bond 0.00126 / 0.07 ( 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 191 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 173 time to evaluate : 0.377 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 58 SER cc_start: 0.8726 (t) cc_final: 0.8190 (t) REVERT: C 93 GLU cc_start: 0.8939 (mp0) cc_final: 0.8715 (mp0) REVERT: D 94 GLU cc_start: 0.9275 (OUTLIER) cc_final: 0.8642 (mp0) REVERT: D 106 GLU cc_start: 0.7845 (mm-30) cc_final: 0.7537 (mm-30) REVERT: E 60 GLU cc_start: 0.8670 (pm20) cc_final: 0.8386 (pm20) REVERT: F 26 ASN cc_start: 0.8769 (m-40) cc_final: 0.8466 (m-40) REVERT: G 74 ASN cc_start: 0.8693 (t0) cc_final: 0.8452 (t0) REVERT: G 91 ASP cc_start: 0.8811 (t0) cc_final: 0.8434 (t70) REVERT: G 111 ASN cc_start: 0.8035 (m-40) cc_final: 0.7779 (m110) outliers start: 18 outliers final: 11 residues processed: 182 average time/residue: 0.1255 time to fit residues: 32.5407 Evaluate side-chains 175 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 163 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 77 GLN Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain K residue 153 LEU 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: 0.0030 chunk 97 optimal weight: 20.0000 chunk 10 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 74 optimal weight: 20.0000 chunk 78 optimal weight: 20.0000 chunk 60 optimal weight: 4.9990 chunk 94 optimal weight: 20.0000 chunk 77 optimal weight: 20.0000 overall best weight: 2.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 85 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.095343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.060390 restraints weight = 37613.042| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 2.11 r_work: 0.2808 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.3607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13842 Z= 0.194 Angle : 0.644 9.694 19832 Z= 0.377 Chirality : 0.041 0.207 2240 Planarity : 0.004 0.046 1530 Dihedral : 29.269 171.160 4128 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 2.25 % Allowed : 11.36 % Favored : 86.39 % 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: 2.88 (0.28), residues: 883 helix: 2.67 (0.20), residues: 665 sheet: None (None), residues: 0 loop : -0.59 (0.36), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 87 TYR 0.016 0.001 TYR H 84 PHE 0.025 0.002 PHE L 90 TRP 0.013 0.003 TRP L 51 HIS 0.004 0.001 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.19 (13824) covalent geometry : angle 0.64365 / 0.38 (19832) hydrogen bonds : bond 0.05554 / 3.72 ( 850) hydrogen bonds : angle 3.30695 / 2.38 ( 2171) Misc. bond : bond 0.00119 / 0.06 ( 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 193 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 176 time to evaluate : 0.405 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: 0.8765 (t) cc_final: 0.8355 (t) REVERT: A 60 GLU cc_start: 0.8388 (pm20) cc_final: 0.8137 (pm20) REVERT: C 93 GLU cc_start: 0.8900 (mp0) cc_final: 0.8690 (mp0) REVERT: D 94 GLU cc_start: 0.9261 (OUTLIER) cc_final: 0.8651 (mp0) REVERT: D 106 GLU cc_start: 0.7833 (mm-30) cc_final: 0.7501 (mm-30) REVERT: E 60 GLU cc_start: 0.8659 (pm20) cc_final: 0.8374 (pm20) REVERT: F 26 ASN cc_start: 0.8792 (m-40) cc_final: 0.8451 (m-40) REVERT: G 74 ASN cc_start: 0.8699 (t0) cc_final: 0.8467 (t0) REVERT: G 91 ASP cc_start: 0.8807 (t0) cc_final: 0.8407 (t70) REVERT: G 111 ASN cc_start: 0.7985 (m-40) cc_final: 0.7721 (m110) REVERT: G 116 LEU cc_start: 0.7533 (OUTLIER) cc_final: 0.6804 (mp) outliers start: 17 outliers final: 13 residues processed: 184 average time/residue: 0.1271 time to fit residues: 33.5051 Evaluate side-chains 182 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 167 time to evaluate : 0.378 ------------------------------------------------------------------------------- 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 58 SER Chi-restraints excluded: chain E residue 61 LEU 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 77 THR Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain K residue 153 LEU Chi-restraints excluded: chain K residue 182 THR 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: 3.9990 chunk 75 optimal weight: 20.0000 chunk 48 optimal weight: 3.9990 chunk 37 optimal weight: 8.9990 chunk 7 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 8 optimal weight: 0.9980 chunk 103 optimal weight: 9.9990 chunk 65 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 78 optimal weight: 20.0000 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.095634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.060803 restraints weight = 37845.881| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 2.12 r_work: 0.2821 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.3798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13842 Z= 0.175 Angle : 0.631 9.924 19832 Z= 0.371 Chirality : 0.040 0.207 2240 Planarity : 0.004 0.045 1530 Dihedral : 29.211 170.148 4128 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 2.11 % Allowed : 12.02 % Favored : 85.87 % 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: 2.90 (0.28), residues: 883 helix: 2.65 (0.20), residues: 667 sheet: None (None), residues: 0 loop : -0.50 (0.37), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 201 TYR 0.018 0.001 TYR H 84 PHE 0.043 0.002 PHE K 187 TRP 0.008 0.003 TRP L 51 HIS 0.004 0.001 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.18 (13824) covalent geometry : angle 0.63077 / 0.37 (19832) hydrogen bonds : bond 0.05237 / 3.52 ( 850) hydrogen bonds : angle 3.23459 / 2.32 ( 2171) Misc. bond : bond 0.00028 / 0.02 ( 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 192 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 176 time to evaluate : 0.323 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 58 SER cc_start: 0.8838 (t) cc_final: 0.8551 (t) REVERT: D 94 GLU cc_start: 0.9234 (OUTLIER) cc_final: 0.8655 (mp0) REVERT: E 59 THR cc_start: 0.9504 (p) cc_final: 0.9237 (p) REVERT: E 60 GLU cc_start: 0.8649 (pm20) cc_final: 0.8170 (pm20) REVERT: G 74 ASN cc_start: 0.8659 (t0) cc_final: 0.8442 (t0) REVERT: G 91 ASP cc_start: 0.8798 (t0) cc_final: 0.8350 (t70) REVERT: G 111 ASN cc_start: 0.7904 (m-40) cc_final: 0.7642 (m110) outliers start: 16 outliers final: 9 residues processed: 182 average time/residue: 0.1232 time to fit residues: 32.1063 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 : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 123 LYS 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 K residue 153 LEU Chi-restraints excluded: chain K residue 182 THR 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: 20.0000 chunk 48 optimal weight: 0.8980 chunk 53 optimal weight: 8.9990 chunk 41 optimal weight: 0.5980 chunk 100 optimal weight: 8.9990 chunk 9 optimal weight: 0.0970 chunk 11 optimal weight: 3.9990 chunk 75 optimal weight: 20.0000 chunk 5 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 overall best weight: 2.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.095788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.061003 restraints weight = 37547.292| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 2.11 r_work: 0.2827 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.3882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13842 Z= 0.166 Angle : 0.630 12.070 19832 Z= 0.371 Chirality : 0.040 0.205 2240 Planarity : 0.004 0.042 1530 Dihedral : 29.200 169.526 4128 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 2.11 % Allowed : 12.81 % 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: 2.94 (0.28), residues: 883 helix: 2.70 (0.20), residues: 665 sheet: None (None), residues: 0 loop : -0.53 (0.37), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG K 201 TYR 0.017 0.001 TYR H 84 PHE 0.041 0.002 PHE K 187 TRP 0.009 0.002 TRP L 51 HIS 0.004 0.001 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.17 (13824) covalent geometry : angle 0.63013 / 0.37 (19832) hydrogen bonds : bond 0.05153 / 3.46 ( 850) hydrogen bonds : angle 3.25629 / 2.35 ( 2171) Misc. bond : bond 0.00006 / 0.00 ( 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 189 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 173 time to evaluate : 0.361 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: A 58 SER cc_start: 0.8837 (t) cc_final: 0.7982 (t) REVERT: A 60 GLU cc_start: 0.8263 (pm20) cc_final: 0.7678 (pm20) REVERT: D 94 GLU cc_start: 0.9223 (OUTLIER) cc_final: 0.8644 (mp0) REVERT: D 106 GLU cc_start: 0.7918 (mm-30) cc_final: 0.7605 (mm-30) REVERT: E 59 THR cc_start: 0.9501 (p) cc_final: 0.9220 (p) REVERT: E 60 GLU cc_start: 0.8629 (pm20) cc_final: 0.8128 (pm20) REVERT: G 74 ASN cc_start: 0.8664 (t0) cc_final: 0.8269 (t0) REVERT: G 91 ASP cc_start: 0.8784 (t0) cc_final: 0.8501 (t0) REVERT: G 111 ASN cc_start: 0.7914 (m-40) cc_final: 0.7628 (m110) outliers start: 16 outliers final: 10 residues processed: 180 average time/residue: 0.1225 time to fit residues: 31.4490 Evaluate side-chains 181 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 170 time to evaluate : 0.381 ------------------------------------------------------------------------------- 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 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 K residue 153 LEU Chi-restraints excluded: chain K residue 182 THR 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: 3.9990 chunk 75 optimal weight: 20.0000 chunk 103 optimal weight: 4.9990 chunk 73 optimal weight: 30.0000 chunk 30 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 10 optimal weight: 1.9990 chunk 91 optimal weight: 20.0000 chunk 78 optimal weight: 20.0000 chunk 31 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.095354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.060502 restraints weight = 38103.871| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 2.11 r_work: 0.2807 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.3956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 13842 Z= 0.206 Angle : 0.666 10.872 19832 Z= 0.384 Chirality : 0.041 0.215 2240 Planarity : 0.004 0.043 1530 Dihedral : 29.270 169.046 4128 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.72 % Allowed : 13.47 % Favored : 84.81 % 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: 2.87 (0.28), residues: 883 helix: 2.67 (0.20), residues: 665 sheet: None (None), residues: 0 loop : -0.63 (0.37), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 87 TYR 0.018 0.001 TYR H 84 PHE 0.030 0.002 PHE K 187 TRP 0.007 0.002 TRP L 51 HIS 0.005 0.001 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.21 (13824) covalent geometry : angle 0.66645 / 0.38 (19832) hydrogen bonds : bond 0.05409 / 3.63 ( 850) hydrogen bonds : angle 3.36977 / 2.42 ( 2171) Misc. bond : bond 0.00115 / 0.06 ( 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 179 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 166 time to evaluate : 0.363 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 58 SER cc_start: 0.8878 (t) cc_final: 0.8026 (t) REVERT: A 60 GLU cc_start: 0.8253 (pm20) cc_final: 0.7661 (pm20) REVERT: C 39 ASN cc_start: 0.8915 (m-40) cc_final: 0.8648 (t0) REVERT: D 94 GLU cc_start: 0.9239 (OUTLIER) cc_final: 0.8657 (mp0) REVERT: D 106 GLU cc_start: 0.7971 (mm-30) cc_final: 0.7636 (mm-30) REVERT: E 60 GLU cc_start: 0.8671 (pm20) cc_final: 0.8375 (pm20) REVERT: G 74 ASN cc_start: 0.8723 (t0) cc_final: 0.8339 (t0) REVERT: G 91 ASP cc_start: 0.8787 (t0) cc_final: 0.8499 (t0) REVERT: G 111 ASN cc_start: 0.7935 (m-40) cc_final: 0.7699 (p0) outliers start: 13 outliers final: 10 residues processed: 170 average time/residue: 0.1145 time to fit residues: 27.8156 Evaluate side-chains 175 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 164 time to evaluate : 0.258 ------------------------------------------------------------------------------- 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 58 SER Chi-restraints excluded: chain E residue 77 GLN Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain K residue 153 LEU Chi-restraints excluded: chain K residue 182 THR 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: 50.0000 chunk 19 optimal weight: 4.9990 chunk 101 optimal weight: 5.9990 chunk 41 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 65 optimal weight: 10.0000 chunk 85 optimal weight: 50.0000 chunk 78 optimal weight: 20.0000 chunk 108 optimal weight: 7.9990 chunk 47 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 94 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.095489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.058776 restraints weight = 38211.155| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 2.17 r_work: 0.2796 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.4028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13842 Z= 0.197 Angle : 0.655 10.427 19832 Z= 0.379 Chirality : 0.041 0.216 2240 Planarity : 0.004 0.043 1530 Dihedral : 29.297 168.290 4128 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.59 % Allowed : 13.74 % Favored : 84.68 % 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: 2.85 (0.28), residues: 883 helix: 2.65 (0.20), residues: 665 sheet: None (None), residues: 0 loop : -0.63 (0.38), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 201 TYR 0.019 0.001 TYR H 84 PHE 0.045 0.002 PHE K 187 TRP 0.007 0.002 TRP L 51 HIS 0.004 0.001 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.20 (13824) covalent geometry : angle 0.65550 / 0.38 (19832) hydrogen bonds : bond 0.05304 / 3.57 ( 850) hydrogen bonds : angle 3.38089 / 2.43 ( 2171) Misc. bond : bond 0.00034 / 0.02 ( 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 177 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 SER cc_start: 0.8861 (t) cc_final: 0.8068 (t) REVERT: A 60 GLU cc_start: 0.8213 (pm20) cc_final: 0.7626 (pm20) REVERT: D 94 GLU cc_start: 0.9246 (OUTLIER) cc_final: 0.8670 (mp0) REVERT: D 106 GLU cc_start: 0.7965 (mm-30) cc_final: 0.7637 (mm-30) REVERT: E 60 GLU cc_start: 0.8638 (pm20) cc_final: 0.8131 (pm20) REVERT: G 74 ASN cc_start: 0.8709 (t0) cc_final: 0.8327 (t0) REVERT: G 91 ASP cc_start: 0.8820 (t0) cc_final: 0.8351 (t70) REVERT: G 111 ASN cc_start: 0.7948 (m-40) cc_final: 0.7734 (p0) outliers start: 12 outliers final: 10 residues processed: 169 average time/residue: 0.1246 time to fit residues: 29.7885 Evaluate side-chains 174 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 163 time to evaluate : 0.372 ------------------------------------------------------------------------------- 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 58 SER Chi-restraints excluded: chain E residue 77 GLN Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain K residue 182 THR 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: 30.0000 chunk 53 optimal weight: 9.9990 chunk 97 optimal weight: 30.0000 chunk 7 optimal weight: 0.8980 chunk 83 optimal weight: 30.0000 chunk 100 optimal weight: 0.6980 chunk 49 optimal weight: 0.8980 chunk 86 optimal weight: 50.0000 chunk 56 optimal weight: 9.9990 chunk 51 optimal weight: 2.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.096307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.059950 restraints weight = 38302.287| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 2.18 r_work: 0.2827 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.4166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13842 Z= 0.154 Angle : 0.647 20.000 19832 Z= 0.373 Chirality : 0.040 0.207 2240 Planarity : 0.004 0.042 1530 Dihedral : 29.180 167.607 4128 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 2.11 % Allowed : 13.21 % Favored : 84.68 % 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: 2.96 (0.28), residues: 883 helix: 2.70 (0.20), residues: 667 sheet: None (None), residues: 0 loop : -0.51 (0.38), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 87 TYR 0.019 0.001 TYR H 84 PHE 0.043 0.002 PHE K 187 TRP 0.011 0.002 TRP L 51 HIS 0.003 0.001 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.15 (13824) covalent geometry : angle 0.64673 / 0.37 (19832) hydrogen bonds : bond 0.04870 / 3.27 ( 850) hydrogen bonds : angle 3.26689 / 2.34 ( 2171) Misc. bond : bond 0.00011 / 0.01 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3329.09 seconds wall clock time: 57 minutes 26.91 seconds (3446.91 seconds total)