Starting phenix.real_space_refine on Sat Sep 12 03:32:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7d20_30552/09_2026/7d20_30552.cif Found real_map, /net/cci-nas-00/data/ceres_data/7d20_30552/09_2026/7d20_30552.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7d20_30552/09_2026/7d20_30552.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7d20_30552/09_2026/7d20_30552.map" model { file = "/net/cci-nas-00/data/ceres_data/7d20_30552/09_2026/7d20_30552.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7d20_30552/09_2026/7d20_30552.cif" } resolution = 3.0 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= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1358 atoms to isotropic. 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 272 5.49 5 S 14 5.16 5 C 7237 2.51 5 N 2397 2.21 5 O 2916 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.00s 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: 12836 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 732 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 2, 'TRANS': 86} Chain: "E" Number of atoms: 749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 749 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "B" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "C" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 824 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "D" Number of atoms: 729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 729 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "F" Number of atoms: 699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 699 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 85} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 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: "I" Number of atoms: 2768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 2768 Classifications: {'DNA': 136} Link IDs: {'rna3p': 135} Chain: "J" Number of atoms: 2808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 2808 Classifications: {'DNA': 136} Link IDs: {'rna3p': 135} Chain: "K" Number of atoms: 1330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1330 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 3, 'TRANS': 162} Chain: "H" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Time building chain proxies: 3.01, per 1000 atoms: 0.23 Number of scatterers: 12836 At special positions: 0 Unit cell: (118.65, 99.75, 116.55, 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 14 16.00 P 272 15.00 O 2916 8.00 N 2397 7.00 C 7237 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.22 Conformation dependent library (CDL) restraints added in 514.1 milliseconds 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1694 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 12 sheets defined 61.9% alpha, 6.0% beta 132 base pairs and 237 stacking pairs defined. Time for finding SS restraints: 1.83 Creating SS restraints... Processing helix chain 'A' and resid 47 through 56 removed outlier: 3.758A pdb=" N LYS A 53 " --> pdb=" O LYS A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 75 Processing helix chain 'A' and resid 87 through 114 removed outlier: 4.010A pdb=" N LEU A 92 " --> pdb=" O ALA A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 127 removed outlier: 3.854A pdb=" N VAL A 126 " --> pdb=" O PHE A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 132 removed outlier: 3.592A pdb=" N ARG A 131 " --> pdb=" O GLN A 127 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 55 Processing helix chain 'E' and resid 63 through 78 removed outlier: 3.575A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL E 76 " --> pdb=" O ARG E 72 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 110 removed outlier: 3.833A pdb=" N LEU E 92 " --> pdb=" O ALA E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 134 removed outlier: 3.620A pdb=" N ARG E 133 " --> pdb=" O ALA E 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.581A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 removed outlier: 3.606A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.397A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASN C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.569A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.616A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 124 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.618A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.524A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.568A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 92 through 97 Processing helix chain 'K' and resid 194 through 213 Processing helix chain 'K' and resid 254 through 264 removed outlier: 3.885A pdb=" N GLU K 259 " --> pdb=" O ALA K 255 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N ALA K 260 " --> pdb=" O LYS K 256 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN K 264 " --> pdb=" O ALA K 260 " (cutoff:3.500A) Processing helix chain 'K' and resid 340 through 347 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 103 through 124 Processing sheet with id=AA1, first strand: chain 'A' and resid 120 through 121 Processing sheet with id=AA2, first strand: chain 'E' and resid 85 through 86 removed outlier: 7.260A pdb=" N ASN E 85 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'E' and resid 120 through 121 Processing sheet with id=AA4, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA5, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.401A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA7, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.913A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.034A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB1, first strand: chain 'K' and resid 218 through 223 removed outlier: 3.931A pdb=" N GLY K 227 " --> pdb=" O ILE K 223 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 241 through 244 removed outlier: 7.160A pdb=" N LEU K 320 " --> pdb=" O VAL K 242 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N GLU K 244 " --> pdb=" O LEU K 318 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N LEU K 318 " --> pdb=" O GLU K 244 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL K 315 " --> pdb=" O ILE K 312 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 248 through 250 removed outlier: 3.685A pdb=" N CYS K 283 " --> pdb=" O ILE K 250 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N PHE K 275 " --> pdb=" O TYR K 282 " (cutoff:3.500A) 423 hydrogen bonds defined for protein. 1248 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 341 hydrogen bonds 682 hydrogen bond angles 0 basepair planarities 132 basepair parallelities 237 stacking parallelities Total time for adding SS restraints: 2.88 Time building geometry restraints manager: 1.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2145 1.33 - 1.45: 4532 1.45 - 1.57: 6382 1.57 - 1.69: 542 1.69 - 1.81: 22 Bond restraints: 13623 Sorted by residual: bond pdb=" C3' DG J -4 " pdb=" O3' DG J -4 " ideal model delta sigma weight residual 1.435 1.380 0.055 1.30e-02 5.92e+03 1.82e+01 bond pdb=" C3' DA J -14 " pdb=" O3' DA J -14 " ideal model delta sigma weight residual 1.435 1.381 0.054 1.30e-02 5.92e+03 1.70e+01 bond pdb=" C3' DC I -4 " pdb=" O3' DC I -4 " ideal model delta sigma weight residual 1.435 1.382 0.053 1.30e-02 5.92e+03 1.69e+01 bond pdb=" C3' DG J 27 " pdb=" O3' DG J 27 " ideal model delta sigma weight residual 1.435 1.385 0.050 1.30e-02 5.92e+03 1.50e+01 bond pdb=" C3' DA J 16 " pdb=" O3' DA J 16 " ideal model delta sigma weight residual 1.435 1.388 0.047 1.30e-02 5.92e+03 1.33e+01 ... (remaining 13618 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.49: 19533 5.49 - 10.97: 19 10.97 - 16.46: 0 16.46 - 21.95: 1 21.95 - 27.43: 1 Bond angle restraints: 19554 Sorted by residual: angle pdb=" O3' DG J 20 " pdb=" P DG J 21 " pdb=" OP1 DG J 21 " ideal model delta sigma weight residual 108.00 80.57 27.43 3.00e+00 1.11e-01 8.36e+01 angle pdb=" N VAL E 119 " pdb=" CA VAL E 119 " pdb=" C VAL E 119 " ideal model delta sigma weight residual 113.71 106.10 7.61 9.50e-01 1.11e+00 6.41e+01 angle pdb=" O3' DG J 20 " pdb=" P DG J 21 " pdb=" OP2 DG J 21 " ideal model delta sigma weight residual 108.00 87.00 21.00 3.00e+00 1.11e-01 4.90e+01 angle pdb=" O4' DG I 28 " pdb=" C4' DG I 28 " pdb=" C3' DG I 28 " ideal model delta sigma weight residual 106.00 102.89 3.11 6.00e-01 2.78e+00 2.70e+01 angle pdb=" N3 DT J 22 " pdb=" C4 DT J 22 " pdb=" O4 DT J 22 " ideal model delta sigma weight residual 119.90 122.75 -2.85 6.00e-01 2.78e+00 2.26e+01 ... (remaining 19549 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.94: 5845 32.94 - 65.88: 1564 65.88 - 98.82: 53 98.82 - 131.76: 1 131.76 - 164.71: 1 Dihedral angle restraints: 7464 sinusoidal: 4830 harmonic: 2634 Sorted by residual: dihedral pdb=" CA THR E 113 " pdb=" C THR E 113 " pdb=" N LEU E 114 " pdb=" CA LEU E 114 " ideal model delta harmonic sigma weight residual 180.00 150.65 29.35 0 5.00e+00 4.00e-02 3.45e+01 dihedral pdb=" CA ILE F 29 " pdb=" C ILE F 29 " pdb=" N THR F 30 " pdb=" CA THR F 30 " ideal model delta harmonic sigma weight residual -180.00 -160.25 -19.75 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA PRO H 103 " pdb=" C PRO H 103 " pdb=" N GLY H 104 " pdb=" CA GLY H 104 " ideal model delta harmonic sigma weight residual 180.00 -160.33 -19.67 0 5.00e+00 4.00e-02 1.55e+01 ... (remaining 7461 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.403: 2211 0.403 - 0.805: 0 0.805 - 1.208: 0 1.208 - 1.610: 0 1.610 - 2.013: 1 Chirality restraints: 2212 Sorted by residual: chirality pdb=" P DG J 21 " pdb=" OP1 DG J 21 " pdb=" OP2 DG J 21 " pdb=" O5' DG J 21 " both_signs ideal model delta sigma weight residual True 2.34 0.32 2.01 2.00e-01 2.50e+01 1.01e+02 chirality pdb=" C3' DC I 7 " pdb=" C4' DC I 7 " pdb=" O3' DC I 7 " pdb=" C2' DC I 7 " both_signs ideal model delta sigma weight residual False -2.73 -2.52 -0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" C3' DG J 8 " pdb=" C4' DG J 8 " pdb=" O3' DG J 8 " pdb=" C2' DG J 8 " both_signs ideal model delta sigma weight residual False -2.73 -2.55 -0.18 2.00e-01 2.50e+01 7.72e-01 ... (remaining 2209 not shown) Planarity restraints: 1531 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG I 26 " 0.029 2.00e-02 2.50e+03 1.24e-02 4.61e+00 pdb=" N9 DG I 26 " -0.026 2.00e-02 2.50e+03 pdb=" C8 DG I 26 " -0.006 2.00e-02 2.50e+03 pdb=" N7 DG I 26 " -0.007 2.00e-02 2.50e+03 pdb=" C5 DG I 26 " 0.002 2.00e-02 2.50e+03 pdb=" C6 DG I 26 " 0.003 2.00e-02 2.50e+03 pdb=" O6 DG I 26 " 0.011 2.00e-02 2.50e+03 pdb=" N1 DG I 26 " 0.003 2.00e-02 2.50e+03 pdb=" C2 DG I 26 " -0.001 2.00e-02 2.50e+03 pdb=" N2 DG I 26 " -0.007 2.00e-02 2.50e+03 pdb=" N3 DG I 26 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DG I 26 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I -35 " 0.030 2.00e-02 2.50e+03 1.29e-02 4.55e+00 pdb=" N9 DA I -35 " -0.027 2.00e-02 2.50e+03 pdb=" C8 DA I -35 " -0.003 2.00e-02 2.50e+03 pdb=" N7 DA I -35 " -0.003 2.00e-02 2.50e+03 pdb=" C5 DA I -35 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DA I -35 " 0.003 2.00e-02 2.50e+03 pdb=" N6 DA I -35 " 0.011 2.00e-02 2.50e+03 pdb=" N1 DA I -35 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DA I -35 " -0.001 2.00e-02 2.50e+03 pdb=" N3 DA I -35 " -0.007 2.00e-02 2.50e+03 pdb=" C4 DA I -35 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC J 24 " -0.002 2.00e-02 2.50e+03 1.32e-02 3.91e+00 pdb=" N1 DC J 24 " 0.004 2.00e-02 2.50e+03 pdb=" C2 DC J 24 " -0.031 2.00e-02 2.50e+03 pdb=" O2 DC J 24 " 0.018 2.00e-02 2.50e+03 pdb=" N3 DC J 24 " 0.008 2.00e-02 2.50e+03 pdb=" C4 DC J 24 " -0.012 2.00e-02 2.50e+03 pdb=" N4 DC J 24 " 0.005 2.00e-02 2.50e+03 pdb=" C5 DC J 24 " 0.005 2.00e-02 2.50e+03 pdb=" C6 DC J 24 " 0.005 2.00e-02 2.50e+03 ... (remaining 1528 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.38: 38 2.38 - 3.01: 6761 3.01 - 3.64: 21719 3.64 - 4.27: 34416 4.27 - 4.90: 50373 Nonbonded interactions: 113307 Sorted by model distance: nonbonded pdb=" OXT GLY B 102 " pdb=" ND2 ASN H 67 " model vdw 1.752 3.120 nonbonded pdb=" OG1 THR A 79 " pdb=" O VAL A 82 " model vdw 2.039 3.040 nonbonded pdb=" O ALA K 255 " pdb=" OH TYR K 274 " model vdw 2.088 3.040 nonbonded pdb=" OD2 ASP D 68 " pdb=" OH TYR F 98 " model vdw 2.121 3.040 nonbonded pdb=" OH TYR B 98 " pdb=" OD2 ASP H 68 " model vdw 2.132 3.040 ... (remaining 113302 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 46 through 134) } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 23 through 102) } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 12 through 118) } ncs_group { reference = (chain 'D' and resid 33 through 124) 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.370 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 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 : 0.010 0.071 13623 Z= 0.674 Angle : 0.932 27.433 19554 Z= 0.723 Chirality : 0.066 2.013 2212 Planarity : 0.004 0.039 1531 Dihedral : 28.627 164.706 5770 Min Nonbonded Distance : 1.752 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % 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: -3.29 (0.23), residues: 896 helix: -1.58 (0.18), residues: 561 sheet: -3.38 (0.76), residues: 26 loop : -3.03 (0.29), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 118 TYR 0.015 0.002 TYR K 274 PHE 0.027 0.002 PHE G 25 TRP 0.006 0.002 TRP K 349 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00992 / 0.67 (13623) covalent geometry : angle 0.93225 / 0.72 (19554) hydrogen bonds : bond 0.10803 / 7.04 ( 764) hydrogen bonds : angle 4.82231 / 3.35 ( 1930) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 LYS cc_start: 0.8397 (tttt) cc_final: 0.7809 (tttp) REVERT: E 53 LYS cc_start: 0.8337 (ttmt) cc_final: 0.7983 (ttmm) REVERT: E 59 HIS cc_start: 0.7451 (m-70) cc_final: 0.6808 (m170) REVERT: E 131 ARG cc_start: 0.8275 (tmt-80) cc_final: 0.8042 (ttp80) REVERT: B 44 LYS cc_start: 0.8510 (tttt) cc_final: 0.8292 (tttt) REVERT: C 15 LYS cc_start: 0.8510 (pttm) cc_final: 0.8251 (pttt) REVERT: C 36 LYS cc_start: 0.8870 (ptmm) cc_final: 0.8542 (ptpt) REVERT: C 50 TYR cc_start: 0.8890 (t80) cc_final: 0.8543 (t80) REVERT: C 75 LYS cc_start: 0.8255 (mttp) cc_final: 0.8032 (mtpp) REVERT: C 90 ASP cc_start: 0.7868 (t0) cc_final: 0.7547 (t0) REVERT: C 95 LYS cc_start: 0.8820 (ttmt) cc_final: 0.8407 (mtpp) REVERT: C 104 GLN cc_start: 0.8798 (mm-40) cc_final: 0.8291 (mm110) REVERT: D 51 ASP cc_start: 0.7960 (p0) cc_final: 0.7621 (p0) REVERT: D 76 GLU cc_start: 0.8022 (tp30) cc_final: 0.7530 (tp30) REVERT: D 85 LYS cc_start: 0.9043 (mtpt) cc_final: 0.8761 (mtmm) REVERT: G 19 SER cc_start: 0.9475 (t) cc_final: 0.9122 (p) REVERT: K 218 MET cc_start: 0.5989 (mpp) cc_final: 0.5753 (mpp) REVERT: K 310 HIS cc_start: 0.7529 (t70) cc_final: 0.6996 (t70) outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 0.8170 time to fit residues: 139.3322 Evaluate side-chains 121 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 20.0000 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 30.0000 chunk 62 optimal weight: 50.0000 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 50.0000 chunk 106 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 HIS E 59 HIS E 95 GLN E 115 HIS B 27 GLN C 24 GLN D 47 GLN D 49 HIS D 84 ASN D 95 GLN F 18 HIS F 27 GLN F 75 HIS F 93 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 95 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.162398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.098171 restraints weight = 20608.886| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.38 r_work: 0.3005 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7091 moved from start: 0.1319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13623 Z= 0.154 Angle : 0.757 25.950 19554 Z= 0.410 Chirality : 0.064 1.985 2212 Planarity : 0.005 0.058 1531 Dihedral : 31.609 165.060 3983 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.51 % Allowed : 14.42 % Favored : 83.07 % 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: -1.18 (0.26), residues: 896 helix: 0.11 (0.21), residues: 575 sheet: -2.82 (0.68), residues: 41 loop : -2.23 (0.32), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 92 TYR 0.017 0.002 TYR G 57 PHE 0.012 0.001 PHE K 241 TRP 0.007 0.001 TRP K 349 HIS 0.005 0.001 HIS C 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.15 (13623) covalent geometry : angle 0.75705 / 0.41 (19554) hydrogen bonds : bond 0.04673 / 3.11 ( 764) hydrogen bonds : angle 3.54709 / 2.46 ( 1930) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 133 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 LYS cc_start: 0.7663 (tttt) cc_final: 0.7161 (tttm) REVERT: E 59 HIS cc_start: 0.7151 (m90) cc_final: 0.6452 (m90) REVERT: E 131 ARG cc_start: 0.8332 (ttt-90) cc_final: 0.7742 (ttp-110) REVERT: C 19 SER cc_start: 0.9048 (t) cc_final: 0.8566 (p) REVERT: C 29 ARG cc_start: 0.7311 (OUTLIER) cc_final: 0.6363 (ttp-170) REVERT: C 36 LYS cc_start: 0.8161 (ptmm) cc_final: 0.7943 (ptpt) REVERT: C 75 LYS cc_start: 0.7627 (mttp) cc_final: 0.7373 (mtpp) REVERT: C 92 GLU cc_start: 0.8181 (mm-30) cc_final: 0.7131 (mt-10) REVERT: C 95 LYS cc_start: 0.8245 (ttmt) cc_final: 0.7887 (mtpp) REVERT: C 104 GLN cc_start: 0.8417 (mm-40) cc_final: 0.7693 (mm110) REVERT: D 47 GLN cc_start: 0.8267 (mt0) cc_final: 0.8037 (mt0) REVERT: D 76 GLU cc_start: 0.7496 (tp30) cc_final: 0.6862 (tp30) REVERT: D 85 LYS cc_start: 0.8806 (mtpt) cc_final: 0.8444 (mtmm) REVERT: F 21 VAL cc_start: 0.5599 (OUTLIER) cc_final: 0.5171 (p) REVERT: F 84 MET cc_start: 0.7372 (mmm) cc_final: 0.7026 (mmt) REVERT: G 19 SER cc_start: 0.9248 (t) cc_final: 0.8996 (p) REVERT: G 36 LYS cc_start: 0.8557 (pptt) cc_final: 0.8034 (pttt) REVERT: G 40 SER cc_start: 0.9019 (OUTLIER) cc_final: 0.8818 (p) REVERT: K 310 HIS cc_start: 0.7157 (t70) cc_final: 0.6524 (t70) outliers start: 19 outliers final: 6 residues processed: 144 average time/residue: 0.7017 time to fit residues: 108.0719 Evaluate side-chains 126 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 117 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 29 ARG Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain D residue 59 MET Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 87 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 47 optimal weight: 0.9980 chunk 78 optimal weight: 20.0000 chunk 105 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 67 optimal weight: 20.0000 chunk 97 optimal weight: 7.9990 chunk 104 optimal weight: 0.5980 chunk 54 optimal weight: 0.7980 chunk 33 optimal weight: 6.9990 chunk 100 optimal weight: 30.0000 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 127 GLN B 25 ASN F 27 GLN F 93 GLN G 31 HIS G 110 ASN ** K 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.161593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.096834 restraints weight = 20681.975| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 2.44 r_work: 0.2941 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7043 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13623 Z= 0.166 Angle : 0.727 26.067 19554 Z= 0.393 Chirality : 0.063 1.959 2212 Planarity : 0.004 0.070 1531 Dihedral : 31.432 165.995 3983 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.65 % Allowed : 18.12 % Favored : 79.23 % 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: -0.28 (0.27), residues: 896 helix: 0.78 (0.21), residues: 575 sheet: -2.69 (0.66), residues: 44 loop : -1.73 (0.34), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 71 TYR 0.020 0.002 TYR K 282 PHE 0.011 0.001 PHE K 275 TRP 0.006 0.001 TRP K 349 HIS 0.004 0.001 HIS C 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.17 (13623) covalent geometry : angle 0.72742 / 0.39 (19554) hydrogen bonds : bond 0.04379 / 2.88 ( 764) hydrogen bonds : angle 3.30381 / 2.28 ( 1930) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 122 time to evaluate : 0.234 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 LYS cc_start: 0.7586 (tttt) cc_final: 0.7106 (tttm) REVERT: E 59 HIS cc_start: 0.7189 (m90) cc_final: 0.6461 (m90) REVERT: E 60 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8105 (mt) REVERT: E 120 THR cc_start: 0.8132 (m) cc_final: 0.7777 (p) REVERT: E 131 ARG cc_start: 0.8244 (ttt-90) cc_final: 0.7660 (ttp-110) REVERT: C 15 LYS cc_start: 0.7371 (pttt) cc_final: 0.7084 (pmtt) REVERT: C 19 SER cc_start: 0.9038 (t) cc_final: 0.8573 (p) REVERT: C 36 LYS cc_start: 0.8090 (ptmm) cc_final: 0.7819 (ptpt) REVERT: C 75 LYS cc_start: 0.7578 (mttp) cc_final: 0.7328 (mtpp) REVERT: C 92 GLU cc_start: 0.8181 (mm-30) cc_final: 0.7158 (mt-10) REVERT: C 95 LYS cc_start: 0.8254 (ttmt) cc_final: 0.7919 (mtpp) REVERT: C 104 GLN cc_start: 0.8483 (mm-40) cc_final: 0.7659 (mm110) REVERT: D 85 LYS cc_start: 0.8711 (mtpt) cc_final: 0.8372 (mtmm) REVERT: F 84 MET cc_start: 0.7359 (mmm) cc_final: 0.6850 (mmt) REVERT: G 19 SER cc_start: 0.9227 (t) cc_final: 0.8998 (p) REVERT: G 36 LYS cc_start: 0.8418 (pptt) cc_final: 0.7927 (pttt) REVERT: K 310 HIS cc_start: 0.7137 (t70) cc_final: 0.6462 (t-90) REVERT: H 99 ARG cc_start: 0.7801 (OUTLIER) cc_final: 0.7561 (ttp80) outliers start: 20 outliers final: 11 residues processed: 136 average time/residue: 0.6983 time to fit residues: 101.7407 Evaluate side-chains 126 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 113 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain K residue 307 THR Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain H residue 99 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 10.0000 chunk 89 optimal weight: 20.0000 chunk 71 optimal weight: 20.0000 chunk 21 optimal weight: 1.9990 chunk 74 optimal weight: 50.0000 chunk 80 optimal weight: 20.0000 chunk 76 optimal weight: 50.0000 chunk 65 optimal weight: 30.0000 chunk 62 optimal weight: 50.0000 chunk 107 optimal weight: 0.9980 overall best weight: 6.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 127 GLN C 24 GLN F 27 GLN F 93 GLN G 110 ASN ** K 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 109 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.157391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.091680 restraints weight = 20817.624| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 2.37 r_work: 0.2852 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.075 13623 Z= 0.413 Angle : 0.882 26.343 19554 Z= 0.457 Chirality : 0.067 1.914 2212 Planarity : 0.006 0.055 1531 Dihedral : 31.818 167.818 3983 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 4.63 % Allowed : 17.99 % Favored : 77.38 % 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: -0.61 (0.27), residues: 896 helix: 0.43 (0.21), residues: 578 sheet: -2.54 (0.71), residues: 44 loop : -1.69 (0.35), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 71 TYR 0.020 0.002 TYR H 40 PHE 0.026 0.003 PHE G 25 TRP 0.007 0.002 TRP E 86 HIS 0.007 0.002 HIS E 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00940 / 0.41 (13623) covalent geometry : angle 0.88226 / 0.46 (19554) hydrogen bonds : bond 0.05564 / 3.66 ( 764) hydrogen bonds : angle 3.58512 / 2.46 ( 1930) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 125 time to evaluate : 0.270 Fit side-chains REVERT: A 53 LYS cc_start: 0.7683 (tttt) cc_final: 0.7174 (tttm) REVERT: E 59 HIS cc_start: 0.7313 (m90) cc_final: 0.6640 (m90) REVERT: E 131 ARG cc_start: 0.8316 (ttt-90) cc_final: 0.7703 (ttp-110) REVERT: C 15 LYS cc_start: 0.7409 (pttt) cc_final: 0.7091 (pmtt) REVERT: C 19 SER cc_start: 0.9019 (t) cc_final: 0.8506 (p) REVERT: C 36 LYS cc_start: 0.8238 (ptmm) cc_final: 0.7956 (ptpt) REVERT: C 50 TYR cc_start: 0.8357 (t80) cc_final: 0.8061 (t80) REVERT: C 75 LYS cc_start: 0.7608 (mttp) cc_final: 0.7359 (mtpp) REVERT: C 90 ASP cc_start: 0.6837 (t0) cc_final: 0.6319 (t0) REVERT: C 95 LYS cc_start: 0.8185 (ttmt) cc_final: 0.7846 (mtpp) REVERT: D 76 GLU cc_start: 0.7745 (tp30) cc_final: 0.7156 (tp30) REVERT: D 85 LYS cc_start: 0.8803 (mtpt) cc_final: 0.8448 (mtmm) REVERT: D 105 GLU cc_start: 0.7922 (tp30) cc_final: 0.7660 (tp30) REVERT: F 21 VAL cc_start: 0.5708 (OUTLIER) cc_final: 0.5316 (p) REVERT: F 84 MET cc_start: 0.7345 (mmm) cc_final: 0.6964 (mmt) REVERT: G 19 SER cc_start: 0.9218 (t) cc_final: 0.8985 (p) REVERT: G 36 LYS cc_start: 0.8495 (pptt) cc_final: 0.8002 (pttt) REVERT: G 92 GLU cc_start: 0.8284 (mt-10) cc_final: 0.8073 (mt-10) REVERT: G 100 VAL cc_start: 0.8894 (OUTLIER) cc_final: 0.8615 (p) REVERT: H 105 GLU cc_start: 0.7754 (mm-30) cc_final: 0.7137 (tp30) REVERT: H 121 TYR cc_start: 0.8404 (t80) cc_final: 0.8169 (t80) outliers start: 35 outliers final: 23 residues processed: 145 average time/residue: 0.6431 time to fit residues: 100.1257 Evaluate side-chains 145 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 120 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 59 MET Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain K residue 307 THR Chi-restraints excluded: chain H residue 87 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 5 optimal weight: 0.8980 chunk 88 optimal weight: 6.9990 chunk 55 optimal weight: 0.7980 chunk 76 optimal weight: 50.0000 chunk 87 optimal weight: 50.0000 chunk 53 optimal weight: 0.6980 chunk 63 optimal weight: 50.0000 chunk 82 optimal weight: 20.0000 chunk 23 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 84 optimal weight: 20.0000 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 127 GLN C 104 GLN F 27 GLN ** K 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.161160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.096137 restraints weight = 20533.140| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 2.37 r_work: 0.2998 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7105 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13623 Z= 0.155 Angle : 0.722 26.009 19554 Z= 0.388 Chirality : 0.063 1.959 2212 Planarity : 0.004 0.068 1531 Dihedral : 31.444 167.731 3983 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.31 % Allowed : 20.50 % Favored : 76.19 % 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: 0.17 (0.28), residues: 896 helix: 1.03 (0.21), residues: 579 sheet: -2.36 (0.74), residues: 44 loop : -1.37 (0.36), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 71 TYR 0.015 0.002 TYR D 40 PHE 0.008 0.001 PHE G 25 TRP 0.006 0.001 TRP K 349 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.15 (13623) covalent geometry : angle 0.72185 / 0.39 (19554) hydrogen bonds : bond 0.04038 / 2.68 ( 764) hydrogen bonds : angle 3.25213 / 2.24 ( 1930) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 119 time to evaluate : 0.322 Fit side-chains revert: symmetry clash REVERT: A 50 GLU cc_start: 0.6973 (tt0) cc_final: 0.6764 (tt0) REVERT: A 53 LYS cc_start: 0.7629 (tttt) cc_final: 0.7107 (tttm) REVERT: E 59 HIS cc_start: 0.7147 (m90) cc_final: 0.6450 (m90) REVERT: E 63 ARG cc_start: 0.6979 (mmp-170) cc_final: 0.6657 (mmp80) REVERT: E 131 ARG cc_start: 0.8295 (ttt-90) cc_final: 0.7697 (ttp-110) REVERT: B 43 VAL cc_start: 0.8633 (t) cc_final: 0.8390 (m) REVERT: B 74 GLU cc_start: 0.8479 (mt-10) cc_final: 0.8248 (mt-10) REVERT: C 15 LYS cc_start: 0.7454 (pttt) cc_final: 0.7152 (pmtt) REVERT: C 19 SER cc_start: 0.9051 (t) cc_final: 0.8512 (p) REVERT: C 29 ARG cc_start: 0.7315 (OUTLIER) cc_final: 0.5933 (ttp-170) REVERT: C 36 LYS cc_start: 0.8165 (ptmm) cc_final: 0.7930 (ptpt) REVERT: C 75 LYS cc_start: 0.7614 (mttp) cc_final: 0.7351 (mtpp) REVERT: C 90 ASP cc_start: 0.6795 (t0) cc_final: 0.6148 (t0) REVERT: C 92 GLU cc_start: 0.8184 (mm-30) cc_final: 0.7229 (mt-10) REVERT: C 95 LYS cc_start: 0.8297 (ttmt) cc_final: 0.7984 (mtpp) REVERT: D 85 LYS cc_start: 0.8738 (mtpt) cc_final: 0.8409 (mtmm) REVERT: F 21 VAL cc_start: 0.5550 (OUTLIER) cc_final: 0.5138 (p) REVERT: F 84 MET cc_start: 0.7282 (mmm) cc_final: 0.6865 (mmp) REVERT: G 19 SER cc_start: 0.9245 (t) cc_final: 0.9015 (p) REVERT: G 36 LYS cc_start: 0.8386 (pptt) cc_final: 0.7925 (pttt) REVERT: G 92 GLU cc_start: 0.8291 (mt-10) cc_final: 0.8035 (mt-10) REVERT: G 100 VAL cc_start: 0.8746 (t) cc_final: 0.8512 (p) REVERT: K 310 HIS cc_start: 0.7276 (t70) cc_final: 0.6543 (t-90) outliers start: 25 outliers final: 11 residues processed: 136 average time/residue: 0.6783 time to fit residues: 98.9404 Evaluate side-chains 123 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 110 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 29 ARG Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain K residue 307 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 107 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 86 optimal weight: 40.0000 chunk 78 optimal weight: 20.0000 chunk 63 optimal weight: 50.0000 chunk 4 optimal weight: 0.1980 chunk 93 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 72 optimal weight: 20.0000 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 127 GLN C 104 GLN F 27 GLN F 93 GLN ** K 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.162203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.097268 restraints weight = 20416.852| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 2.37 r_work: 0.3020 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7101 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13623 Z= 0.143 Angle : 0.704 25.913 19554 Z= 0.379 Chirality : 0.062 1.951 2212 Planarity : 0.004 0.048 1531 Dihedral : 31.224 168.171 3983 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.17 % Allowed : 20.90 % Favored : 75.93 % 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: 0.61 (0.28), residues: 896 helix: 1.36 (0.21), residues: 578 sheet: -2.30 (0.72), residues: 44 loop : -1.15 (0.36), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 71 TYR 0.025 0.002 TYR B 88 PHE 0.008 0.001 PHE A 67 TRP 0.005 0.001 TRP E 47 HIS 0.003 0.001 HIS C 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.14 (13623) covalent geometry : angle 0.70429 / 0.38 (19554) hydrogen bonds : bond 0.03974 / 2.64 ( 764) hydrogen bonds : angle 3.11852 / 2.14 ( 1930) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 119 time to evaluate : 0.383 Fit side-chains REVERT: A 53 LYS cc_start: 0.7478 (tttt) cc_final: 0.7033 (tttp) REVERT: A 92 LEU cc_start: 0.6957 (OUTLIER) cc_final: 0.6724 (tp) REVERT: E 59 HIS cc_start: 0.7096 (m90) cc_final: 0.6407 (m90) REVERT: E 131 ARG cc_start: 0.8261 (ttt-90) cc_final: 0.7710 (ttp-110) REVERT: B 74 GLU cc_start: 0.8401 (mt-10) cc_final: 0.8135 (mt-10) REVERT: B 77 LYS cc_start: 0.8821 (mttm) cc_final: 0.8581 (mppt) REVERT: C 15 LYS cc_start: 0.7425 (pttt) cc_final: 0.7143 (pmtt) REVERT: C 19 SER cc_start: 0.9075 (t) cc_final: 0.8588 (p) REVERT: C 36 LYS cc_start: 0.8117 (ptmm) cc_final: 0.7857 (ptpt) REVERT: C 72 ASP cc_start: 0.8070 (m-30) cc_final: 0.7860 (m-30) REVERT: C 75 LYS cc_start: 0.7577 (mttp) cc_final: 0.7358 (mtpp) REVERT: C 90 ASP cc_start: 0.6806 (t0) cc_final: 0.6185 (t0) REVERT: C 92 GLU cc_start: 0.8218 (mm-30) cc_final: 0.7280 (mt-10) REVERT: C 95 LYS cc_start: 0.8296 (ttmt) cc_final: 0.7977 (mtpp) REVERT: D 85 LYS cc_start: 0.8758 (mtpt) cc_final: 0.8436 (mtmm) REVERT: D 105 GLU cc_start: 0.7753 (tp30) cc_final: 0.7120 (tp30) REVERT: F 21 VAL cc_start: 0.5779 (OUTLIER) cc_final: 0.5411 (p) REVERT: G 19 SER cc_start: 0.9190 (t) cc_final: 0.8966 (p) REVERT: G 36 LYS cc_start: 0.8228 (pptt) cc_final: 0.7886 (pttt) REVERT: G 92 GLU cc_start: 0.8330 (mt-10) cc_final: 0.7951 (mt-10) REVERT: G 100 VAL cc_start: 0.8757 (t) cc_final: 0.8535 (p) REVERT: G 110 ASN cc_start: 0.7677 (m-40) cc_final: 0.7466 (t0) REVERT: K 310 HIS cc_start: 0.7270 (t70) cc_final: 0.6519 (t-90) REVERT: H 42 TYR cc_start: 0.6081 (OUTLIER) cc_final: 0.5772 (m-80) REVERT: H 105 GLU cc_start: 0.7656 (mm-30) cc_final: 0.7201 (tp30) outliers start: 24 outliers final: 11 residues processed: 136 average time/residue: 0.7053 time to fit residues: 102.6926 Evaluate side-chains 127 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 113 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain K residue 307 THR Chi-restraints excluded: chain H residue 42 TYR Chi-restraints excluded: chain H residue 99 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 0.9990 chunk 75 optimal weight: 50.0000 chunk 15 optimal weight: 3.9990 chunk 18 optimal weight: 0.0670 chunk 49 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 76 optimal weight: 50.0000 chunk 71 optimal weight: 20.0000 chunk 82 optimal weight: 20.0000 chunk 85 optimal weight: 30.0000 chunk 7 optimal weight: 2.9990 overall best weight: 2.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 127 GLN C 104 GLN F 25 ASN F 27 GLN ** K 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.161712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.096664 restraints weight = 20466.722| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 2.36 r_work: 0.2990 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7137 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 13623 Z= 0.170 Angle : 0.720 25.941 19554 Z= 0.383 Chirality : 0.062 1.938 2212 Planarity : 0.004 0.046 1531 Dihedral : 31.239 169.419 3983 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.17 % Allowed : 21.69 % Favored : 75.13 % 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: 0.76 (0.28), residues: 896 helix: 1.49 (0.21), residues: 578 sheet: -2.38 (0.69), residues: 44 loop : -1.09 (0.36), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 71 TYR 0.038 0.002 TYR B 88 PHE 0.010 0.001 PHE G 25 TRP 0.005 0.001 TRP K 349 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.17 (13623) covalent geometry : angle 0.72031 / 0.38 (19554) hydrogen bonds : bond 0.04015 / 2.68 ( 764) hydrogen bonds : angle 3.09476 / 2.12 ( 1930) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 115 time to evaluate : 0.359 Fit side-chains revert: symmetry clash REVERT: A 53 LYS cc_start: 0.7480 (tttt) cc_final: 0.7044 (tttp) REVERT: A 92 LEU cc_start: 0.7056 (OUTLIER) cc_final: 0.6824 (tp) REVERT: E 59 HIS cc_start: 0.7174 (m90) cc_final: 0.6500 (m90) REVERT: E 63 ARG cc_start: 0.7022 (mmp-170) cc_final: 0.6701 (mmp80) REVERT: E 83 ASP cc_start: 0.8692 (m-30) cc_final: 0.7571 (p0) REVERT: E 131 ARG cc_start: 0.8300 (ttt-90) cc_final: 0.7725 (ttp-110) REVERT: B 77 LYS cc_start: 0.8827 (mttm) cc_final: 0.8585 (mppt) REVERT: C 15 LYS cc_start: 0.7385 (pttt) cc_final: 0.7093 (pmtt) REVERT: C 19 SER cc_start: 0.9087 (t) cc_final: 0.8606 (p) REVERT: C 36 LYS cc_start: 0.8148 (ptmm) cc_final: 0.7903 (ptpt) REVERT: C 72 ASP cc_start: 0.8037 (m-30) cc_final: 0.7833 (m-30) REVERT: C 75 LYS cc_start: 0.7583 (mttp) cc_final: 0.7366 (mtpp) REVERT: C 90 ASP cc_start: 0.6845 (t0) cc_final: 0.6208 (t0) REVERT: C 92 GLU cc_start: 0.8243 (mm-30) cc_final: 0.7317 (mt-10) REVERT: C 95 LYS cc_start: 0.8339 (ttmt) cc_final: 0.8010 (mtpp) REVERT: C 104 GLN cc_start: 0.8545 (mm-40) cc_final: 0.8181 (mt0) REVERT: D 85 LYS cc_start: 0.8722 (mtpt) cc_final: 0.8404 (mtmm) REVERT: D 105 GLU cc_start: 0.7750 (tp30) cc_final: 0.7187 (tp30) REVERT: F 21 VAL cc_start: 0.5685 (OUTLIER) cc_final: 0.5332 (p) REVERT: G 19 SER cc_start: 0.9258 (t) cc_final: 0.9020 (p) REVERT: G 36 LYS cc_start: 0.8201 (pptt) cc_final: 0.7883 (pttt) REVERT: G 92 GLU cc_start: 0.8389 (mt-10) cc_final: 0.7940 (mt-10) REVERT: G 110 ASN cc_start: 0.7688 (m-40) cc_final: 0.7484 (t0) REVERT: K 310 HIS cc_start: 0.7245 (t70) cc_final: 0.6493 (t-90) REVERT: H 105 GLU cc_start: 0.7676 (mm-30) cc_final: 0.7183 (tp30) outliers start: 24 outliers final: 15 residues processed: 130 average time/residue: 0.6900 time to fit residues: 96.1163 Evaluate side-chains 127 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain K residue 307 THR Chi-restraints excluded: chain H residue 99 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 0 optimal weight: 8.9990 chunk 57 optimal weight: 0.8980 chunk 75 optimal weight: 50.0000 chunk 91 optimal weight: 40.0000 chunk 84 optimal weight: 20.0000 chunk 18 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 79 optimal weight: 20.0000 chunk 105 optimal weight: 0.0040 chunk 77 optimal weight: 30.0000 chunk 44 optimal weight: 8.9990 overall best weight: 2.3394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 127 GLN B 93 GLN F 27 GLN ** K 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 49 HIS H 84 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.161248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.095908 restraints weight = 20361.725| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 2.37 r_work: 0.2973 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7143 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13623 Z= 0.181 Angle : 0.725 25.940 19554 Z= 0.383 Chirality : 0.061 1.929 2212 Planarity : 0.004 0.050 1531 Dihedral : 31.244 170.289 3983 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.17 % Allowed : 22.49 % Favored : 74.34 % 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: 0.85 (0.28), residues: 896 helix: 1.55 (0.21), residues: 578 sheet: -2.38 (0.71), residues: 44 loop : -1.04 (0.36), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 71 TYR 0.045 0.002 TYR B 88 PHE 0.010 0.001 PHE C 25 TRP 0.015 0.001 TRP A 47 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.18 (13623) covalent geometry : angle 0.72485 / 0.38 (19554) hydrogen bonds : bond 0.04082 / 2.72 ( 764) hydrogen bonds : angle 3.10509 / 2.13 ( 1930) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 121 time to evaluate : 0.361 Fit side-chains REVERT: A 53 LYS cc_start: 0.7344 (tttt) cc_final: 0.6936 (tttp) REVERT: A 92 LEU cc_start: 0.7046 (OUTLIER) cc_final: 0.6812 (tp) REVERT: E 59 HIS cc_start: 0.7161 (m90) cc_final: 0.6521 (m90) REVERT: E 63 ARG cc_start: 0.7068 (mmp-170) cc_final: 0.6748 (mmp80) REVERT: E 83 ASP cc_start: 0.8717 (m-30) cc_final: 0.7609 (p0) REVERT: E 131 ARG cc_start: 0.8329 (ttt-90) cc_final: 0.7735 (ttp-110) REVERT: B 44 LYS cc_start: 0.8270 (tttt) cc_final: 0.8042 (tttp) REVERT: B 74 GLU cc_start: 0.8345 (mt-10) cc_final: 0.8069 (mt-10) REVERT: B 77 LYS cc_start: 0.8814 (mttm) cc_final: 0.8561 (mppt) REVERT: C 15 LYS cc_start: 0.7379 (pttt) cc_final: 0.7072 (pttm) REVERT: C 19 SER cc_start: 0.9093 (t) cc_final: 0.8635 (p) REVERT: C 36 LYS cc_start: 0.8121 (ptmm) cc_final: 0.7855 (ptpt) REVERT: C 75 LYS cc_start: 0.7503 (mttp) cc_final: 0.7295 (mtpp) REVERT: C 90 ASP cc_start: 0.6835 (t0) cc_final: 0.6194 (t0) REVERT: C 92 GLU cc_start: 0.8299 (mm-30) cc_final: 0.7284 (mt-10) REVERT: C 95 LYS cc_start: 0.8302 (ttmt) cc_final: 0.7977 (mtpp) REVERT: D 85 LYS cc_start: 0.8749 (mtpt) cc_final: 0.8409 (mtmm) REVERT: D 105 GLU cc_start: 0.7769 (tp30) cc_final: 0.7217 (tp30) REVERT: F 21 VAL cc_start: 0.5799 (OUTLIER) cc_final: 0.5480 (p) REVERT: G 19 SER cc_start: 0.9251 (t) cc_final: 0.8994 (p) REVERT: G 36 LYS cc_start: 0.8204 (pptt) cc_final: 0.7905 (pttt) REVERT: G 92 GLU cc_start: 0.8395 (mt-10) cc_final: 0.7861 (mt-10) REVERT: G 110 ASN cc_start: 0.7674 (m-40) cc_final: 0.7469 (t0) REVERT: K 272 MET cc_start: 0.2392 (tpt) cc_final: 0.0812 (tpt) REVERT: K 310 HIS cc_start: 0.7355 (t70) cc_final: 0.6661 (t-90) REVERT: H 105 GLU cc_start: 0.7755 (mm-30) cc_final: 0.7270 (tp30) outliers start: 24 outliers final: 14 residues processed: 139 average time/residue: 0.6959 time to fit residues: 103.4199 Evaluate side-chains 130 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 114 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain K residue 307 THR Chi-restraints excluded: chain H residue 99 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 11 optimal weight: 1.9990 chunk 81 optimal weight: 20.0000 chunk 105 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 84 optimal weight: 20.0000 chunk 9 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 101 optimal weight: 10.0000 chunk 34 optimal weight: 0.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 89 GLN E 89 GLN C 24 GLN C 104 GLN D 47 GLN F 27 GLN ** K 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.161566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.096372 restraints weight = 20481.375| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 2.38 r_work: 0.2988 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7112 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13623 Z= 0.173 Angle : 0.724 25.896 19554 Z= 0.382 Chirality : 0.061 1.930 2212 Planarity : 0.004 0.050 1531 Dihedral : 31.200 171.065 3983 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.78 % Allowed : 22.62 % Favored : 74.60 % 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: 1.00 (0.28), residues: 896 helix: 1.66 (0.21), residues: 577 sheet: -2.42 (0.72), residues: 44 loop : -0.90 (0.37), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 71 TYR 0.047 0.002 TYR B 88 PHE 0.008 0.001 PHE C 25 TRP 0.005 0.001 TRP A 47 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.17 (13623) covalent geometry : angle 0.72382 / 0.38 (19554) hydrogen bonds : bond 0.03994 / 2.66 ( 764) hydrogen bonds : angle 3.09062 / 2.12 ( 1930) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 118 time to evaluate : 0.303 Fit side-chains REVERT: A 53 LYS cc_start: 0.7326 (tttt) cc_final: 0.6915 (tttp) REVERT: A 92 LEU cc_start: 0.6998 (OUTLIER) cc_final: 0.6761 (tp) REVERT: E 59 HIS cc_start: 0.7124 (m90) cc_final: 0.6489 (m90) REVERT: E 60 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.8014 (mt) REVERT: E 63 ARG cc_start: 0.7036 (mmp-170) cc_final: 0.6719 (mmp80) REVERT: E 83 ASP cc_start: 0.8728 (m-30) cc_final: 0.7644 (p0) REVERT: E 131 ARG cc_start: 0.8315 (ttt-90) cc_final: 0.7717 (ttp-110) REVERT: B 44 LYS cc_start: 0.8244 (tttt) cc_final: 0.8016 (tttp) REVERT: B 74 GLU cc_start: 0.8261 (mt-10) cc_final: 0.8002 (mt-10) REVERT: B 77 LYS cc_start: 0.8827 (mttm) cc_final: 0.8601 (mppt) REVERT: C 15 LYS cc_start: 0.7376 (pttt) cc_final: 0.7086 (pttm) REVERT: C 19 SER cc_start: 0.9088 (t) cc_final: 0.8634 (p) REVERT: C 36 LYS cc_start: 0.8102 (ptmm) cc_final: 0.7848 (ptpt) REVERT: C 75 LYS cc_start: 0.7431 (mttp) cc_final: 0.7230 (mtpp) REVERT: C 90 ASP cc_start: 0.6782 (t0) cc_final: 0.6146 (t0) REVERT: C 92 GLU cc_start: 0.8276 (mm-30) cc_final: 0.7277 (mt-10) REVERT: C 95 LYS cc_start: 0.8319 (ttmt) cc_final: 0.8008 (mtpp) REVERT: D 85 LYS cc_start: 0.8743 (mtpt) cc_final: 0.8393 (mtmm) REVERT: D 105 GLU cc_start: 0.7725 (tp30) cc_final: 0.7509 (tp30) REVERT: D 108 LYS cc_start: 0.6723 (mmtt) cc_final: 0.6350 (mmtt) REVERT: F 21 VAL cc_start: 0.5997 (OUTLIER) cc_final: 0.5675 (p) REVERT: G 19 SER cc_start: 0.9252 (t) cc_final: 0.8998 (p) REVERT: G 36 LYS cc_start: 0.8156 (pptt) cc_final: 0.7863 (pttt) REVERT: G 92 GLU cc_start: 0.8292 (mt-10) cc_final: 0.7839 (mt-10) REVERT: G 110 ASN cc_start: 0.7794 (m-40) cc_final: 0.7593 (t0) REVERT: K 310 HIS cc_start: 0.7326 (t70) cc_final: 0.6635 (t-90) REVERT: H 62 MET cc_start: 0.8310 (tpt) cc_final: 0.7828 (mmm) REVERT: H 105 GLU cc_start: 0.7699 (mm-30) cc_final: 0.7424 (tp30) outliers start: 21 outliers final: 14 residues processed: 132 average time/residue: 0.7032 time to fit residues: 99.2227 Evaluate side-chains 129 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 112 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain K residue 307 THR Chi-restraints excluded: chain H residue 99 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 100 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 108 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 chunk 112 optimal weight: 0.9980 chunk 101 optimal weight: 6.9990 chunk 63 optimal weight: 50.0000 chunk 76 optimal weight: 50.0000 chunk 13 optimal weight: 1.9990 chunk 90 optimal weight: 7.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 24 GLN F 27 GLN ** K 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.161980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.096689 restraints weight = 20648.936| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 2.38 r_work: 0.3008 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7127 moved from start: 0.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13623 Z= 0.160 Angle : 0.716 25.881 19554 Z= 0.378 Chirality : 0.061 1.928 2212 Planarity : 0.004 0.059 1531 Dihedral : 31.129 171.637 3983 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.65 % Allowed : 22.75 % Favored : 74.60 % 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: 1.12 (0.28), residues: 896 helix: 1.75 (0.21), residues: 577 sheet: -2.33 (0.73), residues: 44 loop : -0.86 (0.37), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 71 TYR 0.044 0.002 TYR B 88 PHE 0.008 0.001 PHE K 275 TRP 0.006 0.001 TRP A 47 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.16 (13623) covalent geometry : angle 0.71623 / 0.38 (19554) hydrogen bonds : bond 0.03968 / 2.65 ( 764) hydrogen bonds : angle 3.07095 / 2.11 ( 1930) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 116 time to evaluate : 0.321 Fit side-chains REVERT: A 53 LYS cc_start: 0.7328 (tttt) cc_final: 0.6921 (tttp) REVERT: A 92 LEU cc_start: 0.6991 (OUTLIER) cc_final: 0.6742 (tp) REVERT: E 59 HIS cc_start: 0.7165 (m90) cc_final: 0.6480 (m90) REVERT: E 60 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.7978 (mt) REVERT: E 63 ARG cc_start: 0.6997 (mmp-170) cc_final: 0.6678 (mmp80) REVERT: E 83 ASP cc_start: 0.8727 (m-30) cc_final: 0.7705 (p0) REVERT: E 131 ARG cc_start: 0.8306 (ttt-90) cc_final: 0.7719 (ttp-110) REVERT: B 44 LYS cc_start: 0.8259 (tttt) cc_final: 0.8033 (tttp) REVERT: B 77 LYS cc_start: 0.8834 (mttm) cc_final: 0.8591 (mppt) REVERT: C 15 LYS cc_start: 0.7359 (pttt) cc_final: 0.7073 (pttm) REVERT: C 19 SER cc_start: 0.9094 (t) cc_final: 0.8639 (p) REVERT: C 36 LYS cc_start: 0.7979 (ptmm) cc_final: 0.7708 (ptpt) REVERT: C 75 LYS cc_start: 0.7471 (mttp) cc_final: 0.7269 (mtpp) REVERT: C 90 ASP cc_start: 0.6839 (t0) cc_final: 0.6169 (t0) REVERT: C 92 GLU cc_start: 0.8295 (mm-30) cc_final: 0.7299 (mt-10) REVERT: C 95 LYS cc_start: 0.8352 (ttmt) cc_final: 0.8052 (mtpp) REVERT: C 104 GLN cc_start: 0.8318 (mt0) cc_final: 0.8093 (mt0) REVERT: D 85 LYS cc_start: 0.8778 (mtpt) cc_final: 0.8445 (mtmm) REVERT: D 105 GLU cc_start: 0.7739 (tp30) cc_final: 0.7536 (tp30) REVERT: D 108 LYS cc_start: 0.6746 (mmtt) cc_final: 0.6351 (mmtt) REVERT: F 21 VAL cc_start: 0.6103 (OUTLIER) cc_final: 0.5737 (m) REVERT: G 19 SER cc_start: 0.9285 (t) cc_final: 0.9039 (p) REVERT: G 36 LYS cc_start: 0.8153 (pptt) cc_final: 0.7858 (pttt) REVERT: G 92 GLU cc_start: 0.8266 (mt-10) cc_final: 0.7850 (mt-10) REVERT: K 272 MET cc_start: 0.2734 (tpt) cc_final: 0.1939 (tpt) REVERT: K 310 HIS cc_start: 0.7349 (t70) cc_final: 0.6655 (t-90) REVERT: H 62 MET cc_start: 0.8403 (tpt) cc_final: 0.7921 (mmm) REVERT: H 105 GLU cc_start: 0.7696 (mm-30) cc_final: 0.7189 (tp30) outliers start: 20 outliers final: 15 residues processed: 132 average time/residue: 0.7180 time to fit residues: 101.2694 Evaluate side-chains 130 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 112 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain K residue 307 THR Chi-restraints excluded: chain H residue 99 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 65 optimal weight: 30.0000 chunk 105 optimal weight: 0.9980 chunk 101 optimal weight: 50.0000 chunk 55 optimal weight: 0.0870 chunk 32 optimal weight: 5.9990 chunk 108 optimal weight: 6.9990 chunk 35 optimal weight: 6.9990 chunk 75 optimal weight: 50.0000 chunk 58 optimal weight: 9.9990 chunk 88 optimal weight: 5.9990 chunk 56 optimal weight: 0.8980 overall best weight: 2.7962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 24 GLN D 47 GLN F 25 ASN F 27 GLN ** K 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.161083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.095591 restraints weight = 20499.059| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 2.35 r_work: 0.2977 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7149 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13623 Z= 0.199 Angle : 0.740 25.877 19554 Z= 0.386 Chirality : 0.061 1.917 2212 Planarity : 0.004 0.062 1531 Dihedral : 31.247 172.552 3983 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.25 % Allowed : 23.15 % Favored : 74.60 % 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: 1.05 (0.28), residues: 896 helix: 1.68 (0.21), residues: 577 sheet: -2.36 (0.73), residues: 44 loop : -0.87 (0.37), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 71 TYR 0.048 0.002 TYR B 88 PHE 0.010 0.002 PHE C 25 TRP 0.005 0.001 TRP K 349 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.20 (13623) covalent geometry : angle 0.74029 / 0.39 (19554) hydrogen bonds : bond 0.04219 / 2.81 ( 764) hydrogen bonds : angle 3.11280 / 2.14 ( 1930) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4235.70 seconds wall clock time: 72 minutes 48.43 seconds (4368.43 seconds total)