Starting phenix.real_space_refine on Sat Jul 4 01:49:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nqu_49676/07_2026/9nqu_49676.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nqu_49676/07_2026/9nqu_49676.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9nqu_49676/07_2026/9nqu_49676.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nqu_49676/07_2026/9nqu_49676.map" model { file = "/net/cci-nas-00/data/ceres_data/9nqu_49676/07_2026/9nqu_49676.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nqu_49676/07_2026/9nqu_49676.cif" } resolution = 3.16 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= 0.021 sd= 1.197 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: 7 Type Number sf(0) Gaussians Fe 1 7.16 5 Zn 1 6.06 5 P 370 5.49 5 S 30 5.16 5 C 9772 2.51 5 N 3209 2.21 5 O 3975 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17358 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 800 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "B" Number of atoms: 614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 614 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 1, 'TRANS': 75} Chain: "C" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 832 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "D" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 960 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 6, 'TRANS': 113} Chain: "F" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 619 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "G" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 821 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} 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: 3771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 3771 Classifications: {'DNA': 185} Link IDs: {'rna3p': 184} Chain: "J" Number of atoms: 3814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 3814 Classifications: {'DNA': 185} Link IDs: {'rna3p': 184} Chain: "K" Number of atoms: 3649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 455, 3649 Classifications: {'peptide': 455} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 430} Chain breaks: 1 Chain: "K" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 16 Ad-hoc single atom residues: {' FE': 1} Unusual residues: {' ZN': 1, 'OH0': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 1 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 16842 SG CYS K1573 46.578 39.262 40.088 1.00 80.93 S ATOM 16865 SG CYS K1576 48.324 35.892 39.143 1.00 84.43 S ATOM 17058 SG CYS K1600 45.731 37.109 37.005 1.00110.58 S ATOM 17077 SG CYS K1603 44.908 35.847 40.609 1.00110.36 S Time building chain proxies: 3.48, per 1000 atoms: 0.20 Number of scatterers: 17358 At special positions: 0 Unit cell: (104.244, 132.276, 162.936, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 Fe 1 26.01 S 30 16.00 P 370 15.00 O 3975 8.00 N 3209 7.00 C 9772 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.41 Conformation dependent library (CDL) restraints added in 615.0 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K1702 " pdb="ZN ZN K1702 " - pdb=" SG CYS K1576 " pdb="ZN ZN K1702 " - pdb=" SG CYS K1600 " pdb="ZN ZN K1702 " - pdb=" SG CYS K1573 " pdb="ZN ZN K1702 " - pdb=" SG CYS K1603 " Number of angles added : 6 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2302 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 13 sheets defined 58.3% alpha, 5.0% beta 182 base pairs and 318 stacking pairs defined. Time for finding SS restraints: 2.17 Creating SS restraints... Processing helix chain 'A' and resid 44 through 56 removed outlier: 3.580A pdb=" N LEU A 48 " --> pdb=" O GLY A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.877A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.711A pdb=" N ALA A 114 " --> pdb=" O ALA A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 130 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: 3.714A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 Processing helix chain 'C' and resid 16 through 22 removed outlier: 3.532A pdb=" N ARG C 20 " --> pdb=" O THR C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.511A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 34 through 46 removed outlier: 3.546A pdb=" N LYS D 40 " --> pdb=" O VAL D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 101 through 121 Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.632A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 72 removed outlier: 4.386A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 34 through 46 removed outlier: 3.714A pdb=" N LYS H 40 " --> pdb=" O VAL H 36 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 101 through 121 Processing helix chain 'K' and resid 1175 through 1180 Processing helix chain 'K' and resid 1190 through 1196 removed outlier: 3.969A pdb=" N ALA K1194 " --> pdb=" O SER K1190 " (cutoff:3.500A) Processing helix chain 'K' and resid 1196 through 1204 removed outlier: 3.505A pdb=" N LEU K1200 " --> pdb=" O SER K1196 " (cutoff:3.500A) Processing helix chain 'K' and resid 1215 through 1221 Processing helix chain 'K' and resid 1223 through 1227 Processing helix chain 'K' and resid 1228 through 1234 Processing helix chain 'K' and resid 1274 through 1291 removed outlier: 4.774A pdb=" N GLN K1287 " --> pdb=" O ALA K1283 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N GLU K1288 " --> pdb=" O SER K1284 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU K1290 " --> pdb=" O PHE K1286 " (cutoff:3.500A) Processing helix chain 'K' and resid 1338 through 1345 Processing helix chain 'K' and resid 1359 through 1365 removed outlier: 3.641A pdb=" N GLY K1365 " --> pdb=" O SER K1362 " (cutoff:3.500A) Processing helix chain 'K' and resid 1390 through 1394 removed outlier: 4.300A pdb=" N PHE K1394 " --> pdb=" O ASN K1391 " (cutoff:3.500A) Processing helix chain 'K' and resid 1412 through 1414 No H-bonds generated for 'chain 'K' and resid 1412 through 1414' Processing helix chain 'K' and resid 1415 through 1426 removed outlier: 3.574A pdb=" N SER K1420 " --> pdb=" O TRP K1416 " (cutoff:3.500A) Processing helix chain 'K' and resid 1487 through 1504 removed outlier: 3.733A pdb=" N TYR K1491 " --> pdb=" O THR K1487 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU K1496 " --> pdb=" O GLN K1492 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N ARG K1497 " --> pdb=" O LEU K1493 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TYR K1498 " --> pdb=" O ALA K1494 " (cutoff:3.500A) Processing helix chain 'K' and resid 1511 through 1522 Processing helix chain 'K' and resid 1527 through 1552 removed outlier: 4.010A pdb=" N CYS K1537 " --> pdb=" O MET K1533 " (cutoff:3.500A) Processing helix chain 'K' and resid 1600 through 1608 removed outlier: 3.513A pdb=" N ARG K1605 " --> pdb=" O GLU K1601 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ARG K1606 " --> pdb=" O GLY K1602 " (cutoff:3.500A) Processing helix chain 'K' and resid 1621 through 1632 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.165A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.385A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.280A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.958A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.144A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43 removed outlier: 6.925A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'K' and resid 1210 through 1213 Processing sheet with id=AB1, first strand: chain 'K' and resid 1246 through 1247 Processing sheet with id=AB2, first strand: chain 'K' and resid 1383 through 1388 removed outlier: 3.744A pdb=" N VAL K1470 " --> pdb=" O THR K1385 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N GLY K1387 " --> pdb=" O HIS K1468 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N HIS K1468 " --> pdb=" O GLY K1387 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 1560 through 1561 removed outlier: 5.587A pdb=" N ALA K1560 " --> pdb=" O GLU K1618 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'K' and resid 1585 through 1588 523 hydrogen bonds defined for protein. 1518 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 465 hydrogen bonds 930 hydrogen bond angles 0 basepair planarities 182 basepair parallelities 318 stacking parallelities Total time for adding SS restraints: 4.27 Time building geometry restraints manager: 1.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2029 1.31 - 1.43: 6737 1.43 - 1.56: 8904 1.56 - 1.69: 738 1.69 - 1.81: 47 Bond restraints: 18455 Sorted by residual: bond pdb=" N OH0 K1703 " pdb=" C6 OH0 K1703 " ideal model delta sigma weight residual 1.340 1.453 -0.113 2.00e-02 2.50e+03 3.21e+01 bond pdb=" C3' DT I 30 " pdb=" C2' DT I 30 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.34e+01 bond pdb=" C3' DC I 42 " pdb=" C2' DC I 42 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.31e+01 bond pdb=" C3' DC I 0 " pdb=" C2' DC I 0 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.30e+01 bond pdb=" N VAL K1467 " pdb=" CA VAL K1467 " ideal model delta sigma weight residual 1.461 1.499 -0.038 1.08e-02 8.57e+03 1.26e+01 ... (remaining 18450 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 25033 1.81 - 3.63: 1315 3.63 - 5.44: 121 5.44 - 7.25: 76 7.25 - 9.06: 11 Bond angle restraints: 26556 Sorted by residual: angle pdb=" O4' DT I -26 " pdb=" C4' DT I -26 " pdb=" C3' DT I -26 " ideal model delta sigma weight residual 106.00 103.01 2.99 6.00e-01 2.78e+00 2.48e+01 angle pdb=" N3 DT J 9 " pdb=" C4 DT J 9 " pdb=" O4 DT J 9 " ideal model delta sigma weight residual 119.90 122.49 -2.59 6.00e-01 2.78e+00 1.86e+01 angle pdb=" N3 DT J -61 " pdb=" C4 DT J -61 " pdb=" O4 DT J -61 " ideal model delta sigma weight residual 119.90 122.47 -2.57 6.00e-01 2.78e+00 1.84e+01 angle pdb=" N3 DT J 31 " pdb=" C4 DT J 31 " pdb=" O4 DT J 31 " ideal model delta sigma weight residual 119.90 122.42 -2.52 6.00e-01 2.78e+00 1.77e+01 angle pdb=" O4' DG J -49 " pdb=" C4' DG J -49 " pdb=" C3' DG J -49 " ideal model delta sigma weight residual 106.00 103.49 2.51 6.00e-01 2.78e+00 1.75e+01 ... (remaining 26551 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.63: 8220 35.63 - 71.26: 1834 71.26 - 106.89: 32 106.89 - 142.52: 4 142.52 - 178.15: 9 Dihedral angle restraints: 10099 sinusoidal: 6530 harmonic: 3569 Sorted by residual: dihedral pdb=" C2 OH0 K1703 " pdb=" C3 OH0 K1703 " pdb=" C4 OH0 K1703 " pdb=" C5 OH0 K1703 " ideal model delta sinusoidal sigma weight residual 94.30 -78.54 172.84 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C6 OH0 K1703 " pdb=" N OH0 K1703 " pdb=" C7 OH0 K1703 " pdb=" C8 OH0 K1703 " ideal model delta sinusoidal sigma weight residual 89.05 -127.75 -143.20 1 3.00e+01 1.11e-03 1.92e+01 dihedral pdb=" O OH0 K1703 " pdb=" N OH0 K1703 " pdb=" C7 OH0 K1703 " pdb=" C8 OH0 K1703 " ideal model delta sinusoidal sigma weight residual -73.92 52.23 -126.15 1 3.00e+01 1.11e-03 1.70e+01 ... (remaining 10096 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.130: 2912 0.130 - 0.259: 39 0.259 - 0.389: 1 0.389 - 0.519: 14 0.519 - 0.648: 27 Chirality restraints: 2993 Sorted by residual: chirality pdb=" P DA I -92 " pdb=" OP1 DA I -92 " pdb=" OP2 DA I -92 " pdb=" O5' DA I -92 " both_signs ideal model delta sigma weight residual True 2.34 -2.98 -0.65 2.00e-01 2.50e+01 1.05e+01 chirality pdb=" P DA J -92 " pdb=" OP1 DA J -92 " pdb=" OP2 DA J -92 " pdb=" O5' DA J -92 " both_signs ideal model delta sigma weight residual True 2.34 -2.97 -0.63 2.00e-01 2.50e+01 1.01e+01 chirality pdb=" P DT J -16 " pdb=" OP1 DT J -16 " pdb=" OP2 DT J -16 " pdb=" O5' DT J -16 " both_signs ideal model delta sigma weight residual True 2.34 -2.94 -0.61 2.00e-01 2.50e+01 9.20e+00 ... (remaining 2990 not shown) Planarity restraints: 2088 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE K1583 " 0.017 2.00e-02 2.50e+03 3.46e-02 1.20e+01 pdb=" C ILE K1583 " -0.060 2.00e-02 2.50e+03 pdb=" O ILE K1583 " 0.023 2.00e-02 2.50e+03 pdb=" N LEU K1584 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER K1516 " 0.015 2.00e-02 2.50e+03 2.94e-02 8.65e+00 pdb=" C SER K1516 " -0.051 2.00e-02 2.50e+03 pdb=" O SER K1516 " 0.019 2.00e-02 2.50e+03 pdb=" N TRP K1517 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG K1605 " -0.219 9.50e-02 1.11e+02 9.81e-02 5.90e+00 pdb=" NE ARG K1605 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG K1605 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG K1605 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG K1605 " -0.008 2.00e-02 2.50e+03 ... (remaining 2085 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 66 2.59 - 3.17: 14714 3.17 - 3.74: 31879 3.74 - 4.32: 44083 4.32 - 4.90: 62246 Nonbonded interactions: 152988 Sorted by model distance: nonbonded pdb=" OE2 GLU K1390 " pdb="FE FE K1701 " model vdw 2.012 3.000 nonbonded pdb=" NE2 HIS K1388 " pdb="FE FE K1701 " model vdw 2.099 3.080 nonbonded pdb=" OE1 GLU K1390 " pdb="FE FE K1701 " model vdw 2.195 3.000 nonbonded pdb=" OG1 THR K1355 " pdb=" N SER K1362 " model vdw 2.208 3.120 nonbonded pdb=" NE2 HIS K1468 " pdb="FE FE K1701 " model vdw 2.219 3.080 ... (remaining 152983 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 'B' selection = (chain 'F' and resid 25 through 101) } ncs_group { reference = (chain 'C' and resid 12 through 118) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 29 through 121) 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: 2.580 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: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 20.100 Find NCS groups from input model: 0.200 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:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6973 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 : 0.007 0.214 18460 Z= 0.548 Angle : 0.882 9.065 26562 Z= 0.666 Chirality : 0.078 0.648 2993 Planarity : 0.005 0.098 2088 Dihedral : 28.781 178.149 7797 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 38.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 1.83 % Allowed : 26.37 % Favored : 71.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: 0.16 (0.25), residues: 1209 helix: 1.72 (0.21), residues: 657 sheet: -3.32 (0.58), residues: 62 loop : -1.74 (0.27), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K1607 TYR 0.013 0.001 TYR K1157 PHE 0.012 0.001 PHE K1422 TRP 0.021 0.002 TRP K1264 HIS 0.004 0.001 HIS K1414 Details of bonding type rmsd/Z covalent geometry : bond 0.00641 / 0.53 (18455) covalent geometry : angle 0.87957 / 0.67 (26556) hydrogen bonds : bond 0.12865 / 8.76 ( 988) hydrogen bonds : angle 5.24671 / 3.95 ( 2448) metal coordination : bond 0.00735 / 0.45 ( 4) metal coordination : angle 4.82425 / 3.07 ( 6) Misc. bond : bond 0.21424 / 14.28 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 248 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 1415 TYR cc_start: 0.6374 (OUTLIER) cc_final: 0.4315 (m-80) REVERT: K 1475 TRP cc_start: 0.6369 (OUTLIER) cc_final: 0.5630 (m-90) outliers start: 19 outliers final: 12 residues processed: 262 average time/residue: 0.1746 time to fit residues: 63.2971 Evaluate side-chains 224 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 210 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain K residue 1207 ARG Chi-restraints excluded: chain K residue 1355 THR Chi-restraints excluded: chain K residue 1377 TYR Chi-restraints excluded: chain K residue 1380 VAL Chi-restraints excluded: chain K residue 1385 THR Chi-restraints excluded: chain K residue 1414 HIS Chi-restraints excluded: chain K residue 1415 TYR Chi-restraints excluded: chain K residue 1419 ILE Chi-restraints excluded: chain K residue 1475 TRP Chi-restraints excluded: chain K residue 1478 ASN Chi-restraints excluded: chain K residue 1521 ARG Chi-restraints excluded: chain K residue 1577 ASP Chi-restraints excluded: chain K residue 1611 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 98 optimal weight: 20.0000 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 20.0000 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 50.0000 chunk 149 optimal weight: 0.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 106 HIS H 46 HIS K1320 ASN K1343 GLN ** K1398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K1468 HIS ** K1471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K1492 GLN ** K1544 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.132301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.112955 restraints weight = 58078.021| |-----------------------------------------------------------------------------| r_work (start): 0.3789 rms_B_bonded: 2.14 r_work: 0.3644 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.161 18460 Z= 0.294 Angle : 0.839 12.321 26562 Z= 0.453 Chirality : 0.053 0.253 2993 Planarity : 0.006 0.046 2088 Dihedral : 31.545 176.317 5434 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 16.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 6.93 % Allowed : 21.66 % Favored : 71.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -0.01 (0.25), residues: 1209 helix: 1.52 (0.21), residues: 673 sheet: -3.09 (0.59), residues: 46 loop : -1.95 (0.26), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 96 TYR 0.022 0.002 TYR K1157 PHE 0.043 0.003 PHE K1422 TRP 0.029 0.004 TRP K1469 HIS 0.012 0.002 HIS K1414 Details of bonding type rmsd/Z covalent geometry : bond 0.00631 / 0.29 (18455) covalent geometry : angle 0.83015 / 0.45 (26556) hydrogen bonds : bond 0.06743 / 4.59 ( 988) hydrogen bonds : angle 4.17002 / 3.18 ( 2448) metal coordination : bond 0.01690 / 0.92 ( 4) metal coordination : angle 8.33158 / 5.09 ( 6) Misc. bond : bond 0.00647 / 0.43 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 207 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 92 ARG cc_start: 0.8636 (OUTLIER) cc_final: 0.7841 (ttm-80) REVERT: F 92 ARG cc_start: 0.8891 (OUTLIER) cc_final: 0.8253 (ttp80) REVERT: G 36 LYS cc_start: 0.8783 (mptt) cc_final: 0.8499 (mmtm) REVERT: H 48 ASP cc_start: 0.8771 (p0) cc_final: 0.8557 (p0) REVERT: K 1418 THR cc_start: 0.7332 (OUTLIER) cc_final: 0.6934 (m) REVERT: K 1566 LYS cc_start: 0.5976 (OUTLIER) cc_final: 0.4469 (tmtt) outliers start: 72 outliers final: 42 residues processed: 262 average time/residue: 0.1717 time to fit residues: 63.4950 Evaluate side-chains 240 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 194 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain K residue 1183 THR Chi-restraints excluded: chain K residue 1207 ARG Chi-restraints excluded: chain K residue 1211 THR Chi-restraints excluded: chain K residue 1212 VAL Chi-restraints excluded: chain K residue 1230 LYS Chi-restraints excluded: chain K residue 1269 SER Chi-restraints excluded: chain K residue 1287 GLN Chi-restraints excluded: chain K residue 1322 HIS Chi-restraints excluded: chain K residue 1348 LEU Chi-restraints excluded: chain K residue 1376 LEU Chi-restraints excluded: chain K residue 1377 TYR Chi-restraints excluded: chain K residue 1380 VAL Chi-restraints excluded: chain K residue 1414 HIS Chi-restraints excluded: chain K residue 1418 THR Chi-restraints excluded: chain K residue 1419 ILE Chi-restraints excluded: chain K residue 1441 ASP Chi-restraints excluded: chain K residue 1445 SER Chi-restraints excluded: chain K residue 1452 PHE Chi-restraints excluded: chain K residue 1478 ASN Chi-restraints excluded: chain K residue 1519 VAL Chi-restraints excluded: chain K residue 1521 ARG Chi-restraints excluded: chain K residue 1529 ASP Chi-restraints excluded: chain K residue 1566 LYS Chi-restraints excluded: chain K residue 1577 ASP Chi-restraints excluded: chain K residue 1595 THR Chi-restraints excluded: chain K residue 1611 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 19 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 126 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 96 optimal weight: 20.0000 chunk 48 optimal weight: 0.6980 chunk 80 optimal weight: 20.0000 chunk 107 optimal weight: 20.0000 chunk 124 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN B 93 GLN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN D 60 ASN K1249 GLN K1471 GLN ** K1490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K1540 GLN ** K1544 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.135765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.116981 restraints weight = 59286.271| |-----------------------------------------------------------------------------| r_work (start): 0.3850 rms_B_bonded: 2.05 r_work: 0.3717 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 18460 Z= 0.150 Angle : 0.668 9.316 26562 Z= 0.380 Chirality : 0.046 0.230 2993 Planarity : 0.005 0.051 2088 Dihedral : 31.393 173.821 5428 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 4.62 % Allowed : 24.25 % Favored : 71.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: 0.59 (0.25), residues: 1209 helix: 2.04 (0.21), residues: 667 sheet: -3.01 (0.54), residues: 57 loop : -1.62 (0.27), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 96 TYR 0.021 0.002 TYR G 50 PHE 0.029 0.002 PHE K1422 TRP 0.026 0.002 TRP K1469 HIS 0.006 0.001 HIS K1363 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.15 (18455) covalent geometry : angle 0.66246 / 0.38 (26556) hydrogen bonds : bond 0.04775 / 3.21 ( 988) hydrogen bonds : angle 3.64252 / 2.79 ( 2448) metal coordination : bond 0.00805 / 0.54 ( 4) metal coordination : angle 5.66732 / 3.43 ( 6) Misc. bond : bond 0.00482 / 0.32 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 216 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 GLN cc_start: 0.8745 (mt0) cc_final: 0.8504 (mt0) REVERT: B 88 TYR cc_start: 0.8942 (m-10) cc_final: 0.8732 (m-10) REVERT: C 13 LYS cc_start: 0.8039 (tppt) cc_final: 0.7782 (tptt) REVERT: D 105 LYS cc_start: 0.8660 (mtmm) cc_final: 0.8202 (mtmm) REVERT: F 92 ARG cc_start: 0.8833 (OUTLIER) cc_final: 0.8235 (ttp80) REVERT: F 93 GLN cc_start: 0.8483 (mp10) cc_final: 0.7898 (mp10) REVERT: G 36 LYS cc_start: 0.8809 (mptt) cc_final: 0.8496 (mmtm) REVERT: H 48 ASP cc_start: 0.8677 (p0) cc_final: 0.8410 (p0) REVERT: K 1390 GLU cc_start: 0.5589 (mp0) cc_final: 0.5299 (mp0) REVERT: K 1418 THR cc_start: 0.7293 (OUTLIER) cc_final: 0.6957 (m) REVERT: K 1430 TYR cc_start: 0.5105 (OUTLIER) cc_final: 0.4795 (p90) REVERT: K 1586 VAL cc_start: 0.5960 (m) cc_final: 0.5748 (p) outliers start: 48 outliers final: 24 residues processed: 254 average time/residue: 0.1534 time to fit residues: 55.2712 Evaluate side-chains 229 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 202 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 37 TYR Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain K residue 1183 THR Chi-restraints excluded: chain K residue 1207 ARG Chi-restraints excluded: chain K residue 1210 ILE Chi-restraints excluded: chain K residue 1211 THR Chi-restraints excluded: chain K residue 1212 VAL Chi-restraints excluded: chain K residue 1264 TRP Chi-restraints excluded: chain K residue 1269 SER Chi-restraints excluded: chain K residue 1274 THR Chi-restraints excluded: chain K residue 1287 GLN Chi-restraints excluded: chain K residue 1368 ILE Chi-restraints excluded: chain K residue 1376 LEU Chi-restraints excluded: chain K residue 1377 TYR Chi-restraints excluded: chain K residue 1380 VAL Chi-restraints excluded: chain K residue 1414 HIS Chi-restraints excluded: chain K residue 1418 THR Chi-restraints excluded: chain K residue 1419 ILE Chi-restraints excluded: chain K residue 1430 TYR Chi-restraints excluded: chain K residue 1529 ASP Chi-restraints excluded: chain K residue 1553 VAL Chi-restraints excluded: chain K residue 1577 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 93 optimal weight: 20.0000 chunk 22 optimal weight: 9.9990 chunk 132 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 109 optimal weight: 0.4980 chunk 3 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 123 optimal weight: 3.9990 chunk 102 optimal weight: 20.0000 chunk 5 optimal weight: 0.8980 chunk 68 optimal weight: 0.6980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN D 60 ASN ** K1454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1599 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 = 0.4176 r_free = 0.4176 target = 0.134826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.116024 restraints weight = 58797.228| |-----------------------------------------------------------------------------| r_work (start): 0.3829 rms_B_bonded: 2.10 r_work: 0.3704 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 18460 Z= 0.158 Angle : 0.660 8.511 26562 Z= 0.374 Chirality : 0.045 0.224 2993 Planarity : 0.004 0.044 2088 Dihedral : 31.326 174.209 5418 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 3.95 % Allowed : 23.77 % Favored : 72.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: 0.81 (0.25), residues: 1209 helix: 2.25 (0.21), residues: 661 sheet: -2.79 (0.58), residues: 57 loop : -1.55 (0.27), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K1221 TYR 0.015 0.001 TYR K1377 PHE 0.024 0.002 PHE K1422 TRP 0.026 0.002 TRP K1469 HIS 0.022 0.002 HIS K1544 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.16 (18455) covalent geometry : angle 0.65436 / 0.37 (26556) hydrogen bonds : bond 0.04705 / 3.15 ( 988) hydrogen bonds : angle 3.58287 / 2.74 ( 2448) metal coordination : bond 0.00831 / 0.50 ( 4) metal coordination : angle 5.62023 / 3.34 ( 6) Misc. bond : bond 0.00089 / 0.06 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 206 time to evaluate : 0.501 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8335 (pm20) cc_final: 0.8134 (pm20) REVERT: B 88 TYR cc_start: 0.8957 (m-10) cc_final: 0.8747 (m-10) REVERT: C 13 LYS cc_start: 0.8050 (tppt) cc_final: 0.7835 (tptt) REVERT: F 84 MET cc_start: 0.8709 (mmm) cc_final: 0.8481 (mmm) REVERT: F 92 ARG cc_start: 0.8840 (OUTLIER) cc_final: 0.8281 (ttp80) REVERT: F 93 GLN cc_start: 0.8482 (mp10) cc_final: 0.7898 (mp10) REVERT: G 36 LYS cc_start: 0.8769 (mptt) cc_final: 0.8433 (mmtm) REVERT: H 48 ASP cc_start: 0.8684 (p0) cc_final: 0.8433 (p0) REVERT: K 1390 GLU cc_start: 0.5643 (mp0) cc_final: 0.5363 (mp0) REVERT: K 1418 THR cc_start: 0.7298 (OUTLIER) cc_final: 0.7030 (m) REVERT: K 1428 VAL cc_start: 0.2974 (OUTLIER) cc_final: 0.2694 (t) outliers start: 41 outliers final: 27 residues processed: 233 average time/residue: 0.1792 time to fit residues: 58.9504 Evaluate side-chains 229 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 199 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain K residue 1183 THR Chi-restraints excluded: chain K residue 1207 ARG Chi-restraints excluded: chain K residue 1211 THR Chi-restraints excluded: chain K residue 1264 TRP Chi-restraints excluded: chain K residue 1322 HIS Chi-restraints excluded: chain K residue 1377 TYR Chi-restraints excluded: chain K residue 1380 VAL Chi-restraints excluded: chain K residue 1414 HIS Chi-restraints excluded: chain K residue 1418 THR Chi-restraints excluded: chain K residue 1419 ILE Chi-restraints excluded: chain K residue 1428 VAL Chi-restraints excluded: chain K residue 1493 LEU Chi-restraints excluded: chain K residue 1529 ASP Chi-restraints excluded: chain K residue 1553 VAL Chi-restraints excluded: chain K residue 1567 ASP Chi-restraints excluded: chain K residue 1573 CYS Chi-restraints excluded: chain K residue 1577 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 38 optimal weight: 0.9980 chunk 138 optimal weight: 0.9990 chunk 118 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 143 optimal weight: 0.4980 chunk 41 optimal weight: 8.9990 chunk 42 optimal weight: 1.9990 chunk 124 optimal weight: 0.1980 chunk 56 optimal weight: 8.9990 chunk 28 optimal weight: 4.9990 chunk 142 optimal weight: 0.0870 overall best weight: 0.5560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN C 104 GLN H 60 ASN ** K1239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.136131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.117626 restraints weight = 58550.118| |-----------------------------------------------------------------------------| r_work (start): 0.3863 rms_B_bonded: 2.04 r_work: 0.3727 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 18460 Z= 0.137 Angle : 0.636 9.641 26562 Z= 0.363 Chirality : 0.044 0.226 2993 Planarity : 0.004 0.046 2088 Dihedral : 31.240 179.715 5418 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 3.56 % Allowed : 25.22 % Favored : 71.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: 1.01 (0.25), residues: 1209 helix: 2.34 (0.21), residues: 664 sheet: -2.72 (0.65), residues: 49 loop : -1.38 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K1221 TYR 0.012 0.001 TYR K1281 PHE 0.013 0.002 PHE K1422 TRP 0.027 0.002 TRP K1469 HIS 0.022 0.002 HIS K1544 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.14 (18455) covalent geometry : angle 0.63156 / 0.36 (26556) hydrogen bonds : bond 0.04294 / 2.88 ( 988) hydrogen bonds : angle 3.44696 / 2.64 ( 2448) metal coordination : bond 0.00622 / 0.40 ( 4) metal coordination : angle 4.94591 / 2.84 ( 6) Misc. bond : bond 0.00082 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 206 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 15 LYS cc_start: 0.8791 (mtmm) cc_final: 0.8394 (ptpp) REVERT: F 92 ARG cc_start: 0.8822 (OUTLIER) cc_final: 0.8300 (ttp80) REVERT: G 36 LYS cc_start: 0.8805 (mptt) cc_final: 0.8447 (mmtm) REVERT: H 48 ASP cc_start: 0.8690 (p0) cc_final: 0.8450 (p0) REVERT: H 65 ASP cc_start: 0.9103 (t0) cc_final: 0.8709 (t0) REVERT: K 1418 THR cc_start: 0.7389 (OUTLIER) cc_final: 0.7066 (m) REVERT: K 1428 VAL cc_start: 0.2843 (OUTLIER) cc_final: 0.2605 (t) outliers start: 37 outliers final: 24 residues processed: 231 average time/residue: 0.1728 time to fit residues: 56.9703 Evaluate side-chains 229 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 202 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain K residue 1183 THR Chi-restraints excluded: chain K residue 1211 THR Chi-restraints excluded: chain K residue 1240 THR Chi-restraints excluded: chain K residue 1269 SER Chi-restraints excluded: chain K residue 1322 HIS Chi-restraints excluded: chain K residue 1368 ILE Chi-restraints excluded: chain K residue 1377 TYR Chi-restraints excluded: chain K residue 1380 VAL Chi-restraints excluded: chain K residue 1414 HIS Chi-restraints excluded: chain K residue 1418 THR Chi-restraints excluded: chain K residue 1419 ILE Chi-restraints excluded: chain K residue 1428 VAL Chi-restraints excluded: chain K residue 1445 SER Chi-restraints excluded: chain K residue 1493 LEU Chi-restraints excluded: chain K residue 1529 ASP Chi-restraints excluded: chain K residue 1553 VAL Chi-restraints excluded: chain K residue 1573 CYS Chi-restraints excluded: chain K residue 1577 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 75 optimal weight: 30.0000 chunk 113 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 93 optimal weight: 20.0000 chunk 15 optimal weight: 3.9990 chunk 143 optimal weight: 1.9990 chunk 141 optimal weight: 0.0670 chunk 35 optimal weight: 8.9990 chunk 48 optimal weight: 1.9990 chunk 150 optimal weight: 3.9990 chunk 70 optimal weight: 0.5980 overall best weight: 1.0722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN ** K1446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1544 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.136055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.117366 restraints weight = 58650.879| |-----------------------------------------------------------------------------| r_work (start): 0.3850 rms_B_bonded: 2.10 r_work: 0.3718 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 18460 Z= 0.142 Angle : 0.627 9.899 26562 Z= 0.359 Chirality : 0.044 0.222 2993 Planarity : 0.004 0.046 2088 Dihedral : 31.176 174.114 5414 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 3.75 % Allowed : 24.35 % Favored : 71.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: 1.09 (0.25), residues: 1209 helix: 2.41 (0.20), residues: 666 sheet: -2.65 (0.59), residues: 60 loop : -1.32 (0.28), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 83 TYR 0.011 0.001 TYR K1281 PHE 0.015 0.002 PHE K1632 TRP 0.030 0.002 TRP K1469 HIS 0.018 0.002 HIS K1239 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.14 (18455) covalent geometry : angle 0.62256 / 0.36 (26556) hydrogen bonds : bond 0.04310 / 2.90 ( 988) hydrogen bonds : angle 3.38286 / 2.59 ( 2448) metal coordination : bond 0.00601 / 0.37 ( 4) metal coordination : angle 4.77063 / 2.71 ( 6) Misc. bond : bond 0.00003 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 203 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 92 ARG cc_start: 0.8379 (OUTLIER) cc_final: 0.7616 (ttm-80) REVERT: B 95 ARG cc_start: 0.8766 (OUTLIER) cc_final: 0.8097 (mmm160) REVERT: C 15 LYS cc_start: 0.8712 (mtmm) cc_final: 0.8352 (ptpp) REVERT: G 36 LYS cc_start: 0.8792 (mptt) cc_final: 0.8466 (mmtm) REVERT: H 48 ASP cc_start: 0.8600 (p0) cc_final: 0.8369 (p0) REVERT: H 65 ASP cc_start: 0.9089 (t0) cc_final: 0.8733 (t0) REVERT: K 1418 THR cc_start: 0.7324 (OUTLIER) cc_final: 0.7024 (m) REVERT: K 1428 VAL cc_start: 0.2704 (OUTLIER) cc_final: 0.2446 (t) REVERT: K 1475 TRP cc_start: 0.6325 (OUTLIER) cc_final: 0.6101 (m-90) REVERT: K 1593 ARG cc_start: 0.7458 (OUTLIER) cc_final: 0.7177 (mmm160) outliers start: 39 outliers final: 26 residues processed: 228 average time/residue: 0.1735 time to fit residues: 56.0254 Evaluate side-chains 230 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 198 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain K residue 1183 THR Chi-restraints excluded: chain K residue 1210 ILE Chi-restraints excluded: chain K residue 1211 THR Chi-restraints excluded: chain K residue 1264 TRP Chi-restraints excluded: chain K residue 1269 SER Chi-restraints excluded: chain K residue 1322 HIS Chi-restraints excluded: chain K residue 1357 THR Chi-restraints excluded: chain K residue 1377 TYR Chi-restraints excluded: chain K residue 1414 HIS Chi-restraints excluded: chain K residue 1418 THR Chi-restraints excluded: chain K residue 1419 ILE Chi-restraints excluded: chain K residue 1428 VAL Chi-restraints excluded: chain K residue 1454 GLN Chi-restraints excluded: chain K residue 1475 TRP Chi-restraints excluded: chain K residue 1493 LEU Chi-restraints excluded: chain K residue 1529 ASP Chi-restraints excluded: chain K residue 1553 VAL Chi-restraints excluded: chain K residue 1573 CYS Chi-restraints excluded: chain K residue 1577 ASP Chi-restraints excluded: chain K residue 1593 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 42 optimal weight: 0.9980 chunk 114 optimal weight: 1.9990 chunk 76 optimal weight: 30.0000 chunk 72 optimal weight: 0.9980 chunk 78 optimal weight: 20.0000 chunk 29 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 chunk 95 optimal weight: 20.0000 chunk 90 optimal weight: 50.0000 chunk 17 optimal weight: 3.9990 chunk 122 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN ** K1239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1544 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.136735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.118037 restraints weight = 59405.226| |-----------------------------------------------------------------------------| r_work (start): 0.3865 rms_B_bonded: 2.06 r_work: 0.3746 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 18460 Z= 0.135 Angle : 0.624 10.022 26562 Z= 0.357 Chirality : 0.043 0.235 2993 Planarity : 0.004 0.046 2088 Dihedral : 31.116 170.438 5413 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 3.56 % Allowed : 25.22 % Favored : 71.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: 1.23 (0.25), residues: 1209 helix: 2.48 (0.20), residues: 668 sheet: -2.47 (0.60), residues: 60 loop : -1.23 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 83 TYR 0.011 0.001 TYR K1571 PHE 0.012 0.002 PHE K1409 TRP 0.031 0.002 TRP K1469 HIS 0.014 0.001 HIS K1544 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.14 (18455) covalent geometry : angle 0.62006 / 0.36 (26556) hydrogen bonds : bond 0.04130 / 2.76 ( 988) hydrogen bonds : angle 3.31115 / 2.52 ( 2448) metal coordination : bond 0.00545 / 0.34 ( 4) metal coordination : angle 4.44367 / 2.50 ( 6) Misc. bond : bond 0.00029 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 203 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 95 ARG cc_start: 0.8763 (OUTLIER) cc_final: 0.8107 (mmm160) REVERT: C 15 LYS cc_start: 0.8691 (mtmm) cc_final: 0.8356 (ptpp) REVERT: C 92 GLU cc_start: 0.8660 (mt-10) cc_final: 0.8401 (mt-10) REVERT: E 94 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.7830 (mp0) REVERT: E 125 GLN cc_start: 0.8431 (mt0) cc_final: 0.8203 (mp10) REVERT: G 36 LYS cc_start: 0.8815 (mptt) cc_final: 0.8473 (mmtm) REVERT: H 48 ASP cc_start: 0.8592 (p0) cc_final: 0.8368 (p0) REVERT: H 65 ASP cc_start: 0.9061 (t0) cc_final: 0.8701 (t0) REVERT: K 1418 THR cc_start: 0.7176 (OUTLIER) cc_final: 0.6862 (m) outliers start: 37 outliers final: 25 residues processed: 227 average time/residue: 0.1685 time to fit residues: 54.4010 Evaluate side-chains 227 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 199 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain K residue 1183 THR Chi-restraints excluded: chain K residue 1210 ILE Chi-restraints excluded: chain K residue 1211 THR Chi-restraints excluded: chain K residue 1269 SER Chi-restraints excluded: chain K residue 1322 HIS Chi-restraints excluded: chain K residue 1357 THR Chi-restraints excluded: chain K residue 1368 ILE Chi-restraints excluded: chain K residue 1377 TYR Chi-restraints excluded: chain K residue 1414 HIS Chi-restraints excluded: chain K residue 1418 THR Chi-restraints excluded: chain K residue 1419 ILE Chi-restraints excluded: chain K residue 1454 GLN Chi-restraints excluded: chain K residue 1493 LEU Chi-restraints excluded: chain K residue 1529 ASP Chi-restraints excluded: chain K residue 1544 HIS Chi-restraints excluded: chain K residue 1573 CYS Chi-restraints excluded: chain K residue 1577 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 45 optimal weight: 6.9990 chunk 85 optimal weight: 20.0000 chunk 94 optimal weight: 20.0000 chunk 103 optimal weight: 20.0000 chunk 25 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 36 optimal weight: 8.9990 chunk 48 optimal weight: 1.9990 chunk 142 optimal weight: 4.9990 chunk 107 optimal weight: 20.0000 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN K1180 ASN ** K1239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K1540 GLN ** K1599 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.133552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.114839 restraints weight = 58340.908| |-----------------------------------------------------------------------------| r_work (start): 0.3820 rms_B_bonded: 1.97 r_work: 0.3684 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 18460 Z= 0.216 Angle : 0.689 9.906 26562 Z= 0.385 Chirality : 0.046 0.231 2993 Planarity : 0.005 0.060 2088 Dihedral : 31.221 169.238 5413 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 3.56 % Allowed : 25.89 % Favored : 70.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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 (0.25), residues: 1209 helix: 2.26 (0.20), residues: 672 sheet: -2.45 (0.64), residues: 59 loop : -1.34 (0.28), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K1207 TYR 0.017 0.002 TYR B 88 PHE 0.052 0.003 PHE K1536 TRP 0.043 0.003 TRP K1264 HIS 0.013 0.002 HIS K1239 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.22 (18455) covalent geometry : angle 0.68391 / 0.38 (26556) hydrogen bonds : bond 0.05205 / 3.52 ( 988) hydrogen bonds : angle 3.56393 / 2.70 ( 2448) metal coordination : bond 0.00942 / 0.51 ( 4) metal coordination : angle 5.77983 / 3.38 ( 6) Misc. bond : bond 0.00073 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 193 time to evaluate : 0.511 Fit side-chains revert: symmetry clash REVERT: B 93 GLN cc_start: 0.8707 (mm-40) cc_final: 0.8448 (mm-40) REVERT: B 95 ARG cc_start: 0.8827 (OUTLIER) cc_final: 0.8114 (mmm160) REVERT: C 15 LYS cc_start: 0.8715 (mtmm) cc_final: 0.8305 (ptpp) REVERT: F 84 MET cc_start: 0.8838 (mmm) cc_final: 0.8562 (mmm) REVERT: H 48 ASP cc_start: 0.8644 (p0) cc_final: 0.8423 (p0) REVERT: H 65 ASP cc_start: 0.9148 (t0) cc_final: 0.8772 (t0) REVERT: K 1415 TYR cc_start: 0.6709 (OUTLIER) cc_final: 0.4697 (m-80) REVERT: K 1418 THR cc_start: 0.7378 (OUTLIER) cc_final: 0.7050 (m) outliers start: 37 outliers final: 30 residues processed: 215 average time/residue: 0.1740 time to fit residues: 52.8219 Evaluate side-chains 222 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 189 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain K residue 1180 ASN Chi-restraints excluded: chain K residue 1183 THR Chi-restraints excluded: chain K residue 1210 ILE Chi-restraints excluded: chain K residue 1211 THR Chi-restraints excluded: chain K residue 1264 TRP Chi-restraints excluded: chain K residue 1268 SER Chi-restraints excluded: chain K residue 1269 SER Chi-restraints excluded: chain K residue 1322 HIS Chi-restraints excluded: chain K residue 1357 THR Chi-restraints excluded: chain K residue 1377 TYR Chi-restraints excluded: chain K residue 1414 HIS Chi-restraints excluded: chain K residue 1415 TYR Chi-restraints excluded: chain K residue 1418 THR Chi-restraints excluded: chain K residue 1419 ILE Chi-restraints excluded: chain K residue 1454 GLN Chi-restraints excluded: chain K residue 1493 LEU Chi-restraints excluded: chain K residue 1529 ASP Chi-restraints excluded: chain K residue 1553 VAL Chi-restraints excluded: chain K residue 1567 ASP Chi-restraints excluded: chain K residue 1573 CYS Chi-restraints excluded: chain K residue 1577 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 85 optimal weight: 20.0000 chunk 33 optimal weight: 6.9990 chunk 130 optimal weight: 0.9990 chunk 16 optimal weight: 6.9990 chunk 89 optimal weight: 20.0000 chunk 119 optimal weight: 4.9990 chunk 88 optimal weight: 20.0000 chunk 132 optimal weight: 0.0870 chunk 13 optimal weight: 1.9990 chunk 73 optimal weight: 50.0000 chunk 8 optimal weight: 1.9990 overall best weight: 2.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K1180 ASN ** K1239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.134318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.115567 restraints weight = 59141.389| |-----------------------------------------------------------------------------| r_work (start): 0.3819 rms_B_bonded: 1.98 r_work: 0.3689 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 18460 Z= 0.173 Angle : 0.667 10.133 26562 Z= 0.373 Chirality : 0.045 0.239 2993 Planarity : 0.004 0.051 2088 Dihedral : 31.200 168.448 5413 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 3.66 % Allowed : 25.89 % Favored : 70.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: 1.01 (0.25), residues: 1209 helix: 2.30 (0.20), residues: 672 sheet: -2.47 (0.63), residues: 59 loop : -1.37 (0.28), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K1451 TYR 0.020 0.001 TYR B 88 PHE 0.039 0.002 PHE K1536 TRP 0.044 0.003 TRP K1469 HIS 0.014 0.002 HIS K1544 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.17 (18455) covalent geometry : angle 0.66182 / 0.37 (26556) hydrogen bonds : bond 0.04576 / 3.07 ( 988) hydrogen bonds : angle 3.52459 / 2.67 ( 2448) metal coordination : bond 0.00730 / 0.42 ( 4) metal coordination : angle 5.58687 / 3.23 ( 6) Misc. bond : bond 0.00008 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 193 time to evaluate : 0.463 Fit side-chains revert: symmetry clash REVERT: B 93 GLN cc_start: 0.8699 (mm-40) cc_final: 0.8437 (mm-40) REVERT: B 95 ARG cc_start: 0.8791 (OUTLIER) cc_final: 0.8096 (mmm160) REVERT: C 15 LYS cc_start: 0.8711 (mtmm) cc_final: 0.8326 (ptpp) REVERT: E 94 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.7754 (mp0) REVERT: E 125 GLN cc_start: 0.8409 (mt0) cc_final: 0.8161 (mp10) REVERT: F 84 MET cc_start: 0.8775 (mmm) cc_final: 0.8488 (mmm) REVERT: H 48 ASP cc_start: 0.8637 (p0) cc_final: 0.8411 (p0) REVERT: H 65 ASP cc_start: 0.9118 (t0) cc_final: 0.8741 (t0) REVERT: K 1418 THR cc_start: 0.7289 (OUTLIER) cc_final: 0.6880 (m) outliers start: 38 outliers final: 33 residues processed: 216 average time/residue: 0.1675 time to fit residues: 51.3559 Evaluate side-chains 227 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 191 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain K residue 1180 ASN Chi-restraints excluded: chain K residue 1183 THR Chi-restraints excluded: chain K residue 1185 SER Chi-restraints excluded: chain K residue 1210 ILE Chi-restraints excluded: chain K residue 1211 THR Chi-restraints excluded: chain K residue 1264 TRP Chi-restraints excluded: chain K residue 1268 SER Chi-restraints excluded: chain K residue 1269 SER Chi-restraints excluded: chain K residue 1322 HIS Chi-restraints excluded: chain K residue 1357 THR Chi-restraints excluded: chain K residue 1377 TYR Chi-restraints excluded: chain K residue 1380 VAL Chi-restraints excluded: chain K residue 1414 HIS Chi-restraints excluded: chain K residue 1418 THR Chi-restraints excluded: chain K residue 1419 ILE Chi-restraints excluded: chain K residue 1454 GLN Chi-restraints excluded: chain K residue 1493 LEU Chi-restraints excluded: chain K residue 1529 ASP Chi-restraints excluded: chain K residue 1553 VAL Chi-restraints excluded: chain K residue 1567 ASP Chi-restraints excluded: chain K residue 1573 CYS Chi-restraints excluded: chain K residue 1577 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 21 optimal weight: 0.9980 chunk 99 optimal weight: 20.0000 chunk 79 optimal weight: 20.0000 chunk 69 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 chunk 66 optimal weight: 7.9990 chunk 132 optimal weight: 5.9990 chunk 91 optimal weight: 50.0000 chunk 60 optimal weight: 5.9990 chunk 109 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K1239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.134063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.115217 restraints weight = 58516.141| |-----------------------------------------------------------------------------| r_work (start): 0.3817 rms_B_bonded: 1.95 r_work: 0.3683 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 18460 Z= 0.186 Angle : 0.672 10.084 26562 Z= 0.375 Chirality : 0.045 0.238 2993 Planarity : 0.004 0.052 2088 Dihedral : 31.190 168.219 5413 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 3.56 % Allowed : 25.70 % Favored : 70.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: 0.99 (0.25), residues: 1209 helix: 2.29 (0.20), residues: 672 sheet: -2.55 (0.63), residues: 59 loop : -1.38 (0.28), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K1451 TYR 0.024 0.002 TYR B 88 PHE 0.035 0.002 PHE K1536 TRP 0.047 0.003 TRP K1469 HIS 0.013 0.002 HIS K1544 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.19 (18455) covalent geometry : angle 0.66666 / 0.37 (26556) hydrogen bonds : bond 0.04680 / 3.14 ( 988) hydrogen bonds : angle 3.54222 / 2.68 ( 2448) metal coordination : bond 0.00801 / 0.46 ( 4) metal coordination : angle 5.65450 / 3.29 ( 6) Misc. bond : bond 0.00022 / 0.01 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 192 time to evaluate : 0.593 Fit side-chains revert: symmetry clash REVERT: B 93 GLN cc_start: 0.8727 (mm-40) cc_final: 0.8459 (mm-40) REVERT: B 95 ARG cc_start: 0.8815 (OUTLIER) cc_final: 0.8102 (mmm160) REVERT: C 15 LYS cc_start: 0.8710 (mtmm) cc_final: 0.8326 (ptpp) REVERT: E 125 GLN cc_start: 0.8438 (mt0) cc_final: 0.8168 (mp10) REVERT: F 84 MET cc_start: 0.8785 (mmm) cc_final: 0.8555 (mmm) REVERT: G 71 ARG cc_start: 0.8578 (ttp-110) cc_final: 0.8155 (ttp-110) REVERT: H 48 ASP cc_start: 0.8666 (p0) cc_final: 0.8437 (p0) REVERT: H 65 ASP cc_start: 0.9154 (t0) cc_final: 0.8755 (t0) REVERT: K 1415 TYR cc_start: 0.6582 (OUTLIER) cc_final: 0.4664 (m-80) REVERT: K 1418 THR cc_start: 0.7422 (OUTLIER) cc_final: 0.7036 (m) outliers start: 37 outliers final: 30 residues processed: 214 average time/residue: 0.1759 time to fit residues: 53.3194 Evaluate side-chains 223 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 190 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain K residue 1183 THR Chi-restraints excluded: chain K residue 1185 SER Chi-restraints excluded: chain K residue 1210 ILE Chi-restraints excluded: chain K residue 1211 THR Chi-restraints excluded: chain K residue 1264 TRP Chi-restraints excluded: chain K residue 1268 SER Chi-restraints excluded: chain K residue 1269 SER Chi-restraints excluded: chain K residue 1322 HIS Chi-restraints excluded: chain K residue 1357 THR Chi-restraints excluded: chain K residue 1377 TYR Chi-restraints excluded: chain K residue 1380 VAL Chi-restraints excluded: chain K residue 1415 TYR Chi-restraints excluded: chain K residue 1418 THR Chi-restraints excluded: chain K residue 1419 ILE Chi-restraints excluded: chain K residue 1454 GLN Chi-restraints excluded: chain K residue 1493 LEU Chi-restraints excluded: chain K residue 1529 ASP Chi-restraints excluded: chain K residue 1553 VAL Chi-restraints excluded: chain K residue 1567 ASP Chi-restraints excluded: chain K residue 1573 CYS Chi-restraints excluded: chain K residue 1577 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 121 optimal weight: 2.9990 chunk 135 optimal weight: 0.9990 chunk 110 optimal weight: 8.9990 chunk 80 optimal weight: 20.0000 chunk 22 optimal weight: 0.4980 chunk 55 optimal weight: 4.9990 chunk 116 optimal weight: 0.0020 chunk 41 optimal weight: 7.9990 chunk 122 optimal weight: 3.9990 chunk 143 optimal weight: 0.8980 chunk 125 optimal weight: 0.0270 overall best weight: 0.4848 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 75 HIS ** K1239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.136201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.117734 restraints weight = 59111.065| |-----------------------------------------------------------------------------| r_work (start): 0.3858 rms_B_bonded: 1.89 r_work: 0.3729 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.088 18460 Z= 0.136 Angle : 0.651 10.193 26562 Z= 0.366 Chirality : 0.044 0.259 2993 Planarity : 0.005 0.052 2088 Dihedral : 31.098 168.193 5411 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.69 % Allowed : 26.76 % Favored : 70.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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 (0.25), residues: 1209 helix: 2.45 (0.21), residues: 668 sheet: -2.42 (0.61), residues: 60 loop : -1.29 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG K1451 TYR 0.024 0.001 TYR B 88 PHE 0.042 0.002 PHE K1536 TRP 0.046 0.003 TRP K1469 HIS 0.016 0.002 HIS K1414 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.14 (18455) covalent geometry : angle 0.64616 / 0.37 (26556) hydrogen bonds : bond 0.04172 / 2.78 ( 988) hydrogen bonds : angle 3.39438 / 2.57 ( 2448) metal coordination : bond 0.00526 / 0.36 ( 4) metal coordination : angle 5.06676 / 2.80 ( 6) Misc. bond : bond 0.00050 / 0.03 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4434.03 seconds wall clock time: 76 minutes 34.29 seconds (4594.29 seconds total)