Starting phenix.real_space_refine on Sun Aug 24 06:10:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nqu_49676/08_2025/9nqu_49676.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nqu_49676/08_2025/9nqu_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_49676/08_2025/9nqu_49676.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nqu_49676/08_2025/9nqu_49676.map" model { file = "/net/cci-nas-00/data/ceres_data/9nqu_49676/08_2025/9nqu_49676.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nqu_49676/08_2025/9nqu_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-2.0-5787/lib/python3.9/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, 17 Unusual residues: {' FE': 1, ' ZN': 1, 'OH0': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: 4.08, per 1000 atoms: 0.24 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: 1.59 Conformation dependent library (CDL) restraints added in 588.0 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 2.90 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: 4.41 Time building geometry restraints manager: 2.13 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=" 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 bond pdb=" N VAL K1523 " pdb=" CA VAL K1523 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.14e-02 7.69e+03 1.24e+01 bond pdb=" N ILE K1323 " pdb=" CA ILE K1323 " ideal model delta sigma weight residual 1.456 1.497 -0.040 1.14e-02 7.69e+03 1.24e+01 bond pdb=" N GLN E 19 " pdb=" CA GLN E 19 " ideal model delta sigma weight residual 1.459 1.491 -0.032 9.10e-03 1.21e+04 1.22e+01 ... (remaining 18450 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 25502 1.81 - 3.63: 850 3.63 - 5.44: 117 5.44 - 7.25: 76 7.25 - 9.06: 11 Bond angle restraints: 26556 Sorted by residual: angle pdb=" C ASN K1398 " pdb=" CA ASN K1398 " pdb=" CB ASN K1398 " ideal model delta sigma weight residual 109.71 117.02 -7.31 1.83e+00 2.99e-01 1.60e+01 angle pdb=" N TRP K1517 " pdb=" CA TRP K1517 " pdb=" C TRP K1517 " ideal model delta sigma weight residual 110.97 115.30 -4.33 1.09e+00 8.42e-01 1.58e+01 angle pdb=" N GLY K1610 " pdb=" CA GLY K1610 " pdb=" C GLY K1610 " ideal model delta sigma weight residual 113.18 104.12 9.06 2.37e+00 1.78e-01 1.46e+01 angle pdb=" CA ILE K1323 " pdb=" C ILE K1323 " pdb=" O ILE K1323 " ideal model delta sigma weight residual 121.28 116.86 4.42 1.16e+00 7.43e-01 1.45e+01 angle pdb=" N SER K1251 " pdb=" CA SER K1251 " pdb=" C SER K1251 " ideal model delta sigma weight residual 110.80 103.03 7.77 2.13e+00 2.20e-01 1.33e+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 - 0.128: 2915 0.128 - 0.255: 36 0.255 - 0.383: 1 0.383 - 0.510: 16 0.510 - 0.638: 25 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 2.35 -2.98 -0.64 2.00e-01 2.50e+01 1.02e+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 2.35 -2.97 -0.62 2.00e-01 2.50e+01 9.73e+00 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 2.35 -2.94 -0.60 2.00e-01 2.50e+01 8.89e+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 2.260 nonbonded pdb=" NE2 HIS K1388 " pdb="FE FE K1701 " model vdw 2.099 2.340 nonbonded pdb=" OE1 GLU K1390 " pdb="FE FE K1701 " model vdw 2.195 2.260 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 2.340 ... (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: 2.460 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: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 22.290 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6802 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.214 18460 Z= 0.326 Angle : 0.790 9.065 26562 Z= 0.453 Chirality : 0.073 0.638 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 aren 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 covalent geometry : bond 0.00500 (18455) covalent geometry : angle 0.78663 (26556) hydrogen bonds : bond 0.12865 ( 988) hydrogen bonds : angle 5.24671 ( 2448) metal coordination : bond 0.00735 ( 4) metal coordination : angle 4.82425 ( 6) Misc. bond : bond 0.21424 ( 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 : 0.485 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: 0.1967 time to fit residues: 70.7512 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 : 0.470 ------------------------------------------------------------------------------- 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: 7.9990 chunk 107 optimal weight: 6.9990 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: 7.9990 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 30.0000 chunk 149 optimal weight: 0.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 60 ASN D 106 HIS H 46 HIS K1320 ASN ** K1329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K1343 GLN ** K1375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K1468 HIS ** 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.131417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.111870 restraints weight = 58694.071| |-----------------------------------------------------------------------------| r_work (start): 0.3765 rms_B_bonded: 2.17 r_work: 0.3623 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.108 18460 Z= 0.327 Angle : 0.729 12.799 26562 Z= 0.412 Chirality : 0.043 0.204 2993 Planarity : 0.005 0.046 2088 Dihedral : 31.259 174.659 5434 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 6.35 % Allowed : 22.91 % 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 aren not related in a simple way. whole: 0.07 (0.25), residues: 1209 helix: 1.65 (0.21), residues: 672 sheet: -3.04 (0.56), residues: 57 loop : -1.97 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K1207 TYR 0.018 0.002 TYR K1157 PHE 0.044 0.003 PHE K1422 TRP 0.029 0.003 TRP K1469 HIS 0.010 0.002 HIS K1414 Details of bonding type rmsd covalent geometry : bond 0.00747 (18455) covalent geometry : angle 0.72010 (26556) hydrogen bonds : bond 0.05741 ( 988) hydrogen bonds : angle 4.03026 ( 2448) metal coordination : bond 0.01403 ( 4) metal coordination : angle 7.50702 ( 6) Misc. bond : bond 0.00126 ( 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 270 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 204 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 GLN cc_start: 0.8778 (mt0) cc_final: 0.8577 (mt0) REVERT: B 92 ARG cc_start: 0.8604 (OUTLIER) cc_final: 0.7804 (ttm-80) REVERT: D 90 GLU cc_start: 0.8676 (mp0) cc_final: 0.8452 (mp0) REVERT: F 92 ARG cc_start: 0.8887 (OUTLIER) cc_final: 0.8221 (ttp80) REVERT: G 36 LYS cc_start: 0.8786 (mptt) cc_final: 0.8464 (mmtm) REVERT: G 73 ASN cc_start: 0.8630 (t0) cc_final: 0.8308 (t0) REVERT: H 89 ARG cc_start: 0.8791 (mmm-85) cc_final: 0.8587 (mmm160) REVERT: K 1415 TYR cc_start: 0.6580 (OUTLIER) cc_final: 0.4220 (m-80) REVERT: K 1418 THR cc_start: 0.7412 (OUTLIER) cc_final: 0.7016 (m) outliers start: 66 outliers final: 40 residues processed: 255 average time/residue: 0.1886 time to fit residues: 66.8817 Evaluate side-chains 237 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 193 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET 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 37 TYR Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 92 ARG 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 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 1230 LYS Chi-restraints excluded: chain K residue 1236 SER 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 1287 GLN Chi-restraints excluded: chain K residue 1322 HIS Chi-restraints excluded: chain K residue 1348 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 1415 TYR 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 1478 ASN Chi-restraints excluded: chain K residue 1521 ARG Chi-restraints excluded: chain K residue 1529 ASP 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: 3.9990 chunk 29 optimal weight: 0.8980 chunk 60 optimal weight: 0.9990 chunk 126 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 96 optimal weight: 5.9990 chunk 48 optimal weight: 0.9980 chunk 80 optimal weight: 5.9990 chunk 107 optimal weight: 7.9990 chunk 124 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN B 93 GLN ** K1446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.135760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.116376 restraints weight = 58903.791| |-----------------------------------------------------------------------------| r_work (start): 0.3849 rms_B_bonded: 1.87 r_work: 0.3725 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 18460 Z= 0.163 Angle : 0.595 7.491 26562 Z= 0.344 Chirality : 0.036 0.173 2993 Planarity : 0.004 0.044 2088 Dihedral : 30.818 174.612 5428 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 3.66 % Allowed : 23.58 % Favored : 72.76 % 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 aren not related in a simple way. whole: 0.77 (0.25), residues: 1209 helix: 2.22 (0.20), residues: 669 sheet: -3.22 (0.57), residues: 55 loop : -1.57 (0.28), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 96 TYR 0.013 0.001 TYR K1571 PHE 0.023 0.002 PHE K1422 TRP 0.021 0.002 TRP K1469 HIS 0.005 0.001 HIS K1544 Details of bonding type rmsd covalent geometry : bond 0.00362 (18455) covalent geometry : angle 0.58981 (26556) hydrogen bonds : bond 0.03888 ( 988) hydrogen bonds : angle 3.39837 ( 2448) metal coordination : bond 0.00686 ( 4) metal coordination : angle 5.40300 ( 6) Misc. bond : bond 0.00003 ( 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 251 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 213 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 93 GLN cc_start: 0.8575 (mm-40) cc_final: 0.8349 (mm110) REVERT: C 13 LYS cc_start: 0.8149 (tppt) cc_final: 0.7947 (tptt) REVERT: F 50 ILE cc_start: 0.9068 (tp) cc_final: 0.8858 (tp) REVERT: G 36 LYS cc_start: 0.8817 (mptt) cc_final: 0.8461 (mmtm) REVERT: H 65 ASP cc_start: 0.9076 (t0) cc_final: 0.8712 (t0) REVERT: K 1418 THR cc_start: 0.7104 (OUTLIER) cc_final: 0.6897 (m) REVERT: K 1475 TRP cc_start: 0.6269 (OUTLIER) cc_final: 0.6043 (m-90) outliers start: 38 outliers final: 21 residues processed: 243 average time/residue: 0.1762 time to fit residues: 60.4687 Evaluate side-chains 218 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 195 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 73 THR 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 1211 THR Chi-restraints excluded: chain K residue 1287 GLN 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 1445 SER Chi-restraints excluded: chain K residue 1475 TRP 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 1611 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 93 optimal weight: 10.0000 chunk 22 optimal weight: 9.9990 chunk 132 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 109 optimal weight: 7.9990 chunk 3 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 102 optimal weight: 6.9990 chunk 5 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN ** K1398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K1471 GLN ** K1490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K1540 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.134416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.115783 restraints weight = 59391.294| |-----------------------------------------------------------------------------| r_work (start): 0.3834 rms_B_bonded: 1.98 r_work: 0.3697 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 18460 Z= 0.185 Angle : 0.606 10.069 26562 Z= 0.348 Chirality : 0.037 0.175 2993 Planarity : 0.004 0.043 2088 Dihedral : 30.829 173.951 5416 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 4.43 % Allowed : 23.87 % Favored : 71.70 % 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 aren not related in a simple way. whole: 0.89 (0.25), residues: 1209 helix: 2.33 (0.21), residues: 668 sheet: -3.10 (0.55), residues: 58 loop : -1.53 (0.28), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K1221 TYR 0.013 0.001 TYR K1157 PHE 0.041 0.002 PHE K1422 TRP 0.027 0.002 TRP K1469 HIS 0.021 0.001 HIS K1544 Details of bonding type rmsd covalent geometry : bond 0.00415 (18455) covalent geometry : angle 0.59985 (26556) hydrogen bonds : bond 0.04069 ( 988) hydrogen bonds : angle 3.42262 ( 2448) metal coordination : bond 0.00733 ( 4) metal coordination : angle 5.67243 ( 6) Misc. bond : bond 0.00005 ( 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: 46 poor density : 201 time to evaluate : 0.458 Fit side-chains revert: symmetry clash REVERT: B 84 MET cc_start: 0.8774 (tpp) cc_final: 0.8363 (mmm) REVERT: C 15 LYS cc_start: 0.8666 (mtmm) cc_final: 0.8380 (ptpp) REVERT: G 36 LYS cc_start: 0.8803 (mptt) cc_final: 0.8426 (mmtm) REVERT: H 65 ASP cc_start: 0.9095 (t0) cc_final: 0.8696 (t0) REVERT: K 1352 MET cc_start: 0.4890 (mtt) cc_final: 0.4602 (mtt) REVERT: K 1418 THR cc_start: 0.7384 (OUTLIER) cc_final: 0.6984 (m) outliers start: 46 outliers final: 28 residues processed: 233 average time/residue: 0.1705 time to fit residues: 56.4507 Evaluate side-chains 222 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 193 time to evaluate : 0.573 ------------------------------------------------------------------------------- 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 80 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain D residue 43 LYS 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 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 1211 THR Chi-restraints excluded: chain K residue 1212 VAL Chi-restraints excluded: chain K residue 1229 THR Chi-restraints excluded: chain K residue 1245 THR Chi-restraints excluded: chain K residue 1264 TRP Chi-restraints excluded: chain K residue 1287 GLN Chi-restraints excluded: chain K residue 1322 HIS Chi-restraints excluded: chain K residue 1325 LYS Chi-restraints excluded: chain K residue 1377 TYR Chi-restraints excluded: chain K residue 1418 THR Chi-restraints excluded: chain K residue 1419 ILE 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 1577 ASP Chi-restraints excluded: chain K residue 1611 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 38 optimal weight: 2.9990 chunk 138 optimal weight: 0.2980 chunk 118 optimal weight: 0.5980 chunk 24 optimal weight: 3.9990 chunk 143 optimal weight: 0.8980 chunk 41 optimal weight: 9.9990 chunk 42 optimal weight: 0.9980 chunk 124 optimal weight: 5.9990 chunk 56 optimal weight: 8.9990 chunk 28 optimal weight: 0.9990 chunk 142 optimal weight: 5.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN D 60 ASN F 75 HIS ** K1398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1454 GLN ** 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 = 0.4212 r_free = 0.4212 target = 0.136777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.117955 restraints weight = 59182.193| |-----------------------------------------------------------------------------| r_work (start): 0.3863 rms_B_bonded: 2.06 r_work: 0.3739 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7173 moved from start: 0.3080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 18460 Z= 0.147 Angle : 0.579 8.068 26562 Z= 0.336 Chirality : 0.036 0.245 2993 Planarity : 0.004 0.051 2088 Dihedral : 30.513 173.875 5413 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 3.85 % Allowed : 24.45 % Favored : 71.70 % 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 aren not related in a simple way. whole: 1.23 (0.25), residues: 1209 helix: 2.58 (0.20), residues: 670 sheet: -3.01 (0.57), residues: 60 loop : -1.32 (0.28), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K1521 TYR 0.015 0.001 TYR K1157 PHE 0.031 0.002 PHE K1422 TRP 0.023 0.002 TRP K1469 HIS 0.022 0.002 HIS K1544 Details of bonding type rmsd covalent geometry : bond 0.00318 (18455) covalent geometry : angle 0.57582 (26556) hydrogen bonds : bond 0.03584 ( 988) hydrogen bonds : angle 3.15994 ( 2448) metal coordination : bond 0.00525 ( 4) metal coordination : angle 4.11160 ( 6) Misc. bond : bond 0.00020 ( 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 241 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 201 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 84 MET cc_start: 0.8674 (tpp) cc_final: 0.8376 (mmm) REVERT: B 92 ARG cc_start: 0.8342 (OUTLIER) cc_final: 0.7727 (ttm-80) REVERT: C 15 LYS cc_start: 0.8574 (mtmm) cc_final: 0.8338 (ptpp) REVERT: E 125 GLN cc_start: 0.8538 (mt0) cc_final: 0.8190 (mp10) REVERT: G 36 LYS cc_start: 0.8822 (mptt) cc_final: 0.8439 (mmtm) REVERT: H 65 ASP cc_start: 0.9084 (t0) cc_final: 0.8642 (t0) REVERT: K 1187 TYR cc_start: 0.5574 (OUTLIER) cc_final: 0.4458 (t80) REVERT: K 1378 MET cc_start: 0.5831 (mmp) cc_final: 0.5543 (mmp) REVERT: K 1418 THR cc_start: 0.7129 (OUTLIER) cc_final: 0.6712 (m) outliers start: 40 outliers final: 26 residues processed: 228 average time/residue: 0.1755 time to fit residues: 56.2221 Evaluate side-chains 224 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 195 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 122 LYS 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 D residue 43 LYS Chi-restraints excluded: chain D residue 110 GLU 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 H residue 105 LYS Chi-restraints excluded: chain K residue 1183 THR Chi-restraints excluded: chain K residue 1187 TYR Chi-restraints excluded: chain K residue 1211 THR Chi-restraints excluded: chain K residue 1264 TRP Chi-restraints excluded: chain K residue 1287 GLN 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 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 1611 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 75 optimal weight: 10.0000 chunk 113 optimal weight: 0.6980 chunk 65 optimal weight: 0.9990 chunk 93 optimal weight: 8.9990 chunk 15 optimal weight: 2.9990 chunk 143 optimal weight: 0.3980 chunk 141 optimal weight: 0.8980 chunk 35 optimal weight: 8.9990 chunk 48 optimal weight: 6.9990 chunk 150 optimal weight: 0.9990 chunk 70 optimal weight: 4.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN ** K1398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1490 GLN ** 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 = 0.4222 r_free = 0.4222 target = 0.137407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.118612 restraints weight = 59375.874| |-----------------------------------------------------------------------------| r_work (start): 0.3883 rms_B_bonded: 2.10 r_work: 0.3759 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 moved from start: 0.3358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18460 Z= 0.146 Angle : 0.575 10.133 26562 Z= 0.332 Chirality : 0.035 0.170 2993 Planarity : 0.004 0.048 2088 Dihedral : 30.353 173.492 5413 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 4.14 % Allowed : 24.83 % Favored : 71.03 % 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 aren not related in a simple way. whole: 1.47 (0.25), residues: 1209 helix: 2.69 (0.20), residues: 673 sheet: -2.77 (0.58), residues: 60 loop : -1.13 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K1521 TYR 0.010 0.001 TYR K1281 PHE 0.026 0.002 PHE K1422 TRP 0.027 0.002 TRP K1469 HIS 0.022 0.002 HIS K1544 Details of bonding type rmsd covalent geometry : bond 0.00320 (18455) covalent geometry : angle 0.57295 (26556) hydrogen bonds : bond 0.03553 ( 988) hydrogen bonds : angle 3.07298 ( 2448) metal coordination : bond 0.00437 ( 4) metal coordination : angle 3.57269 ( 6) Misc. bond : bond 0.00021 ( 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 249 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 206 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 129 ARG cc_start: 0.8452 (tpt90) cc_final: 0.8128 (tpt90) REVERT: B 84 MET cc_start: 0.8618 (tpp) cc_final: 0.8363 (mmm) REVERT: B 92 ARG cc_start: 0.8347 (OUTLIER) cc_final: 0.7548 (ttm-80) REVERT: B 95 ARG cc_start: 0.8760 (OUTLIER) cc_final: 0.8190 (mmm160) REVERT: C 15 LYS cc_start: 0.8534 (mtmm) cc_final: 0.8334 (ptpp) REVERT: E 125 GLN cc_start: 0.8459 (mt0) cc_final: 0.8125 (mp10) REVERT: F 92 ARG cc_start: 0.8845 (ttp80) cc_final: 0.8611 (ttp80) REVERT: G 36 LYS cc_start: 0.8859 (mptt) cc_final: 0.8521 (mmtm) REVERT: H 65 ASP cc_start: 0.9036 (t0) cc_final: 0.8603 (t0) REVERT: H 102 GLU cc_start: 0.7801 (mm-30) cc_final: 0.6807 (mm-30) REVERT: K 1187 TYR cc_start: 0.5588 (OUTLIER) cc_final: 0.4731 (t80) REVERT: K 1418 THR cc_start: 0.6991 (OUTLIER) cc_final: 0.6642 (m) outliers start: 43 outliers final: 29 residues processed: 232 average time/residue: 0.1791 time to fit residues: 58.4376 Evaluate side-chains 230 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 197 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain B residue 80 THR 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 D residue 43 LYS Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain D residue 120 SER 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 1187 TYR 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 1287 GLN Chi-restraints excluded: chain K residue 1322 HIS Chi-restraints excluded: chain K residue 1325 LYS 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 1493 LEU Chi-restraints excluded: chain K residue 1529 ASP Chi-restraints excluded: chain K residue 1552 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 42 optimal weight: 0.8980 chunk 114 optimal weight: 0.8980 chunk 76 optimal weight: 7.9990 chunk 72 optimal weight: 0.9980 chunk 78 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 95 optimal weight: 6.9990 chunk 90 optimal weight: 10.0000 chunk 17 optimal weight: 4.9990 chunk 122 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K1239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K1490 GLN K1548 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.137831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.119066 restraints weight = 59744.062| |-----------------------------------------------------------------------------| r_work (start): 0.3881 rms_B_bonded: 2.21 r_work: 0.3763 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7165 moved from start: 0.3545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18460 Z= 0.147 Angle : 0.580 11.430 26562 Z= 0.332 Chirality : 0.035 0.169 2993 Planarity : 0.004 0.046 2088 Dihedral : 30.262 173.314 5411 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 4.14 % Allowed : 24.64 % 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 aren not related in a simple way. whole: 1.58 (0.25), residues: 1209 helix: 2.76 (0.20), residues: 674 sheet: -2.54 (0.60), residues: 60 loop : -1.08 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K1593 TYR 0.011 0.001 TYR D 80 PHE 0.024 0.002 PHE K1422 TRP 0.029 0.002 TRP K1469 HIS 0.020 0.002 HIS K1544 Details of bonding type rmsd covalent geometry : bond 0.00320 (18455) covalent geometry : angle 0.57695 (26556) hydrogen bonds : bond 0.03539 ( 988) hydrogen bonds : angle 3.07045 ( 2448) metal coordination : bond 0.00401 ( 4) metal coordination : angle 3.72980 ( 6) Misc. bond : bond 0.00003 ( 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 247 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 204 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 129 ARG cc_start: 0.8477 (tpt90) cc_final: 0.8132 (tpt90) REVERT: B 84 MET cc_start: 0.8610 (tpp) cc_final: 0.8363 (mmm) REVERT: B 92 ARG cc_start: 0.8393 (OUTLIER) cc_final: 0.7520 (ttm-80) REVERT: B 95 ARG cc_start: 0.8764 (OUTLIER) cc_final: 0.8189 (mmm160) REVERT: E 125 GLN cc_start: 0.8527 (mt0) cc_final: 0.8244 (mp10) REVERT: F 92 ARG cc_start: 0.8841 (ttp80) cc_final: 0.8568 (ttp80) REVERT: G 36 LYS cc_start: 0.8821 (mptt) cc_final: 0.8464 (mmtm) REVERT: H 65 ASP cc_start: 0.9066 (t0) cc_final: 0.8634 (t0) REVERT: K 1187 TYR cc_start: 0.5579 (OUTLIER) cc_final: 0.4685 (t80) REVERT: K 1377 TYR cc_start: 0.6420 (OUTLIER) cc_final: 0.5008 (p90) REVERT: K 1418 THR cc_start: 0.7036 (OUTLIER) cc_final: 0.6722 (m) outliers start: 43 outliers final: 25 residues processed: 234 average time/residue: 0.1798 time to fit residues: 59.0566 Evaluate side-chains 226 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 196 time to evaluate : 0.493 ------------------------------------------------------------------------------- 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 80 THR 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 D residue 43 LYS Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain D residue 120 SER 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 1187 TYR Chi-restraints excluded: chain K residue 1210 ILE Chi-restraints excluded: chain K residue 1211 THR Chi-restraints excluded: chain K residue 1268 SER Chi-restraints excluded: chain K residue 1287 GLN 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 45 optimal weight: 0.9980 chunk 85 optimal weight: 6.9990 chunk 94 optimal weight: 7.9990 chunk 103 optimal weight: 6.9990 chunk 25 optimal weight: 0.0870 chunk 5 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 142 optimal weight: 4.9990 chunk 107 optimal weight: 8.9990 overall best weight: 1.4162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 27 GLN K1180 ASN ** K1239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K1514 HIS K1540 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.136282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.117175 restraints weight = 59137.715| |-----------------------------------------------------------------------------| r_work (start): 0.3859 rms_B_bonded: 2.17 r_work: 0.3728 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.3546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 18460 Z= 0.168 Angle : 0.598 12.371 26562 Z= 0.341 Chirality : 0.036 0.169 2993 Planarity : 0.004 0.037 2088 Dihedral : 30.320 173.451 5411 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.75 % Allowed : 25.12 % 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 aren not related in a simple way. whole: 1.39 (0.25), residues: 1209 helix: 2.60 (0.20), residues: 681 sheet: -2.61 (0.59), residues: 62 loop : -1.21 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 83 TYR 0.011 0.001 TYR D 80 PHE 0.025 0.002 PHE K1422 TRP 0.040 0.002 TRP K1469 HIS 0.019 0.002 HIS K1544 Details of bonding type rmsd covalent geometry : bond 0.00374 (18455) covalent geometry : angle 0.59502 (26556) hydrogen bonds : bond 0.03811 ( 988) hydrogen bonds : angle 3.18770 ( 2448) metal coordination : bond 0.00542 ( 4) metal coordination : angle 4.11793 ( 6) Misc. bond : bond 0.00019 ( 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 236 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 197 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 129 ARG cc_start: 0.8468 (tpt90) cc_final: 0.8170 (tpt90) REVERT: B 84 MET cc_start: 0.8628 (tpp) cc_final: 0.8309 (mmm) REVERT: B 92 ARG cc_start: 0.8381 (OUTLIER) cc_final: 0.7547 (ttm-80) REVERT: B 95 ARG cc_start: 0.8796 (OUTLIER) cc_final: 0.8193 (mmm160) REVERT: E 125 GLN cc_start: 0.8485 (mt0) cc_final: 0.8214 (mp10) REVERT: G 36 LYS cc_start: 0.8832 (mptt) cc_final: 0.8482 (mmtm) REVERT: G 71 ARG cc_start: 0.8608 (ttm110) cc_final: 0.8399 (ttm110) REVERT: H 65 ASP cc_start: 0.9092 (t0) cc_final: 0.8682 (t0) REVERT: K 1187 TYR cc_start: 0.5714 (OUTLIER) cc_final: 0.4724 (t80) REVERT: K 1377 TYR cc_start: 0.6649 (OUTLIER) cc_final: 0.5682 (p90) outliers start: 39 outliers final: 32 residues processed: 226 average time/residue: 0.1752 time to fit residues: 55.7325 Evaluate side-chains 229 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 193 time to evaluate : 0.502 ------------------------------------------------------------------------------- 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 80 THR 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 D residue 43 LYS Chi-restraints excluded: chain D residue 120 SER 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 1180 ASN Chi-restraints excluded: chain K residue 1183 THR Chi-restraints excluded: chain K residue 1187 TYR 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 1287 GLN 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 1419 ILE Chi-restraints excluded: chain K residue 1493 LEU Chi-restraints excluded: chain K residue 1514 HIS Chi-restraints excluded: chain K residue 1529 ASP Chi-restraints excluded: chain K residue 1544 HIS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 85 optimal weight: 6.9990 chunk 33 optimal weight: 0.7980 chunk 130 optimal weight: 0.9980 chunk 16 optimal weight: 4.9990 chunk 89 optimal weight: 8.9990 chunk 119 optimal weight: 0.9980 chunk 88 optimal weight: 8.9990 chunk 132 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 73 optimal weight: 30.0000 chunk 8 optimal weight: 2.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 68 ASN ** K1239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1454 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 = 0.4205 r_free = 0.4205 target = 0.136568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.118213 restraints weight = 59362.470| |-----------------------------------------------------------------------------| r_work (start): 0.3868 rms_B_bonded: 1.94 r_work: 0.3729 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7185 moved from start: 0.3611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 18460 Z= 0.164 Angle : 0.599 13.076 26562 Z= 0.342 Chirality : 0.036 0.206 2993 Planarity : 0.004 0.039 2088 Dihedral : 30.287 173.590 5411 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.75 % Allowed : 25.31 % Favored : 70.93 % 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 aren not related in a simple way. whole: 1.36 (0.25), residues: 1209 helix: 2.59 (0.20), residues: 681 sheet: -2.64 (0.59), residues: 62 loop : -1.24 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 83 TYR 0.023 0.001 TYR D 118 PHE 0.023 0.002 PHE K1422 TRP 0.041 0.002 TRP K1469 HIS 0.019 0.001 HIS K1544 Details of bonding type rmsd covalent geometry : bond 0.00366 (18455) covalent geometry : angle 0.59600 (26556) hydrogen bonds : bond 0.03726 ( 988) hydrogen bonds : angle 3.18674 ( 2448) metal coordination : bond 0.00524 ( 4) metal coordination : angle 4.09867 ( 6) Misc. bond : bond 0.00022 ( 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 236 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 197 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 129 ARG cc_start: 0.8480 (tpt90) cc_final: 0.8188 (tpt90) REVERT: B 84 MET cc_start: 0.8590 (tpp) cc_final: 0.8283 (mmm) REVERT: B 92 ARG cc_start: 0.8437 (OUTLIER) cc_final: 0.7580 (ttm-80) REVERT: B 95 ARG cc_start: 0.8777 (OUTLIER) cc_final: 0.8210 (mmm160) REVERT: E 125 GLN cc_start: 0.8497 (mt0) cc_final: 0.8239 (mp10) REVERT: F 92 ARG cc_start: 0.8866 (ttp80) cc_final: 0.8569 (ttp80) REVERT: G 36 LYS cc_start: 0.8840 (mptt) cc_final: 0.8487 (mmtm) REVERT: G 71 ARG cc_start: 0.8650 (ttm110) cc_final: 0.8446 (ttm110) REVERT: H 65 ASP cc_start: 0.9071 (t0) cc_final: 0.8654 (t0) REVERT: K 1186 ILE cc_start: 0.1500 (OUTLIER) cc_final: 0.1294 (mm) REVERT: K 1187 TYR cc_start: 0.5756 (OUTLIER) cc_final: 0.4660 (t80) REVERT: K 1377 TYR cc_start: 0.6629 (OUTLIER) cc_final: 0.5557 (p90) REVERT: K 1418 THR cc_start: 0.7071 (OUTLIER) cc_final: 0.6815 (m) outliers start: 39 outliers final: 31 residues processed: 228 average time/residue: 0.1715 time to fit residues: 54.9893 Evaluate side-chains 231 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 194 time to evaluate : 0.484 ------------------------------------------------------------------------------- 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 80 THR 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 102 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 87 SER 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 1186 ILE Chi-restraints excluded: chain K residue 1187 TYR Chi-restraints excluded: chain K residue 1210 ILE Chi-restraints excluded: chain K residue 1211 THR Chi-restraints excluded: chain K residue 1268 SER 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 1357 THR Chi-restraints excluded: chain K residue 1367 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 1493 LEU Chi-restraints excluded: chain K residue 1529 ASP Chi-restraints excluded: chain K residue 1544 HIS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 21 optimal weight: 0.9990 chunk 99 optimal weight: 7.9990 chunk 79 optimal weight: 7.9990 chunk 69 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 132 optimal weight: 2.9990 chunk 91 optimal weight: 30.0000 chunk 60 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 68 ASN K1180 ASN ** K1398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1514 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 = 0.4187 r_free = 0.4187 target = 0.135461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.116350 restraints weight = 58655.417| |-----------------------------------------------------------------------------| r_work (start): 0.3836 rms_B_bonded: 2.13 r_work: 0.3697 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.3599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 18460 Z= 0.185 Angle : 0.618 12.489 26562 Z= 0.351 Chirality : 0.037 0.189 2993 Planarity : 0.004 0.037 2088 Dihedral : 30.377 173.898 5411 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 3.95 % Allowed : 25.31 % 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 aren not related in a simple way. whole: 1.27 (0.25), residues: 1209 helix: 2.50 (0.20), residues: 682 sheet: -2.56 (0.59), residues: 62 loop : -1.28 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 83 TYR 0.025 0.002 TYR D 118 PHE 0.024 0.002 PHE K1422 TRP 0.044 0.003 TRP K1469 HIS 0.018 0.001 HIS K1544 Details of bonding type rmsd covalent geometry : bond 0.00416 (18455) covalent geometry : angle 0.61206 (26556) hydrogen bonds : bond 0.03958 ( 988) hydrogen bonds : angle 3.28409 ( 2448) metal coordination : bond 0.00569 ( 4) metal coordination : angle 5.48199 ( 6) Misc. bond : bond 0.00024 ( 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 230 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 189 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 129 ARG cc_start: 0.8495 (tpt90) cc_final: 0.8131 (tpt90) REVERT: B 92 ARG cc_start: 0.8463 (OUTLIER) cc_final: 0.7590 (ttm-80) REVERT: B 95 ARG cc_start: 0.8823 (OUTLIER) cc_final: 0.8215 (mmm160) REVERT: D 56 MET cc_start: 0.8966 (tpp) cc_final: 0.8760 (mmm) REVERT: E 125 GLN cc_start: 0.8568 (mt0) cc_final: 0.8307 (mp10) REVERT: G 36 LYS cc_start: 0.8848 (mptt) cc_final: 0.8495 (mmtm) REVERT: G 71 ARG cc_start: 0.8689 (ttm110) cc_final: 0.8487 (ttm110) REVERT: H 65 ASP cc_start: 0.9129 (t0) cc_final: 0.8718 (t0) REVERT: K 1186 ILE cc_start: 0.1449 (OUTLIER) cc_final: 0.1216 (mm) REVERT: K 1187 TYR cc_start: 0.5916 (OUTLIER) cc_final: 0.4711 (t80) REVERT: K 1377 TYR cc_start: 0.6606 (OUTLIER) cc_final: 0.5549 (p90) REVERT: K 1418 THR cc_start: 0.7173 (OUTLIER) cc_final: 0.6906 (m) outliers start: 41 outliers final: 32 residues processed: 222 average time/residue: 0.1759 time to fit residues: 55.0739 Evaluate side-chains 226 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 188 time to evaluate : 0.494 ------------------------------------------------------------------------------- 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 80 THR 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 43 LYS Chi-restraints excluded: chain D residue 120 SER 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 1180 ASN Chi-restraints excluded: chain K residue 1183 THR Chi-restraints excluded: chain K residue 1186 ILE Chi-restraints excluded: chain K residue 1187 TYR 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 1287 GLN Chi-restraints excluded: chain K residue 1322 HIS Chi-restraints excluded: chain K residue 1357 THR Chi-restraints excluded: chain K residue 1367 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 1493 LEU Chi-restraints excluded: chain K residue 1529 ASP Chi-restraints excluded: chain K residue 1544 HIS Chi-restraints excluded: chain K residue 1553 VAL 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: 0.0870 chunk 110 optimal weight: 0.5980 chunk 80 optimal weight: 6.9990 chunk 22 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 116 optimal weight: 0.9990 chunk 41 optimal weight: 8.9990 chunk 122 optimal weight: 2.9990 chunk 143 optimal weight: 4.9990 chunk 125 optimal weight: 1.9990 overall best weight: 0.9362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 68 ASN ** K1239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1454 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 = 0.4188 r_free = 0.4188 target = 0.135637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.116478 restraints weight = 59087.480| |-----------------------------------------------------------------------------| r_work (start): 0.3845 rms_B_bonded: 2.16 r_work: 0.3706 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.3602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.303 18460 Z= 0.220 Angle : 0.817 58.875 26562 Z= 0.467 Chirality : 0.039 0.847 2993 Planarity : 0.004 0.036 2088 Dihedral : 30.379 173.919 5411 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 3.95 % Allowed : 24.83 % Favored : 71.22 % Cbeta Deviations : 0.09 % 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 aren not related in a simple way. whole: 1.27 (0.25), residues: 1209 helix: 2.50 (0.20), residues: 682 sheet: -2.55 (0.59), residues: 62 loop : -1.28 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 83 TYR 0.022 0.002 TYR D 118 PHE 0.023 0.002 PHE K1422 TRP 0.037 0.003 TRP K1469 HIS 0.018 0.001 HIS K1544 Details of bonding type rmsd covalent geometry : bond 0.00506 (18455) covalent geometry : angle 0.81260 (26556) hydrogen bonds : bond 0.04055 ( 988) hydrogen bonds : angle 3.32880 ( 2448) metal coordination : bond 0.00611 ( 4) metal coordination : angle 5.46586 ( 6) Misc. bond : bond 0.00015 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4541.36 seconds wall clock time: 78 minutes 33.85 seconds (4713.85 seconds total)