Starting phenix.real_space_refine on Sun Aug 24 00:11:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8atf_15647/08_2025/8atf_15647.cif Found real_map, /net/cci-nas-00/data/ceres_data/8atf_15647/08_2025/8atf_15647.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8atf_15647/08_2025/8atf_15647.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8atf_15647/08_2025/8atf_15647.map" model { file = "/net/cci-nas-00/data/ceres_data/8atf_15647/08_2025/8atf_15647.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8atf_15647/08_2025/8atf_15647.cif" } resolution = 3.45 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 288 5.49 5 S 35 5.16 5 C 9014 2.51 5 N 2908 2.21 5 O 3474 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 124 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: 15719 Number of models: 1 Model: "" Number of chains: 13 Chain: "G" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3661 Classifications: {'peptide': 442} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 428} Chain breaks: 3 Chain: "H" Number of atoms: 264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 264 Classifications: {'peptide': 31} Link IDs: {'PTRANS': 1, 'TRANS': 29} Chain: "K" Number of atoms: 2915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2915 Classifications: {'DNA': 143} Link IDs: {'rna3p': 142} Chain: "L" Number of atoms: 2948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2948 Classifications: {'DNA': 143} Link IDs: {'rna3p': 142} Chain: "M" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 784 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "N" Number of atoms: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 622 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "O" 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: "P" 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: "Q" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "R" Number of atoms: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 622 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "S" 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: "T" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 708 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "G" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.59, per 1000 atoms: 0.23 Number of scatterers: 15719 At special positions: 0 Unit cell: (120.726, 140.847, 145.083, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 35 16.00 P 288 15.00 O 3474 8.00 N 2908 7.00 C 9014 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.13 Conformation dependent library (CDL) restraints added in 529.0 milliseconds Enol-peptide restraints added in 1.2 microseconds 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2300 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 12 sheets defined 66.7% alpha, 6.0% beta 141 base pairs and 267 stacking pairs defined. Time for finding SS restraints: 2.65 Creating SS restraints... Processing helix chain 'G' and resid 973 through 990 Processing helix chain 'G' and resid 1002 through 1018 removed outlier: 3.522A pdb=" N GLN G1006 " --> pdb=" O GLY G1002 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N MET G1011 " --> pdb=" O SER G1007 " (cutoff:3.500A) Processing helix chain 'G' and resid 1029 through 1031 No H-bonds generated for 'chain 'G' and resid 1029 through 1031' Processing helix chain 'G' and resid 1032 through 1044 Processing helix chain 'G' and resid 1055 through 1064 removed outlier: 4.015A pdb=" N VAL G1061 " --> pdb=" O ALA G1057 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS G1064 " --> pdb=" O LYS G1060 " (cutoff:3.500A) Processing helix chain 'G' and resid 1086 through 1092 Processing helix chain 'G' and resid 1092 through 1097 Processing helix chain 'G' and resid 1108 through 1113 Processing helix chain 'G' and resid 1117 through 1124 Processing helix chain 'G' and resid 1142 through 1154 removed outlier: 3.758A pdb=" N LEU G1146 " --> pdb=" O ASN G1142 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU G1149 " --> pdb=" O GLU G1145 " (cutoff:3.500A) Processing helix chain 'G' and resid 1160 through 1166 Processing helix chain 'G' and resid 1184 through 1194 removed outlier: 3.594A pdb=" N MET G1192 " --> pdb=" O LYS G1188 " (cutoff:3.500A) Processing helix chain 'G' and resid 1202 through 1206 Processing helix chain 'G' and resid 1223 through 1236 Processing helix chain 'G' and resid 1260 through 1270 Processing helix chain 'G' and resid 1271 through 1274 Processing helix chain 'G' and resid 1544 through 1551 Processing helix chain 'G' and resid 1552 through 1569 removed outlier: 3.630A pdb=" N GLU G1560 " --> pdb=" O ALA G1556 " (cutoff:3.500A) Processing helix chain 'G' and resid 1578 through 1592 removed outlier: 3.665A pdb=" N ILE G1582 " --> pdb=" O MET G1578 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU G1587 " --> pdb=" O ASP G1583 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR G1588 " --> pdb=" O LEU G1584 " (cutoff:3.500A) Processing helix chain 'G' and resid 1604 through 1618 removed outlier: 4.020A pdb=" N ARG G1609 " --> pdb=" O LEU G1605 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASP G1610 " --> pdb=" O GLU G1606 " (cutoff:3.500A) Processing helix chain 'G' and resid 1628 through 1632 Processing helix chain 'G' and resid 1651 through 1660 removed outlier: 3.836A pdb=" N ASP G1655 " --> pdb=" O ASN G1651 " (cutoff:3.500A) Processing helix chain 'G' and resid 1681 through 1702 removed outlier: 3.746A pdb=" N ARG G1685 " --> pdb=" O THR G1681 " (cutoff:3.500A) Processing helix chain 'H' and resid 390 through 416 removed outlier: 3.638A pdb=" N GLU H 397 " --> pdb=" O ARG H 393 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS H 398 " --> pdb=" O ASN H 394 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE H 403 " --> pdb=" O ARG H 399 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU H 412 " --> pdb=" O VAL H 408 " (cutoff:3.500A) Processing helix chain 'M' and resid 44 through 55 Processing helix chain 'M' and resid 63 through 76 Processing helix chain 'M' and resid 85 through 114 Processing helix chain 'M' and resid 120 through 132 removed outlier: 3.717A pdb=" N ILE M 124 " --> pdb=" O MET M 120 " (cutoff:3.500A) Processing helix chain 'N' and resid 25 through 29 Processing helix chain 'N' and resid 30 through 41 Processing helix chain 'N' and resid 49 through 76 removed outlier: 3.617A pdb=" N GLU N 53 " --> pdb=" O LEU N 49 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASP N 68 " --> pdb=" O ASN N 64 " (cutoff:3.500A) Processing helix chain 'N' and resid 82 through 92 Processing helix chain 'O' and resid 16 through 21 Processing helix chain 'O' and resid 26 through 37 Processing helix chain 'O' and resid 45 through 72 removed outlier: 4.051A pdb=" N VAL O 49 " --> pdb=" O ALA O 45 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU O 65 " --> pdb=" O GLU O 61 " (cutoff:3.500A) Processing helix chain 'O' and resid 79 through 90 removed outlier: 3.506A pdb=" N LEU O 83 " --> pdb=" O ILE O 79 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP O 90 " --> pdb=" O ALA O 86 " (cutoff:3.500A) Processing helix chain 'O' and resid 90 through 97 Processing helix chain 'O' and resid 112 through 116 Processing helix chain 'P' and resid 37 through 49 removed outlier: 3.518A pdb=" N LYS P 43 " --> pdb=" O VAL P 39 " (cutoff:3.500A) Processing helix chain 'P' and resid 55 through 84 Processing helix chain 'P' and resid 90 through 102 removed outlier: 3.574A pdb=" N ILE P 94 " --> pdb=" O THR P 90 " (cutoff:3.500A) Processing helix chain 'P' and resid 103 through 124 removed outlier: 3.577A pdb=" N ALA P 107 " --> pdb=" O PRO P 103 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS P 108 " --> pdb=" O GLY P 104 " (cutoff:3.500A) Processing helix chain 'Q' and resid 44 through 55 Processing helix chain 'Q' and resid 63 through 76 Processing helix chain 'Q' and resid 85 through 114 removed outlier: 3.934A pdb=" N VAL Q 89 " --> pdb=" O GLN Q 85 " (cutoff:3.500A) Processing helix chain 'Q' and resid 120 through 131 removed outlier: 3.696A pdb=" N ILE Q 124 " --> pdb=" O MET Q 120 " (cutoff:3.500A) Processing helix chain 'R' and resid 25 through 29 Processing helix chain 'R' and resid 30 through 41 Processing helix chain 'R' and resid 49 through 76 removed outlier: 3.549A pdb=" N GLU R 53 " --> pdb=" O LEU R 49 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASN R 64 " --> pdb=" O VAL R 60 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASP R 68 " --> pdb=" O ASN R 64 " (cutoff:3.500A) Processing helix chain 'R' and resid 82 through 91 Processing helix chain 'S' and resid 16 through 21 Processing helix chain 'S' and resid 26 through 37 Processing helix chain 'S' and resid 45 through 73 removed outlier: 4.189A pdb=" N VAL S 49 " --> pdb=" O ALA S 45 " (cutoff:3.500A) Processing helix chain 'S' and resid 79 through 90 removed outlier: 3.531A pdb=" N ASP S 90 " --> pdb=" O ALA S 86 " (cutoff:3.500A) Processing helix chain 'S' and resid 90 through 97 Processing helix chain 'T' and resid 37 through 49 Processing helix chain 'T' and resid 55 through 84 Processing helix chain 'T' and resid 91 through 102 Processing helix chain 'T' and resid 104 through 124 removed outlier: 3.823A pdb=" N LYS T 108 " --> pdb=" O GLY T 104 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 1049 through 1052 removed outlier: 4.451A pdb=" N SER G1085 " --> pdb=" O TYR G1052 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N PHE G1024 " --> pdb=" O MET G1082 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N THR G1084 " --> pdb=" O PHE G1024 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N VAL G1026 " --> pdb=" O THR G1084 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N GLN G1102 " --> pdb=" O ASN G1130 " (cutoff:3.500A) removed outlier: 8.768A pdb=" N LEU G1132 " --> pdb=" O GLN G1102 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N MET G1104 " --> pdb=" O LEU G1132 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N LEU G1134 " --> pdb=" O MET G1104 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LEU G1106 " --> pdb=" O LEU G1134 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY G 993 " --> pdb=" O ARG G1131 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ILE G 994 " --> pdb=" O LEU G1199 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 1214 through 1220 removed outlier: 6.379A pdb=" N ILE G1214 " --> pdb=" O VAL G1673 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N ARG G1675 " --> pdb=" O ILE G1214 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE G1216 " --> pdb=" O ARG G1675 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N ILE G1677 " --> pdb=" O ILE G1216 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N VAL G1218 " --> pdb=" O ILE G1677 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N VAL G1643 " --> pdb=" O TYR G1674 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N LEU G1676 " --> pdb=" O VAL G1643 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N PHE G1645 " --> pdb=" O LEU G1676 " (cutoff:3.500A) removed outlier: 8.738A pdb=" N THR G1678 " --> pdb=" O PHE G1645 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LEU G1573 " --> pdb=" O ILE G1644 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N CYS G1597 " --> pdb=" O LEU G1625 " (cutoff:3.500A) removed outlier: 8.375A pdb=" N SER G1627 " --> pdb=" O CYS G1597 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N LEU G1599 " --> pdb=" O SER G1627 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'M' and resid 83 through 84 removed outlier: 6.760A pdb=" N ARG M 83 " --> pdb=" O VAL N 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'M' and resid 118 through 119 Processing sheet with id=AA5, first strand: chain 'N' and resid 97 through 98 Processing sheet with id=AA6, first strand: chain 'O' and resid 42 through 43 removed outlier: 7.200A pdb=" N ARG O 42 " --> pdb=" O ILE P 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'O' and resid 77 through 78 Processing sheet with id=AA8, first strand: chain 'O' and resid 100 through 102 removed outlier: 6.768A pdb=" N THR O 101 " --> pdb=" O TYR R 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'Q' and resid 83 through 84 removed outlier: 6.876A pdb=" N ARG Q 83 " --> pdb=" O VAL R 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'Q' and resid 118 through 119 Processing sheet with id=AB2, first strand: chain 'S' and resid 42 through 43 removed outlier: 7.178A pdb=" N ARG S 42 " --> pdb=" O ILE T 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'S' and resid 77 through 78 563 hydrogen bonds defined for protein. 1653 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 363 hydrogen bonds 726 hydrogen bond angles 0 basepair planarities 141 basepair parallelities 267 stacking parallelities Total time for adding SS restraints: 4.01 Time building geometry restraints manager: 1.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 2342 1.32 - 1.46: 6757 1.46 - 1.60: 6870 1.60 - 1.74: 557 1.74 - 1.88: 62 Bond restraints: 16588 Sorted by residual: bond pdb=" C4 ADP G2000 " pdb=" C5 ADP G2000 " ideal model delta sigma weight residual 1.490 1.385 0.105 2.00e-02 2.50e+03 2.73e+01 bond pdb=" C GLN T 95 " pdb=" O GLN T 95 " ideal model delta sigma weight residual 1.237 1.182 0.055 1.17e-02 7.31e+03 2.22e+01 bond pdb=" C5 ADP G2000 " pdb=" C6 ADP G2000 " ideal model delta sigma weight residual 1.490 1.399 0.091 2.00e-02 2.50e+03 2.06e+01 bond pdb=" CA SER M 96 " pdb=" CB SER M 96 " ideal model delta sigma weight residual 1.528 1.458 0.071 1.59e-02 3.96e+03 1.98e+01 bond pdb=" CG ASP G1092 " pdb=" OD2 ASP G1092 " ideal model delta sigma weight residual 1.249 1.322 -0.073 1.90e-02 2.77e+03 1.46e+01 ... (remaining 16583 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.92: 22183 3.92 - 7.83: 1339 7.83 - 11.75: 85 11.75 - 15.66: 6 15.66 - 19.58: 1 Bond angle restraints: 23614 Sorted by residual: angle pdb=" O3' DC L -25 " pdb=" P DT L -24 " pdb=" O5' DT L -24 " ideal model delta sigma weight residual 104.00 92.97 11.03 1.50e+00 4.44e-01 5.41e+01 angle pdb=" NE ARG M 52 " pdb=" CZ ARG M 52 " pdb=" NH1 ARG M 52 " ideal model delta sigma weight residual 121.50 114.19 7.31 1.00e+00 1.00e+00 5.34e+01 angle pdb=" NE ARG M 52 " pdb=" CZ ARG M 52 " pdb=" NH2 ARG M 52 " ideal model delta sigma weight residual 119.20 125.74 -6.54 9.00e-01 1.23e+00 5.29e+01 angle pdb=" O3' DA K -5 " pdb=" P DC K -4 " pdb=" O5' DC K -4 " ideal model delta sigma weight residual 104.00 94.08 9.92 1.50e+00 4.44e-01 4.38e+01 angle pdb=" O3' DT L 15 " pdb=" C3' DT L 15 " pdb=" C2' DT L 15 " ideal model delta sigma weight residual 111.50 101.63 9.87 1.50e+00 4.44e-01 4.33e+01 ... (remaining 23609 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.73: 8034 35.73 - 71.46: 1208 71.46 - 107.18: 22 107.18 - 142.91: 1 142.91 - 178.64: 1 Dihedral angle restraints: 9266 sinusoidal: 5712 harmonic: 3554 Sorted by residual: dihedral pdb=" CA ARG G1664 " pdb=" C ARG G1664 " pdb=" N LEU G1665 " pdb=" CA LEU G1665 " ideal model delta harmonic sigma weight residual 180.00 147.93 32.07 0 5.00e+00 4.00e-02 4.12e+01 dihedral pdb=" CA GLU G 998 " pdb=" C GLU G 998 " pdb=" N MET G 999 " pdb=" CA MET G 999 " ideal model delta harmonic sigma weight residual -180.00 -151.32 -28.68 0 5.00e+00 4.00e-02 3.29e+01 dihedral pdb=" CA PRO P 103 " pdb=" C PRO P 103 " pdb=" N GLY P 104 " pdb=" CA GLY P 104 " ideal model delta harmonic sigma weight residual 180.00 151.93 28.07 0 5.00e+00 4.00e-02 3.15e+01 ... (remaining 9263 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.130: 2178 0.130 - 0.259: 385 0.259 - 0.389: 90 0.389 - 0.518: 7 0.518 - 0.648: 5 Chirality restraints: 2665 Sorted by residual: chirality pdb=" P DG L -70 " pdb=" OP1 DG L -70 " pdb=" OP2 DG L -70 " pdb=" O5' DG L -70 " both_signs ideal model delta sigma weight residual True 2.35 -2.99 -0.65 2.00e-01 2.50e+01 1.05e+01 chirality pdb=" P DT K -72 " pdb=" OP1 DT K -72 " pdb=" OP2 DT K -72 " pdb=" O5' DT K -72 " both_signs ideal model delta sigma weight residual True 2.35 -2.98 -0.63 2.00e-01 2.50e+01 1.00e+01 chirality pdb=" P DA L -12 " pdb=" OP1 DA L -12 " pdb=" OP2 DA L -12 " pdb=" O5' DA L -12 " both_signs ideal model delta sigma weight residual True 2.35 -2.98 -0.63 2.00e-01 2.50e+01 1.00e+01 ... (remaining 2662 not shown) Planarity restraints: 1991 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR S 50 " 0.127 2.00e-02 2.50e+03 7.14e-02 1.02e+02 pdb=" CG TYR S 50 " -0.062 2.00e-02 2.50e+03 pdb=" CD1 TYR S 50 " -0.031 2.00e-02 2.50e+03 pdb=" CD2 TYR S 50 " -0.114 2.00e-02 2.50e+03 pdb=" CE1 TYR S 50 " -0.042 2.00e-02 2.50e+03 pdb=" CE2 TYR S 50 " 0.036 2.00e-02 2.50e+03 pdb=" CZ TYR S 50 " 0.038 2.00e-02 2.50e+03 pdb=" OH TYR S 50 " 0.047 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC K 37 " 0.136 2.00e-02 2.50e+03 6.21e-02 8.69e+01 pdb=" N1 DC K 37 " -0.065 2.00e-02 2.50e+03 pdb=" C2 DC K 37 " -0.039 2.00e-02 2.50e+03 pdb=" O2 DC K 37 " -0.040 2.00e-02 2.50e+03 pdb=" N3 DC K 37 " 0.016 2.00e-02 2.50e+03 pdb=" C4 DC K 37 " 0.024 2.00e-02 2.50e+03 pdb=" N4 DC K 37 " 0.059 2.00e-02 2.50e+03 pdb=" C5 DC K 37 " -0.035 2.00e-02 2.50e+03 pdb=" C6 DC K 37 " -0.057 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP G1053 " -0.059 2.00e-02 2.50e+03 5.66e-02 8.01e+01 pdb=" CG TRP G1053 " 0.140 2.00e-02 2.50e+03 pdb=" CD1 TRP G1053 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP G1053 " 0.040 2.00e-02 2.50e+03 pdb=" NE1 TRP G1053 " -0.051 2.00e-02 2.50e+03 pdb=" CE2 TRP G1053 " -0.036 2.00e-02 2.50e+03 pdb=" CE3 TRP G1053 " -0.037 2.00e-02 2.50e+03 pdb=" CZ2 TRP G1053 " 0.031 2.00e-02 2.50e+03 pdb=" CZ3 TRP G1053 " -0.023 2.00e-02 2.50e+03 pdb=" CH2 TRP G1053 " 0.015 2.00e-02 2.50e+03 ... (remaining 1988 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 334 2.65 - 3.21: 12956 3.21 - 3.78: 26423 3.78 - 4.34: 37829 4.34 - 4.90: 53371 Nonbonded interactions: 130913 Sorted by model distance: nonbonded pdb=" O HIS R 75 " pdb=" NH2 ARG T 92 " model vdw 2.090 3.120 nonbonded pdb=" OP2 DA K 17 " pdb=" NH2 ARG Q 69 " model vdw 2.201 3.120 nonbonded pdb=" O SER Q 57 " pdb=" NH1 ARG R 40 " model vdw 2.300 3.120 nonbonded pdb=" NH2 ARG S 32 " pdb=" OE1 GLU T 35 " model vdw 2.324 3.120 nonbonded pdb=" O PHE N 100 " pdb=" C GLY N 101 " model vdw 2.344 3.270 ... (remaining 130908 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 'M' selection = (chain 'Q' and resid 40 through 134) } ncs_group { reference = chain 'N' selection = chain 'R' } ncs_group { reference = chain 'O' selection = chain 'S' } ncs_group { reference = (chain 'P' and resid 34 through 124) selection = chain 'T' } 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: 1.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 18.020 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: 0.010 Load rotamer database and sin/cos tables:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 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 : 0.013 0.105 16588 Z= 0.729 Angle : 1.988 19.581 23614 Z= 1.223 Chirality : 0.111 0.648 2665 Planarity : 0.026 0.255 1991 Dihedral : 25.037 178.640 6966 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.67 % Allowed : 3.10 % Favored : 96.23 % Rotamer: Outliers : 1.81 % Allowed : 6.29 % Favored : 91.90 % Cbeta Deviations : 0.35 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.09 (0.20), residues: 1193 helix: -1.38 (0.15), residues: 777 sheet: 0.55 (0.64), residues: 68 loop : -1.34 (0.28), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.069 0.006 ARG G1608 TYR 0.127 0.017 TYR S 50 PHE 0.077 0.017 PHE G1152 TRP 0.140 0.024 TRP G1053 HIS 0.030 0.006 HIS S 31 Details of bonding type rmsd covalent geometry : bond 0.01307 (16588) covalent geometry : angle 1.98759 (23614) hydrogen bonds : bond 0.19597 ( 926) hydrogen bonds : angle 6.35867 ( 2379) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 324 time to evaluate : 0.495 Fit side-chains REVERT: G 978 LYS cc_start: 0.8055 (mmmt) cc_final: 0.7478 (tptt) REVERT: G 1035 ASN cc_start: 0.7945 (t0) cc_final: 0.7641 (t0) REVERT: G 1135 THR cc_start: 0.8591 (t) cc_final: 0.8266 (t) REVERT: G 1205 HIS cc_start: 0.7080 (m170) cc_final: 0.6855 (m170) REVERT: G 1552 SER cc_start: 0.9273 (t) cc_final: 0.8985 (p) REVERT: G 1563 ARG cc_start: 0.7545 (ttt180) cc_final: 0.7277 (ttm-80) REVERT: G 1606 GLU cc_start: 0.8799 (mt-10) cc_final: 0.8351 (tp30) REVERT: G 1647 ASP cc_start: 0.9364 (p0) cc_final: 0.9108 (t70) REVERT: G 1651 ASN cc_start: 0.8925 (t0) cc_final: 0.8563 (t0) REVERT: G 1659 MET cc_start: 0.8556 (ptp) cc_final: 0.8333 (ptt) REVERT: G 1660 ASP cc_start: 0.8356 (m-30) cc_final: 0.7882 (m-30) REVERT: M 52 ARG cc_start: 0.7710 (mtt-85) cc_final: 0.7128 (ttm-80) REVERT: M 53 ARG cc_start: 0.7572 (ttt180) cc_final: 0.7255 (ttm170) REVERT: M 56 LYS cc_start: 0.7122 (ttmt) cc_final: 0.6881 (mttt) REVERT: M 63 ARG cc_start: 0.7164 (mmm-85) cc_final: 0.6913 (mmt-90) REVERT: M 129 ARG cc_start: 0.8395 (ttt180) cc_final: 0.8006 (tpt-90) REVERT: O 72 ASP cc_start: 0.8317 (m-30) cc_final: 0.8110 (m-30) REVERT: P 35 GLU cc_start: 0.8343 (pt0) cc_final: 0.7763 (mt-10) REVERT: P 51 ASP cc_start: 0.8291 (m-30) cc_final: 0.7931 (p0) REVERT: Q 90 MET cc_start: 0.8372 (mmp) cc_final: 0.8036 (tpt) REVERT: R 95 ARG cc_start: 0.8166 (OUTLIER) cc_final: 0.7804 (ttm110) REVERT: S 104 GLN cc_start: 0.8158 (mm-40) cc_final: 0.7936 (mt0) REVERT: S 111 ILE cc_start: 0.8882 (OUTLIER) cc_final: 0.8546 (mt) outliers start: 19 outliers final: 5 residues processed: 338 average time/residue: 0.1791 time to fit residues: 80.5698 Evaluate side-chains 213 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 206 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 1089 VAL Chi-restraints excluded: chain G residue 1153 ILE Chi-restraints excluded: chain M residue 61 LEU Chi-restraints excluded: chain N residue 100 PHE Chi-restraints excluded: chain R residue 95 ARG Chi-restraints excluded: chain S residue 43 VAL Chi-restraints excluded: chain S residue 111 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.0980 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G1130 ASN ** G1657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 25 ASN N 75 HIS ** P 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 84 ASN P 95 GLN Q 39 HIS R 25 ASN R 75 HIS T 82 HIS T 95 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.147798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.111508 restraints weight = 23876.273| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 1.36 r_work: 0.3199 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16588 Z= 0.173 Angle : 0.663 6.149 23614 Z= 0.387 Chirality : 0.039 0.140 2665 Planarity : 0.004 0.036 1991 Dihedral : 28.565 173.823 4499 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 2.48 % Allowed : 11.14 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.98 (0.23), residues: 1193 helix: 1.19 (0.18), residues: 789 sheet: 1.13 (0.65), residues: 68 loop : -0.62 (0.31), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG R 45 TYR 0.025 0.001 TYR G1018 PHE 0.016 0.001 PHE M 67 TRP 0.030 0.003 TRP G1053 HIS 0.004 0.001 HIS T 82 Details of bonding type rmsd covalent geometry : bond 0.00377 (16588) covalent geometry : angle 0.66292 (23614) hydrogen bonds : bond 0.04723 ( 926) hydrogen bonds : angle 3.15620 ( 2379) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 219 time to evaluate : 0.483 Fit side-chains revert: symmetry clash REVERT: G 981 ASN cc_start: 0.7975 (OUTLIER) cc_final: 0.7589 (t0) REVERT: G 1058 ASP cc_start: 0.7983 (m-30) cc_final: 0.7671 (m-30) REVERT: G 1143 MET cc_start: 0.7359 (mpp) cc_final: 0.6486 (tpp) REVERT: G 1229 MET cc_start: 0.8819 (mtp) cc_final: 0.8603 (mtt) REVERT: G 1274 PHE cc_start: 0.7274 (m-80) cc_final: 0.6928 (m-80) REVERT: G 1694 GLU cc_start: 0.8163 (tt0) cc_final: 0.7811 (tp30) REVERT: M 52 ARG cc_start: 0.7857 (mtt-85) cc_final: 0.6545 (ttt90) REVERT: M 53 ARG cc_start: 0.8697 (ttt180) cc_final: 0.8430 (ttp-110) REVERT: M 61 LEU cc_start: 0.9133 (OUTLIER) cc_final: 0.8911 (mt) REVERT: N 49 LEU cc_start: 0.8733 (mm) cc_final: 0.8418 (mt) REVERT: P 51 ASP cc_start: 0.7816 (m-30) cc_final: 0.7548 (p0) REVERT: P 84 ASN cc_start: 0.8677 (m-40) cc_final: 0.8370 (m110) REVERT: R 80 THR cc_start: 0.9358 (m) cc_final: 0.9141 (p) REVERT: S 13 LYS cc_start: 0.7401 (tttt) cc_final: 0.7030 (tptp) REVERT: T 71 GLU cc_start: 0.7666 (mt-10) cc_final: 0.7389 (mp0) outliers start: 26 outliers final: 13 residues processed: 240 average time/residue: 0.1576 time to fit residues: 51.1556 Evaluate side-chains 187 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 172 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 981 ASN Chi-restraints excluded: chain G residue 1014 LEU Chi-restraints excluded: chain G residue 1089 VAL Chi-restraints excluded: chain G residue 1123 LEU Chi-restraints excluded: chain G residue 1166 GLU Chi-restraints excluded: chain G residue 1260 LEU Chi-restraints excluded: chain G residue 1669 LYS Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain M residue 61 LEU Chi-restraints excluded: chain Q residue 118 THR Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain S residue 43 VAL Chi-restraints excluded: chain S residue 110 ASN Chi-restraints excluded: chain T residue 122 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 133 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 17 optimal weight: 0.9980 chunk 57 optimal weight: 4.9990 chunk 115 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 95 optimal weight: 1.9990 chunk 119 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G1263 GLN G1577 GLN ** N 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 75 HIS O 38 ASN P 63 ASN P 84 ASN Q 39 HIS Q 68 GLN S 31 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.144217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.107210 restraints weight = 24145.517| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 1.37 r_work: 0.3133 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.3622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 16588 Z= 0.224 Angle : 0.647 6.361 23614 Z= 0.374 Chirality : 0.040 0.157 2665 Planarity : 0.005 0.040 1991 Dihedral : 28.536 169.763 4489 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 3.71 % Allowed : 12.95 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 1.50 (0.24), residues: 1193 helix: 1.64 (0.18), residues: 785 sheet: 0.95 (0.63), residues: 68 loop : -0.44 (0.32), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G1592 TYR 0.018 0.002 TYR O 50 PHE 0.014 0.002 PHE G1164 TRP 0.022 0.002 TRP G1053 HIS 0.005 0.001 HIS N 75 Details of bonding type rmsd covalent geometry : bond 0.00517 (16588) covalent geometry : angle 0.64682 (23614) hydrogen bonds : bond 0.05067 ( 926) hydrogen bonds : angle 3.07138 ( 2379) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 184 time to evaluate : 0.470 Fit side-chains revert: symmetry clash REVERT: G 981 ASN cc_start: 0.8132 (OUTLIER) cc_final: 0.7768 (t0) REVERT: G 1190 LEU cc_start: 0.8185 (tp) cc_final: 0.7903 (mp) REVERT: G 1274 PHE cc_start: 0.7660 (m-80) cc_final: 0.7171 (m-80) REVERT: M 52 ARG cc_start: 0.7912 (mtt-85) cc_final: 0.6471 (ttt90) REVERT: M 133 GLU cc_start: 0.8317 (mt-10) cc_final: 0.8114 (mt-10) REVERT: N 49 LEU cc_start: 0.8661 (mm) cc_final: 0.8421 (mt) REVERT: P 51 ASP cc_start: 0.7785 (m-30) cc_final: 0.7484 (p0) REVERT: R 80 THR cc_start: 0.9412 (m) cc_final: 0.8999 (p) REVERT: S 13 LYS cc_start: 0.7527 (tttt) cc_final: 0.7202 (tptp) REVERT: S 71 ARG cc_start: 0.8023 (mtt180) cc_final: 0.7817 (mtt180) REVERT: T 71 GLU cc_start: 0.7820 (mt-10) cc_final: 0.7574 (mt-10) REVERT: T 113 GLU cc_start: 0.8304 (mp0) cc_final: 0.7744 (mp0) outliers start: 39 outliers final: 32 residues processed: 210 average time/residue: 0.1330 time to fit residues: 39.4950 Evaluate side-chains 198 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 165 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 981 ASN Chi-restraints excluded: chain G residue 1005 VAL Chi-restraints excluded: chain G residue 1014 LEU Chi-restraints excluded: chain G residue 1041 SER Chi-restraints excluded: chain G residue 1089 VAL Chi-restraints excluded: chain G residue 1123 LEU Chi-restraints excluded: chain G residue 1153 ILE Chi-restraints excluded: chain G residue 1162 ASP Chi-restraints excluded: chain G residue 1166 GLU Chi-restraints excluded: chain G residue 1206 VAL Chi-restraints excluded: chain G residue 1218 VAL Chi-restraints excluded: chain G residue 1260 LEU Chi-restraints excluded: chain G residue 1578 MET Chi-restraints excluded: chain G residue 1621 ILE Chi-restraints excluded: chain G residue 1623 ILE Chi-restraints excluded: chain G residue 1659 MET Chi-restraints excluded: chain G residue 1669 LYS Chi-restraints excluded: chain H residue 408 VAL Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain M residue 61 LEU Chi-restraints excluded: chain M residue 120 MET Chi-restraints excluded: chain N residue 73 THR Chi-restraints excluded: chain O residue 107 VAL Chi-restraints excluded: chain Q residue 118 THR Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain R residue 66 ILE Chi-restraints excluded: chain S residue 43 VAL Chi-restraints excluded: chain S residue 76 THR Chi-restraints excluded: chain S residue 100 VAL Chi-restraints excluded: chain S residue 110 ASN Chi-restraints excluded: chain T residue 34 LYS Chi-restraints excluded: chain T residue 122 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 131 optimal weight: 4.9990 chunk 106 optimal weight: 3.9990 chunk 138 optimal weight: 2.9990 chunk 74 optimal weight: 7.9990 chunk 45 optimal weight: 7.9990 chunk 26 optimal weight: 0.8980 chunk 91 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 128 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 47 optimal weight: 7.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G1130 ASN ** N 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 63 ASN ** P 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 63 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.144597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.107824 restraints weight = 24003.451| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 1.35 r_work: 0.3147 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.4008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 16588 Z= 0.199 Angle : 0.602 5.971 23614 Z= 0.347 Chirality : 0.037 0.137 2665 Planarity : 0.004 0.039 1991 Dihedral : 28.451 167.757 4489 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 4.57 % Allowed : 13.24 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 1.82 (0.24), residues: 1193 helix: 1.98 (0.18), residues: 783 sheet: 0.75 (0.66), residues: 68 loop : -0.51 (0.32), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG O 71 TYR 0.016 0.002 TYR O 50 PHE 0.013 0.002 PHE G1164 TRP 0.019 0.002 TRP G1147 HIS 0.003 0.001 HIS P 109 Details of bonding type rmsd covalent geometry : bond 0.00456 (16588) covalent geometry : angle 0.60174 (23614) hydrogen bonds : bond 0.04503 ( 926) hydrogen bonds : angle 2.92031 ( 2379) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 179 time to evaluate : 0.439 Fit side-chains revert: symmetry clash REVERT: G 981 ASN cc_start: 0.8138 (OUTLIER) cc_final: 0.7880 (t0) REVERT: G 1190 LEU cc_start: 0.8219 (tp) cc_final: 0.7878 (mp) REVERT: M 52 ARG cc_start: 0.7799 (mtt-85) cc_final: 0.6501 (ttt90) REVERT: P 51 ASP cc_start: 0.7786 (m-30) cc_final: 0.7428 (p0) REVERT: R 80 THR cc_start: 0.9394 (m) cc_final: 0.9026 (p) REVERT: S 13 LYS cc_start: 0.7602 (tttt) cc_final: 0.7275 (tptp) REVERT: S 19 SER cc_start: 0.9368 (p) cc_final: 0.9066 (p) REVERT: T 71 GLU cc_start: 0.7786 (mt-10) cc_final: 0.7562 (mt-10) REVERT: T 86 ARG cc_start: 0.8607 (mmm-85) cc_final: 0.8188 (mmt-90) REVERT: T 113 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.7950 (mp0) outliers start: 48 outliers final: 33 residues processed: 213 average time/residue: 0.1258 time to fit residues: 37.9438 Evaluate side-chains 207 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 172 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 981 ASN Chi-restraints excluded: chain G residue 1005 VAL Chi-restraints excluded: chain G residue 1014 LEU Chi-restraints excluded: chain G residue 1041 SER Chi-restraints excluded: chain G residue 1123 LEU Chi-restraints excluded: chain G residue 1153 ILE Chi-restraints excluded: chain G residue 1162 ASP Chi-restraints excluded: chain G residue 1166 GLU Chi-restraints excluded: chain G residue 1206 VAL Chi-restraints excluded: chain G residue 1260 LEU Chi-restraints excluded: chain G residue 1578 MET Chi-restraints excluded: chain G residue 1621 ILE Chi-restraints excluded: chain G residue 1623 ILE Chi-restraints excluded: chain G residue 1633 LEU Chi-restraints excluded: chain G residue 1659 MET Chi-restraints excluded: chain G residue 1669 LYS Chi-restraints excluded: chain G residue 1691 LEU Chi-restraints excluded: chain G residue 1699 VAL Chi-restraints excluded: chain H residue 408 VAL Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain M residue 58 THR Chi-restraints excluded: chain M residue 61 LEU Chi-restraints excluded: chain M residue 120 MET Chi-restraints excluded: chain N residue 73 THR Chi-restraints excluded: chain O residue 107 VAL Chi-restraints excluded: chain P residue 61 ILE Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain R residue 66 ILE Chi-restraints excluded: chain S residue 43 VAL Chi-restraints excluded: chain S residue 76 THR Chi-restraints excluded: chain S residue 99 LYS Chi-restraints excluded: chain S residue 100 VAL Chi-restraints excluded: chain T residue 113 GLU Chi-restraints excluded: chain T residue 122 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 115 optimal weight: 0.6980 chunk 99 optimal weight: 0.6980 chunk 12 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 40 optimal weight: 9.9990 chunk 2 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 120 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 63 ASN P 84 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.147551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.110836 restraints weight = 23982.052| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 1.36 r_work: 0.3191 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.4341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16588 Z= 0.150 Angle : 0.544 5.799 23614 Z= 0.318 Chirality : 0.034 0.143 2665 Planarity : 0.004 0.035 1991 Dihedral : 28.132 166.766 4488 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 3.05 % Allowed : 14.48 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 2.30 (0.24), residues: 1193 helix: 2.37 (0.18), residues: 781 sheet: 0.85 (0.67), residues: 67 loop : -0.31 (0.33), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G1580 TYR 0.011 0.001 TYR O 50 PHE 0.009 0.001 PHE G1164 TRP 0.017 0.002 TRP G1147 HIS 0.002 0.000 HIS P 109 Details of bonding type rmsd covalent geometry : bond 0.00331 (16588) covalent geometry : angle 0.54443 (23614) hydrogen bonds : bond 0.03666 ( 926) hydrogen bonds : angle 2.68455 ( 2379) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 180 time to evaluate : 0.466 Fit side-chains REVERT: G 981 ASN cc_start: 0.8091 (OUTLIER) cc_final: 0.7847 (t0) REVERT: G 1190 LEU cc_start: 0.8110 (tp) cc_final: 0.7760 (mp) REVERT: G 1581 MET cc_start: 0.9000 (tpp) cc_final: 0.8799 (tpp) REVERT: G 1659 MET cc_start: 0.8803 (OUTLIER) cc_final: 0.8521 (ptt) REVERT: M 52 ARG cc_start: 0.7818 (mtt-85) cc_final: 0.6614 (ttt90) REVERT: P 42 TYR cc_start: 0.8219 (t80) cc_final: 0.7973 (t80) REVERT: P 51 ASP cc_start: 0.7835 (m-30) cc_final: 0.7615 (p0) REVERT: P 63 ASN cc_start: 0.8369 (OUTLIER) cc_final: 0.8047 (m-40) REVERT: R 74 GLU cc_start: 0.8426 (tp30) cc_final: 0.8020 (mt-10) REVERT: R 80 THR cc_start: 0.9380 (m) cc_final: 0.9041 (p) REVERT: S 13 LYS cc_start: 0.7637 (tttt) cc_final: 0.7299 (tptp) REVERT: S 19 SER cc_start: 0.9343 (p) cc_final: 0.9022 (p) REVERT: T 71 GLU cc_start: 0.7708 (mt-10) cc_final: 0.7478 (mt-10) REVERT: T 86 ARG cc_start: 0.8581 (mmm-85) cc_final: 0.8138 (mmt-90) REVERT: T 113 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.8087 (mp0) outliers start: 32 outliers final: 21 residues processed: 201 average time/residue: 0.1514 time to fit residues: 42.5088 Evaluate side-chains 190 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 165 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 981 ASN Chi-restraints excluded: chain G residue 1014 LEU Chi-restraints excluded: chain G residue 1041 SER Chi-restraints excluded: chain G residue 1123 LEU Chi-restraints excluded: chain G residue 1153 ILE Chi-restraints excluded: chain G residue 1166 GLU Chi-restraints excluded: chain G residue 1206 VAL Chi-restraints excluded: chain G residue 1218 VAL Chi-restraints excluded: chain G residue 1260 LEU Chi-restraints excluded: chain G residue 1578 MET Chi-restraints excluded: chain G residue 1659 MET Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain M residue 61 LEU Chi-restraints excluded: chain M residue 120 MET Chi-restraints excluded: chain N residue 49 LEU Chi-restraints excluded: chain N residue 73 THR Chi-restraints excluded: chain O residue 107 VAL Chi-restraints excluded: chain P residue 63 ASN Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain S residue 43 VAL Chi-restraints excluded: chain S residue 99 LYS Chi-restraints excluded: chain T residue 34 LYS Chi-restraints excluded: chain T residue 113 GLU Chi-restraints excluded: chain T residue 122 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 130 optimal weight: 2.9990 chunk 101 optimal weight: 4.9990 chunk 75 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 chunk 129 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 116 optimal weight: 0.5980 chunk 115 optimal weight: 0.5980 chunk 20 optimal weight: 7.9990 chunk 7 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 63 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.147722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.110932 restraints weight = 23874.253| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 1.35 r_work: 0.3192 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.4403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16588 Z= 0.145 Angle : 0.540 5.740 23614 Z= 0.315 Chirality : 0.034 0.135 2665 Planarity : 0.004 0.035 1991 Dihedral : 28.137 166.569 4488 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 3.24 % Allowed : 14.67 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 2.47 (0.24), residues: 1193 helix: 2.50 (0.18), residues: 781 sheet: 0.79 (0.68), residues: 67 loop : -0.23 (0.33), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG O 71 TYR 0.009 0.001 TYR T 40 PHE 0.009 0.001 PHE G1164 TRP 0.016 0.001 TRP G1147 HIS 0.003 0.001 HIS N 75 Details of bonding type rmsd covalent geometry : bond 0.00317 (16588) covalent geometry : angle 0.53961 (23614) hydrogen bonds : bond 0.03640 ( 926) hydrogen bonds : angle 2.66096 ( 2379) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 170 time to evaluate : 0.503 Fit side-chains REVERT: G 981 ASN cc_start: 0.8095 (OUTLIER) cc_final: 0.7834 (t0) REVERT: G 1143 MET cc_start: 0.7544 (mpp) cc_final: 0.6857 (mmt) REVERT: G 1190 LEU cc_start: 0.8035 (tp) cc_final: 0.7374 (mm) REVERT: G 1581 MET cc_start: 0.8990 (tpp) cc_final: 0.8771 (tpp) REVERT: M 52 ARG cc_start: 0.7756 (mtt-85) cc_final: 0.6529 (ttt90) REVERT: P 42 TYR cc_start: 0.8210 (t80) cc_final: 0.7975 (t80) REVERT: P 51 ASP cc_start: 0.7789 (m-30) cc_final: 0.7572 (p0) REVERT: Q 70 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.8815 (tp) REVERT: R 80 THR cc_start: 0.9375 (m) cc_final: 0.9042 (p) REVERT: S 13 LYS cc_start: 0.7635 (tttt) cc_final: 0.7274 (tptp) REVERT: S 19 SER cc_start: 0.9340 (p) cc_final: 0.9020 (p) REVERT: T 71 GLU cc_start: 0.7731 (mt-10) cc_final: 0.7507 (mt-10) REVERT: T 86 ARG cc_start: 0.8557 (mmm-85) cc_final: 0.8129 (mmt-90) REVERT: T 113 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.8074 (mp0) outliers start: 34 outliers final: 23 residues processed: 192 average time/residue: 0.1331 time to fit residues: 36.4006 Evaluate side-chains 191 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 165 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 981 ASN Chi-restraints excluded: chain G residue 1014 LEU Chi-restraints excluded: chain G residue 1041 SER Chi-restraints excluded: chain G residue 1123 LEU Chi-restraints excluded: chain G residue 1153 ILE Chi-restraints excluded: chain G residue 1162 ASP Chi-restraints excluded: chain G residue 1166 GLU Chi-restraints excluded: chain G residue 1206 VAL Chi-restraints excluded: chain G residue 1218 VAL Chi-restraints excluded: chain G residue 1260 LEU Chi-restraints excluded: chain G residue 1578 MET Chi-restraints excluded: chain M residue 58 THR Chi-restraints excluded: chain M residue 61 LEU Chi-restraints excluded: chain M residue 120 MET Chi-restraints excluded: chain N residue 49 LEU Chi-restraints excluded: chain N residue 80 THR Chi-restraints excluded: chain O residue 107 VAL Chi-restraints excluded: chain P residue 61 ILE Chi-restraints excluded: chain Q residue 70 LEU Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain S residue 43 VAL Chi-restraints excluded: chain S residue 100 VAL Chi-restraints excluded: chain T residue 34 LYS Chi-restraints excluded: chain T residue 113 GLU Chi-restraints excluded: chain T residue 122 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 107 optimal weight: 0.9990 chunk 87 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 141 optimal weight: 5.9990 chunk 129 optimal weight: 0.5980 chunk 75 optimal weight: 0.9990 chunk 57 optimal weight: 4.9990 chunk 133 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 28 optimal weight: 0.8980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.147491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.110602 restraints weight = 23827.474| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 1.35 r_work: 0.3189 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.4461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16588 Z= 0.152 Angle : 0.542 6.459 23614 Z= 0.316 Chirality : 0.034 0.134 2665 Planarity : 0.004 0.036 1991 Dihedral : 28.165 166.383 4488 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.62 % Allowed : 14.00 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 2.48 (0.24), residues: 1193 helix: 2.51 (0.18), residues: 781 sheet: 0.72 (0.68), residues: 67 loop : -0.21 (0.33), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G1580 TYR 0.010 0.001 TYR Q 54 PHE 0.008 0.001 PHE Q 67 TRP 0.015 0.001 TRP G1147 HIS 0.003 0.001 HIS N 75 Details of bonding type rmsd covalent geometry : bond 0.00337 (16588) covalent geometry : angle 0.54204 (23614) hydrogen bonds : bond 0.03752 ( 926) hydrogen bonds : angle 2.67064 ( 2379) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 169 time to evaluate : 0.595 Fit side-chains REVERT: G 981 ASN cc_start: 0.8089 (OUTLIER) cc_final: 0.7830 (t0) REVERT: G 1154 MET cc_start: 0.6450 (mmm) cc_final: 0.6250 (mmm) REVERT: G 1190 LEU cc_start: 0.8032 (tp) cc_final: 0.7747 (mp) REVERT: G 1581 MET cc_start: 0.8992 (tpp) cc_final: 0.8768 (tpp) REVERT: M 52 ARG cc_start: 0.7769 (mtt-85) cc_final: 0.6551 (ttt90) REVERT: P 42 TYR cc_start: 0.8221 (t80) cc_final: 0.7966 (t80) REVERT: P 51 ASP cc_start: 0.7801 (m-30) cc_final: 0.7532 (p0) REVERT: Q 70 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.8831 (tp) REVERT: R 80 THR cc_start: 0.9372 (m) cc_final: 0.9025 (p) REVERT: S 13 LYS cc_start: 0.7660 (tttt) cc_final: 0.7279 (tptp) REVERT: S 19 SER cc_start: 0.9337 (p) cc_final: 0.9015 (p) REVERT: T 71 GLU cc_start: 0.7727 (mt-10) cc_final: 0.7505 (mt-10) REVERT: T 86 ARG cc_start: 0.8580 (mmm-85) cc_final: 0.8160 (mmt-90) REVERT: T 101 LEU cc_start: 0.8538 (mm) cc_final: 0.8270 (mm) REVERT: T 113 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.8091 (mp0) outliers start: 38 outliers final: 27 residues processed: 195 average time/residue: 0.1267 time to fit residues: 35.5399 Evaluate side-chains 196 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 166 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 981 ASN Chi-restraints excluded: chain G residue 1014 LEU Chi-restraints excluded: chain G residue 1041 SER Chi-restraints excluded: chain G residue 1123 LEU Chi-restraints excluded: chain G residue 1153 ILE Chi-restraints excluded: chain G residue 1162 ASP Chi-restraints excluded: chain G residue 1206 VAL Chi-restraints excluded: chain G residue 1218 VAL Chi-restraints excluded: chain G residue 1260 LEU Chi-restraints excluded: chain G residue 1544 SER Chi-restraints excluded: chain G residue 1578 MET Chi-restraints excluded: chain G residue 1633 LEU Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain M residue 58 THR Chi-restraints excluded: chain M residue 61 LEU Chi-restraints excluded: chain M residue 120 MET Chi-restraints excluded: chain N residue 49 LEU Chi-restraints excluded: chain N residue 73 THR Chi-restraints excluded: chain N residue 80 THR Chi-restraints excluded: chain O residue 107 VAL Chi-restraints excluded: chain P residue 61 ILE Chi-restraints excluded: chain Q residue 70 LEU Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain S residue 43 VAL Chi-restraints excluded: chain S residue 99 LYS Chi-restraints excluded: chain S residue 100 VAL Chi-restraints excluded: chain T residue 34 LYS Chi-restraints excluded: chain T residue 90 THR Chi-restraints excluded: chain T residue 113 GLU Chi-restraints excluded: chain T residue 122 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 47 optimal weight: 8.9990 chunk 73 optimal weight: 6.9990 chunk 88 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 67 optimal weight: 5.9990 chunk 54 optimal weight: 4.9990 chunk 121 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.143879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.106484 restraints weight = 24020.191| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 1.36 r_work: 0.3126 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.4395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 16588 Z= 0.229 Angle : 0.605 6.957 23614 Z= 0.345 Chirality : 0.038 0.144 2665 Planarity : 0.004 0.037 1991 Dihedral : 28.647 166.254 4488 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.43 % Allowed : 14.86 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 2.09 (0.24), residues: 1193 helix: 2.24 (0.18), residues: 782 sheet: 0.42 (0.68), residues: 67 loop : -0.42 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG O 71 TYR 0.017 0.002 TYR O 50 PHE 0.009 0.002 PHE Q 67 TRP 0.018 0.002 TRP G1147 HIS 0.003 0.001 HIS N 75 Details of bonding type rmsd covalent geometry : bond 0.00535 (16588) covalent geometry : angle 0.60495 (23614) hydrogen bonds : bond 0.04962 ( 926) hydrogen bonds : angle 2.92432 ( 2379) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 170 time to evaluate : 0.307 Fit side-chains REVERT: G 981 ASN cc_start: 0.8102 (OUTLIER) cc_final: 0.7881 (t0) REVERT: G 1107 ASP cc_start: 0.8356 (t0) cc_final: 0.8120 (t0) REVERT: G 1143 MET cc_start: 0.7675 (mpp) cc_final: 0.6951 (mmt) REVERT: G 1190 LEU cc_start: 0.8131 (tp) cc_final: 0.7396 (mm) REVERT: M 52 ARG cc_start: 0.7839 (mtt-85) cc_final: 0.6549 (ttt90) REVERT: P 42 TYR cc_start: 0.8326 (t80) cc_final: 0.8078 (t80) REVERT: P 51 ASP cc_start: 0.7950 (m-30) cc_final: 0.7600 (p0) REVERT: S 13 LYS cc_start: 0.7710 (tttt) cc_final: 0.7337 (tptp) REVERT: S 19 SER cc_start: 0.9382 (p) cc_final: 0.9085 (p) REVERT: T 86 ARG cc_start: 0.8731 (mmm-85) cc_final: 0.8349 (mmt-90) REVERT: T 113 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.7689 (mp0) outliers start: 36 outliers final: 31 residues processed: 195 average time/residue: 0.1140 time to fit residues: 32.1597 Evaluate side-chains 196 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 163 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 981 ASN Chi-restraints excluded: chain G residue 1014 LEU Chi-restraints excluded: chain G residue 1041 SER Chi-restraints excluded: chain G residue 1123 LEU Chi-restraints excluded: chain G residue 1153 ILE Chi-restraints excluded: chain G residue 1162 ASP Chi-restraints excluded: chain G residue 1206 VAL Chi-restraints excluded: chain G residue 1218 VAL Chi-restraints excluded: chain G residue 1260 LEU Chi-restraints excluded: chain G residue 1544 SER Chi-restraints excluded: chain G residue 1578 MET Chi-restraints excluded: chain G residue 1633 LEU Chi-restraints excluded: chain G residue 1699 VAL Chi-restraints excluded: chain H residue 412 LEU Chi-restraints excluded: chain H residue 419 THR Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain M residue 58 THR Chi-restraints excluded: chain M residue 120 MET Chi-restraints excluded: chain N residue 49 LEU Chi-restraints excluded: chain N residue 73 THR Chi-restraints excluded: chain N residue 80 THR Chi-restraints excluded: chain O residue 107 VAL Chi-restraints excluded: chain P residue 61 ILE Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 66 ILE Chi-restraints excluded: chain S residue 43 VAL Chi-restraints excluded: chain S residue 76 THR Chi-restraints excluded: chain S residue 99 LYS Chi-restraints excluded: chain S residue 100 VAL Chi-restraints excluded: chain T residue 34 LYS Chi-restraints excluded: chain T residue 90 THR Chi-restraints excluded: chain T residue 113 GLU Chi-restraints excluded: chain T residue 122 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 132 optimal weight: 3.9990 chunk 141 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 48 optimal weight: 7.9990 chunk 60 optimal weight: 4.9990 chunk 113 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 chunk 83 optimal weight: 0.5980 chunk 72 optimal weight: 5.9990 chunk 101 optimal weight: 3.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.146237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.109283 restraints weight = 23893.351| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 1.34 r_work: 0.3170 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.4573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 16588 Z= 0.160 Angle : 0.554 6.801 23614 Z= 0.320 Chirality : 0.035 0.137 2665 Planarity : 0.004 0.037 1991 Dihedral : 28.336 166.071 4486 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 3.05 % Allowed : 15.71 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 2.26 (0.24), residues: 1193 helix: 2.39 (0.18), residues: 782 sheet: 0.28 (0.68), residues: 67 loop : -0.36 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG O 71 TYR 0.011 0.001 TYR O 50 PHE 0.009 0.001 PHE Q 67 TRP 0.017 0.002 TRP G1147 HIS 0.003 0.001 HIS N 75 Details of bonding type rmsd covalent geometry : bond 0.00361 (16588) covalent geometry : angle 0.55385 (23614) hydrogen bonds : bond 0.03985 ( 926) hydrogen bonds : angle 2.74650 ( 2379) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 168 time to evaluate : 0.317 Fit side-chains REVERT: G 1107 ASP cc_start: 0.8072 (t0) cc_final: 0.7727 (t0) REVERT: G 1143 MET cc_start: 0.7342 (mpp) cc_final: 0.6718 (tpp) REVERT: G 1190 LEU cc_start: 0.8016 (tp) cc_final: 0.7736 (mp) REVERT: G 1581 MET cc_start: 0.8845 (tpp) cc_final: 0.8628 (tpp) REVERT: M 52 ARG cc_start: 0.7651 (mtt-85) cc_final: 0.6463 (ttt90) REVERT: P 42 TYR cc_start: 0.8140 (t80) cc_final: 0.7877 (t80) REVERT: P 51 ASP cc_start: 0.7686 (m-30) cc_final: 0.7468 (p0) REVERT: S 13 LYS cc_start: 0.7704 (tttt) cc_final: 0.7382 (tptp) REVERT: S 19 SER cc_start: 0.9311 (p) cc_final: 0.8968 (p) REVERT: S 72 ASP cc_start: 0.6933 (OUTLIER) cc_final: 0.6199 (m-30) REVERT: T 71 GLU cc_start: 0.7266 (mt-10) cc_final: 0.7063 (mp0) REVERT: T 86 ARG cc_start: 0.8550 (mmm-85) cc_final: 0.8213 (mmt-90) REVERT: T 113 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.7565 (mp0) outliers start: 32 outliers final: 25 residues processed: 191 average time/residue: 0.1304 time to fit residues: 35.8253 Evaluate side-chains 192 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 165 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 1014 LEU Chi-restraints excluded: chain G residue 1041 SER Chi-restraints excluded: chain G residue 1123 LEU Chi-restraints excluded: chain G residue 1153 ILE Chi-restraints excluded: chain G residue 1162 ASP Chi-restraints excluded: chain G residue 1206 VAL Chi-restraints excluded: chain G residue 1218 VAL Chi-restraints excluded: chain G residue 1260 LEU Chi-restraints excluded: chain G residue 1544 SER Chi-restraints excluded: chain G residue 1578 MET Chi-restraints excluded: chain G residue 1633 LEU Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain M residue 58 THR Chi-restraints excluded: chain M residue 120 MET Chi-restraints excluded: chain N residue 49 LEU Chi-restraints excluded: chain N residue 73 THR Chi-restraints excluded: chain N residue 80 THR Chi-restraints excluded: chain P residue 61 ILE Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 66 ILE Chi-restraints excluded: chain S residue 43 VAL Chi-restraints excluded: chain S residue 72 ASP Chi-restraints excluded: chain S residue 99 LYS Chi-restraints excluded: chain S residue 100 VAL Chi-restraints excluded: chain T residue 90 THR Chi-restraints excluded: chain T residue 113 GLU Chi-restraints excluded: chain T residue 122 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 131 optimal weight: 4.9990 chunk 63 optimal weight: 5.9990 chunk 97 optimal weight: 0.5980 chunk 55 optimal weight: 5.9990 chunk 88 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 45 optimal weight: 6.9990 chunk 137 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 74 optimal weight: 8.9990 chunk 72 optimal weight: 5.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.144339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.106866 restraints weight = 23943.566| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 1.36 r_work: 0.3126 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.4531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 16588 Z= 0.223 Angle : 0.600 7.003 23614 Z= 0.342 Chirality : 0.037 0.140 2665 Planarity : 0.004 0.038 1991 Dihedral : 28.654 165.813 4486 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.76 % Allowed : 16.38 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 2.01 (0.24), residues: 1193 helix: 2.21 (0.18), residues: 782 sheet: 0.09 (0.68), residues: 67 loop : -0.46 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG O 71 TYR 0.016 0.002 TYR O 50 PHE 0.010 0.002 PHE Q 67 TRP 0.017 0.002 TRP G1147 HIS 0.003 0.001 HIS G1080 Details of bonding type rmsd covalent geometry : bond 0.00518 (16588) covalent geometry : angle 0.59973 (23614) hydrogen bonds : bond 0.04842 ( 926) hydrogen bonds : angle 2.91468 ( 2379) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 167 time to evaluate : 0.581 Fit side-chains REVERT: G 1107 ASP cc_start: 0.8280 (t0) cc_final: 0.7911 (t0) REVERT: G 1143 MET cc_start: 0.7729 (mpp) cc_final: 0.6981 (mmt) REVERT: G 1190 LEU cc_start: 0.8115 (tp) cc_final: 0.7372 (mm) REVERT: G 1581 MET cc_start: 0.8987 (tpp) cc_final: 0.8711 (tpp) REVERT: M 52 ARG cc_start: 0.7862 (mtt-85) cc_final: 0.6533 (ttt90) REVERT: M 79 LYS cc_start: 0.8338 (tttp) cc_final: 0.7989 (ttpt) REVERT: P 42 TYR cc_start: 0.8350 (t80) cc_final: 0.8120 (t80) REVERT: P 51 ASP cc_start: 0.7979 (m-30) cc_final: 0.7582 (p0) REVERT: S 13 LYS cc_start: 0.7715 (tttt) cc_final: 0.7337 (tptp) REVERT: S 19 SER cc_start: 0.9386 (p) cc_final: 0.9108 (p) REVERT: S 72 ASP cc_start: 0.7358 (OUTLIER) cc_final: 0.6693 (m-30) REVERT: T 71 GLU cc_start: 0.7745 (mt-10) cc_final: 0.7521 (mp0) REVERT: T 86 ARG cc_start: 0.8725 (mmm-85) cc_final: 0.8368 (mmt-90) REVERT: T 113 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.7679 (mp0) outliers start: 29 outliers final: 26 residues processed: 188 average time/residue: 0.1458 time to fit residues: 39.3942 Evaluate side-chains 193 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 165 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 1014 LEU Chi-restraints excluded: chain G residue 1041 SER Chi-restraints excluded: chain G residue 1123 LEU Chi-restraints excluded: chain G residue 1153 ILE Chi-restraints excluded: chain G residue 1162 ASP Chi-restraints excluded: chain G residue 1206 VAL Chi-restraints excluded: chain G residue 1218 VAL Chi-restraints excluded: chain G residue 1260 LEU Chi-restraints excluded: chain G residue 1544 SER Chi-restraints excluded: chain G residue 1578 MET Chi-restraints excluded: chain G residue 1623 ILE Chi-restraints excluded: chain G residue 1633 LEU Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain M residue 58 THR Chi-restraints excluded: chain M residue 120 MET Chi-restraints excluded: chain N residue 49 LEU Chi-restraints excluded: chain N residue 73 THR Chi-restraints excluded: chain N residue 80 THR Chi-restraints excluded: chain P residue 61 ILE Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 66 ILE Chi-restraints excluded: chain S residue 43 VAL Chi-restraints excluded: chain S residue 72 ASP Chi-restraints excluded: chain S residue 99 LYS Chi-restraints excluded: chain S residue 100 VAL Chi-restraints excluded: chain T residue 90 THR Chi-restraints excluded: chain T residue 113 GLU Chi-restraints excluded: chain T residue 122 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 99 optimal weight: 0.9980 chunk 88 optimal weight: 0.5980 chunk 114 optimal weight: 0.9990 chunk 141 optimal weight: 3.9990 chunk 111 optimal weight: 0.6980 chunk 125 optimal weight: 0.7980 chunk 80 optimal weight: 0.9980 chunk 70 optimal weight: 4.9990 chunk 122 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 129 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G1006 GLN ** P 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 67 ASN ** 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 = 0.3858 r_free = 0.3858 target = 0.148560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.111470 restraints weight = 23938.299| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 1.37 r_work: 0.3191 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.4785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16588 Z= 0.143 Angle : 0.540 7.655 23614 Z= 0.312 Chirality : 0.034 0.138 2665 Planarity : 0.003 0.037 1991 Dihedral : 28.151 165.301 4486 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.38 % Allowed : 16.67 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 2.40 (0.25), residues: 1193 helix: 2.53 (0.18), residues: 781 sheet: 0.11 (0.69), residues: 67 loop : -0.33 (0.33), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG O 71 TYR 0.009 0.001 TYR T 121 PHE 0.010 0.001 PHE Q 67 TRP 0.016 0.002 TRP G1147 HIS 0.003 0.001 HIS N 75 Details of bonding type rmsd covalent geometry : bond 0.00314 (16588) covalent geometry : angle 0.54027 (23614) hydrogen bonds : bond 0.03611 ( 926) hydrogen bonds : angle 2.67742 ( 2379) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3778.76 seconds wall clock time: 65 minutes 11.29 seconds (3911.29 seconds total)