Starting phenix.real_space_refine on Sat Jun 14 01:16:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8atf_15647/06_2025/8atf_15647.cif Found real_map, /net/cci-nas-00/data/ceres_data/8atf_15647/06_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_15647/06_2025/8atf_15647.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8atf_15647/06_2025/8atf_15647.map" model { file = "/net/cci-nas-00/data/ceres_data/8atf_15647/06_2025/8atf_15647.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8atf_15647/06_2025/8atf_15647.cif" } resolution = 3.45 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 9.61, per 1000 atoms: 0.61 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: 4.22 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 7.79 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: 8.46 Time building geometry restraints manager: 4.99 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: 2.030 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: 0.570 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 45.780 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.070 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.840 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.140 0.024 TRP G1053 HIS 0.030 0.006 HIS S 31 PHE 0.077 0.017 PHE G1152 TYR 0.127 0.017 TYR S 50 ARG 0.069 0.006 ARG G1608 Details of bonding type rmsd hydrogen bonds : bond 0.19597 ( 926) hydrogen bonds : angle 6.35867 ( 2379) covalent geometry : bond 0.01307 (16588) covalent geometry : angle 1.98759 (23614) *********************** 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 : 1.268 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: 0.3932 time to fit residues: 175.7292 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 : 1.270 ------------------------------------------------------------------------------- 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 122 optimal weight: 0.9990 chunk 109 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 74 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 113 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 84 optimal weight: 0.6980 chunk 131 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G1130 ASN G1657 GLN 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.147360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.111098 restraints weight = 23887.128| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 1.36 r_work: 0.3192 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.3011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16588 Z= 0.188 Angle : 0.672 6.237 23614 Z= 0.392 Chirality : 0.040 0.150 2665 Planarity : 0.004 0.037 1991 Dihedral : 28.581 173.193 4499 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 2.86 % Allowed : 10.86 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.23), residues: 1193 helix: 1.14 (0.18), residues: 790 sheet: 1.11 (0.65), residues: 68 loop : -0.63 (0.31), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP G1053 HIS 0.004 0.001 HIS T 82 PHE 0.016 0.002 PHE G1164 TYR 0.026 0.002 TYR G1018 ARG 0.007 0.001 ARG G1017 Details of bonding type rmsd hydrogen bonds : bond 0.04773 ( 926) hydrogen bonds : angle 3.17774 ( 2379) covalent geometry : bond 0.00402 (16588) covalent geometry : angle 0.67179 (23614) *********************** 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 252 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 222 time to evaluate : 1.410 Fit side-chains revert: symmetry clash REVERT: G 981 ASN cc_start: 0.7963 (OUTLIER) cc_final: 0.7564 (t0) REVERT: G 1058 ASP cc_start: 0.8011 (m-30) cc_final: 0.7693 (m-30) REVERT: G 1143 MET cc_start: 0.7358 (mpp) cc_final: 0.6491 (tpp) REVERT: G 1229 MET cc_start: 0.8862 (mtp) cc_final: 0.8649 (mtt) REVERT: G 1274 PHE cc_start: 0.7345 (m-80) cc_final: 0.7015 (m-80) REVERT: G 1545 MET cc_start: 0.7141 (tpt) cc_final: 0.6908 (tpp) REVERT: G 1694 GLU cc_start: 0.8168 (tt0) cc_final: 0.7833 (tp30) REVERT: M 52 ARG cc_start: 0.7871 (mtt-85) cc_final: 0.6544 (ttt90) REVERT: M 53 ARG cc_start: 0.8693 (ttt180) cc_final: 0.8424 (ttp-110) REVERT: M 61 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8921 (mt) REVERT: N 49 LEU cc_start: 0.8718 (mm) cc_final: 0.8416 (mt) REVERT: P 51 ASP cc_start: 0.7799 (m-30) cc_final: 0.7535 (p0) REVERT: P 84 ASN cc_start: 0.8683 (m-40) cc_final: 0.8372 (m110) REVERT: R 80 THR cc_start: 0.9372 (m) cc_final: 0.9144 (p) REVERT: S 13 LYS cc_start: 0.7420 (tttt) cc_final: 0.7055 (tptp) REVERT: T 71 GLU cc_start: 0.7674 (mt-10) cc_final: 0.7396 (mp0) outliers start: 30 outliers final: 15 residues processed: 245 average time/residue: 0.3854 time to fit residues: 128.8784 Evaluate side-chains 188 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 171 time to evaluate : 1.491 ------------------------------------------------------------------------------- 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 N residue 80 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 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 47 optimal weight: 8.9990 chunk 100 optimal weight: 4.9990 chunk 75 optimal weight: 0.0060 chunk 17 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 overall best weight: 2.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G1263 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.143115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.106155 restraints weight = 23903.943| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 1.37 r_work: 0.3110 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.3664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 16588 Z= 0.257 Angle : 0.685 6.992 23614 Z= 0.393 Chirality : 0.041 0.154 2665 Planarity : 0.005 0.049 1991 Dihedral : 28.725 169.468 4489 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 4.48 % Allowed : 12.38 % Favored : 83.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.24), residues: 1193 helix: 1.50 (0.18), residues: 785 sheet: 0.83 (0.63), residues: 68 loop : -0.57 (0.32), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP G1053 HIS 0.005 0.001 HIS T 49 PHE 0.016 0.002 PHE G1164 TYR 0.022 0.002 TYR O 50 ARG 0.007 0.001 ARG G1664 Details of bonding type rmsd hydrogen bonds : bond 0.05622 ( 926) hydrogen bonds : angle 3.18798 ( 2379) covalent geometry : bond 0.00598 (16588) covalent geometry : angle 0.68511 (23614) *********************** 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 228 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 181 time to evaluate : 1.273 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 981 ASN cc_start: 0.8105 (OUTLIER) cc_final: 0.7735 (t0) REVERT: G 1190 LEU cc_start: 0.8234 (tp) cc_final: 0.7947 (mp) REVERT: G 1274 PHE cc_start: 0.7742 (m-80) cc_final: 0.7225 (m-80) REVERT: M 52 ARG cc_start: 0.7893 (mtt-85) cc_final: 0.6470 (ptm-80) REVERT: N 49 LEU cc_start: 0.8674 (mm) cc_final: 0.8450 (mt) REVERT: P 51 ASP cc_start: 0.7856 (m-30) cc_final: 0.7556 (p0) REVERT: S 13 LYS cc_start: 0.7606 (tttt) cc_final: 0.7254 (tptp) REVERT: S 71 ARG cc_start: 0.8073 (mtt180) cc_final: 0.7872 (mtt180) REVERT: T 71 GLU cc_start: 0.7870 (mt-10) cc_final: 0.7655 (mt-10) outliers start: 47 outliers final: 34 residues processed: 215 average time/residue: 0.3258 time to fit residues: 97.9859 Evaluate side-chains 203 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 168 time to evaluate : 1.417 ------------------------------------------------------------------------------- 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 1621 ILE 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 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 77 ARG 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 2 optimal weight: 0.9990 chunk 99 optimal weight: 0.8980 chunk 48 optimal weight: 7.9990 chunk 90 optimal weight: 0.5980 chunk 72 optimal weight: 5.9990 chunk 75 optimal weight: 3.9990 chunk 120 optimal weight: 0.5980 chunk 123 optimal weight: 0.5980 chunk 89 optimal weight: 0.9990 chunk 138 optimal weight: 1.9990 chunk 19 optimal weight: 0.4980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G1130 ASN G1577 GLN ** N 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 63 ASN P 84 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.147664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.111163 restraints weight = 23834.332| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 1.35 r_work: 0.3193 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.4114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16588 Z= 0.146 Angle : 0.561 5.800 23614 Z= 0.329 Chirality : 0.035 0.163 2665 Planarity : 0.004 0.038 1991 Dihedral : 28.128 167.941 4489 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 3.05 % Allowed : 13.52 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.24), residues: 1193 helix: 2.13 (0.18), residues: 786 sheet: 0.86 (0.64), residues: 68 loop : -0.33 (0.33), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP G1147 HIS 0.002 0.000 HIS T 49 PHE 0.010 0.001 PHE G1164 TYR 0.009 0.001 TYR O 50 ARG 0.005 0.000 ARG M 129 Details of bonding type rmsd hydrogen bonds : bond 0.03697 ( 926) hydrogen bonds : angle 2.75175 ( 2379) covalent geometry : bond 0.00316 (16588) covalent geometry : angle 0.56051 (23614) *********************** 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 220 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 188 time to evaluate : 1.611 Fit side-chains REVERT: G 981 ASN cc_start: 0.8094 (OUTLIER) cc_final: 0.7826 (t0) REVERT: G 1143 MET cc_start: 0.7535 (mpp) cc_final: 0.6798 (mmt) REVERT: G 1190 LEU cc_start: 0.8178 (tp) cc_final: 0.7419 (mm) REVERT: M 52 ARG cc_start: 0.7791 (mtt-85) cc_final: 0.6573 (ttt90) REVERT: M 53 ARG cc_start: 0.8848 (ttt180) cc_final: 0.8416 (ttp80) REVERT: P 42 TYR cc_start: 0.8204 (t80) cc_final: 0.7963 (t80) REVERT: P 51 ASP cc_start: 0.7811 (m-30) cc_final: 0.7451 (p0) REVERT: S 13 LYS cc_start: 0.7542 (tttt) cc_final: 0.7240 (tptp) REVERT: S 19 SER cc_start: 0.9335 (p) cc_final: 0.9007 (p) REVERT: T 71 GLU cc_start: 0.7710 (mt-10) cc_final: 0.7456 (mt-10) REVERT: T 86 ARG cc_start: 0.8579 (mmm-85) cc_final: 0.8136 (mmt-90) REVERT: T 101 LEU cc_start: 0.8605 (mm) cc_final: 0.8240 (mm) REVERT: T 113 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.8066 (mp0) outliers start: 32 outliers final: 19 residues processed: 209 average time/residue: 0.4745 time to fit residues: 138.1178 Evaluate side-chains 188 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 167 time to evaluate : 1.540 ------------------------------------------------------------------------------- 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 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 1633 LEU 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 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 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 134 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 64 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 47 optimal weight: 7.9990 chunk 17 optimal weight: 3.9990 chunk 38 optimal weight: 0.0040 overall best weight: 2.3998 ------------------------------------------------------------------------------- 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 = 0.3781 r_free = 0.3781 target = 0.142415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.105282 restraints weight = 24123.029| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 1.35 r_work: 0.3107 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.4117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 16588 Z= 0.266 Angle : 0.648 7.307 23614 Z= 0.369 Chirality : 0.040 0.148 2665 Planarity : 0.005 0.037 1991 Dihedral : 28.842 167.489 4488 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 4.19 % Allowed : 13.14 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.24), residues: 1193 helix: 1.87 (0.18), residues: 786 sheet: 0.72 (0.66), residues: 67 loop : -0.59 (0.32), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP G1147 HIS 0.004 0.001 HIS P 109 PHE 0.011 0.002 PHE M 67 TYR 0.020 0.002 TYR O 50 ARG 0.005 0.001 ARG G1664 Details of bonding type rmsd hydrogen bonds : bond 0.05420 ( 926) hydrogen bonds : angle 3.06244 ( 2379) covalent geometry : bond 0.00625 (16588) covalent geometry : angle 0.64769 (23614) *********************** 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 210 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 166 time to evaluate : 1.607 Fit side-chains revert: symmetry clash REVERT: G 981 ASN cc_start: 0.8145 (OUTLIER) cc_final: 0.7904 (t0) REVERT: G 1143 MET cc_start: 0.7595 (mpp) cc_final: 0.6832 (mmt) REVERT: G 1190 LEU cc_start: 0.8264 (tp) cc_final: 0.7476 (mm) REVERT: M 52 ARG cc_start: 0.7890 (mtt-85) cc_final: 0.6540 (ttt90) REVERT: P 51 ASP cc_start: 0.7903 (m-30) cc_final: 0.7549 (p0) REVERT: R 92 ARG cc_start: 0.8530 (OUTLIER) cc_final: 0.8027 (tpm-80) REVERT: S 13 LYS cc_start: 0.7694 (tttt) cc_final: 0.7314 (tptp) REVERT: S 19 SER cc_start: 0.9384 (p) cc_final: 0.9097 (p) REVERT: S 110 ASN cc_start: 0.8763 (p0) cc_final: 0.8483 (p0) REVERT: T 71 GLU cc_start: 0.7813 (mt-10) cc_final: 0.7611 (mt-10) REVERT: T 86 ARG cc_start: 0.8765 (mmm-85) cc_final: 0.8379 (mmt-90) REVERT: T 113 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.7644 (mp0) outliers start: 44 outliers final: 34 residues processed: 194 average time/residue: 0.4937 time to fit residues: 144.4228 Evaluate side-chains 200 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 163 time to evaluate : 1.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 981 ASN 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 1544 SER Chi-restraints excluded: chain G residue 1578 MET Chi-restraints excluded: chain G residue 1621 ILE Chi-restraints excluded: chain G residue 1633 LEU 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 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 61 LEU Chi-restraints excluded: chain M residue 107 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 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 R residue 92 ARG 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 90 THR 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 128 optimal weight: 0.3980 chunk 6 optimal weight: 0.9990 chunk 56 optimal weight: 4.9990 chunk 132 optimal weight: 4.9990 chunk 137 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 119 optimal weight: 0.5980 chunk 86 optimal weight: 0.0070 chunk 15 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 chunk 123 optimal weight: 0.5980 overall best weight: 0.5200 ------------------------------------------------------------------------------- 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 = 0.3858 r_free = 0.3858 target = 0.148745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.112098 restraints weight = 24197.343| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 1.38 r_work: 0.3202 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.4490 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= 0.138 Angle : 0.535 5.755 23614 Z= 0.313 Chirality : 0.034 0.130 2665 Planarity : 0.003 0.035 1991 Dihedral : 28.068 166.764 4488 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 2.57 % Allowed : 14.57 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.32 (0.24), residues: 1193 helix: 2.39 (0.18), residues: 782 sheet: 0.77 (0.67), residues: 67 loop : -0.32 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP G1053 HIS 0.002 0.000 HIS N 75 PHE 0.010 0.001 PHE Q 67 TYR 0.008 0.001 TYR O 50 ARG 0.005 0.000 ARG O 71 Details of bonding type rmsd hydrogen bonds : bond 0.03484 ( 926) hydrogen bonds : angle 2.66777 ( 2379) covalent geometry : bond 0.00296 (16588) covalent geometry : angle 0.53464 (23614) *********************** 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 202 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 175 time to evaluate : 1.326 Fit side-chains REVERT: G 981 ASN cc_start: 0.7974 (OUTLIER) cc_final: 0.7747 (t0) REVERT: G 1154 MET cc_start: 0.6176 (mmm) cc_final: 0.5862 (mmm) REVERT: G 1190 LEU cc_start: 0.8065 (tp) cc_final: 0.7737 (mp) REVERT: M 52 ARG cc_start: 0.7565 (mtt-85) cc_final: 0.6411 (ttt90) REVERT: P 42 TYR cc_start: 0.8069 (t80) cc_final: 0.7781 (t80) REVERT: Q 70 LEU cc_start: 0.9144 (OUTLIER) cc_final: 0.8783 (tp) REVERT: S 13 LYS cc_start: 0.7667 (tttt) cc_final: 0.7353 (tptp) REVERT: S 19 SER cc_start: 0.9284 (p) cc_final: 0.8948 (p) REVERT: T 71 GLU cc_start: 0.7269 (mt-10) cc_final: 0.7067 (mt-10) REVERT: T 86 ARG cc_start: 0.8421 (mmm-85) cc_final: 0.8064 (mmt-90) REVERT: T 101 LEU cc_start: 0.8558 (mm) cc_final: 0.8210 (mm) REVERT: T 113 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7670 (mp0) outliers start: 27 outliers final: 17 residues processed: 194 average time/residue: 0.3947 time to fit residues: 108.9823 Evaluate side-chains 187 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 167 time to evaluate : 1.383 ------------------------------------------------------------------------------- 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 1206 VAL Chi-restraints excluded: chain G residue 1260 LEU Chi-restraints excluded: chain G residue 1633 LEU 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 Q residue 70 LEU 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 99 LYS Chi-restraints excluded: chain S residue 100 VAL Chi-restraints excluded: chain T residue 113 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 74 optimal weight: 8.9990 chunk 132 optimal weight: 5.9990 chunk 124 optimal weight: 0.8980 chunk 131 optimal weight: 3.9990 chunk 82 optimal weight: 0.8980 chunk 59 optimal weight: 6.9990 chunk 107 optimal weight: 0.6980 chunk 76 optimal weight: 3.9990 chunk 121 optimal weight: 0.9990 chunk 68 optimal weight: 6.9990 chunk 137 optimal weight: 3.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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** T 63 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.145665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.108420 restraints weight = 24163.305| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 1.36 r_work: 0.3148 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.4466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 16588 Z= 0.193 Angle : 0.571 6.430 23614 Z= 0.328 Chirality : 0.036 0.135 2665 Planarity : 0.004 0.036 1991 Dihedral : 28.410 166.321 4488 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.86 % Allowed : 15.14 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.19 (0.24), residues: 1193 helix: 2.30 (0.18), residues: 782 sheet: 0.70 (0.68), residues: 67 loop : -0.40 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP G1147 HIS 0.003 0.001 HIS N 75 PHE 0.009 0.001 PHE G1065 TYR 0.013 0.001 TYR O 50 ARG 0.005 0.000 ARG O 71 Details of bonding type rmsd hydrogen bonds : bond 0.04350 ( 926) hydrogen bonds : angle 2.80896 ( 2379) covalent geometry : bond 0.00442 (16588) covalent geometry : angle 0.57123 (23614) *********************** 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 199 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 169 time to evaluate : 1.475 Fit side-chains REVERT: G 981 ASN cc_start: 0.8001 (OUTLIER) cc_final: 0.7781 (t0) REVERT: G 1143 MET cc_start: 0.7436 (mpp) cc_final: 0.6894 (mmt) REVERT: G 1154 MET cc_start: 0.6237 (mmm) cc_final: 0.5966 (mmm) REVERT: G 1190 LEU cc_start: 0.8053 (tp) cc_final: 0.7385 (mm) REVERT: M 52 ARG cc_start: 0.7653 (mtt-85) cc_final: 0.6443 (ttt90) REVERT: P 42 TYR cc_start: 0.8111 (t80) cc_final: 0.7840 (t80) REVERT: Q 70 LEU cc_start: 0.9221 (OUTLIER) cc_final: 0.8825 (tp) REVERT: R 92 ARG cc_start: 0.8336 (OUTLIER) cc_final: 0.7860 (tpm-80) REVERT: S 13 LYS cc_start: 0.7678 (tttt) cc_final: 0.7346 (tptp) REVERT: S 19 SER cc_start: 0.9304 (p) cc_final: 0.8977 (p) REVERT: S 71 ARG cc_start: 0.7916 (tpp80) cc_final: 0.7549 (mmt90) REVERT: T 86 ARG cc_start: 0.8590 (mmm-85) cc_final: 0.8254 (mmt-90) REVERT: T 113 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7545 (mp0) outliers start: 30 outliers final: 20 residues processed: 189 average time/residue: 0.3354 time to fit residues: 90.2754 Evaluate side-chains 189 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 165 time to evaluate : 1.432 ------------------------------------------------------------------------------- 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 1260 LEU 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 120 MET Chi-restraints excluded: chain N residue 49 LEU Chi-restraints excluded: chain N residue 73 THR Chi-restraints excluded: chain Q residue 70 LEU Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 66 ILE Chi-restraints excluded: chain R residue 92 ARG 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 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 104 optimal weight: 0.7980 chunk 89 optimal weight: 0.9990 chunk 72 optimal weight: 5.9990 chunk 8 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 15 optimal weight: 4.9990 chunk 85 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 44 optimal weight: 10.0000 chunk 97 optimal weight: 0.6980 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 ** 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 = 0.3849 r_free = 0.3849 target = 0.147864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.110976 restraints weight = 24016.801| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 1.35 r_work: 0.3189 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.4645 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= 0.149 Angle : 0.542 6.214 23614 Z= 0.314 Chirality : 0.034 0.138 2665 Planarity : 0.003 0.035 1991 Dihedral : 28.153 165.849 4486 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.57 % Allowed : 15.81 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.40 (0.24), residues: 1193 helix: 2.47 (0.18), residues: 783 sheet: 0.58 (0.69), residues: 67 loop : -0.28 (0.33), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP G1147 HIS 0.002 0.001 HIS N 75 PHE 0.010 0.001 PHE G1274 TYR 0.010 0.001 TYR O 50 ARG 0.006 0.000 ARG O 71 Details of bonding type rmsd hydrogen bonds : bond 0.03710 ( 926) hydrogen bonds : angle 2.67650 ( 2379) covalent geometry : bond 0.00329 (16588) covalent geometry : angle 0.54244 (23614) *********************** 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 197 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 170 time to evaluate : 1.323 Fit side-chains REVERT: G 981 ASN cc_start: 0.7978 (OUTLIER) cc_final: 0.7757 (t0) REVERT: G 1143 MET cc_start: 0.7399 (mpp) cc_final: 0.6697 (tpp) REVERT: G 1190 LEU cc_start: 0.7988 (tp) cc_final: 0.7721 (mp) REVERT: M 52 ARG cc_start: 0.7638 (mtt-85) cc_final: 0.6494 (ttt90) REVERT: M 133 GLU cc_start: 0.8153 (mt-10) cc_final: 0.7952 (mt-10) REVERT: P 42 TYR cc_start: 0.8054 (t80) cc_final: 0.7785 (t80) REVERT: Q 70 LEU cc_start: 0.9169 (OUTLIER) cc_final: 0.8803 (tp) REVERT: R 92 ARG cc_start: 0.8341 (OUTLIER) cc_final: 0.7858 (tpm-80) REVERT: S 13 LYS cc_start: 0.7679 (tttt) cc_final: 0.7365 (tptp) REVERT: S 19 SER cc_start: 0.9304 (p) cc_final: 0.8960 (p) REVERT: S 71 ARG cc_start: 0.7865 (tpp80) cc_final: 0.7490 (mpt-90) REVERT: T 71 GLU cc_start: 0.7189 (mt-10) cc_final: 0.6941 (mp0) REVERT: T 86 ARG cc_start: 0.8520 (mmm-85) cc_final: 0.8186 (mmt-90) REVERT: T 101 LEU cc_start: 0.8592 (mm) cc_final: 0.8262 (mm) REVERT: T 113 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7658 (mp0) outliers start: 27 outliers final: 20 residues processed: 189 average time/residue: 0.4189 time to fit residues: 111.4109 Evaluate side-chains 188 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 164 time to evaluate : 1.395 ------------------------------------------------------------------------------- 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 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 1633 LEU Chi-restraints excluded: chain M residue 57 SER 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 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 66 ILE Chi-restraints excluded: chain R residue 92 ARG Chi-restraints excluded: chain S residue 43 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 87 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 129 optimal weight: 0.7980 chunk 130 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 23 optimal weight: 10.0000 chunk 49 optimal weight: 6.9990 chunk 116 optimal weight: 0.6980 chunk 48 optimal weight: 7.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 = 0.3834 r_free = 0.3834 target = 0.146661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.109514 restraints weight = 24061.386| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 1.34 r_work: 0.3161 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.4625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 16588 Z= 0.174 Angle : 0.563 7.029 23614 Z= 0.324 Chirality : 0.035 0.133 2665 Planarity : 0.004 0.036 1991 Dihedral : 28.282 165.645 4486 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.76 % Allowed : 15.71 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.34 (0.24), residues: 1193 helix: 2.42 (0.18), residues: 782 sheet: 0.52 (0.69), residues: 67 loop : -0.29 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP G1147 HIS 0.003 0.001 HIS N 75 PHE 0.008 0.001 PHE Q 67 TYR 0.011 0.001 TYR O 50 ARG 0.007 0.000 ARG O 71 Details of bonding type rmsd hydrogen bonds : bond 0.04095 ( 926) hydrogen bonds : angle 2.75747 ( 2379) covalent geometry : bond 0.00396 (16588) covalent geometry : angle 0.56318 (23614) *********************** 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 195 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 166 time to evaluate : 2.281 Fit side-chains REVERT: G 981 ASN cc_start: 0.7989 (OUTLIER) cc_final: 0.7775 (t0) REVERT: G 1143 MET cc_start: 0.7374 (mpp) cc_final: 0.6780 (tpp) REVERT: G 1190 LEU cc_start: 0.8014 (tp) cc_final: 0.7729 (mp) REVERT: M 52 ARG cc_start: 0.7690 (mtt-85) cc_final: 0.6495 (ttt90) REVERT: P 42 TYR cc_start: 0.8082 (t80) cc_final: 0.7804 (t80) REVERT: Q 70 LEU cc_start: 0.9205 (OUTLIER) cc_final: 0.8784 (tp) REVERT: R 92 ARG cc_start: 0.8337 (OUTLIER) cc_final: 0.7895 (tpm-80) REVERT: S 13 LYS cc_start: 0.7716 (tttt) cc_final: 0.7375 (tptp) REVERT: S 19 SER cc_start: 0.9304 (p) cc_final: 0.8975 (p) REVERT: S 71 ARG cc_start: 0.7896 (tpp80) cc_final: 0.7508 (mmt90) REVERT: T 86 ARG cc_start: 0.8568 (mmm-85) cc_final: 0.8235 (mmt-90) REVERT: T 113 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7596 (mp0) outliers start: 29 outliers final: 23 residues processed: 185 average time/residue: 0.4389 time to fit residues: 115.6494 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 : 1.837 ------------------------------------------------------------------------------- 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 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 H residue 419 THR Chi-restraints excluded: chain M residue 57 SER 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 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 66 ILE Chi-restraints excluded: chain R residue 92 ARG 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 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 113 optimal weight: 0.6980 chunk 56 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 122 optimal weight: 0.9990 chunk 51 optimal weight: 4.9990 chunk 67 optimal weight: 5.9990 chunk 141 optimal weight: 0.5980 chunk 54 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 = 0.3832 r_free = 0.3832 target = 0.146503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.109458 restraints weight = 24149.989| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 1.35 r_work: 0.3167 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.4652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 16588 Z= 0.176 Angle : 0.565 7.222 23614 Z= 0.324 Chirality : 0.035 0.135 2665 Planarity : 0.004 0.036 1991 Dihedral : 28.302 165.667 4486 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.57 % Allowed : 15.62 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.32 (0.24), residues: 1193 helix: 2.41 (0.18), residues: 782 sheet: 0.42 (0.69), residues: 67 loop : -0.29 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP G1147 HIS 0.003 0.001 HIS P 109 PHE 0.008 0.001 PHE Q 67 TYR 0.012 0.001 TYR O 50 ARG 0.007 0.000 ARG O 71 Details of bonding type rmsd hydrogen bonds : bond 0.04132 ( 926) hydrogen bonds : angle 2.77517 ( 2379) covalent geometry : bond 0.00401 (16588) covalent geometry : angle 0.56480 (23614) ********************** 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 195 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 168 time to evaluate : 1.678 Fit side-chains REVERT: G 981 ASN cc_start: 0.8092 (OUTLIER) cc_final: 0.7880 (t0) REVERT: G 1143 MET cc_start: 0.7615 (mpp) cc_final: 0.6866 (tpp) REVERT: G 1190 LEU cc_start: 0.8034 (tp) cc_final: 0.7723 (mp) REVERT: M 52 ARG cc_start: 0.7806 (mtt-85) cc_final: 0.6528 (ttt90) REVERT: P 42 TYR cc_start: 0.8221 (t80) cc_final: 0.7958 (t80) REVERT: Q 70 LEU cc_start: 0.9225 (OUTLIER) cc_final: 0.8817 (tp) REVERT: R 92 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.8022 (tpm-80) REVERT: S 13 LYS cc_start: 0.7710 (tttt) cc_final: 0.7343 (tptp) REVERT: S 19 SER cc_start: 0.9362 (p) cc_final: 0.9064 (p) REVERT: S 71 ARG cc_start: 0.8074 (tpp80) cc_final: 0.7653 (mmt90) REVERT: T 71 GLU cc_start: 0.7721 (mp0) cc_final: 0.7287 (mp0) REVERT: T 86 ARG cc_start: 0.8718 (mmm-85) cc_final: 0.8339 (mmt-90) REVERT: T 101 LEU cc_start: 0.8632 (mm) cc_final: 0.8272 (mm) REVERT: T 113 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.7991 (mp0) outliers start: 27 outliers final: 22 residues processed: 186 average time/residue: 0.3300 time to fit residues: 87.0254 Evaluate side-chains 193 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 167 time to evaluate : 1.373 ------------------------------------------------------------------------------- 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 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 H residue 419 THR 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 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 66 ILE Chi-restraints excluded: chain R residue 92 ARG Chi-restraints excluded: chain S residue 43 VAL 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 127 optimal weight: 0.4980 chunk 19 optimal weight: 0.9990 chunk 79 optimal weight: 0.4980 chunk 65 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 110 optimal weight: 0.8980 chunk 136 optimal weight: 0.9980 chunk 113 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 115 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3859 r_free = 0.3859 target = 0.148718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.111937 restraints weight = 24049.578| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 1.35 r_work: 0.3200 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.4798 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= 0.143 Angle : 0.537 7.315 23614 Z= 0.311 Chirality : 0.033 0.137 2665 Planarity : 0.003 0.035 1991 Dihedral : 28.101 165.115 4486 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.19 % Allowed : 16.29 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.55 (0.25), residues: 1193 helix: 2.57 (0.18), residues: 783 sheet: 0.42 (0.70), residues: 67 loop : -0.15 (0.33), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP G1147 HIS 0.002 0.001 HIS P 109 PHE 0.009 0.001 PHE Q 67 TYR 0.010 0.001 TYR T 40 ARG 0.007 0.000 ARG O 71 Details of bonding type rmsd hydrogen bonds : bond 0.03598 ( 926) hydrogen bonds : angle 2.66255 ( 2379) covalent geometry : bond 0.00315 (16588) covalent geometry : angle 0.53742 (23614) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8677.41 seconds wall clock time: 153 minutes 0.81 seconds (9180.81 seconds total)