Starting phenix.real_space_refine on Thu Aug 6 14:05:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8atf_15647/08_2026/8atf_15647.cif Found real_map, /net/cci-nas-00/data/ceres_data/8atf_15647/08_2026/8atf_15647.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8atf_15647/08_2026/8atf_15647.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8atf_15647/08_2026/8atf_15647.map" model { file = "/net/cci-nas-00/data/ceres_data/8atf_15647/08_2026/8atf_15647.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8atf_15647/08_2026/8atf_15647.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8atf_15647/08_2026/8atf_15647.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8atf_15647/08_2026/8atf_15647.cif" } resolution = 3.45 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 288 5.49 5 S 35 5.16 5 C 9014 2.51 5 N 2908 2.21 5 O 3474 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 124 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15719 Number of models: 1 Model: "" Number of chains: 13 Chain: "G" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3661 Classifications: {'peptide': 442} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 428} Chain breaks: 3 Chain: "H" Number of atoms: 264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 264 Classifications: {'peptide': 31} Link IDs: {'PTRANS': 1, 'TRANS': 29} Chain: "K" Number of atoms: 2915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2915 Classifications: {'DNA': 143} Link IDs: {'rna3p': 142} Chain: "L" Number of atoms: 2948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2948 Classifications: {'DNA': 143} Link IDs: {'rna3p': 142} Chain: "M" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 784 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "N" Number of atoms: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 622 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "O" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 821 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "P" Number of atoms: 725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 725 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "Q" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "R" Number of atoms: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 622 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "S" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 821 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "T" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 708 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "G" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.26, per 1000 atoms: 0.21 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: 0.90 Conformation dependent library (CDL) restraints added in 494.6 milliseconds 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: 1.99 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: 3.60 Time building geometry restraints manager: 1.28 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=" N1 DC K -12 " pdb=" C6 DC K -12 " ideal model delta sigma weight residual 1.367 1.331 0.036 6.00e-03 2.78e+04 3.54e+01 bond pdb=" N1 DC K 8 " pdb=" C6 DC K 8 " ideal model delta sigma weight residual 1.367 1.331 0.036 6.00e-03 2.78e+04 3.52e+01 bond pdb=" N1 DC K -23 " pdb=" C6 DC K -23 " ideal model delta sigma weight residual 1.367 1.332 0.035 6.00e-03 2.78e+04 3.34e+01 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=" N1 DC L -58 " pdb=" C6 DC L -58 " ideal model delta sigma weight residual 1.367 1.336 0.031 6.00e-03 2.78e+04 2.72e+01 ... (remaining 16583 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.92: 22180 3.92 - 7.83: 1349 7.83 - 11.75: 78 11.75 - 15.66: 6 15.66 - 19.58: 1 Bond angle restraints: 23614 Sorted by residual: angle pdb=" O4' DG L 23 " pdb=" C1' DG L 23 " pdb=" N9 DG L 23 " ideal model delta sigma weight residual 108.00 114.66 -6.66 7.00e-01 2.04e+00 9.06e+01 angle pdb=" O4' DG K -34 " pdb=" C1' DG K -34 " pdb=" N9 DG K -34 " ideal model delta sigma weight residual 108.00 114.42 -6.42 7.00e-01 2.04e+00 8.42e+01 angle pdb=" O4' DT K 15 " pdb=" C1' DT K 15 " pdb=" N1 DT K 15 " ideal model delta sigma weight residual 108.00 113.79 -5.79 7.00e-01 2.04e+00 6.85e+01 angle pdb=" O4' DG K -68 " pdb=" C1' DG K -68 " pdb=" N9 DG K -68 " ideal model delta sigma weight residual 108.00 113.61 -5.61 7.00e-01 2.04e+00 6.43e+01 angle pdb=" O4' DG L 27 " pdb=" C1' DG L 27 " pdb=" N9 DG L 27 " ideal model delta sigma weight residual 108.00 113.43 -5.43 7.00e-01 2.04e+00 6.01e+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 - 0.132: 2178 0.132 - 0.263: 384 0.263 - 0.395: 91 0.395 - 0.526: 7 0.526 - 0.658: 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 2.34 -2.99 -0.66 2.00e-01 2.50e+01 1.08e+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 2.34 -2.98 -0.64 2.00e-01 2.50e+01 1.03e+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 2.34 -2.98 -0.64 2.00e-01 2.50e+01 1.03e+01 ... (remaining 2662 not shown) Planarity restraints: 1991 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR S 50 " 0.127 2.00e-02 2.50e+03 7.14e-02 1.02e+02 pdb=" CG TYR S 50 " -0.062 2.00e-02 2.50e+03 pdb=" CD1 TYR S 50 " -0.031 2.00e-02 2.50e+03 pdb=" CD2 TYR S 50 " -0.114 2.00e-02 2.50e+03 pdb=" CE1 TYR S 50 " -0.042 2.00e-02 2.50e+03 pdb=" CE2 TYR S 50 " 0.036 2.00e-02 2.50e+03 pdb=" CZ TYR S 50 " 0.038 2.00e-02 2.50e+03 pdb=" OH TYR S 50 " 0.047 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC K 37 " 0.136 2.00e-02 2.50e+03 6.21e-02 8.69e+01 pdb=" N1 DC K 37 " -0.065 2.00e-02 2.50e+03 pdb=" C2 DC K 37 " -0.039 2.00e-02 2.50e+03 pdb=" O2 DC K 37 " -0.040 2.00e-02 2.50e+03 pdb=" N3 DC K 37 " 0.016 2.00e-02 2.50e+03 pdb=" C4 DC K 37 " 0.024 2.00e-02 2.50e+03 pdb=" N4 DC K 37 " 0.059 2.00e-02 2.50e+03 pdb=" C5 DC K 37 " -0.035 2.00e-02 2.50e+03 pdb=" C6 DC K 37 " -0.057 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP G1053 " -0.059 2.00e-02 2.50e+03 5.66e-02 8.01e+01 pdb=" CG TRP G1053 " 0.140 2.00e-02 2.50e+03 pdb=" CD1 TRP G1053 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP G1053 " 0.040 2.00e-02 2.50e+03 pdb=" NE1 TRP G1053 " -0.051 2.00e-02 2.50e+03 pdb=" CE2 TRP G1053 " -0.036 2.00e-02 2.50e+03 pdb=" CE3 TRP G1053 " -0.037 2.00e-02 2.50e+03 pdb=" CZ2 TRP G1053 " 0.031 2.00e-02 2.50e+03 pdb=" CZ3 TRP G1053 " -0.023 2.00e-02 2.50e+03 pdb=" CH2 TRP G1053 " 0.015 2.00e-02 2.50e+03 ... (remaining 1988 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 334 2.65 - 3.21: 12956 3.21 - 3.78: 26423 3.78 - 4.34: 37829 4.34 - 4.90: 53371 Nonbonded interactions: 130913 Sorted by model distance: nonbonded pdb=" O HIS R 75 " pdb=" NH2 ARG T 92 " model vdw 2.090 3.120 nonbonded pdb=" OP2 DA K 17 " pdb=" NH2 ARG Q 69 " model vdw 2.201 3.120 nonbonded pdb=" O SER Q 57 " pdb=" NH1 ARG R 40 " model vdw 2.300 3.120 nonbonded pdb=" NH2 ARG S 32 " pdb=" OE1 GLU T 35 " model vdw 2.324 3.120 nonbonded pdb=" O PHE N 100 " pdb=" C GLY N 101 " model vdw 2.344 3.270 ... (remaining 130908 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'M' selection = (chain 'Q' and resid 40 through 134) } ncs_group { reference = chain 'N' selection = chain 'R' } ncs_group { reference = chain 'O' selection = chain 'S' } ncs_group { reference = (chain 'P' and resid 34 through 124) selection = chain 'T' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.530 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 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= 0.947 Angle : 1.990 19.581 23614 Z= 1.397 Chirality : 0.113 0.658 2665 Planarity : 0.026 0.255 1991 Dihedral : 25.037 178.640 6966 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.67 % Allowed : 3.10 % Favored : 96.23 % Rotamer: Outliers : 1.81 % Allowed : 6.29 % Favored : 91.90 % Cbeta Deviations : 0.35 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.09 (0.20), residues: 1193 helix: -1.38 (0.15), residues: 777 sheet: 0.55 (0.64), residues: 68 loop : -1.34 (0.28), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.069 0.006 ARG G1608 TYR 0.127 0.017 TYR S 50 PHE 0.077 0.017 PHE G1152 TRP 0.140 0.024 TRP G1053 HIS 0.030 0.006 HIS S 31 Details of bonding type rmsd/Z covalent geometry : bond 0.01332 / 0.95 (16588) covalent geometry : angle 1.99011 / 1.40 (23614) hydrogen bonds : bond 0.19597 / 13.17 ( 926) hydrogen bonds : angle 6.35867 / 4.45 ( 2379) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 324 time to evaluate : 0.468 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: 0.6914 (mmt-90) REVERT: M 129 ARG cc_start: 0.8395 (ttt180) cc_final: 0.8006 (tpt-90) REVERT: O 17 ARG cc_start: 0.8160 (mtt180) cc_final: 0.7875 (mmm-85) REVERT: O 72 ASP cc_start: 0.8317 (m-30) cc_final: 0.8109 (m-30) REVERT: P 35 GLU cc_start: 0.8343 (pt0) cc_final: 0.7764 (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: 0.8035 (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: 0.1583 time to fit residues: 72.0947 Evaluate side-chains 216 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 209 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 1089 VAL Chi-restraints excluded: chain G residue 1153 ILE Chi-restraints excluded: chain M residue 61 LEU Chi-restraints excluded: chain N residue 100 PHE Chi-restraints excluded: chain R residue 95 ARG Chi-restraints excluded: chain S residue 43 VAL Chi-restraints excluded: chain S residue 111 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.0980 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 10.0000 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 S 31 HIS T 82 HIS T 95 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.147280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.110677 restraints weight = 23960.765| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 1.38 r_work: 0.3177 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16588 Z= 0.197 Angle : 0.853 8.280 23614 Z= 0.476 Chirality : 0.058 0.292 2665 Planarity : 0.006 0.109 1991 Dihedral : 28.708 174.379 4499 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 2.57 % Allowed : 11.33 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.23), residues: 1193 helix: 0.86 (0.17), residues: 789 sheet: 1.00 (0.63), residues: 68 loop : -0.78 (0.30), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG G1017 TYR 0.032 0.002 TYR G1018 PHE 0.020 0.002 PHE G1164 TRP 0.035 0.003 TRP G1053 HIS 0.006 0.001 HIS G1663 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.20 (16588) covalent geometry : angle 0.85279 / 0.48 (23614) hydrogen bonds : bond 0.06379 / 4.24 ( 926) hydrogen bonds : angle 3.47452 / 2.41 ( 2379) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 220 time to evaluate : 0.420 Fit side-chains revert: symmetry clash REVERT: G 981 ASN cc_start: 0.7963 (OUTLIER) cc_final: 0.7625 (t0) REVERT: G 1143 MET cc_start: 0.7445 (mpp) cc_final: 0.6601 (tpp) REVERT: G 1274 PHE cc_start: 0.7324 (m-80) cc_final: 0.7046 (m-80) REVERT: G 1545 MET cc_start: 0.7154 (tpt) cc_final: 0.6921 (tpp) REVERT: G 1552 SER cc_start: 0.8624 (t) cc_final: 0.8259 (p) REVERT: G 1694 GLU cc_start: 0.8295 (tt0) cc_final: 0.7903 (tp30) REVERT: M 52 ARG cc_start: 0.8016 (mtt-85) cc_final: 0.6606 (ttt90) REVERT: N 49 LEU cc_start: 0.8758 (mm) cc_final: 0.8473 (mt) REVERT: P 51 ASP cc_start: 0.7855 (m-30) cc_final: 0.7598 (p0) REVERT: P 84 ASN cc_start: 0.8710 (m-40) cc_final: 0.8499 (m110) REVERT: Q 59 GLU cc_start: 0.8662 (pt0) cc_final: 0.8441 (pt0) REVERT: S 13 LYS cc_start: 0.7458 (tttt) cc_final: 0.7067 (tptp) REVERT: T 46 LYS cc_start: 0.8755 (ttmm) cc_final: 0.8397 (ttmm) outliers start: 27 outliers final: 12 residues processed: 237 average time/residue: 0.1431 time to fit residues: 46.8756 Evaluate side-chains 191 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 178 time to evaluate : 0.449 ------------------------------------------------------------------------------- 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 1260 LEU Chi-restraints excluded: chain G residue 1688 LYS Chi-restraints excluded: chain M residue 58 THR Chi-restraints excluded: chain M residue 61 LEU Chi-restraints excluded: chain Q residue 118 THR Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain S residue 43 VAL Chi-restraints excluded: chain T residue 34 LYS Chi-restraints excluded: chain T residue 90 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 133 optimal weight: 0.8980 chunk 25 optimal weight: 4.9990 chunk 17 optimal weight: 0.3980 chunk 57 optimal weight: 10.0000 chunk 115 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 51 optimal weight: 9.9990 chunk 95 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 66 optimal weight: 9.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G1130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G1263 GLN G1577 GLN O 38 ASN P 63 ASN Q 39 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.146628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.109750 restraints weight = 24187.963| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 1.38 r_work: 0.3164 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.3182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16588 Z= 0.161 Angle : 0.723 9.006 23614 Z= 0.410 Chirality : 0.052 0.304 2665 Planarity : 0.005 0.058 1991 Dihedral : 28.994 172.942 4489 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 3.24 % Allowed : 12.19 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.24), residues: 1193 helix: 1.55 (0.18), residues: 792 sheet: 0.77 (0.63), residues: 68 loop : -0.54 (0.32), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G1017 TYR 0.021 0.002 TYR G1018 PHE 0.015 0.002 PHE G1164 TRP 0.030 0.002 TRP G1053 HIS 0.005 0.001 HIS G1151 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.16 (16588) covalent geometry : angle 0.72347 / 0.41 (23614) hydrogen bonds : bond 0.05315 / 3.53 ( 926) hydrogen bonds : angle 3.10024 / 2.16 ( 2379) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 195 time to evaluate : 0.457 Fit side-chains REVERT: G 981 ASN cc_start: 0.7937 (OUTLIER) cc_final: 0.7546 (t0) REVERT: G 1058 ASP cc_start: 0.7676 (m-30) cc_final: 0.7287 (m-30) REVERT: G 1143 MET cc_start: 0.7156 (mpp) cc_final: 0.6546 (tpp) REVERT: G 1229 MET cc_start: 0.8637 (mtp) cc_final: 0.8376 (mtt) REVERT: G 1274 PHE cc_start: 0.7366 (m-80) cc_final: 0.6951 (m-80) REVERT: G 1694 GLU cc_start: 0.7923 (tt0) cc_final: 0.7663 (tp30) REVERT: M 52 ARG cc_start: 0.7728 (mtt-85) cc_final: 0.6513 (ttt90) REVERT: M 53 ARG cc_start: 0.8735 (ttp80) cc_final: 0.8286 (ttp-110) REVERT: N 49 LEU cc_start: 0.8750 (mm) cc_final: 0.8400 (mt) REVERT: P 84 ASN cc_start: 0.8650 (m-40) cc_final: 0.8394 (m110) REVERT: S 13 LYS cc_start: 0.7467 (tttt) cc_final: 0.7133 (tptp) REVERT: T 113 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7753 (mp0) outliers start: 34 outliers final: 18 residues processed: 217 average time/residue: 0.1379 time to fit residues: 42.0178 Evaluate side-chains 184 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 164 time to evaluate : 0.438 ------------------------------------------------------------------------------- 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 1162 ASP Chi-restraints excluded: chain G residue 1166 GLU Chi-restraints excluded: chain G residue 1206 VAL Chi-restraints excluded: chain G residue 1260 LEU Chi-restraints excluded: chain G residue 1578 MET Chi-restraints excluded: chain G residue 1623 ILE Chi-restraints excluded: chain G residue 1691 LEU Chi-restraints excluded: chain H residue 408 VAL Chi-restraints excluded: chain M residue 58 THR Chi-restraints excluded: chain M residue 61 LEU Chi-restraints excluded: chain N residue 80 THR Chi-restraints excluded: chain Q residue 118 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 113 GLU Chi-restraints excluded: chain T residue 122 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 131 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 chunk 138 optimal weight: 0.6980 chunk 74 optimal weight: 20.0000 chunk 45 optimal weight: 8.9990 chunk 26 optimal weight: 0.9980 chunk 91 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 chunk 128 optimal weight: 1.9990 chunk 28 optimal weight: 7.9990 chunk 47 optimal weight: 20.0000 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G1130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 38 ASN P 63 ASN Q 39 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.142426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.105031 restraints weight = 23900.164| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 1.35 r_work: 0.3105 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.3474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 16588 Z= 0.224 Angle : 0.756 12.742 23614 Z= 0.413 Chirality : 0.053 0.277 2665 Planarity : 0.005 0.047 1991 Dihedral : 29.154 169.131 4489 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.52 % Allowed : 13.71 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.24), residues: 1193 helix: 1.58 (0.18), residues: 785 sheet: 0.55 (0.65), residues: 68 loop : -0.68 (0.32), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG T 79 TYR 0.019 0.002 TYR O 50 PHE 0.020 0.002 PHE G1164 TRP 0.018 0.002 TRP G1053 HIS 0.006 0.001 HIS N 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00496 / 0.22 (16588) covalent geometry : angle 0.75642 / 0.41 (23614) hydrogen bonds : bond 0.05726 / 3.79 ( 926) hydrogen bonds : angle 3.16219 / 2.20 ( 2379) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 174 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 981 ASN cc_start: 0.8106 (OUTLIER) cc_final: 0.7696 (t0) REVERT: G 1143 MET cc_start: 0.7457 (mpp) cc_final: 0.6731 (mmt) REVERT: G 1229 MET cc_start: 0.8878 (mtp) cc_final: 0.8618 (mtt) REVERT: G 1274 PHE cc_start: 0.7643 (m-80) cc_final: 0.7178 (m-80) REVERT: G 1581 MET cc_start: 0.8925 (tpp) cc_final: 0.8637 (tpp) REVERT: G 1694 GLU cc_start: 0.8088 (tt0) cc_final: 0.7843 (tp30) REVERT: M 52 ARG cc_start: 0.7939 (mtt-85) cc_final: 0.6691 (ttt90) REVERT: N 49 LEU cc_start: 0.8695 (mm) cc_final: 0.8378 (mt) REVERT: P 84 ASN cc_start: 0.8893 (m-40) cc_final: 0.8573 (m110) REVERT: S 13 LYS cc_start: 0.7517 (tttt) cc_final: 0.7216 (tptp) REVERT: T 71 GLU cc_start: 0.7881 (mt-10) cc_final: 0.7643 (mt-10) outliers start: 37 outliers final: 27 residues processed: 200 average time/residue: 0.1301 time to fit residues: 37.1813 Evaluate side-chains 191 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 163 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 981 ASN Chi-restraints excluded: chain G residue 1001 LEU Chi-restraints excluded: chain G residue 1005 VAL 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 1162 ASP Chi-restraints excluded: chain G residue 1166 GLU Chi-restraints excluded: chain G residue 1260 LEU Chi-restraints excluded: chain G residue 1578 MET Chi-restraints excluded: chain G residue 1699 VAL Chi-restraints excluded: chain H residue 408 VAL Chi-restraints excluded: chain M residue 58 THR Chi-restraints excluded: chain M residue 61 LEU Chi-restraints excluded: chain N residue 73 THR Chi-restraints excluded: chain N residue 80 THR Chi-restraints excluded: chain O residue 107 VAL Chi-restraints excluded: chain 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 110 ASN Chi-restraints excluded: chain T residue 34 LYS Chi-restraints excluded: chain T residue 90 THR Chi-restraints excluded: chain T residue 122 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 115 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 40 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 chunk 93 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 chunk 58 optimal weight: 10.0000 chunk 120 optimal weight: 0.6980 chunk 85 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G1130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 63 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.146009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.108998 restraints weight = 24037.353| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 1.36 r_work: 0.3154 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.3763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16588 Z= 0.137 Angle : 0.642 8.206 23614 Z= 0.367 Chirality : 0.047 0.282 2665 Planarity : 0.004 0.039 1991 Dihedral : 28.882 171.141 4489 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 2.29 % Allowed : 14.76 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.80 (0.24), residues: 1193 helix: 1.98 (0.18), residues: 785 sheet: 0.58 (0.64), residues: 68 loop : -0.52 (0.32), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G1664 TYR 0.011 0.001 TYR T 40 PHE 0.012 0.001 PHE G1164 TRP 0.021 0.002 TRP G1147 HIS 0.003 0.001 HIS N 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.14 (16588) covalent geometry : angle 0.64201 / 0.37 (23614) hydrogen bonds : bond 0.04450 / 2.96 ( 926) hydrogen bonds : angle 2.88135 / 2.02 ( 2379) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 177 time to evaluate : 0.342 Fit side-chains REVERT: G 981 ASN cc_start: 0.8098 (OUTLIER) cc_final: 0.7834 (t0) REVERT: G 1143 MET cc_start: 0.7446 (mpp) cc_final: 0.6678 (tpp) REVERT: G 1190 LEU cc_start: 0.8200 (tp) cc_final: 0.7842 (mp) REVERT: G 1229 MET cc_start: 0.8831 (mtp) cc_final: 0.8542 (mtt) REVERT: G 1274 PHE cc_start: 0.7362 (m-80) cc_final: 0.6861 (m-80) REVERT: G 1581 MET cc_start: 0.8924 (tpp) cc_final: 0.8600 (tpp) REVERT: G 1694 GLU cc_start: 0.8118 (tt0) cc_final: 0.7885 (tp30) REVERT: M 52 ARG cc_start: 0.7884 (mtt-85) cc_final: 0.6659 (ttt90) REVERT: N 49 LEU cc_start: 0.8633 (mm) cc_final: 0.8357 (mt) REVERT: S 13 LYS cc_start: 0.7503 (tttt) cc_final: 0.7230 (tptp) REVERT: T 46 LYS cc_start: 0.8687 (ttmm) cc_final: 0.8402 (ttmm) REVERT: T 71 GLU cc_start: 0.7734 (mt-10) cc_final: 0.7510 (mt-10) REVERT: T 113 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.8096 (mp0) outliers start: 24 outliers final: 16 residues processed: 192 average time/residue: 0.1390 time to fit residues: 37.9784 Evaluate side-chains 184 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 166 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 981 ASN Chi-restraints excluded: chain G residue 998 GLU Chi-restraints excluded: chain G residue 1014 LEU Chi-restraints excluded: chain G residue 1089 VAL Chi-restraints excluded: chain G residue 1162 ASP Chi-restraints excluded: chain G residue 1166 GLU Chi-restraints excluded: chain G residue 1192 MET 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 H residue 408 VAL Chi-restraints excluded: chain M residue 61 LEU Chi-restraints excluded: chain N residue 73 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 113 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 130 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 107 optimal weight: 0.0970 chunk 129 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 116 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 7 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G1130 ASN P 63 ASN Q 68 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.145606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.108474 restraints weight = 23821.441| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 1.35 r_work: 0.3156 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.3952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16588 Z= 0.145 Angle : 0.626 7.798 23614 Z= 0.355 Chirality : 0.046 0.269 2665 Planarity : 0.004 0.038 1991 Dihedral : 28.860 168.520 4489 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.76 % Allowed : 15.62 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.99 (0.24), residues: 1193 helix: 2.13 (0.18), residues: 785 sheet: 0.55 (0.65), residues: 68 loop : -0.44 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G1580 TYR 0.017 0.001 TYR G1018 PHE 0.014 0.001 PHE G1164 TRP 0.015 0.002 TRP G1147 HIS 0.005 0.001 HIS N 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.14 (16588) covalent geometry : angle 0.62554 / 0.36 (23614) hydrogen bonds : bond 0.04429 / 2.95 ( 926) hydrogen bonds : angle 2.80064 / 1.96 ( 2379) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 175 time to evaluate : 0.466 Fit side-chains REVERT: G 981 ASN cc_start: 0.8104 (OUTLIER) cc_final: 0.7874 (t0) REVERT: G 1143 MET cc_start: 0.7534 (mpp) cc_final: 0.6863 (mmt) REVERT: G 1190 LEU cc_start: 0.8129 (tp) cc_final: 0.7433 (mm) REVERT: G 1274 PHE cc_start: 0.7519 (m-80) cc_final: 0.6990 (m-80) REVERT: G 1581 MET cc_start: 0.8966 (tpp) cc_final: 0.8631 (tpp) REVERT: G 1694 GLU cc_start: 0.8072 (tt0) cc_final: 0.7830 (tp30) REVERT: M 52 ARG cc_start: 0.7863 (mtt-85) cc_final: 0.6660 (ttt90) REVERT: N 49 LEU cc_start: 0.8606 (mm) cc_final: 0.8353 (mt) REVERT: Q 70 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.8885 (tp) REVERT: T 71 GLU cc_start: 0.7718 (mt-10) cc_final: 0.7494 (mt-10) REVERT: T 113 GLU cc_start: 0.8418 (mp0) cc_final: 0.8209 (mp0) outliers start: 29 outliers final: 22 residues processed: 194 average time/residue: 0.1413 time to fit residues: 38.7760 Evaluate side-chains 190 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 166 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 981 ASN Chi-restraints excluded: chain G residue 998 GLU Chi-restraints excluded: chain G residue 1014 LEU Chi-restraints excluded: chain G residue 1082 MET Chi-restraints excluded: chain G residue 1123 LEU Chi-restraints excluded: chain G residue 1162 ASP Chi-restraints excluded: chain G residue 1166 GLU Chi-restraints excluded: chain G residue 1192 MET 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 61 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 49 LEU 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 110 ASN Chi-restraints excluded: chain T residue 34 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 107 optimal weight: 0.7980 chunk 87 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 141 optimal weight: 0.8980 chunk 129 optimal weight: 0.8980 chunk 75 optimal weight: 0.6980 chunk 57 optimal weight: 9.9990 chunk 133 optimal weight: 0.5980 chunk 64 optimal weight: 9.9990 chunk 28 optimal weight: 6.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 63 ASN ** P 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.147428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.110486 restraints weight = 23885.915| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 1.36 r_work: 0.3182 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.4122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 16588 Z= 0.129 Angle : 0.601 8.521 23614 Z= 0.343 Chirality : 0.044 0.267 2665 Planarity : 0.003 0.035 1991 Dihedral : 28.768 168.585 4488 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 2.48 % Allowed : 16.19 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.23 (0.24), residues: 1193 helix: 2.34 (0.18), residues: 785 sheet: 0.47 (0.65), residues: 68 loop : -0.36 (0.32), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G1580 TYR 0.011 0.001 TYR P 42 PHE 0.011 0.001 PHE G1164 TRP 0.017 0.001 TRP G1147 HIS 0.004 0.001 HIS N 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.13 (16588) covalent geometry : angle 0.60112 / 0.34 (23614) hydrogen bonds : bond 0.04124 / 2.76 ( 926) hydrogen bonds : angle 2.73704 / 1.92 ( 2379) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 180 time to evaluate : 0.441 Fit side-chains REVERT: G 981 ASN cc_start: 0.8090 (OUTLIER) cc_final: 0.7846 (t0) REVERT: G 1143 MET cc_start: 0.7596 (mpp) cc_final: 0.6927 (mmt) REVERT: G 1190 LEU cc_start: 0.8127 (tp) cc_final: 0.7425 (mm) REVERT: G 1694 GLU cc_start: 0.8038 (tt0) cc_final: 0.7807 (tp30) REVERT: M 52 ARG cc_start: 0.7842 (mtt-85) cc_final: 0.6638 (ttt90) REVERT: N 49 LEU cc_start: 0.8600 (mm) cc_final: 0.8366 (mt) REVERT: T 71 GLU cc_start: 0.7723 (mt-10) cc_final: 0.7508 (mt-10) REVERT: T 113 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.8109 (mp0) outliers start: 26 outliers final: 19 residues processed: 196 average time/residue: 0.1430 time to fit residues: 39.9361 Evaluate side-chains 192 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 171 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 981 ASN Chi-restraints excluded: chain G residue 998 GLU 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 1162 ASP Chi-restraints excluded: chain G residue 1166 GLU Chi-restraints excluded: chain G residue 1192 MET 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 1659 MET Chi-restraints excluded: chain H residue 408 VAL Chi-restraints excluded: chain M residue 61 LEU 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 99 LYS Chi-restraints excluded: chain T residue 34 LYS Chi-restraints excluded: chain T residue 113 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 47 optimal weight: 20.0000 chunk 73 optimal weight: 10.0000 chunk 88 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 101 optimal weight: 0.9980 chunk 21 optimal weight: 8.9990 chunk 67 optimal weight: 10.0000 chunk 54 optimal weight: 10.0000 chunk 121 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 chunk 94 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 63 ASN ** P 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.147452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.110393 restraints weight = 24014.054| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 1.37 r_work: 0.3179 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.4240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16588 Z= 0.134 Angle : 0.595 6.742 23614 Z= 0.339 Chirality : 0.043 0.267 2665 Planarity : 0.004 0.036 1991 Dihedral : 28.745 167.777 4488 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.76 % Allowed : 16.19 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.32 (0.24), residues: 1193 helix: 2.40 (0.18), residues: 787 sheet: 0.44 (0.66), residues: 68 loop : -0.29 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G1580 TYR 0.013 0.001 TYR P 42 PHE 0.012 0.001 PHE G1164 TRP 0.015 0.001 TRP G1147 HIS 0.005 0.001 HIS N 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.13 (16588) covalent geometry : angle 0.59528 / 0.34 (23614) hydrogen bonds : bond 0.04205 / 2.82 ( 926) hydrogen bonds : angle 2.72512 / 1.91 ( 2379) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 178 time to evaluate : 0.450 Fit side-chains REVERT: G 981 ASN cc_start: 0.7995 (OUTLIER) cc_final: 0.7752 (t0) REVERT: G 1143 MET cc_start: 0.7419 (mpp) cc_final: 0.6896 (mmt) REVERT: G 1190 LEU cc_start: 0.8102 (tp) cc_final: 0.7410 (mm) REVERT: M 52 ARG cc_start: 0.7661 (mtt-85) cc_final: 0.6576 (ttt90) REVERT: Q 70 LEU cc_start: 0.9188 (OUTLIER) cc_final: 0.8817 (tp) REVERT: S 19 SER cc_start: 0.9321 (p) cc_final: 0.9001 (p) REVERT: S 110 ASN cc_start: 0.8397 (p0) cc_final: 0.8145 (p0) REVERT: T 101 LEU cc_start: 0.8471 (mm) cc_final: 0.8255 (mm) REVERT: T 113 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7762 (mp0) outliers start: 29 outliers final: 22 residues processed: 195 average time/residue: 0.1477 time to fit residues: 40.9676 Evaluate side-chains 195 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 170 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 981 ASN Chi-restraints excluded: chain G residue 998 GLU Chi-restraints excluded: chain G residue 1014 LEU Chi-restraints excluded: chain G residue 1123 LEU Chi-restraints excluded: chain G residue 1162 ASP Chi-restraints excluded: chain G residue 1192 MET 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 G residue 1659 MET Chi-restraints excluded: chain H residue 408 VAL 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 80 THR Chi-restraints excluded: chain Q residue 70 LEU Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 132 optimal weight: 0.0770 chunk 141 optimal weight: 0.6980 chunk 5 optimal weight: 8.9990 chunk 17 optimal weight: 4.9990 chunk 48 optimal weight: 20.0000 chunk 60 optimal weight: 10.0000 chunk 113 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 chunk 72 optimal weight: 10.0000 chunk 101 optimal weight: 4.9990 overall best weight: 1.0540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** P 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 84 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 = 0.3840 r_free = 0.3840 target = 0.147154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.110007 restraints weight = 24013.715| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 1.36 r_work: 0.3172 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.4311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16588 Z= 0.143 Angle : 0.599 7.754 23614 Z= 0.339 Chirality : 0.043 0.265 2665 Planarity : 0.004 0.041 1991 Dihedral : 28.759 167.841 4488 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.57 % Allowed : 16.86 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.36 (0.24), residues: 1193 helix: 2.46 (0.18), residues: 781 sheet: 0.44 (0.66), residues: 68 loop : -0.32 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G1580 TYR 0.011 0.001 TYR O 50 PHE 0.011 0.001 PHE G1164 TRP 0.015 0.001 TRP G1147 HIS 0.004 0.001 HIS N 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.14 (16588) covalent geometry : angle 0.59928 / 0.34 (23614) hydrogen bonds : bond 0.04271 / 2.85 ( 926) hydrogen bonds : angle 2.74634 / 1.92 ( 2379) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 168 time to evaluate : 0.374 Fit side-chains REVERT: G 981 ASN cc_start: 0.8005 (OUTLIER) cc_final: 0.7768 (t0) REVERT: G 1190 LEU cc_start: 0.8102 (tp) cc_final: 0.7795 (mp) REVERT: M 52 ARG cc_start: 0.7614 (mtt-85) cc_final: 0.6472 (ttt90) REVERT: Q 70 LEU cc_start: 0.9199 (OUTLIER) cc_final: 0.8831 (tp) REVERT: S 110 ASN cc_start: 0.8512 (p0) cc_final: 0.8204 (p0) REVERT: T 113 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7704 (mp0) outliers start: 27 outliers final: 22 residues processed: 185 average time/residue: 0.1328 time to fit residues: 35.1386 Evaluate side-chains 190 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 165 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 981 ASN Chi-restraints excluded: chain G residue 998 GLU 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 1162 ASP Chi-restraints excluded: chain G residue 1192 MET 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 G residue 1659 MET Chi-restraints excluded: chain M residue 58 THR Chi-restraints excluded: chain M residue 61 LEU Chi-restraints excluded: chain Q residue 70 LEU Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain R residue 66 ILE Chi-restraints excluded: chain S residue 43 VAL Chi-restraints excluded: chain S residue 76 THR Chi-restraints excluded: chain S residue 99 LYS Chi-restraints excluded: chain S residue 100 VAL Chi-restraints excluded: chain T residue 34 LYS Chi-restraints excluded: chain T residue 113 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 131 optimal weight: 4.9990 chunk 63 optimal weight: 9.9990 chunk 97 optimal weight: 0.0870 chunk 55 optimal weight: 10.0000 chunk 88 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 45 optimal weight: 7.9990 chunk 137 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 74 optimal weight: 30.0000 chunk 72 optimal weight: 9.9990 overall best weight: 1.2164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 63 ASN ** P 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.146682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.109556 restraints weight = 24034.268| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 1.37 r_work: 0.3166 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.4351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16588 Z= 0.152 Angle : 0.606 7.105 23614 Z= 0.341 Chirality : 0.043 0.266 2665 Planarity : 0.004 0.036 1991 Dihedral : 28.789 167.556 4488 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.67 % Allowed : 16.86 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.32 (0.24), residues: 1193 helix: 2.41 (0.18), residues: 781 sheet: 0.44 (0.66), residues: 68 loop : -0.29 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G1580 TYR 0.012 0.001 TYR O 50 PHE 0.011 0.001 PHE G1164 TRP 0.015 0.001 TRP G1147 HIS 0.005 0.001 HIS N 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.15 (16588) covalent geometry : angle 0.60597 / 0.34 (23614) hydrogen bonds : bond 0.04451 / 2.97 ( 926) hydrogen bonds : angle 2.79455 / 1.96 ( 2379) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 167 time to evaluate : 0.481 Fit side-chains REVERT: G 981 ASN cc_start: 0.8123 (OUTLIER) cc_final: 0.7886 (t0) REVERT: G 1143 MET cc_start: 0.7664 (mpp) cc_final: 0.7007 (mmt) REVERT: G 1190 LEU cc_start: 0.8131 (tp) cc_final: 0.7400 (mm) REVERT: M 52 ARG cc_start: 0.7818 (mtt-85) cc_final: 0.6535 (ttt90) REVERT: S 110 ASN cc_start: 0.8655 (p0) cc_final: 0.8372 (p0) REVERT: T 113 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.8013 (mp0) outliers start: 28 outliers final: 23 residues processed: 184 average time/residue: 0.1376 time to fit residues: 36.6559 Evaluate side-chains 190 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 165 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 981 ASN Chi-restraints excluded: chain G residue 998 GLU 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 1162 ASP Chi-restraints excluded: chain G residue 1192 MET 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 G residue 1659 MET Chi-restraints excluded: chain H residue 408 VAL 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 R residue 30 THR Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain R residue 66 ILE Chi-restraints excluded: chain S residue 43 VAL Chi-restraints excluded: chain S residue 76 THR Chi-restraints excluded: chain S residue 99 LYS Chi-restraints excluded: chain S residue 100 VAL Chi-restraints excluded: chain T residue 113 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 99 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 114 optimal weight: 0.3980 chunk 141 optimal weight: 1.9990 chunk 111 optimal weight: 0.8980 chunk 125 optimal weight: 0.7980 chunk 80 optimal weight: 0.9990 chunk 70 optimal weight: 10.0000 chunk 122 optimal weight: 0.0770 chunk 29 optimal weight: 1.9990 chunk 129 optimal weight: 0.5980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 63 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.148243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.111447 restraints weight = 23878.159| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 1.35 r_work: 0.3204 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.4507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 16588 Z= 0.123 Angle : 0.570 8.433 23614 Z= 0.327 Chirality : 0.041 0.264 2665 Planarity : 0.003 0.034 1991 Dihedral : 28.616 167.535 4488 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 2.19 % Allowed : 17.14 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.54 (0.24), residues: 1193 helix: 2.57 (0.18), residues: 781 sheet: 0.51 (0.67), residues: 68 loop : -0.18 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G1580 TYR 0.010 0.001 TYR T 40 PHE 0.008 0.001 PHE G1164 TRP 0.018 0.002 TRP G1147 HIS 0.003 0.001 HIS N 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.12 (16588) covalent geometry : angle 0.56953 / 0.33 (23614) hydrogen bonds : bond 0.03900 / 2.62 ( 926) hydrogen bonds : angle 2.69780 / 1.90 ( 2379) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3643.48 seconds wall clock time: 62 minutes 50.96 seconds (3770.96 seconds total)