Starting phenix.real_space_refine on Sat Jul 4 13:19:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yny_39431/07_2026/8yny_39431.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yny_39431/07_2026/8yny_39431.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8yny_39431/07_2026/8yny_39431.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yny_39431/07_2026/8yny_39431.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8yny_39431/07_2026/8yny_39431.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yny_39431/07_2026/8yny_39431.map" } resolution = 4.52 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= 0.003 sd= 0.094 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 386 5.49 5 S 30 5.16 5 C 12247 2.51 5 N 3895 2.21 5 O 4829 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21387 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 743 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "B" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 646 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "C" Number of atoms: 743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 743 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain: "D" Number of atoms: 699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 699 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "E" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 738 Classifications: {'peptide': 90} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "F" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 619 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "G" Number of atoms: 741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 741 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain: "H" Number of atoms: 699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 699 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "I" Number of atoms: 2794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 2794 Classifications: {'DNA': 137} Link IDs: {'rna3p': 136} Chain: "J" Number of atoms: 2783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 2783 Classifications: {'DNA': 135} Link IDs: {'rna3p': 134} Chain: "K" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 351 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Chain: "W" Number of atoms: 2072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 2072 Classifications: {'RNA': 97} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p_pur': 48, 'rna3p_pyr': 38} Link IDs: {'rna2p': 11, 'rna3p': 85} Chain: "X" Number of atoms: 7759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 941, 7759 Classifications: {'peptide': 941} Link IDs: {'PTRANS': 26, 'TRANS': 914} Chain breaks: 13 Time building chain proxies: 4.60, per 1000 atoms: 0.22 Number of scatterers: 21387 At special positions: 0 Unit cell: (106.575, 115.71, 190.312, 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 30 16.00 P 386 15.00 O 4829 8.00 N 3895 7.00 C 12247 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.75 Conformation dependent library (CDL) restraints added in 608.4 milliseconds 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3126 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 8 sheets defined 64.7% alpha, 5.1% beta 167 base pairs and 277 stacking pairs defined. Time for finding SS restraints: 2.99 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 removed outlier: 3.660A pdb=" N ARG A 49 " --> pdb=" O THR A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 79 removed outlier: 3.901A pdb=" N LEU A 70 " --> pdb=" O PRO A 66 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.527A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 47 through 76 Processing helix chain 'B' and resid 82 through 94 Processing helix chain 'C' and resid 17 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.290A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.915A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 88 through 99 Processing helix chain 'D' and resid 103 through 121 Processing helix chain 'E' and resid 47 through 57 Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.791A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.980A pdb=" N ASP E 106 " --> pdb=" O GLY E 102 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ALA E 111 " --> pdb=" O THR E 107 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ILE E 112 " --> pdb=" O ASN E 108 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N HIS E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.544A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 removed outlier: 3.619A pdb=" N GLY F 28 " --> pdb=" O ASN F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 47 through 77 removed outlier: 3.798A pdb=" N TYR F 51 " --> pdb=" O SER F 47 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLU F 52 " --> pdb=" O GLY F 48 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 through 38 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.042A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 4.105A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLN G 84 " --> pdb=" O PRO G 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 98 removed outlier: 3.681A pdb=" N LEU G 96 " --> pdb=" O GLU G 92 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 82 Processing helix chain 'H' and resid 87 through 99 removed outlier: 3.772A pdb=" N ILE H 91 " --> pdb=" O THR H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 121 Processing helix chain 'X' and resid 59 through 91 removed outlier: 4.512A pdb=" N ASN X 88 " --> pdb=" O GLU X 84 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N GLU X 89 " --> pdb=" O ILE X 85 " (cutoff:3.500A) Processing helix chain 'X' and resid 95 through 104 removed outlier: 3.733A pdb=" N HIS X 99 " --> pdb=" O ASP X 95 " (cutoff:3.500A) Processing helix chain 'X' and resid 121 through 132 removed outlier: 3.552A pdb=" N GLU X 125 " --> pdb=" O ASN X 121 " (cutoff:3.500A) Processing helix chain 'X' and resid 134 through 145 removed outlier: 3.795A pdb=" N LEU X 138 " --> pdb=" O THR X 134 " (cutoff:3.500A) Processing helix chain 'X' and resid 150 through 164 Processing helix chain 'X' and resid 315 through 343 removed outlier: 3.789A pdb=" N ALA X 319 " --> pdb=" O ALA X 315 " (cutoff:3.500A) Processing helix chain 'X' and resid 343 through 353 removed outlier: 3.819A pdb=" N ASP X 353 " --> pdb=" O GLU X 349 " (cutoff:3.500A) Processing helix chain 'X' and resid 358 through 364 Processing helix chain 'X' and resid 368 through 383 Proline residue: X 378 - end of helix Processing helix chain 'X' and resid 387 through 395 Processing helix chain 'X' and resid 405 through 410 removed outlier: 4.158A pdb=" N GLY X 408 " --> pdb=" O PHE X 405 " (cutoff:3.500A) Processing helix chain 'X' and resid 411 through 427 removed outlier: 4.204A pdb=" N HIS X 415 " --> pdb=" O PRO X 411 " (cutoff:3.500A) Processing helix chain 'X' and resid 430 through 436 Processing helix chain 'X' and resid 436 through 446 Processing helix chain 'X' and resid 477 through 482 Processing helix chain 'X' and resid 483 through 494 Processing helix chain 'X' and resid 512 through 525 Processing helix chain 'X' and resid 591 through 598 Processing helix chain 'X' and resid 614 through 626 Processing helix chain 'X' and resid 628 through 637 Processing helix chain 'X' and resid 644 through 654 Processing helix chain 'X' and resid 663 through 668 Processing helix chain 'X' and resid 679 through 685 Processing helix chain 'X' and resid 692 through 698 Processing helix chain 'X' and resid 702 through 709 removed outlier: 4.070A pdb=" N GLU X 706 " --> pdb=" O LEU X 702 " (cutoff:3.500A) Processing helix chain 'X' and resid 720 through 727 Processing helix chain 'X' and resid 730 through 751 Processing helix chain 'X' and resid 926 through 940 Processing helix chain 'X' and resid 959 through 971 removed outlier: 3.637A pdb=" N VAL X 963 " --> pdb=" O LYS X 959 " (cutoff:3.500A) Processing helix chain 'X' and resid 980 through 999 removed outlier: 3.701A pdb=" N ALA X 987 " --> pdb=" O HIS X 983 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N TYR X 988 " --> pdb=" O ALA X 984 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLY X 994 " --> pdb=" O ASN X 990 " (cutoff:3.500A) Processing helix chain 'X' and resid 1001 through 1007 Processing helix chain 'X' and resid 1041 through 1047 removed outlier: 4.248A pdb=" N PHE X1045 " --> pdb=" O ILE X1042 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS X1047 " --> pdb=" O ASN X1044 " (cutoff:3.500A) Processing helix chain 'X' and resid 1077 through 1089 Processing helix chain 'X' and resid 1127 through 1132 Processing helix chain 'X' and resid 1168 through 1177 removed outlier: 4.160A pdb=" N SER X1172 " --> pdb=" O ILE X1168 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N SER X1173 " --> pdb=" O MET X1169 " (cutoff:3.500A) Processing helix chain 'X' and resid 1177 through 1185 Processing helix chain 'X' and resid 1191 through 1195 Processing helix chain 'X' and resid 1229 through 1241 Processing helix chain 'X' and resid 1254 through 1262 Processing helix chain 'X' and resid 1262 through 1281 Processing helix chain 'X' and resid 1283 through 1298 removed outlier: 3.617A pdb=" N LEU X1287 " --> pdb=" O ALA X1283 " (cutoff:3.500A) Processing helix chain 'X' and resid 1301 through 1313 Processing helix chain 'X' and resid 1314 through 1316 No H-bonds generated for 'chain 'X' and resid 1314 through 1316' Processing helix chain 'X' and resid 1339 through 1345 removed outlier: 3.678A pdb=" N ASP X1344 " --> pdb=" O LYS X1340 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 42 through 43 removed outlier: 6.982A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'C' and resid 100 through 101 Processing sheet with id=AA3, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AA4, first strand: chain 'X' and resid 954 through 957 removed outlier: 4.168A pdb=" N ASN X 758 " --> pdb=" O TYR X 5 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'X' and resid 29 through 33 Processing sheet with id=AA6, first strand: chain 'X' and resid 1156 through 1167 removed outlier: 5.704A pdb=" N LYS X1156 " --> pdb=" O GLU X1150 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLU X1150 " --> pdb=" O LYS X1156 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N LYS X1158 " --> pdb=" O LYS X1148 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N LYS X1148 " --> pdb=" O LYS X1158 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL X1160 " --> pdb=" O VAL X1146 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N VAL X1146 " --> pdb=" O VAL X1160 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N GLU X1162 " --> pdb=" O LEU X1144 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N LEU X1144 " --> pdb=" O GLU X1162 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LEU X1164 " --> pdb=" O SER X1142 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N SER X1142 " --> pdb=" O LEU X1164 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N ILE X1166 " --> pdb=" O ALA X1140 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ILE X1196 " --> pdb=" O LEU X1144 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'X' and resid 1220 through 1222 removed outlier: 3.841A pdb=" N SER X1202 " --> pdb=" O LEU X1214 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N LEU X1203 " --> pdb=" O ILE X1348 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE X1348 " --> pdb=" O LEU X1203 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLU X1205 " --> pdb=" O THR X1346 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N THR X1346 " --> pdb=" O GLU X1205 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'X' and resid 1324 through 1325 761 hydrogen bonds defined for protein. 2256 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 431 hydrogen bonds 854 hydrogen bond angles 0 basepair planarities 167 basepair parallelities 277 stacking parallelities Total time for adding SS restraints: 6.31 Time building geometry restraints manager: 2.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4252 1.33 - 1.45: 6775 1.45 - 1.57: 10716 1.57 - 1.69: 768 1.69 - 1.81: 55 Bond restraints: 22566 Sorted by residual: bond pdb=" C3' DT J 66 " pdb=" C2' DT J 66 " ideal model delta sigma weight residual 1.516 1.546 -0.030 8.00e-03 1.56e+04 1.38e+01 bond pdb=" C3' DC I 52 " pdb=" C2' DC I 52 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.35e+01 bond pdb=" C3' DT I 111 " pdb=" C2' DT I 111 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.34e+01 bond pdb=" C3' DG J -21 " pdb=" C2' DG J -21 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.31e+01 bond pdb=" C3' DG J 23 " pdb=" C2' DG J 23 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.17e+01 ... (remaining 22561 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.25: 31135 2.25 - 4.51: 827 4.51 - 6.76: 139 6.76 - 9.01: 28 9.01 - 11.26: 4 Bond angle restraints: 32133 Sorted by residual: angle pdb=" O5' DG I 23 " pdb=" C5' DG I 23 " pdb=" C4' DG I 23 " ideal model delta sigma weight residual 109.40 115.26 -5.86 8.00e-01 1.56e+00 5.37e+01 angle pdb=" O5' DC J 52 " pdb=" C5' DC J 52 " pdb=" C4' DC J 52 " ideal model delta sigma weight residual 109.40 114.77 -5.37 8.00e-01 1.56e+00 4.50e+01 angle pdb=" O4' DG I 47 " pdb=" C1' DG I 47 " pdb=" N9 DG I 47 " ideal model delta sigma weight residual 108.00 112.20 -4.20 7.00e-01 2.04e+00 3.60e+01 angle pdb=" O4' DT J 22 " pdb=" C1' DT J 22 " pdb=" N1 DT J 22 " ideal model delta sigma weight residual 108.00 112.01 -4.01 7.00e-01 2.04e+00 3.28e+01 angle pdb=" O3' DT I 17 " pdb=" P DC I 18 " pdb=" O5' DC I 18 " ideal model delta sigma weight residual 104.00 95.46 8.54 1.50e+00 4.44e-01 3.24e+01 ... (remaining 32128 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.57: 10809 31.57 - 63.13: 1977 63.13 - 94.70: 143 94.70 - 126.27: 11 126.27 - 157.84: 4 Dihedral angle restraints: 12944 sinusoidal: 8120 harmonic: 4824 Sorted by residual: dihedral pdb=" CA TYR F 98 " pdb=" C TYR F 98 " pdb=" N GLY F 99 " pdb=" CA GLY F 99 " ideal model delta harmonic sigma weight residual 180.00 153.07 26.93 0 5.00e+00 4.00e-02 2.90e+01 dihedral pdb=" C4' A W 28 " pdb=" O4' A W 28 " pdb=" C1' A W 28 " pdb=" C2' A W 28 " ideal model delta sinusoidal sigma weight residual -21.00 7.49 -28.49 1 8.00e+00 1.56e-02 1.82e+01 dihedral pdb=" C3' A W 28 " pdb=" C4' A W 28 " pdb=" O4' A W 28 " pdb=" C1' A W 28 " ideal model delta sinusoidal sigma weight residual -2.00 -28.60 26.60 1 8.00e+00 1.56e-02 1.59e+01 ... (remaining 12941 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.124: 3606 0.124 - 0.248: 47 0.248 - 0.372: 0 0.372 - 0.496: 3 0.496 - 0.620: 46 Chirality restraints: 3702 Sorted by residual: chirality pdb=" P DG I 28 " pdb=" OP1 DG I 28 " pdb=" OP2 DG I 28 " pdb=" O5' DG I 28 " both_signs ideal model delta sigma weight residual True 2.34 -2.96 -0.62 2.00e-01 2.50e+01 9.62e+00 chirality pdb=" P DG I 47 " pdb=" OP1 DG I 47 " pdb=" OP2 DG I 47 " pdb=" O5' DG I 47 " both_signs ideal model delta sigma weight residual True 2.34 -2.95 -0.62 2.00e-01 2.50e+01 9.57e+00 chirality pdb=" P DT J 68 " pdb=" OP1 DT J 68 " pdb=" OP2 DT J 68 " pdb=" O5' DT J 68 " both_signs ideal model delta sigma weight residual True 2.34 -2.95 -0.62 2.00e-01 2.50e+01 9.52e+00 ... (remaining 3699 not shown) Planarity restraints: 2702 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DC I 100 " 0.006 2.00e-02 2.50e+03 2.71e-02 1.65e+01 pdb=" N1 DC I 100 " -0.010 2.00e-02 2.50e+03 pdb=" C2 DC I 100 " 0.068 2.00e-02 2.50e+03 pdb=" O2 DC I 100 " -0.033 2.00e-02 2.50e+03 pdb=" N3 DC I 100 " -0.023 2.00e-02 2.50e+03 pdb=" C4 DC I 100 " 0.000 2.00e-02 2.50e+03 pdb=" N4 DC I 100 " 0.008 2.00e-02 2.50e+03 pdb=" C5 DC I 100 " -0.010 2.00e-02 2.50e+03 pdb=" C6 DC I 100 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG J -18 " -0.020 2.00e-02 2.50e+03 1.57e-02 7.37e+00 pdb=" N9 DG J -18 " 0.023 2.00e-02 2.50e+03 pdb=" C8 DG J -18 " 0.006 2.00e-02 2.50e+03 pdb=" N7 DG J -18 " 0.003 2.00e-02 2.50e+03 pdb=" C5 DG J -18 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DG J -18 " -0.005 2.00e-02 2.50e+03 pdb=" O6 DG J -18 " -0.008 2.00e-02 2.50e+03 pdb=" N1 DG J -18 " 0.012 2.00e-02 2.50e+03 pdb=" C2 DG J -18 " -0.035 2.00e-02 2.50e+03 pdb=" N2 DG J -18 " 0.023 2.00e-02 2.50e+03 pdb=" N3 DG J -18 " 0.000 2.00e-02 2.50e+03 pdb=" C4 DG J -18 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG J 38 " -0.034 2.00e-02 2.50e+03 1.53e-02 7.03e+00 pdb=" N9 DG J 38 " 0.038 2.00e-02 2.50e+03 pdb=" C8 DG J 38 " 0.006 2.00e-02 2.50e+03 pdb=" N7 DG J 38 " 0.002 2.00e-02 2.50e+03 pdb=" C5 DG J 38 " -0.005 2.00e-02 2.50e+03 pdb=" C6 DG J 38 " -0.008 2.00e-02 2.50e+03 pdb=" O6 DG J 38 " -0.006 2.00e-02 2.50e+03 pdb=" N1 DG J 38 " -0.002 2.00e-02 2.50e+03 pdb=" C2 DG J 38 " 0.005 2.00e-02 2.50e+03 pdb=" N2 DG J 38 " 0.004 2.00e-02 2.50e+03 pdb=" N3 DG J 38 " 0.003 2.00e-02 2.50e+03 pdb=" C4 DG J 38 " -0.003 2.00e-02 2.50e+03 ... (remaining 2699 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.74: 2067 2.74 - 3.28: 23061 3.28 - 3.82: 43980 3.82 - 4.36: 50281 4.36 - 4.90: 70903 Nonbonded interactions: 190292 Sorted by model distance: nonbonded pdb=" O2' C W 8 " pdb=" OP1 C W 9 " model vdw 2.194 3.040 nonbonded pdb=" O2' A W 42 " pdb=" OP1 G W 43 " model vdw 2.202 3.040 nonbonded pdb=" NH1 ARG E 116 " pdb=" OP2 DC J -2 " model vdw 2.207 3.120 nonbonded pdb=" O ALA X 149 " pdb=" OH TYR X 430 " model vdw 2.211 3.040 nonbonded pdb=" OP1 G W 16 " pdb=" NH2 ARG X 74 " model vdw 2.213 3.120 ... (remaining 190287 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 'A' and resid 46 through 134) selection = (chain 'E' and resid 46 through 134) } ncs_group { reference = (chain 'B' and resid 25 through 102) selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 16 through 109) selection = (chain 'G' and resid 16 through 109) } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.760 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: 0.260 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 23.360 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 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 : 0.006 0.051 22566 Z= 0.458 Angle : 0.875 11.263 32133 Z= 0.653 Chirality : 0.077 0.620 3702 Planarity : 0.004 0.043 2702 Dihedral : 25.386 157.836 9818 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 24.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.14 % Allowed : 7.49 % Favored : 92.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.54 (0.20), residues: 1609 helix: 1.07 (0.16), residues: 942 sheet: 0.09 (0.59), residues: 75 loop : -0.67 (0.25), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG X1210 TYR 0.016 0.002 TYR C 57 PHE 0.013 0.002 PHE X1313 TRP 0.006 0.001 TRP X 464 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00570 / 0.46 (22566) covalent geometry : angle 0.87457 / 0.65 (32133) hydrogen bonds : bond 0.13676 / 9.38 ( 1192) hydrogen bonds : angle 6.24768 / 4.50 ( 3110) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 97 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 99 average time/residue: 0.1566 time to fit residues: 24.2401 Evaluate side-chains 53 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 98 optimal weight: 30.0000 chunk 194 optimal weight: 9.9990 chunk 107 optimal weight: 0.0010 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 40.0000 chunk 77 optimal weight: 40.0000 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 40.0000 overall best weight: 6.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN G 24 GLN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 14 ASN X 129 HIS X 415 HIS X 459 ASN ** X 698 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 979 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 980 ASN X1256 GLN X1317 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.036094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.029803 restraints weight = 365631.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.030340 restraints weight = 255055.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.030690 restraints weight = 196637.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.030947 restraints weight = 165217.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.031132 restraints weight = 145868.909| |-----------------------------------------------------------------------------| r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 22566 Z= 0.222 Angle : 0.761 12.351 32133 Z= 0.430 Chirality : 0.050 0.300 3702 Planarity : 0.005 0.051 2702 Dihedral : 29.546 158.266 6426 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 22.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 0.14 % Allowed : 3.61 % Favored : 96.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.49 (0.20), residues: 1609 helix: 1.05 (0.15), residues: 1012 sheet: -0.68 (0.50), residues: 90 loop : -0.84 (0.27), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG G 81 TYR 0.019 0.002 TYR D 37 PHE 0.019 0.002 PHE X1313 TRP 0.012 0.002 TRP X 464 HIS 0.008 0.002 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.22 (22566) covalent geometry : angle 0.76137 / 0.43 (32133) hydrogen bonds : bond 0.08916 / 6.12 ( 1192) hydrogen bonds : angle 4.70020 / 3.42 ( 3110) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 70 time to evaluate : 0.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 PHE cc_start: 0.9150 (t80) cc_final: 0.8702 (t80) REVERT: A 90 MET cc_start: 0.9440 (mmp) cc_final: 0.9173 (mmm) REVERT: B 85 ASP cc_start: 0.9143 (m-30) cc_final: 0.8886 (m-30) REVERT: D 106 HIS cc_start: 0.9565 (m90) cc_final: 0.9207 (m90) REVERT: H 68 GLU cc_start: 0.9363 (tt0) cc_final: 0.8659 (pt0) REVERT: H 79 HIS cc_start: 0.9525 (m90) cc_final: 0.9153 (m90) REVERT: X 383 MET cc_start: 0.9112 (ttm) cc_final: 0.8816 (ttm) REVERT: X 751 MET cc_start: 0.9272 (ttm) cc_final: 0.9071 (ttp) outliers start: 2 outliers final: 0 residues processed: 72 average time/residue: 0.1492 time to fit residues: 17.5806 Evaluate side-chains 55 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 2 optimal weight: 20.0000 chunk 96 optimal weight: 50.0000 chunk 108 optimal weight: 0.0970 chunk 140 optimal weight: 1.9990 chunk 51 optimal weight: 30.0000 chunk 30 optimal weight: 8.9990 chunk 11 optimal weight: 20.0000 chunk 93 optimal weight: 30.0000 chunk 138 optimal weight: 6.9990 chunk 1 optimal weight: 7.9990 chunk 16 optimal weight: 0.9980 overall best weight: 3.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 698 HIS X 723 HIS X1234 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.036348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.029980 restraints weight = 363232.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.030566 restraints weight = 244432.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.030926 restraints weight = 183991.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.031204 restraints weight = 153463.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.031402 restraints weight = 134437.310| |-----------------------------------------------------------------------------| r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.177 22566 Z= 0.157 Angle : 0.661 8.031 32133 Z= 0.380 Chirality : 0.045 0.262 3702 Planarity : 0.005 0.053 2702 Dihedral : 29.529 160.457 6426 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 18.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.78 (0.20), residues: 1609 helix: 1.31 (0.16), residues: 1009 sheet: -0.69 (0.53), residues: 78 loop : -0.77 (0.26), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 63 TYR 0.012 0.002 TYR X1232 PHE 0.049 0.002 PHE C 25 TRP 0.008 0.001 TRP X 464 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.16 (22566) covalent geometry : angle 0.66093 / 0.38 (32133) hydrogen bonds : bond 0.06153 / 4.21 ( 1192) hydrogen bonds : angle 4.40120 / 3.19 ( 3110) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 PHE cc_start: 0.9077 (t80) cc_final: 0.8626 (t80) REVERT: A 90 MET cc_start: 0.9405 (mmp) cc_final: 0.9170 (mmm) REVERT: A 120 MET cc_start: 0.7233 (mpp) cc_final: 0.6683 (mpp) REVERT: D 105 LYS cc_start: 0.9576 (pttm) cc_final: 0.9306 (ptpp) REVERT: D 106 HIS cc_start: 0.9491 (m90) cc_final: 0.9170 (m90) REVERT: E 94 GLU cc_start: 0.9433 (tm-30) cc_final: 0.9099 (tm-30) REVERT: F 97 LEU cc_start: 0.8786 (tp) cc_final: 0.8236 (mt) REVERT: H 59 MET cc_start: 0.9774 (mmm) cc_final: 0.9480 (mmm) REVERT: H 66 ILE cc_start: 0.9349 (pt) cc_final: 0.9147 (pt) REVERT: H 77 LEU cc_start: 0.9784 (tt) cc_final: 0.9559 (pp) REVERT: X 383 MET cc_start: 0.9097 (ttm) cc_final: 0.8771 (ttm) REVERT: X 419 LEU cc_start: 0.9555 (tt) cc_final: 0.9316 (mt) REVERT: X 751 MET cc_start: 0.9260 (ttm) cc_final: 0.9006 (ttp) outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.1426 time to fit residues: 15.7870 Evaluate side-chains 56 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 36 optimal weight: 7.9990 chunk 139 optimal weight: 0.3980 chunk 161 optimal weight: 30.0000 chunk 196 optimal weight: 20.0000 chunk 190 optimal weight: 5.9990 chunk 82 optimal weight: 50.0000 chunk 3 optimal weight: 4.9990 chunk 113 optimal weight: 4.9990 chunk 88 optimal weight: 50.0000 chunk 109 optimal weight: 30.0000 chunk 122 optimal weight: 30.0000 overall best weight: 4.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.035644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.029400 restraints weight = 368641.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.029932 restraints weight = 251894.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.030270 restraints weight = 193170.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.030530 restraints weight = 161686.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.030627 restraints weight = 142724.482| |-----------------------------------------------------------------------------| r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 22566 Z= 0.172 Angle : 0.655 10.557 32133 Z= 0.374 Chirality : 0.044 0.256 3702 Planarity : 0.004 0.057 2702 Dihedral : 29.479 165.489 6426 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 19.66 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.11 % Favored : 97.82 % Rotamer: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.84 (0.21), residues: 1609 helix: 1.35 (0.16), residues: 1015 sheet: -0.78 (0.51), residues: 88 loop : -0.74 (0.27), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 96 TYR 0.020 0.002 TYR H 37 PHE 0.023 0.002 PHE C 25 TRP 0.008 0.001 TRP X 464 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.17 (22566) covalent geometry : angle 0.65464 / 0.37 (32133) hydrogen bonds : bond 0.07343 / 5.05 ( 1192) hydrogen bonds : angle 4.29161 / 3.11 ( 3110) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 PHE cc_start: 0.9123 (t80) cc_final: 0.8668 (t80) REVERT: A 90 MET cc_start: 0.9435 (mmp) cc_final: 0.9163 (mmm) REVERT: A 120 MET cc_start: 0.7103 (mpp) cc_final: 0.6880 (mpp) REVERT: D 105 LYS cc_start: 0.9575 (pttm) cc_final: 0.9365 (mptt) REVERT: D 106 HIS cc_start: 0.9530 (m90) cc_final: 0.9282 (m90) REVERT: H 68 GLU cc_start: 0.9321 (tt0) cc_final: 0.8986 (tm-30) REVERT: H 77 LEU cc_start: 0.9746 (tt) cc_final: 0.9518 (pp) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.1416 time to fit residues: 15.4628 Evaluate side-chains 53 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 77 optimal weight: 50.0000 chunk 135 optimal weight: 5.9990 chunk 12 optimal weight: 10.0000 chunk 53 optimal weight: 30.0000 chunk 115 optimal weight: 20.0000 chunk 183 optimal weight: 2.9990 chunk 72 optimal weight: 50.0000 chunk 172 optimal weight: 9.9990 chunk 52 optimal weight: 7.9990 chunk 195 optimal weight: 9.9990 chunk 28 optimal weight: 5.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 GLN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X1308 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.034504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.028220 restraints weight = 383467.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.028804 restraints weight = 253833.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.029154 restraints weight = 189569.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.029425 restraints weight = 157129.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.029613 restraints weight = 136989.275| |-----------------------------------------------------------------------------| r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 22566 Z= 0.196 Angle : 0.671 9.595 32133 Z= 0.382 Chirality : 0.045 0.263 3702 Planarity : 0.005 0.096 2702 Dihedral : 29.655 167.800 6426 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 21.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.20), residues: 1609 helix: 1.32 (0.16), residues: 1016 sheet: -0.62 (0.55), residues: 77 loop : -0.76 (0.27), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 76 TYR 0.021 0.002 TYR G 57 PHE 0.021 0.002 PHE C 25 TRP 0.008 0.001 TRP X 464 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.20 (22566) covalent geometry : angle 0.67059 / 0.38 (32133) hydrogen bonds : bond 0.07970 / 5.46 ( 1192) hydrogen bonds : angle 4.34121 / 3.14 ( 3110) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 PHE cc_start: 0.9219 (t80) cc_final: 0.8752 (t80) REVERT: A 90 MET cc_start: 0.9386 (mmp) cc_final: 0.9060 (mmm) REVERT: C 41 GLU cc_start: 0.9742 (tm-30) cc_final: 0.9352 (pp20) REVERT: D 105 LYS cc_start: 0.9535 (pttm) cc_final: 0.9333 (ptpp) REVERT: D 106 HIS cc_start: 0.9604 (m90) cc_final: 0.9386 (m90) REVERT: H 68 GLU cc_start: 0.9254 (tt0) cc_final: 0.9048 (tm-30) REVERT: H 77 LEU cc_start: 0.9738 (tt) cc_final: 0.9506 (pp) REVERT: X 751 MET cc_start: 0.9356 (ttm) cc_final: 0.9119 (ttm) outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 0.1385 time to fit residues: 14.4839 Evaluate side-chains 49 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 32 optimal weight: 2.9990 chunk 58 optimal weight: 7.9990 chunk 35 optimal weight: 9.9990 chunk 92 optimal weight: 40.0000 chunk 71 optimal weight: 30.0000 chunk 24 optimal weight: 7.9990 chunk 43 optimal weight: 0.7980 chunk 194 optimal weight: 3.9990 chunk 60 optimal weight: 20.0000 chunk 193 optimal weight: 9.9990 chunk 96 optimal weight: 50.0000 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.034730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.028412 restraints weight = 380000.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.029028 restraints weight = 250543.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.029386 restraints weight = 185565.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.029662 restraints weight = 153569.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.029852 restraints weight = 133864.461| |-----------------------------------------------------------------------------| r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.2932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 22566 Z= 0.163 Angle : 0.646 10.073 32133 Z= 0.367 Chirality : 0.044 0.263 3702 Planarity : 0.004 0.060 2702 Dihedral : 29.620 167.544 6426 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 19.25 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.36 % Favored : 97.58 % Rotamer: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.91 (0.21), residues: 1609 helix: 1.41 (0.16), residues: 1015 sheet: -0.69 (0.52), residues: 78 loop : -0.73 (0.27), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 81 TYR 0.017 0.002 TYR G 39 PHE 0.021 0.002 PHE X 351 TRP 0.010 0.001 TRP X 464 HIS 0.009 0.001 HIS X 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.16 (22566) covalent geometry : angle 0.64553 / 0.37 (32133) hydrogen bonds : bond 0.06583 / 4.50 ( 1192) hydrogen bonds : angle 4.23922 / 3.08 ( 3110) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 PHE cc_start: 0.9200 (t80) cc_final: 0.8731 (t80) REVERT: A 90 MET cc_start: 0.9380 (mmp) cc_final: 0.9054 (mmm) REVERT: A 120 MET cc_start: 0.6661 (mpp) cc_final: 0.6350 (mpp) REVERT: C 41 GLU cc_start: 0.9723 (tm-30) cc_final: 0.9339 (pp20) REVERT: D 68 GLU cc_start: 0.9574 (pt0) cc_final: 0.9297 (pp20) REVERT: D 105 LYS cc_start: 0.9545 (pttm) cc_final: 0.9343 (ptpp) REVERT: D 106 HIS cc_start: 0.9584 (m90) cc_final: 0.9372 (m90) REVERT: E 94 GLU cc_start: 0.9655 (tm-30) cc_final: 0.9316 (tm-30) REVERT: H 68 GLU cc_start: 0.9251 (tt0) cc_final: 0.9011 (tm-30) REVERT: H 77 LEU cc_start: 0.9676 (tt) cc_final: 0.9424 (pp) REVERT: X 751 MET cc_start: 0.9361 (ttm) cc_final: 0.9036 (ttm) outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.1407 time to fit residues: 14.6467 Evaluate side-chains 54 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 1 optimal weight: 0.0570 chunk 27 optimal weight: 0.4980 chunk 109 optimal weight: 6.9990 chunk 122 optimal weight: 40.0000 chunk 51 optimal weight: 20.0000 chunk 80 optimal weight: 50.0000 chunk 76 optimal weight: 50.0000 chunk 93 optimal weight: 40.0000 chunk 32 optimal weight: 6.9990 chunk 34 optimal weight: 20.0000 chunk 193 optimal weight: 10.0000 overall best weight: 4.9106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 60 ASN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X1311 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.034462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.028165 restraints weight = 378299.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.028770 restraints weight = 250264.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.029121 restraints weight = 185973.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.029393 restraints weight = 153887.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.029585 restraints weight = 134306.001| |-----------------------------------------------------------------------------| r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.3234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 22566 Z= 0.166 Angle : 0.636 9.339 32133 Z= 0.362 Chirality : 0.043 0.265 3702 Planarity : 0.004 0.065 2702 Dihedral : 29.553 169.624 6426 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 19.35 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.49 % Favored : 97.45 % Rotamer: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.02 (0.21), residues: 1609 helix: 1.48 (0.16), residues: 1013 sheet: -0.37 (0.58), residues: 67 loop : -0.71 (0.26), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 63 TYR 0.015 0.002 TYR G 39 PHE 0.018 0.002 PHE X1105 TRP 0.007 0.001 TRP X 464 HIS 0.007 0.001 HIS X 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.17 (22566) covalent geometry : angle 0.63590 / 0.36 (32133) hydrogen bonds : bond 0.06791 / 4.63 ( 1192) hydrogen bonds : angle 4.17807 / 3.03 ( 3110) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 PHE cc_start: 0.9188 (t80) cc_final: 0.8714 (t80) REVERT: A 90 MET cc_start: 0.9391 (mmp) cc_final: 0.9066 (mmm) REVERT: C 41 GLU cc_start: 0.9712 (tm-30) cc_final: 0.9392 (pp20) REVERT: D 68 GLU cc_start: 0.9507 (pt0) cc_final: 0.9261 (pp20) REVERT: D 106 HIS cc_start: 0.9597 (m90) cc_final: 0.9375 (m90) REVERT: E 94 GLU cc_start: 0.9624 (tm-30) cc_final: 0.9181 (tm-30) REVERT: F 97 LEU cc_start: 0.9188 (mt) cc_final: 0.8587 (mt) REVERT: H 77 LEU cc_start: 0.9684 (tt) cc_final: 0.9443 (pp) REVERT: H 79 HIS cc_start: 0.9473 (m90) cc_final: 0.9149 (m90) REVERT: X 751 MET cc_start: 0.9360 (ttm) cc_final: 0.9020 (ttm) outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.1270 time to fit residues: 13.1390 Evaluate side-chains 52 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 106 optimal weight: 8.9990 chunk 89 optimal weight: 40.0000 chunk 96 optimal weight: 50.0000 chunk 70 optimal weight: 30.0000 chunk 124 optimal weight: 8.9990 chunk 9 optimal weight: 20.0000 chunk 53 optimal weight: 30.0000 chunk 121 optimal weight: 9.9990 chunk 92 optimal weight: 40.0000 chunk 170 optimal weight: 10.0000 chunk 71 optimal weight: 30.0000 overall best weight: 11.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 GLN H 60 ASN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 698 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X1297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.032472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.026418 restraints weight = 399846.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.026969 restraints weight = 264254.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.027294 restraints weight = 198662.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.027553 restraints weight = 165125.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.027731 restraints weight = 144522.638| |-----------------------------------------------------------------------------| r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.3829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.111 22566 Z= 0.302 Angle : 0.773 9.217 32133 Z= 0.441 Chirality : 0.048 0.289 3702 Planarity : 0.006 0.071 2702 Dihedral : 29.953 173.360 6426 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 32.27 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.11 % Favored : 96.83 % Rotamer: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.35 (0.20), residues: 1609 helix: 0.96 (0.15), residues: 1010 sheet: -0.98 (0.55), residues: 82 loop : -0.88 (0.26), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG X 71 TYR 0.027 0.003 TYR D 34 PHE 0.042 0.003 PHE C 25 TRP 0.023 0.003 TRP X 464 HIS 0.009 0.002 HIS X 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00531 / 0.30 (22566) covalent geometry : angle 0.77338 / 0.44 (32133) hydrogen bonds : bond 0.13011 / 8.86 ( 1192) hydrogen bonds : angle 4.75673 / 3.47 ( 3110) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 PHE cc_start: 0.9278 (t80) cc_final: 0.8867 (t80) REVERT: A 90 MET cc_start: 0.9422 (mmp) cc_final: 0.9063 (mmp) REVERT: C 41 GLU cc_start: 0.9658 (tm-30) cc_final: 0.9337 (pp20) REVERT: D 106 HIS cc_start: 0.9647 (m90) cc_final: 0.9402 (m90) REVERT: E 67 PHE cc_start: 0.9192 (t80) cc_final: 0.8930 (t80) REVERT: H 77 LEU cc_start: 0.9592 (tt) cc_final: 0.9321 (pp) REVERT: H 79 HIS cc_start: 0.9503 (m90) cc_final: 0.9161 (m90) REVERT: X 751 MET cc_start: 0.9122 (ttm) cc_final: 0.8627 (ttm) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.1334 time to fit residues: 11.2296 Evaluate side-chains 45 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 34 optimal weight: 10.0000 chunk 144 optimal weight: 10.0000 chunk 55 optimal weight: 5.9990 chunk 25 optimal weight: 10.0000 chunk 174 optimal weight: 20.0000 chunk 79 optimal weight: 50.0000 chunk 152 optimal weight: 8.9990 chunk 124 optimal weight: 8.9990 chunk 156 optimal weight: 7.9990 chunk 171 optimal weight: 0.9990 chunk 53 optimal weight: 30.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 GLN ** D 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 60 ASN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.033179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.027030 restraints weight = 390436.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.027606 restraints weight = 258435.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.027953 restraints weight = 193488.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.028225 restraints weight = 159899.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.028392 restraints weight = 139960.819| |-----------------------------------------------------------------------------| r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.3913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 22566 Z= 0.195 Angle : 0.688 10.293 32133 Z= 0.389 Chirality : 0.046 0.315 3702 Planarity : 0.005 0.072 2702 Dihedral : 29.957 170.849 6426 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 23.94 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.05 % Favored : 96.89 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.54 (0.20), residues: 1609 helix: 1.13 (0.16), residues: 1010 sheet: -1.52 (0.52), residues: 94 loop : -0.71 (0.27), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG D 96 TYR 0.040 0.002 TYR G 39 PHE 0.028 0.002 PHE X 432 TRP 0.013 0.002 TRP X 464 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.19 (22566) covalent geometry : angle 0.68806 / 0.39 (32133) hydrogen bonds : bond 0.08059 / 5.50 ( 1192) hydrogen bonds : angle 4.52782 / 3.29 ( 3110) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 PHE cc_start: 0.9247 (t80) cc_final: 0.8838 (t80) REVERT: A 90 MET cc_start: 0.9413 (mmp) cc_final: 0.9065 (mmm) REVERT: A 120 MET cc_start: 0.6733 (mpp) cc_final: 0.6495 (mpp) REVERT: D 106 HIS cc_start: 0.9648 (m90) cc_final: 0.9388 (m90) REVERT: E 67 PHE cc_start: 0.9046 (t80) cc_final: 0.8840 (t80) REVERT: H 77 LEU cc_start: 0.9485 (tt) cc_final: 0.9221 (pp) REVERT: H 79 HIS cc_start: 0.9449 (m90) cc_final: 0.9125 (m90) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.1260 time to fit residues: 11.6362 Evaluate side-chains 46 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 89 optimal weight: 40.0000 chunk 159 optimal weight: 9.9990 chunk 177 optimal weight: 10.0000 chunk 25 optimal weight: 0.0270 chunk 59 optimal weight: 10.0000 chunk 118 optimal weight: 6.9990 chunk 129 optimal weight: 3.9990 chunk 180 optimal weight: 5.9990 chunk 92 optimal weight: 40.0000 chunk 134 optimal weight: 6.9990 chunk 63 optimal weight: 5.9990 overall best weight: 4.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 60 ASN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 412 HIS X 698 HIS ** X 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.033706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.027487 restraints weight = 385456.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.028086 restraints weight = 253177.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.028427 restraints weight = 188072.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.028715 restraints weight = 155515.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.028864 restraints weight = 135932.437| |-----------------------------------------------------------------------------| r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.4051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 22566 Z= 0.162 Angle : 0.651 8.922 32133 Z= 0.369 Chirality : 0.044 0.318 3702 Planarity : 0.005 0.073 2702 Dihedral : 29.718 170.665 6426 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 19.99 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.92 % Favored : 97.02 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.73 (0.21), residues: 1609 helix: 1.32 (0.16), residues: 1005 sheet: -1.55 (0.51), residues: 94 loop : -0.69 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 63 TYR 0.019 0.002 TYR G 39 PHE 0.024 0.002 PHE C 25 TRP 0.009 0.001 TRP X 464 HIS 0.008 0.001 HIS X 721 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.16 (22566) covalent geometry : angle 0.65132 / 0.37 (32133) hydrogen bonds : bond 0.06285 / 4.27 ( 1192) hydrogen bonds : angle 4.36374 / 3.17 ( 3110) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 PHE cc_start: 0.9205 (t80) cc_final: 0.8749 (t80) REVERT: A 90 MET cc_start: 0.9364 (mmp) cc_final: 0.9046 (mmp) REVERT: A 120 MET cc_start: 0.6739 (mpp) cc_final: 0.6510 (mpp) REVERT: D 106 HIS cc_start: 0.9652 (m90) cc_final: 0.9375 (m90) REVERT: H 77 LEU cc_start: 0.9568 (tt) cc_final: 0.9324 (pp) REVERT: H 79 HIS cc_start: 0.9429 (m90) cc_final: 0.9107 (m90) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.1302 time to fit residues: 11.8891 Evaluate side-chains 45 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 106 optimal weight: 4.9990 chunk 103 optimal weight: 30.0000 chunk 33 optimal weight: 7.9990 chunk 6 optimal weight: 5.9990 chunk 113 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 143 optimal weight: 50.0000 chunk 173 optimal weight: 0.9980 chunk 185 optimal weight: 6.9990 chunk 52 optimal weight: 8.9990 chunk 20 optimal weight: 8.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 60 ASN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.033656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.027446 restraints weight = 388072.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.028040 restraints weight = 252869.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.028389 restraints weight = 186567.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.028661 restraints weight = 154302.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.028843 restraints weight = 134475.920| |-----------------------------------------------------------------------------| r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.4199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 22566 Z= 0.157 Angle : 0.639 9.691 32133 Z= 0.362 Chirality : 0.044 0.298 3702 Planarity : 0.004 0.067 2702 Dihedral : 29.612 174.629 6426 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 19.48 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.67 % Favored : 97.27 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.88 (0.21), residues: 1609 helix: 1.42 (0.16), residues: 1004 sheet: -1.42 (0.52), residues: 93 loop : -0.62 (0.27), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 63 TYR 0.014 0.002 TYR X 515 PHE 0.018 0.002 PHE C 25 TRP 0.009 0.001 TRP X 464 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.16 (22566) covalent geometry : angle 0.63910 / 0.36 (32133) hydrogen bonds : bond 0.06251 / 4.25 ( 1192) hydrogen bonds : angle 4.29297 / 3.12 ( 3110) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2646.50 seconds wall clock time: 47 minutes 17.85 seconds (2837.85 seconds total)