Starting phenix.real_space_refine on Fri Aug 7 10:34:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yny_39431/08_2026/8yny_39431.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yny_39431/08_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8yny_39431/08_2026/8yny_39431.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yny_39431/08_2026/8yny_39431.map" model { file = "/net/cci-nas-00/data/ceres_data/8yny_39431/08_2026/8yny_39431.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yny_39431/08_2026/8yny_39431.cif" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 4.50, per 1000 atoms: 0.21 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: 2.05 Conformation dependent library (CDL) restraints added in 666.6 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: 3.16 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: 6.92 Time building geometry restraints manager: 2.74 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: 30965 2.25 - 4.51: 993 4.51 - 6.76: 143 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=" O5' DC J 53 " pdb=" C5' DC J 53 " pdb=" C4' DC J 53 " ideal model delta sigma weight residual 109.40 113.85 -4.45 8.00e-01 1.56e+00 3.09e+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: 3547 0.124 - 0.248: 106 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: 0.590 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: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 25.540 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.050 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.110 ------------------------------------------------------------------------------- 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= 0.461 Angle : 0.907 11.263 32133 Z= 0.683 Chirality : 0.079 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 0.00573 / 0.46 (22566) covalent geometry : angle 0.90690 / 0.68 (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 : 0.603 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: 0.1723 time to fit residues: 26.6307 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 : 0.635 ------------------------------------------------------------------------------- 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: 50.0000 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: 50.0000 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** ** 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 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.036134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.029879 restraints weight = 365865.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.030403 restraints weight = 253055.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.030735 restraints weight = 194304.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.030993 restraints weight = 164043.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.031187 restraints weight = 144694.921| |-----------------------------------------------------------------------------| r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.1501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.110 22566 Z= 0.221 Angle : 0.778 12.220 32133 Z= 0.431 Chirality : 0.050 0.289 3702 Planarity : 0.005 0.053 2702 Dihedral : 29.438 158.947 6426 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 22.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.14 % Allowed : 3.75 % Favored : 96.11 % 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: 0.51 (0.20), residues: 1609 helix: 1.06 (0.15), residues: 1012 sheet: -0.68 (0.50), residues: 90 loop : -0.83 (0.27), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG G 81 TYR 0.021 0.002 TYR X1201 PHE 0.022 0.002 PHE X1313 TRP 0.013 0.002 TRP X 476 HIS 0.012 0.002 HIS H 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.22 (22566) covalent geometry : angle 0.77769 / 0.43 (32133) hydrogen bonds : bond 0.08882 / 6.09 ( 1192) hydrogen bonds : angle 4.70523 / 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 : 0.659 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: 0.9142 (t80) cc_final: 0.8696 (t80) REVERT: A 90 MET cc_start: 0.9427 (mmp) cc_final: 0.9166 (mmm) REVERT: B 85 ASP cc_start: 0.9152 (m-30) cc_final: 0.8893 (m-30) REVERT: D 106 HIS cc_start: 0.9555 (m90) cc_final: 0.9192 (m90) REVERT: H 68 GLU cc_start: 0.9371 (tt0) cc_final: 0.8655 (pt0) REVERT: H 79 HIS cc_start: 0.9524 (m90) cc_final: 0.9150 (m90) REVERT: X 383 MET cc_start: 0.9083 (ttm) cc_final: 0.8779 (ttm) REVERT: X 751 MET cc_start: 0.8918 (ttm) cc_final: 0.8684 (ttp) outliers start: 2 outliers final: 0 residues processed: 72 average time/residue: 0.1466 time to fit residues: 17.2923 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 : 0.624 ------------------------------------------------------------------------------- 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: 8.9990 chunk 96 optimal weight: 50.0000 chunk 108 optimal weight: 3.9990 chunk 140 optimal weight: 0.8980 chunk 51 optimal weight: 30.0000 chunk 30 optimal weight: 7.9990 chunk 11 optimal weight: 20.0000 chunk 93 optimal weight: 30.0000 chunk 138 optimal weight: 20.0000 chunk 1 optimal weight: 9.9990 chunk 16 optimal weight: 4.9990 overall best weight: 5.3788 ------------------------------------------------------------------------------- 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 129 HIS ** X 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 698 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3181 r_free = 0.3181 target = 0.035851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.029592 restraints weight = 367340.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.030133 restraints weight = 252201.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.030475 restraints weight = 193985.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.030734 restraints weight = 162460.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.030836 restraints weight = 143352.655| |-----------------------------------------------------------------------------| r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.188 22566 Z= 0.178 Angle : 0.688 8.386 32133 Z= 0.390 Chirality : 0.046 0.278 3702 Planarity : 0.005 0.055 2702 Dihedral : 29.481 162.345 6426 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 20.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % 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: 0.70 (0.20), residues: 1609 helix: 1.24 (0.16), residues: 1016 sheet: -0.80 (0.49), residues: 88 loop : -0.80 (0.27), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 63 TYR 0.012 0.002 TYR X1232 PHE 0.034 0.002 PHE C 25 TRP 0.009 0.001 TRP X 464 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.18 (22566) covalent geometry : angle 0.68815 / 0.39 (32133) hydrogen bonds : bond 0.07203 / 4.94 ( 1192) hydrogen bonds : angle 4.46492 / 3.24 ( 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 66 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.667 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: symmetry clash revert: symmetry clash REVERT: A 67 PHE cc_start: 0.9124 (t80) cc_final: 0.8663 (t80) REVERT: A 90 MET cc_start: 0.9426 (mmp) cc_final: 0.9181 (mmm) REVERT: D 105 LYS cc_start: 0.9578 (pttm) cc_final: 0.9309 (mtmm) REVERT: D 106 HIS cc_start: 0.9529 (m90) cc_final: 0.9264 (m90) REVERT: E 94 GLU cc_start: 0.9485 (tm-30) cc_final: 0.9136 (tm-30) REVERT: F 97 LEU cc_start: 0.8658 (tp) cc_final: 0.8211 (mt) REVERT: H 77 LEU cc_start: 0.9790 (tt) cc_final: 0.9561 (pp) REVERT: X 383 MET cc_start: 0.8956 (ttm) cc_final: 0.8594 (ttm) REVERT: X 419 LEU cc_start: 0.9579 (tt) cc_final: 0.9344 (mt) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.1538 time to fit residues: 16.7968 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 : 1.004 ------------------------------------------------------------------------------- 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: 10.0000 chunk 139 optimal weight: 8.9990 chunk 161 optimal weight: 20.0000 chunk 196 optimal weight: 30.0000 chunk 190 optimal weight: 1.9990 chunk 82 optimal weight: 50.0000 chunk 3 optimal weight: 0.2980 chunk 113 optimal weight: 7.9990 chunk 88 optimal weight: 50.0000 chunk 109 optimal weight: 40.0000 chunk 122 optimal weight: 20.0000 overall best weight: 5.8590 ------------------------------------------------------------------------------- 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** G 24 GLN ** 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 = 0.3163 r_free = 0.3163 target = 0.035182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.029000 restraints weight = 378594.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.029523 restraints weight = 260539.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.029849 restraints weight = 200363.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.030091 restraints weight = 168837.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.030276 restraints weight = 149259.627| |-----------------------------------------------------------------------------| r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 22566 Z= 0.188 Angle : 0.684 11.786 32133 Z= 0.385 Chirality : 0.045 0.278 3702 Planarity : 0.005 0.051 2702 Dihedral : 29.487 166.458 6426 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 20.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % 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: 0.74 (0.20), residues: 1609 helix: 1.28 (0.16), residues: 1016 sheet: -0.90 (0.50), residues: 88 loop : -0.78 (0.27), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG X 63 TYR 0.017 0.002 TYR H 37 PHE 0.020 0.002 PHE C 25 TRP 0.009 0.001 TRP X 464 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.19 (22566) covalent geometry : angle 0.68390 / 0.39 (32133) hydrogen bonds : bond 0.07800 / 5.36 ( 1192) hydrogen bonds : angle 4.37636 / 3.17 ( 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 67 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.691 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: 0.9123 (t80) cc_final: 0.8672 (t80) REVERT: A 90 MET cc_start: 0.9420 (mmp) cc_final: 0.9151 (mmm) REVERT: A 120 MET cc_start: 0.7306 (mpp) cc_final: 0.7025 (mpp) REVERT: D 105 LYS cc_start: 0.9578 (pttm) cc_final: 0.9335 (ptpp) REVERT: D 106 HIS cc_start: 0.9479 (m90) cc_final: 0.9212 (m90) REVERT: H 59 MET cc_start: 0.9793 (mmm) cc_final: 0.9513 (mmm) REVERT: H 68 GLU cc_start: 0.9339 (tt0) cc_final: 0.8972 (tm-30) REVERT: H 77 LEU cc_start: 0.9749 (tt) cc_final: 0.9527 (pp) REVERT: X 383 MET cc_start: 0.8583 (ttm) cc_final: 0.8128 (ttm) REVERT: X 751 MET cc_start: 0.9312 (ttm) cc_final: 0.8992 (ttp) outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.1575 time to fit residues: 17.2135 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 : 0.640 ------------------------------------------------------------------------------- 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: 6.9990 chunk 12 optimal weight: 6.9990 chunk 53 optimal weight: 40.0000 chunk 115 optimal weight: 6.9990 chunk 183 optimal weight: 7.9990 chunk 72 optimal weight: 50.0000 chunk 172 optimal weight: 8.9990 chunk 52 optimal weight: 5.9990 chunk 195 optimal weight: 5.9990 chunk 28 optimal weight: 6.9990 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** ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.034423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.028157 restraints weight = 383124.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.028751 restraints weight = 252262.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.029097 restraints weight = 188320.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.029366 restraints weight = 155675.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.029571 restraints weight = 135328.859| |-----------------------------------------------------------------------------| r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 22566 Z= 0.192 Angle : 0.682 10.326 32133 Z= 0.386 Chirality : 0.045 0.286 3702 Planarity : 0.005 0.073 2702 Dihedral : 29.569 167.882 6426 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 21.61 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.49 % Favored : 97.45 % Rotamer: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % 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: 0.75 (0.20), residues: 1609 helix: 1.28 (0.16), residues: 1014 sheet: -1.06 (0.49), residues: 88 loop : -0.73 (0.27), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 76 TYR 0.021 0.002 TYR X 347 PHE 0.020 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 0.00328 / 0.19 (22566) covalent geometry : angle 0.68176 / 0.39 (32133) hydrogen bonds : bond 0.07968 / 5.45 ( 1192) hydrogen bonds : angle 4.39082 / 3.19 ( 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 62 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.658 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: 0.9221 (t80) cc_final: 0.8752 (t80) REVERT: A 90 MET cc_start: 0.9392 (mmp) cc_final: 0.9060 (mmm) REVERT: C 41 GLU cc_start: 0.9735 (tm-30) cc_final: 0.9344 (pp20) REVERT: D 105 LYS cc_start: 0.9547 (pttm) cc_final: 0.9343 (ptpp) REVERT: D 106 HIS cc_start: 0.9589 (m90) cc_final: 0.9370 (m90) REVERT: H 59 MET cc_start: 0.9798 (mmm) cc_final: 0.9552 (mmm) REVERT: H 68 GLU cc_start: 0.9265 (tt0) cc_final: 0.9044 (tm-30) REVERT: H 77 LEU cc_start: 0.9715 (tt) cc_final: 0.9502 (pp) REVERT: X 383 MET cc_start: 0.8902 (ttm) cc_final: 0.8488 (ttm) REVERT: X 751 MET cc_start: 0.9355 (ttm) cc_final: 0.9105 (ttm) outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.1533 time to fit residues: 15.7916 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 : 0.633 ------------------------------------------------------------------------------- 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: 7.9990 chunk 58 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 chunk 92 optimal weight: 40.0000 chunk 71 optimal weight: 30.0000 chunk 24 optimal weight: 10.0000 chunk 43 optimal weight: 0.9990 chunk 194 optimal weight: 6.9990 chunk 60 optimal weight: 9.9990 chunk 193 optimal weight: 9.9990 chunk 96 optimal weight: 50.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- 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 ** 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 = 0.3104 r_free = 0.3104 target = 0.034408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.028093 restraints weight = 380444.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.028689 restraints weight = 252164.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.029045 restraints weight = 188943.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.029318 restraints weight = 156311.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.029525 restraints weight = 136649.504| |-----------------------------------------------------------------------------| r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.2995 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= 0.173 Angle : 0.665 10.525 32133 Z= 0.374 Chirality : 0.045 0.290 3702 Planarity : 0.004 0.061 2702 Dihedral : 29.561 168.559 6426 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 20.01 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.30 % Favored : 97.64 % 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: 0.82 (0.21), residues: 1609 helix: 1.33 (0.16), residues: 1015 sheet: -0.81 (0.53), residues: 78 loop : -0.74 (0.27), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG X 139 TYR 0.019 0.002 TYR G 39 PHE 0.017 0.002 PHE C 25 TRP 0.011 0.001 TRP X 464 HIS 0.012 0.001 HIS X 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.17 (22566) covalent geometry : angle 0.66530 / 0.37 (32133) hydrogen bonds : bond 0.07008 / 4.78 ( 1192) hydrogen bonds : angle 4.31674 / 3.14 ( 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 64 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.616 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: 0.9203 (t80) cc_final: 0.8732 (t80) REVERT: A 90 MET cc_start: 0.9386 (mmp) cc_final: 0.9053 (mmp) REVERT: A 120 MET cc_start: 0.6666 (mpp) cc_final: 0.6342 (mpp) REVERT: C 41 GLU cc_start: 0.9730 (tm-30) cc_final: 0.9350 (pp20) REVERT: D 106 HIS cc_start: 0.9574 (m90) cc_final: 0.9330 (m90) REVERT: E 94 GLU cc_start: 0.9651 (tm-30) cc_final: 0.9208 (tm-30) REVERT: F 97 LEU cc_start: 0.9195 (mt) cc_final: 0.8493 (mt) REVERT: H 68 GLU cc_start: 0.9225 (tt0) cc_final: 0.9008 (tm-30) REVERT: H 77 LEU cc_start: 0.9673 (tt) cc_final: 0.9431 (pp) REVERT: X 383 MET cc_start: 0.8943 (ttm) cc_final: 0.8450 (ttm) REVERT: X 751 MET cc_start: 0.9360 (ttm) cc_final: 0.9020 (ttm) outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.1538 time to fit residues: 16.3584 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 : 0.637 ------------------------------------------------------------------------------- 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: 20.0000 chunk 27 optimal weight: 4.9990 chunk 109 optimal weight: 20.0000 chunk 122 optimal weight: 50.0000 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: 9.9990 overall best weight: 12.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 125 GLN ** 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 44 GLN H 60 ASN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 933 GLN ** 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 = 0.3040 r_free = 0.3040 target = 0.032032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.025988 restraints weight = 404650.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.026532 restraints weight = 269171.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.026852 restraints weight = 202351.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.027103 restraints weight = 168152.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.027253 restraints weight = 148135.290| |-----------------------------------------------------------------------------| r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.3813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.107 22566 Z= 0.320 Angle : 0.841 13.843 32133 Z= 0.467 Chirality : 0.050 0.304 3702 Planarity : 0.006 0.069 2702 Dihedral : 30.040 173.422 6426 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 36.73 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.23 % Favored : 96.71 % Rotamer: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % 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: -0.06 (0.20), residues: 1609 helix: 0.61 (0.15), residues: 1001 sheet: -1.40 (0.48), residues: 93 loop : -0.89 (0.26), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG X 71 TYR 0.034 0.003 TYR G 39 PHE 0.022 0.003 PHE E 67 TRP 0.019 0.003 TRP X 659 HIS 0.008 0.002 HIS X 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00558 / 0.32 (22566) covalent geometry : angle 0.84093 / 0.47 (32133) hydrogen bonds : bond 0.14918 / 10.14 ( 1192) hydrogen bonds : angle 4.96451 / 3.62 ( 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 50 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 PHE cc_start: 0.9219 (t80) cc_final: 0.8819 (t80) REVERT: D 106 HIS cc_start: 0.9658 (m90) cc_final: 0.9404 (m90) REVERT: E 67 PHE cc_start: 0.9252 (t80) cc_final: 0.8976 (t80) REVERT: H 77 LEU cc_start: 0.9531 (tt) cc_final: 0.9220 (pp) REVERT: X 321 MET cc_start: 0.9278 (tpt) cc_final: 0.9056 (tpt) REVERT: X 751 MET cc_start: 0.9082 (ttm) cc_final: 0.8574 (ttm) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.1545 time to fit residues: 13.0382 Evaluate side-chains 43 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.641 ------------------------------------------------------------------------------- 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: 40.0000 chunk 124 optimal weight: 6.9990 chunk 9 optimal weight: 9.9990 chunk 53 optimal weight: 20.0000 chunk 121 optimal weight: 7.9990 chunk 92 optimal weight: 40.0000 chunk 170 optimal weight: 0.6980 chunk 71 optimal weight: 30.0000 overall best weight: 6.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 125 GLN ** 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 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X1295 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.031705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.023788 restraints weight = 392539.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.024443 restraints weight = 255180.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.024878 restraints weight = 190308.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.025204 restraints weight = 155195.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.025408 restraints weight = 134372.571| |-----------------------------------------------------------------------------| r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.3871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.128 22566 Z= 0.200 Angle : 0.718 8.750 32133 Z= 0.403 Chirality : 0.047 0.301 3702 Planarity : 0.005 0.059 2702 Dihedral : 30.036 170.488 6426 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 25.18 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.80 % Favored : 97.14 % Rotamer: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % 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: 0.28 (0.20), residues: 1609 helix: 0.92 (0.16), residues: 1002 sheet: -1.48 (0.49), residues: 98 loop : -0.82 (0.27), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG E 63 TYR 0.016 0.002 TYR X 373 PHE 0.039 0.002 PHE C 25 TRP 0.015 0.002 TRP X 464 HIS 0.007 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.20 (22566) covalent geometry : angle 0.71780 / 0.40 (32133) hydrogen bonds : bond 0.08118 / 5.53 ( 1192) hydrogen bonds : angle 4.62121 / 3.38 ( 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 55 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 67 PHE cc_start: 0.9197 (t80) cc_final: 0.8931 (t80) REVERT: H 77 LEU cc_start: 0.9027 (tt) cc_final: 0.8792 (pp) REVERT: H 79 HIS cc_start: 0.9188 (m90) cc_final: 0.8924 (m90) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.1473 time to fit residues: 13.7717 Evaluate side-chains 41 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.657 ------------------------------------------------------------------------------- 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: 30.0000 chunk 144 optimal weight: 8.9990 chunk 55 optimal weight: 9.9990 chunk 25 optimal weight: 0.3980 chunk 174 optimal weight: 20.0000 chunk 79 optimal weight: 50.0000 chunk 152 optimal weight: 8.9990 chunk 124 optimal weight: 6.9990 chunk 156 optimal weight: 5.9990 chunk 171 optimal weight: 8.9990 chunk 53 optimal weight: 1.9990 overall best weight: 4.8788 ------------------------------------------------------------------------------- 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 412 HIS ** X 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X1295 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.032109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.024081 restraints weight = 386660.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.024763 restraints weight = 247980.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.025235 restraints weight = 183581.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.025576 restraints weight = 148248.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.025805 restraints weight = 127342.571| |-----------------------------------------------------------------------------| r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.4010 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= 0.171 Angle : 0.684 10.010 32133 Z= 0.382 Chirality : 0.045 0.333 3702 Planarity : 0.005 0.061 2702 Dihedral : 29.739 170.508 6426 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 21.51 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.73 % Favored : 97.20 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % 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: 0.47 (0.21), residues: 1609 helix: 1.11 (0.16), residues: 1010 sheet: -1.88 (0.46), residues: 105 loop : -0.72 (0.28), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 63 TYR 0.014 0.002 TYR X 430 PHE 0.029 0.002 PHE X 432 TRP 0.009 0.001 TRP X 464 HIS 0.013 0.001 HIS D 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.17 (22566) covalent geometry : angle 0.68398 / 0.38 (32133) hydrogen bonds : bond 0.06923 / 4.71 ( 1192) hydrogen bonds : angle 4.44011 / 3.24 ( 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 55 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 77 LEU cc_start: 0.9007 (tt) cc_final: 0.8765 (pp) REVERT: H 79 HIS cc_start: 0.9114 (m90) cc_final: 0.8866 (m90) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.1567 time to fit residues: 14.2707 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 : 0.652 ------------------------------------------------------------------------------- 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: 50.0000 chunk 159 optimal weight: 6.9990 chunk 177 optimal weight: 5.9990 chunk 25 optimal weight: 0.0980 chunk 59 optimal weight: 0.7980 chunk 118 optimal weight: 8.9990 chunk 129 optimal weight: 3.9990 chunk 180 optimal weight: 10.0000 chunk 92 optimal weight: 50.0000 chunk 134 optimal weight: 10.0000 chunk 63 optimal weight: 10.0000 overall best weight: 3.5786 ------------------------------------------------------------------------------- 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 = 0.3022 r_free = 0.3022 target = 0.032466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.024397 restraints weight = 383114.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.025087 restraints weight = 247055.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.025553 restraints weight = 182562.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.025890 restraints weight = 148030.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.026109 restraints weight = 127783.627| |-----------------------------------------------------------------------------| r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.4129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 22566 Z= 0.147 Angle : 0.659 10.134 32133 Z= 0.368 Chirality : 0.045 0.350 3702 Planarity : 0.005 0.097 2702 Dihedral : 29.591 174.241 6426 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 19.53 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.55 % Favored : 97.39 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % 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: 1.31 (0.16), residues: 1007 sheet: -1.72 (0.47), residues: 104 loop : -0.59 (0.28), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG X 494 TYR 0.015 0.001 TYR X 515 PHE 0.024 0.002 PHE C 25 TRP 0.026 0.002 TRP X 464 HIS 0.008 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.15 (22566) covalent geometry : angle 0.65950 / 0.37 (32133) hydrogen bonds : bond 0.05717 / 3.88 ( 1192) hydrogen bonds : angle 4.28689 / 3.12 ( 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 56 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.644 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: 0.9248 (t80) cc_final: 0.8903 (t80) REVERT: A 90 MET cc_start: 0.9153 (mmp) cc_final: 0.8949 (mmm) REVERT: E 94 GLU cc_start: 0.9701 (tm-30) cc_final: 0.9414 (tm-30) REVERT: H 77 LEU cc_start: 0.9056 (tt) cc_final: 0.8715 (pp) REVERT: H 79 HIS cc_start: 0.9082 (m90) cc_final: 0.8833 (m90) REVERT: H 97 LEU cc_start: 0.9048 (mt) cc_final: 0.8048 (mt) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.1579 time to fit residues: 14.7360 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 : 0.650 ------------------------------------------------------------------------------- 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: 3.9990 chunk 103 optimal weight: 50.0000 chunk 33 optimal weight: 6.9990 chunk 6 optimal weight: 5.9990 chunk 113 optimal weight: 3.9990 chunk 13 optimal weight: 6.9990 chunk 143 optimal weight: 40.0000 chunk 173 optimal weight: 20.0000 chunk 185 optimal weight: 0.0010 chunk 52 optimal weight: 6.9990 chunk 20 optimal weight: 8.9990 overall best weight: 4.1994 ------------------------------------------------------------------------------- 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 = 0.033634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.027408 restraints weight = 384756.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.027977 restraints weight = 251802.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.028332 restraints weight = 188605.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.028602 restraints weight = 155582.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.028797 restraints weight = 135683.377| |-----------------------------------------------------------------------------| r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.4237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 22566 Z= 0.156 Angle : 0.654 9.462 32133 Z= 0.366 Chirality : 0.044 0.339 3702 Planarity : 0.004 0.060 2702 Dihedral : 29.507 174.437 6426 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 20.17 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.61 % Favored : 97.33 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % 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: 0.69 (0.21), residues: 1609 helix: 1.29 (0.16), residues: 1005 sheet: -1.75 (0.47), residues: 104 loop : -0.64 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG F 92 TYR 0.015 0.002 TYR G 39 PHE 0.022 0.002 PHE C 25 TRP 0.026 0.002 TRP X 464 HIS 0.008 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.16 (22566) covalent geometry : angle 0.65406 / 0.37 (32133) hydrogen bonds : bond 0.06375 / 4.33 ( 1192) hydrogen bonds : angle 4.30164 / 3.13 ( 3110) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3151.58 seconds wall clock time: 56 minutes 2.90 seconds (3362.90 seconds total)