Starting phenix.real_space_refine on Fri Sep 11 01:58:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6gtd_0062/09_2026/6gtd_0062_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6gtd_0062/09_2026/6gtd_0062.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6gtd_0062/09_2026/6gtd_0062_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6gtd_0062/09_2026/6gtd_0062_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6gtd_0062/09_2026/6gtd_0062.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6gtd_0062/09_2026/6gtd_0062.map" } resolution = 4.24 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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 66 5.49 5 S 1 5.16 5 C 3179 2.51 5 N 1515 2.21 5 O 1695 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6456 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1269, 5080 Classifications: {'peptide': 1269} Incomplete info: {'backbone_only': 1217} Link IDs: {'CIS': 2, 'PTRANS': 27, 'TRANS': 1239} Chain breaks: 4 Unresolved chain link angles: 27 Unresolved non-hydrogen bonds: 5609 Unresolved non-hydrogen angles: 7983 Unresolved non-hydrogen dihedrals: 3721 Unresolved non-hydrogen chiralities: 1529 Planarities with less than four sites: {'TYR:plan': 67, 'GLN:plan1': 55, 'GLU:plan': 93, 'PHE:plan': 83, 'ASN:plan1': 97, 'ARG:plan': 33, 'ASP:plan': 97, 'HIS:plan': 18, 'TRP:plan': 8} Unresolved non-hydrogen planarities: 2838 Chain: "B" Number of atoms: 596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 596 Classifications: {'RNA': 28} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 4, 'rna3p_pur': 11, 'rna3p_pyr': 9} Link IDs: {'rna2p': 8, 'rna3p': 19} Chain: "C" Number of atoms: 406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 406 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "D" Number of atoms: 374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 374 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Time building chain proxies: 1.92, per 1000 atoms: 0.30 Number of scatterers: 6456 At special positions: 0 Unit cell: (95.68, 118.976, 102.336, 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 1 16.00 P 66 15.00 O 1695 8.00 N 1515 7.00 C 3179 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: 1.06 Conformation dependent library (CDL) restraints added in 298.9 milliseconds 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 8 sheets defined 35.8% alpha, 2.7% beta 6 base pairs and 23 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 26 through 35 Processing helix chain 'A' and resid 36 through 40 removed outlier: 3.823A pdb=" N ASP A 40 " --> pdb=" O ILE A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 54 Processing helix chain 'A' and resid 59 through 64 Processing helix chain 'A' and resid 72 through 88 removed outlier: 3.651A pdb=" N SER A 80 " --> pdb=" O LEU A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 109 Processing helix chain 'A' and resid 109 through 114 Processing helix chain 'A' and resid 115 through 116 No H-bonds generated for 'chain 'A' and resid 115 through 116' Processing helix chain 'A' and resid 117 through 121 removed outlier: 3.760A pdb=" N LYS A 120 " --> pdb=" O GLU A 117 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN A 121 " --> pdb=" O LYS A 118 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 117 through 121' Processing helix chain 'A' and resid 136 through 149 Processing helix chain 'A' and resid 161 through 163 No H-bonds generated for 'chain 'A' and resid 161 through 163' Processing helix chain 'A' and resid 164 through 171 Processing helix chain 'A' and resid 207 through 215 Processing helix chain 'A' and resid 218 through 224 removed outlier: 3.623A pdb=" N LEU A 221 " --> pdb=" O TYR A 218 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS A 222 " --> pdb=" O GLU A 219 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASP A 223 " --> pdb=" O SER A 220 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N LYS A 224 " --> pdb=" O LEU A 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 218 through 224' Processing helix chain 'A' and resid 230 through 235 Processing helix chain 'A' and resid 239 through 241 No H-bonds generated for 'chain 'A' and resid 239 through 241' Processing helix chain 'A' and resid 281 through 286 Processing helix chain 'A' and resid 305 through 312 Processing helix chain 'A' and resid 356 through 361 removed outlier: 3.640A pdb=" N ALA A 360 " --> pdb=" O GLU A 357 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ALA A 361 " --> pdb=" O GLN A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 377 removed outlier: 3.673A pdb=" N LEU A 374 " --> pdb=" O ILE A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 384 removed outlier: 4.020A pdb=" N ALA A 383 " --> pdb=" O ASP A 380 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLN A 384 " --> pdb=" O LEU A 381 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 380 through 384' Processing helix chain 'A' and resid 396 through 401 Processing helix chain 'A' and resid 401 through 408 removed outlier: 3.751A pdb=" N ASP A 408 " --> pdb=" O GLN A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 414 removed outlier: 3.503A pdb=" N GLY A 414 " --> pdb=" O TYR A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 418 Processing helix chain 'A' and resid 421 through 426 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.907A pdb=" N ILE A 441 " --> pdb=" O GLN A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 462 removed outlier: 3.590A pdb=" N LEU A 458 " --> pdb=" O GLU A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 466 removed outlier: 4.587A pdb=" N HIS A 466 " --> pdb=" O PHE A 463 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 463 through 466' Processing helix chain 'A' and resid 468 through 472 removed outlier: 3.589A pdb=" N GLN A 472 " --> pdb=" O ILE A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 484 removed outlier: 3.510A pdb=" N ALA A 484 " --> pdb=" O ALA A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 495 removed outlier: 4.390A pdb=" N GLU A 491 " --> pdb=" O MET A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 498 No H-bonds generated for 'chain 'A' and resid 496 through 498' Processing helix chain 'A' and resid 516 through 518 No H-bonds generated for 'chain 'A' and resid 516 through 518' Processing helix chain 'A' and resid 519 through 526 removed outlier: 3.626A pdb=" N VAL A 523 " --> pdb=" O ALA A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 532 No H-bonds generated for 'chain 'A' and resid 530 through 532' Processing helix chain 'A' and resid 533 through 540 removed outlier: 3.514A pdb=" N LEU A 537 " --> pdb=" O THR A 533 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N HIS A 538 " --> pdb=" O ASN A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 562 removed outlier: 4.100A pdb=" N PHE A 561 " --> pdb=" O ASP A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 570 removed outlier: 4.124A pdb=" N PHE A 570 " --> pdb=" O GLU A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 579 removed outlier: 3.970A pdb=" N TYR A 579 " --> pdb=" O VAL A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 649 removed outlier: 3.875A pdb=" N GLU A 648 " --> pdb=" O LYS A 644 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASN A 649 " --> pdb=" O ALA A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 672 removed outlier: 3.832A pdb=" N LYS A 671 " --> pdb=" O MET A 668 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL A 672 " --> pdb=" O LEU A 669 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 668 through 672' Processing helix chain 'A' and resid 675 through 679 Processing helix chain 'A' and resid 685 through 690 Processing helix chain 'A' and resid 713 through 730 removed outlier: 3.698A pdb=" N LYS A 719 " --> pdb=" O GLU A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 738 removed outlier: 4.093A pdb=" N ASP A 736 " --> pdb=" O GLU A 733 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N PHE A 737 " --> pdb=" O TRP A 734 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY A 738 " --> pdb=" O LYS A 735 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 733 through 738' Processing helix chain 'A' and resid 749 through 754 Processing helix chain 'A' and resid 772 through 781 Processing helix chain 'A' and resid 871 through 875 removed outlier: 4.267A pdb=" N GLU A 875 " --> pdb=" O ARG A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 904 Processing helix chain 'A' and resid 955 through 961 Processing helix chain 'A' and resid 970 through 985 removed outlier: 4.810A pdb=" N LYS A 981 " --> pdb=" O ILE A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 997 removed outlier: 3.554A pdb=" N HIS A 990 " --> pdb=" O SER A 986 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ILE A 997 " --> pdb=" O ALA A 993 " (cutoff:3.500A) Processing helix chain 'A' and resid 1063 through 1067 removed outlier: 3.622A pdb=" N MET A1067 " --> pdb=" O PHE A1064 " (cutoff:3.500A) Processing helix chain 'A' and resid 1101 through 1112 Processing helix chain 'A' and resid 1174 through 1179 removed outlier: 3.507A pdb=" N LEU A1178 " --> pdb=" O LEU A1174 " (cutoff:3.500A) Processing helix chain 'A' and resid 1191 through 1198 Processing helix chain 'A' and resid 1200 through 1213 removed outlier: 4.023A pdb=" N LEU A1207 " --> pdb=" O PHE A1203 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N THR A1208 " --> pdb=" O PHE A1204 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER A1209 " --> pdb=" O ALA A1205 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL A1210 " --> pdb=" O LYS A1206 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU A1211 " --> pdb=" O LEU A1207 " (cutoff:3.500A) Processing helix chain 'A' and resid 1261 through 1267 removed outlier: 3.916A pdb=" N GLY A1266 " --> pdb=" O ILE A1262 " (cutoff:3.500A) Processing helix chain 'A' and resid 1269 through 1275 Processing helix chain 'A' and resid 1287 through 1297 Processing sheet with id=AA1, first strand: chain 'A' and resid 243 through 244 Processing sheet with id=AA2, first strand: chain 'A' and resid 287 through 288 Processing sheet with id=AA3, first strand: chain 'A' and resid 363 through 364 removed outlier: 4.100A pdb=" N LYS A 368 " --> pdb=" O THR A 364 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 392 through 394 Processing sheet with id=AA5, first strand: chain 'A' and resid 597 through 598 Processing sheet with id=AA6, first strand: chain 'A' and resid 657 through 661 Processing sheet with id=AA7, first strand: chain 'A' and resid 916 through 917 removed outlier: 4.114A pdb=" N ASP A 917 " --> pdb=" O TYR A 925 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N TYR A 925 " --> pdb=" O ASP A 917 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TYR A 926 " --> pdb=" O ASP A 939 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ASP A 939 " --> pdb=" O TYR A 926 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LEU A 928 " --> pdb=" O LYS A 937 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LYS A 937 " --> pdb=" O LEU A 928 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 1150 through 1152 203 hydrogen bonds defined for protein. 558 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 13 hydrogen bonds 22 hydrogen bond angles 0 basepair planarities 6 basepair parallelities 23 stacking parallelities Total time for adding SS restraints: 1.45 Time building geometry restraints manager: 1.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1390 1.31 - 1.43: 2004 1.43 - 1.55: 3088 1.55 - 1.68: 130 1.68 - 1.80: 2 Bond restraints: 6614 Sorted by residual: bond pdb=" N9 A B -2 " pdb=" C4 A B -2 " ideal model delta sigma weight residual 1.374 1.323 0.051 6.00e-03 2.78e+04 7.10e+01 bond pdb=" N9 A B -4 " pdb=" C4 A B -4 " ideal model delta sigma weight residual 1.374 1.325 0.049 6.00e-03 2.78e+04 6.76e+01 bond pdb=" N9 G B 2 " pdb=" C4 G B 2 " ideal model delta sigma weight residual 1.375 1.312 0.063 8.00e-03 1.56e+04 6.15e+01 bond pdb=" N3 A B -4 " pdb=" C4 A B -4 " ideal model delta sigma weight residual 1.344 1.301 0.043 6.00e-03 2.78e+04 5.19e+01 bond pdb=" CA MET A1030 " pdb=" C MET A1030 " ideal model delta sigma weight residual 1.524 1.438 0.087 1.24e-02 6.50e+03 4.87e+01 ... (remaining 6609 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.75: 8306 2.75 - 5.51: 371 5.51 - 8.26: 30 8.26 - 11.01: 4 11.01 - 13.76: 2 Bond angle restraints: 8713 Sorted by residual: angle pdb=" O4' DC C -5 " pdb=" C4' DC C -5 " pdb=" C3' DC C -5 " ideal model delta sigma weight residual 106.00 100.18 5.82 6.00e-01 2.78e+00 9.40e+01 angle pdb=" C LYS A1029 " pdb=" N MET A1030 " pdb=" CA MET A1030 " ideal model delta sigma weight residual 121.18 134.94 -13.76 1.64e+00 3.72e-01 7.04e+01 angle pdb=" CA MET A1030 " pdb=" C MET A1030 " pdb=" N LEU A1031 " ideal model delta sigma weight residual 118.82 108.63 10.19 1.26e+00 6.30e-01 6.54e+01 angle pdb=" C5 G B 0 " pdb=" C4 G B 0 " pdb=" N3 G B 0 " ideal model delta sigma weight residual 128.60 124.70 3.90 5.00e-01 4.00e+00 6.10e+01 angle pdb=" O4 U B -1 " pdb=" C4 U B -1 " pdb=" C5 U B -1 " ideal model delta sigma weight residual 125.90 121.46 4.44 6.00e-01 2.78e+00 5.49e+01 ... (remaining 8708 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.96: 1758 28.96 - 57.92: 278 57.92 - 86.88: 50 86.88 - 115.84: 13 115.84 - 144.80: 1 Dihedral angle restraints: 2100 sinusoidal: 834 harmonic: 1266 Sorted by residual: dihedral pdb=" CA TYR A 178 " pdb=" C TYR A 178 " pdb=" N PHE A 179 " pdb=" CA PHE A 179 " ideal model delta harmonic sigma weight residual 180.00 142.23 37.77 0 5.00e+00 4.00e-02 5.71e+01 dihedral pdb=" CA GLN A1006 " pdb=" C GLN A1006 " pdb=" N ASP A1007 " pdb=" CA ASP A1007 " ideal model delta harmonic sigma weight residual 180.00 -144.63 -35.37 0 5.00e+00 4.00e-02 5.00e+01 dihedral pdb=" CA PHE A1005 " pdb=" C PHE A1005 " pdb=" N GLN A1006 " pdb=" CA GLN A1006 " ideal model delta harmonic sigma weight residual 180.00 -145.75 -34.25 0 5.00e+00 4.00e-02 4.69e+01 ... (remaining 2097 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 173 0.077 - 0.154: 91 0.154 - 0.230: 23 0.230 - 0.307: 4 0.307 - 0.384: 2 Chirality restraints: 293 Sorted by residual: chirality pdb=" C3' DC C -5 " pdb=" C4' DC C -5 " pdb=" O3' DC C -5 " pdb=" C2' DC C -5 " both_signs ideal model delta sigma weight residual False -2.73 -2.35 -0.38 2.00e-01 2.50e+01 3.68e+00 chirality pdb=" C1' U B -16 " pdb=" O4' U B -16 " pdb=" C2' U B -16 " pdb=" N1 U B -16 " both_signs ideal model delta sigma weight residual False 2.47 2.13 0.34 2.00e-01 2.50e+01 2.87e+00 chirality pdb=" C1' U B -5 " pdb=" O4' U B -5 " pdb=" C2' U B -5 " pdb=" N1 U B -5 " both_signs ideal model delta sigma weight residual False 2.47 2.20 0.27 2.00e-01 2.50e+01 1.85e+00 ... (remaining 290 not shown) Planarity restraints: 1330 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U B -16 " -0.037 2.00e-02 2.50e+03 2.36e-02 1.25e+01 pdb=" N1 U B -16 " 0.058 2.00e-02 2.50e+03 pdb=" C2 U B -16 " 0.004 2.00e-02 2.50e+03 pdb=" O2 U B -16 " -0.006 2.00e-02 2.50e+03 pdb=" N3 U B -16 " -0.004 2.00e-02 2.50e+03 pdb=" C4 U B -16 " 0.003 2.00e-02 2.50e+03 pdb=" O4 U B -16 " -0.011 2.00e-02 2.50e+03 pdb=" C5 U B -16 " -0.006 2.00e-02 2.50e+03 pdb=" C6 U B -16 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A B 1 " -0.031 2.00e-02 2.50e+03 1.81e-02 9.06e+00 pdb=" N9 A B 1 " 0.034 2.00e-02 2.50e+03 pdb=" C8 A B 1 " 0.019 2.00e-02 2.50e+03 pdb=" N7 A B 1 " -0.005 2.00e-02 2.50e+03 pdb=" C5 A B 1 " -0.008 2.00e-02 2.50e+03 pdb=" C6 A B 1 " -0.021 2.00e-02 2.50e+03 pdb=" N6 A B 1 " -0.007 2.00e-02 2.50e+03 pdb=" N1 A B 1 " 0.015 2.00e-02 2.50e+03 pdb=" C2 A B 1 " 0.015 2.00e-02 2.50e+03 pdb=" N3 A B 1 " -0.011 2.00e-02 2.50e+03 pdb=" C4 A B 1 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 791 " -0.014 2.00e-02 2.50e+03 2.80e-02 7.82e+00 pdb=" C LYS A 791 " 0.048 2.00e-02 2.50e+03 pdb=" O LYS A 791 " -0.018 2.00e-02 2.50e+03 pdb=" N ASP A 792 " -0.016 2.00e-02 2.50e+03 ... (remaining 1327 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 470 2.69 - 3.24: 6187 3.24 - 3.79: 8956 3.79 - 4.35: 11626 4.35 - 4.90: 15056 Nonbonded interactions: 42295 Sorted by model distance: nonbonded pdb=" N PHE A1064 " pdb=" OP2 DC C -5 " model vdw 2.138 3.120 nonbonded pdb=" O LYS A 613 " pdb=" N ASN A 617 " model vdw 2.306 3.120 nonbonded pdb=" N ARG A 872 " pdb=" OP2 U B -17 " model vdw 2.311 3.120 nonbonded pdb=" O4 U B -15 " pdb=" N6 A B -2 " model vdw 2.319 3.120 nonbonded pdb=" O TRP A 175 " pdb=" N PHE A 179 " model vdw 2.323 3.120 ... (remaining 42290 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.050 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: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.420 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6548 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 : 0.009 0.092 6614 Z= 0.939 Angle : 1.312 13.763 8713 Z= 1.072 Chirality : 0.098 0.384 293 Planarity : 0.005 0.028 1330 Dihedral : 23.088 144.798 2098 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.78 % Favored : 80.22 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.49 % 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: -5.72 (0.17), residues: 1259 helix: -4.37 (0.12), residues: 373 sheet: -4.34 (0.59), residues: 55 loop : -3.72 (0.18), residues: 831 Details of bonding type rmsd/Z covalent geometry : bond 0.00918 / 0.94 ( 6614) covalent geometry : angle 1.31185 / 1.07 ( 8713) hydrogen bonds : bond 0.36744 / 27.88 ( 216) hydrogen bonds : angle 14.64671 / 11.14 ( 580) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.237 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0280 time to fit residues: 0.9431 Evaluate side-chains 13 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 30.0000 chunk 66 optimal weight: 20.0000 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 30.0000 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 30.0000 chunk 91 optimal weight: 10.0000 chunk 55 optimal weight: 30.0000 overall best weight: 6.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.090462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.071253 restraints weight = 35370.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.070739 restraints weight = 41506.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.072125 restraints weight = 31976.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.071021 restraints weight = 23124.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.071334 restraints weight = 23123.468| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6648 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 6614 Z= 0.252 Angle : 0.823 11.745 8713 Z= 0.492 Chirality : 0.077 0.466 293 Planarity : 0.004 0.027 1330 Dihedral : 22.521 150.874 2095 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.60 % Favored : 83.40 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -5.18 (0.19), residues: 1259 helix: -3.31 (0.18), residues: 438 sheet: -4.60 (0.60), residues: 50 loop : -3.63 (0.20), residues: 771 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.25 ( 6614) covalent geometry : angle 0.82348 / 0.49 ( 8713) hydrogen bonds : bond 0.10388 / 8.47 ( 216) hydrogen bonds : angle 9.13869 / 6.95 ( 580) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.242 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0331 time to fit residues: 1.1865 Evaluate side-chains 13 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 63 optimal weight: 30.0000 chunk 19 optimal weight: 40.0000 chunk 68 optimal weight: 40.0000 chunk 37 optimal weight: 50.0000 chunk 49 optimal weight: 30.0000 chunk 34 optimal weight: 0.0670 chunk 3 optimal weight: 8.9990 chunk 7 optimal weight: 0.0670 chunk 113 optimal weight: 50.0000 chunk 70 optimal weight: 30.0000 chunk 77 optimal weight: 0.7980 overall best weight: 7.9862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.090114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.071106 restraints weight = 35140.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.069862 restraints weight = 42001.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.070882 restraints weight = 33472.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.070565 restraints weight = 24223.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.070699 restraints weight = 23021.004| |-----------------------------------------------------------------------------| r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6671 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.105 6614 Z= 0.266 Angle : 0.805 10.042 8713 Z= 0.476 Chirality : 0.076 0.426 293 Planarity : 0.004 0.021 1330 Dihedral : 22.345 151.609 2095 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.33 % Favored : 79.67 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % 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: -4.82 (0.20), residues: 1259 helix: -2.76 (0.20), residues: 453 sheet: -4.68 (0.61), residues: 50 loop : -3.55 (0.20), residues: 756 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.27 ( 6614) covalent geometry : angle 0.80541 / 0.48 ( 8713) hydrogen bonds : bond 0.08530 / 6.74 ( 216) hydrogen bonds : angle 7.62053 / 5.88 ( 580) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.171 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0320 time to fit residues: 1.0894 Evaluate side-chains 13 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 48 optimal weight: 0.0570 chunk 86 optimal weight: 0.0570 chunk 66 optimal weight: 0.0040 chunk 2 optimal weight: 0.9990 chunk 56 optimal weight: 50.0000 chunk 121 optimal weight: 50.0000 chunk 105 optimal weight: 0.0270 chunk 111 optimal weight: 50.0000 chunk 34 optimal weight: 0.4980 chunk 126 optimal weight: 20.0000 chunk 35 optimal weight: 40.0000 overall best weight: 0.1286 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.096245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.076589 restraints weight = 34394.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.075947 restraints weight = 38823.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.076387 restraints weight = 27405.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.076415 restraints weight = 23591.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.077448 restraints weight = 20839.576| |-----------------------------------------------------------------------------| r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6368 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 6614 Z= 0.133 Angle : 0.584 9.717 8713 Z= 0.349 Chirality : 0.053 0.322 293 Planarity : 0.002 0.012 1330 Dihedral : 21.243 153.764 2095 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % 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: -4.21 (0.21), residues: 1259 helix: -2.17 (0.22), residues: 489 sheet: -3.89 (1.16), residues: 14 loop : -3.39 (0.20), residues: 756 Details of bonding type rmsd/Z covalent geometry : bond 0.00189 / 0.13 ( 6614) covalent geometry : angle 0.58449 / 0.35 ( 8713) hydrogen bonds : bond 0.05534 / 4.50 ( 216) hydrogen bonds : angle 6.11901 / 4.71 ( 580) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.144 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0318 time to fit residues: 1.0757 Evaluate side-chains 13 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 124 optimal weight: 9.9990 chunk 118 optimal weight: 30.0000 chunk 71 optimal weight: 20.0000 chunk 50 optimal weight: 9.9990 chunk 26 optimal weight: 30.0000 chunk 38 optimal weight: 3.9990 chunk 22 optimal weight: 0.0060 chunk 79 optimal weight: 9.9990 chunk 76 optimal weight: 30.0000 chunk 110 optimal weight: 40.0000 chunk 119 optimal weight: 2.9990 overall best weight: 5.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.092594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.072916 restraints weight = 35185.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.072250 restraints weight = 39482.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.073078 restraints weight = 29890.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.072842 restraints weight = 23731.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.074349 restraints weight = 20796.357| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6516 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 6614 Z= 0.185 Angle : 0.609 6.975 8713 Z= 0.361 Chirality : 0.058 0.313 293 Planarity : 0.002 0.014 1330 Dihedral : 21.372 151.661 2095 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.61 % Favored : 85.39 % Rotamer: Outliers : 0.00 % Allowed : 100.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % 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: -3.95 (0.22), residues: 1259 helix: -1.69 (0.23), residues: 471 sheet: -4.76 (0.55), residues: 50 loop : -3.26 (0.21), residues: 738 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.18 ( 6614) covalent geometry : angle 0.60869 / 0.36 ( 8713) hydrogen bonds : bond 0.05693 / 4.37 ( 216) hydrogen bonds : angle 5.86916 / 4.56 ( 580) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.172 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0285 time to fit residues: 0.9957 Evaluate side-chains 13 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 58 optimal weight: 8.9990 chunk 28 optimal weight: 50.0000 chunk 21 optimal weight: 50.0000 chunk 112 optimal weight: 20.0000 chunk 54 optimal weight: 50.0000 chunk 48 optimal weight: 50.0000 chunk 71 optimal weight: 5.9990 chunk 44 optimal weight: 50.0000 chunk 8 optimal weight: 30.0000 chunk 62 optimal weight: 0.2980 chunk 90 optimal weight: 9.9990 overall best weight: 9.0590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.090341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.071031 restraints weight = 35657.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.070672 restraints weight = 41218.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.071326 restraints weight = 30702.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.070991 restraints weight = 26991.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.071406 restraints weight = 22634.277| |-----------------------------------------------------------------------------| r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6614 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.113 6614 Z= 0.268 Angle : 0.792 7.937 8713 Z= 0.455 Chirality : 0.071 0.343 293 Planarity : 0.004 0.018 1330 Dihedral : 21.933 150.659 2095 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.14 % Favored : 80.86 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % 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: -4.01 (0.22), residues: 1259 helix: -1.65 (0.23), residues: 456 sheet: -4.84 (0.57), residues: 50 loop : -3.34 (0.20), residues: 753 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.27 ( 6614) covalent geometry : angle 0.79179 / 0.45 ( 8713) hydrogen bonds : bond 0.07869 / 6.17 ( 216) hydrogen bonds : angle 6.31209 / 4.93 ( 580) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.269 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0317 time to fit residues: 1.1064 Evaluate side-chains 13 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 58 optimal weight: 20.0000 chunk 54 optimal weight: 1.9990 chunk 33 optimal weight: 50.0000 chunk 5 optimal weight: 0.0060 chunk 19 optimal weight: 50.0000 chunk 9 optimal weight: 50.0000 chunk 53 optimal weight: 0.0570 chunk 94 optimal weight: 8.9990 chunk 114 optimal weight: 40.0000 chunk 123 optimal weight: 10.0000 chunk 39 optimal weight: 30.0000 overall best weight: 4.2122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.092250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.072725 restraints weight = 35139.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.072292 restraints weight = 39631.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.072529 restraints weight = 33039.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.072535 restraints weight = 26784.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.072700 restraints weight = 24393.033| |-----------------------------------------------------------------------------| r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6540 moved from start: 0.2826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.068 6614 Z= 0.159 Angle : 0.605 7.771 8713 Z= 0.360 Chirality : 0.057 0.326 293 Planarity : 0.002 0.013 1330 Dihedral : 21.576 152.253 2095 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.46 % Favored : 85.54 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % 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: -3.68 (0.23), residues: 1259 helix: -1.26 (0.25), residues: 462 sheet: -4.87 (0.56), residues: 50 loop : -3.22 (0.21), residues: 747 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.16 ( 6614) covalent geometry : angle 0.60530 / 0.36 ( 8713) hydrogen bonds : bond 0.05812 / 4.42 ( 216) hydrogen bonds : angle 5.72370 / 4.47 ( 580) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.230 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0313 time to fit residues: 1.0877 Evaluate side-chains 13 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 24 optimal weight: 50.0000 chunk 39 optimal weight: 30.0000 chunk 51 optimal weight: 20.0000 chunk 117 optimal weight: 9.9990 chunk 36 optimal weight: 0.5980 chunk 14 optimal weight: 9.9990 chunk 3 optimal weight: 9.9990 chunk 68 optimal weight: 30.0000 chunk 91 optimal weight: 10.0000 chunk 17 optimal weight: 20.0000 chunk 6 optimal weight: 30.0000 overall best weight: 8.1190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.090793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.071499 restraints weight = 35227.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.071318 restraints weight = 40379.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.071507 restraints weight = 29927.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.071529 restraints weight = 22793.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.071716 restraints weight = 21711.563| |-----------------------------------------------------------------------------| r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6579 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.104 6614 Z= 0.243 Angle : 0.731 7.566 8713 Z= 0.422 Chirality : 0.067 0.342 293 Planarity : 0.003 0.017 1330 Dihedral : 21.797 150.817 2095 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.78 % Favored : 80.22 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % 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: -3.77 (0.22), residues: 1259 helix: -1.29 (0.24), residues: 464 sheet: -4.92 (0.58), residues: 50 loop : -3.31 (0.21), residues: 745 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.24 ( 6614) covalent geometry : angle 0.73143 / 0.42 ( 8713) hydrogen bonds : bond 0.07200 / 5.58 ( 216) hydrogen bonds : angle 6.00550 / 4.69 ( 580) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.250 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0252 time to fit residues: 0.9155 Evaluate side-chains 13 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 2 optimal weight: 5.9990 chunk 83 optimal weight: 9.9990 chunk 40 optimal weight: 0.9990 chunk 120 optimal weight: 9.9990 chunk 18 optimal weight: 0.0050 chunk 1 optimal weight: 20.0000 chunk 34 optimal weight: 0.0010 chunk 49 optimal weight: 50.0000 chunk 103 optimal weight: 10.0000 chunk 86 optimal weight: 4.9990 chunk 61 optimal weight: 30.0000 overall best weight: 2.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.093618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.073970 restraints weight = 35626.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.073415 restraints weight = 38218.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.073748 restraints weight = 28310.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.073704 restraints weight = 26274.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.073860 restraints weight = 21605.917| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6493 moved from start: 0.3218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6614 Z= 0.121 Angle : 0.535 6.288 8713 Z= 0.322 Chirality : 0.050 0.311 293 Planarity : 0.002 0.011 1330 Dihedral : 21.370 153.081 2095 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.80 % Favored : 89.20 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % 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: -3.35 (0.23), residues: 1259 helix: -0.90 (0.25), residues: 466 sheet: -4.59 (0.78), residues: 30 loop : -3.18 (0.21), residues: 763 Details of bonding type rmsd/Z covalent geometry : bond 0.00161 / 0.12 ( 6614) covalent geometry : angle 0.53454 / 0.32 ( 8713) hydrogen bonds : bond 0.05290 / 4.09 ( 216) hydrogen bonds : angle 5.25581 / 4.11 ( 580) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.210 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0275 time to fit residues: 0.9679 Evaluate side-chains 13 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 1 optimal weight: 20.0000 chunk 59 optimal weight: 0.9980 chunk 70 optimal weight: 30.0000 chunk 3 optimal weight: 10.0000 chunk 79 optimal weight: 0.5980 chunk 31 optimal weight: 5.9990 chunk 50 optimal weight: 40.0000 chunk 110 optimal weight: 30.0000 chunk 113 optimal weight: 50.0000 chunk 42 optimal weight: 40.0000 chunk 92 optimal weight: 5.9990 overall best weight: 4.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.092400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.073607 restraints weight = 34562.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.072707 restraints weight = 40045.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.073260 restraints weight = 31617.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.073250 restraints weight = 24382.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.073393 restraints weight = 23141.589| |-----------------------------------------------------------------------------| r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6516 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.066 6614 Z= 0.162 Angle : 0.572 7.080 8713 Z= 0.341 Chirality : 0.054 0.317 293 Planarity : 0.002 0.012 1330 Dihedral : 21.390 152.198 2095 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.28 % Favored : 83.72 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % 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: -3.42 (0.23), residues: 1259 helix: -0.88 (0.25), residues: 470 sheet: -4.97 (0.55), residues: 50 loop : -3.19 (0.21), residues: 739 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.16 ( 6614) covalent geometry : angle 0.57221 / 0.34 ( 8713) hydrogen bonds : bond 0.05631 / 4.29 ( 216) hydrogen bonds : angle 5.23890 / 4.10 ( 580) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.222 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0313 time to fit residues: 1.0296 Evaluate side-chains 13 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 29 optimal weight: 50.0000 chunk 56 optimal weight: 50.0000 chunk 79 optimal weight: 0.0010 chunk 55 optimal weight: 0.4980 chunk 96 optimal weight: 9.9990 chunk 114 optimal weight: 0.0770 chunk 102 optimal weight: 9.9990 chunk 39 optimal weight: 40.0000 chunk 65 optimal weight: 8.9990 chunk 37 optimal weight: 50.0000 chunk 60 optimal weight: 20.0000 overall best weight: 3.9148 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.092965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.073473 restraints weight = 35148.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.073207 restraints weight = 43094.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.073542 restraints weight = 30318.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.073605 restraints weight = 22756.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.073759 restraints weight = 21180.107| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6495 moved from start: 0.3394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 6614 Z= 0.142 Angle : 0.530 6.747 8713 Z= 0.321 Chirality : 0.050 0.310 293 Planarity : 0.002 0.011 1330 Dihedral : 21.312 152.551 2095 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.11 % Favored : 86.89 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % 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: -3.23 (0.23), residues: 1259 helix: -0.69 (0.26), residues: 464 sheet: -4.91 (0.55), residues: 50 loop : -3.08 (0.21), residues: 745 Details of bonding type rmsd/Z covalent geometry : bond 0.00203 / 0.14 ( 6614) covalent geometry : angle 0.52970 / 0.32 ( 8713) hydrogen bonds : bond 0.05240 / 3.98 ( 216) hydrogen bonds : angle 5.03361 / 3.95 ( 580) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1192.56 seconds wall clock time: 21 minutes 3.15 seconds (1263.15 seconds total)