Starting phenix.real_space_refine on Wed Sep 17 07:33:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6gtd_0062/09_2025/6gtd_0062_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6gtd_0062/09_2025/6gtd_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_2025/6gtd_0062_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6gtd_0062/09_2025/6gtd_0062_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6gtd_0062/09_2025/6gtd_0062.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6gtd_0062/09_2025/6gtd_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-2.0-5805/lib/python3.9/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: 2.15, per 1000 atoms: 0.33 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: 0.88 Conformation dependent library (CDL) restraints added in 328.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.81 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: 1.28 Time building geometry restraints manager: 1.05 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=" 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 bond pdb=" N9 G B 2 " pdb=" C4 G B 2 " ideal model delta sigma weight residual 1.375 1.312 0.063 2.00e-02 2.50e+03 9.83e+00 bond pdb=" N3 U B -16 " pdb=" C4 U B -16 " ideal model delta sigma weight residual 1.380 1.318 0.062 2.00e-02 2.50e+03 9.53e+00 bond pdb=" C1' DA C 3 " pdb=" N9 DA C 3 " ideal model delta sigma weight residual 1.460 1.402 0.058 2.00e-02 2.50e+03 8.41e+00 bond pdb=" C LEU A 824 " pdb=" N ASN A 825 " ideal model delta sigma weight residual 1.330 1.298 0.033 1.19e-02 7.06e+03 7.58e+00 ... (remaining 6609 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.75: 8349 2.75 - 5.51: 330 5.51 - 8.26: 28 8.26 - 11.01: 4 11.01 - 13.76: 2 Bond angle restraints: 8713 Sorted by residual: 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=" N ILE A 128 " pdb=" CA ILE A 128 " pdb=" C ILE A 128 " ideal model delta sigma weight residual 113.16 103.38 9.78 1.49e+00 4.50e-01 4.31e+01 angle pdb=" N LEU A 342 " pdb=" CA LEU A 342 " pdb=" C LEU A 342 " ideal model delta sigma weight residual 111.56 103.21 8.35 1.38e+00 5.25e-01 3.66e+01 angle pdb=" N THR A1222 " pdb=" CA THR A1222 " pdb=" C THR A1222 " ideal model delta sigma weight residual 114.62 107.89 6.73 1.14e+00 7.69e-01 3.49e+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 - 0.067: 187 0.067 - 0.133: 76 0.133 - 0.200: 23 0.200 - 0.267: 4 0.267 - 0.334: 3 Chirality restraints: 293 Sorted by residual: 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 0.33 2.00e-01 2.50e+01 2.78e+00 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 -2.66 -2.35 -0.31 2.00e-01 2.50e+01 2.45e+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 1.78e+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: 1.350 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: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.470 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6505 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 0.087 6614 Z= 0.505 Angle : 1.263 13.763 8713 Z= 0.791 Chirality : 0.082 0.334 293 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 aren 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 covalent geometry : bond 0.00886 ( 6614) covalent geometry : angle 1.26335 ( 8713) hydrogen bonds : bond 0.36744 ( 216) hydrogen bonds : angle 14.64671 ( 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 : 0.225 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0314 time to fit residues: 1.0425 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 : 0.221 ------------------------------------------------------------------------------- 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: 0.8980 chunk 124 optimal weight: 30.0000 chunk 103 optimal weight: 2.9990 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: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.092574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.072454 restraints weight = 34915.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.071683 restraints weight = 37421.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.072524 restraints weight = 31049.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.072075 restraints weight = 25231.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.072425 restraints weight = 22310.039| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6526 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 6614 Z= 0.203 Angle : 0.669 8.968 8713 Z= 0.387 Chirality : 0.049 0.201 293 Planarity : 0.003 0.026 1330 Dihedral : 21.933 153.321 2095 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.42 % Favored : 86.58 % 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 aren not related in a simple way. whole: -4.97 (0.19), residues: 1259 helix: -3.11 (0.18), residues: 467 sheet: -4.30 (0.60), residues: 50 loop : -3.51 (0.20), residues: 742 Details of bonding type rmsd covalent geometry : bond 0.00375 ( 6614) covalent geometry : angle 0.66869 ( 8713) hydrogen bonds : bond 0.05389 ( 216) hydrogen bonds : angle 6.99699 ( 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 : 0.351 Fit side-chains REVERT: A 1 MET cc_start: 0.7920 (ptm) cc_final: 0.7717 (ptt) outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0324 time to fit residues: 1.1356 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 63 optimal weight: 30.0000 chunk 19 optimal weight: 50.0000 chunk 68 optimal weight: 40.0000 chunk 37 optimal weight: 50.0000 chunk 49 optimal weight: 20.0000 chunk 34 optimal weight: 0.0270 chunk 3 optimal weight: 9.9990 chunk 7 optimal weight: 0.0970 chunk 113 optimal weight: 50.0000 chunk 70 optimal weight: 40.0000 chunk 77 optimal weight: 0.9980 overall best weight: 6.2242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.091003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.071644 restraints weight = 34921.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.071399 restraints weight = 38383.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.071729 restraints weight = 28831.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.071716 restraints weight = 22660.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.071801 restraints weight = 21456.822| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6546 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 6614 Z= 0.258 Angle : 0.716 9.818 8713 Z= 0.402 Chirality : 0.052 0.235 293 Planarity : 0.003 0.014 1330 Dihedral : 21.926 150.459 2095 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.67 % Favored : 81.33 % 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 aren not related in a simple way. whole: -4.43 (0.21), residues: 1259 helix: -2.30 (0.21), residues: 481 sheet: -4.56 (0.59), residues: 50 loop : -3.43 (0.21), residues: 728 Details of bonding type rmsd covalent geometry : bond 0.00486 ( 6614) covalent geometry : angle 0.71602 ( 8713) hydrogen bonds : bond 0.06088 ( 216) hydrogen bonds : angle 6.06677 ( 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 : 0.239 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0294 time to fit residues: 1.0283 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 : 0.263 ------------------------------------------------------------------------------- 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: 50.0000 chunk 86 optimal weight: 0.0870 chunk 66 optimal weight: 0.0870 chunk 2 optimal weight: 2.9990 chunk 56 optimal weight: 50.0000 chunk 121 optimal weight: 40.0000 chunk 105 optimal weight: 0.0060 chunk 111 optimal weight: 50.0000 chunk 34 optimal weight: 6.9990 chunk 126 optimal weight: 7.9990 chunk 35 optimal weight: 40.0000 overall best weight: 2.0356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.095226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.075424 restraints weight = 34535.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.073993 restraints weight = 36427.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.074540 restraints weight = 27960.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.074629 restraints weight = 22669.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.074746 restraints weight = 20671.060| |-----------------------------------------------------------------------------| r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6432 moved from start: 0.3536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 6614 Z= 0.121 Angle : 0.516 9.730 8713 Z= 0.284 Chirality : 0.033 0.150 293 Planarity : 0.002 0.009 1330 Dihedral : 21.097 153.693 2095 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.21 % Favored : 90.79 % 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 aren not related in a simple way. whole: -3.77 (0.22), residues: 1259 helix: -1.42 (0.24), residues: 474 sheet: -4.29 (0.77), residues: 30 loop : -3.35 (0.20), residues: 755 Details of bonding type rmsd covalent geometry : bond 0.00233 ( 6614) covalent geometry : angle 0.51555 ( 8713) hydrogen bonds : bond 0.04167 ( 216) hydrogen bonds : angle 4.61069 ( 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 : 0.228 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0310 time to fit residues: 1.0523 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 : 0.227 ------------------------------------------------------------------------------- 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: 40.0000 chunk 118 optimal weight: 10.0000 chunk 71 optimal weight: 7.9990 chunk 50 optimal weight: 40.0000 chunk 26 optimal weight: 50.0000 chunk 38 optimal weight: 20.0000 chunk 22 optimal weight: 20.0000 chunk 79 optimal weight: 0.0000 chunk 76 optimal weight: 20.0000 chunk 110 optimal weight: 30.0000 chunk 119 optimal weight: 1.9990 overall best weight: 7.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.090522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.071744 restraints weight = 36214.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.070671 restraints weight = 44310.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.071256 restraints weight = 33479.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.071095 restraints weight = 28765.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.071145 restraints weight = 24252.554| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6570 moved from start: 0.3136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.108 6614 Z= 0.303 Angle : 0.744 9.649 8713 Z= 0.412 Chirality : 0.056 0.297 293 Planarity : 0.003 0.016 1330 Dihedral : 21.819 152.179 2095 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.54 % Favored : 80.46 % 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 aren not related in a simple way. whole: -3.83 (0.22), residues: 1259 helix: -1.36 (0.24), residues: 476 sheet: -4.72 (0.57), residues: 50 loop : -3.38 (0.21), residues: 733 Details of bonding type rmsd covalent geometry : bond 0.00570 ( 6614) covalent geometry : angle 0.74392 ( 8713) hydrogen bonds : bond 0.06291 ( 216) hydrogen bonds : angle 5.59022 ( 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 : 0.237 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0323 time to fit residues: 1.0876 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 : 0.223 ------------------------------------------------------------------------------- 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: 30.0000 chunk 28 optimal weight: 40.0000 chunk 21 optimal weight: 50.0000 chunk 112 optimal weight: 20.0000 chunk 54 optimal weight: 30.0000 chunk 48 optimal weight: 50.0000 chunk 71 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 8 optimal weight: 30.0000 chunk 62 optimal weight: 9.9990 chunk 90 optimal weight: 10.0000 overall best weight: 9.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.089322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.070435 restraints weight = 36195.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.069814 restraints weight = 42368.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.070760 restraints weight = 32793.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.070007 restraints weight = 27871.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.070249 restraints weight = 23993.135| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6615 moved from start: 0.3409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.130 6614 Z= 0.357 Angle : 0.830 8.804 8713 Z= 0.465 Chirality : 0.063 0.364 293 Planarity : 0.004 0.020 1330 Dihedral : 22.110 149.653 2095 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 15.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.98 % Favored : 81.02 % 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 aren not related in a simple way. whole: -3.93 (0.22), residues: 1259 helix: -1.48 (0.23), residues: 470 sheet: -4.75 (0.63), residues: 50 loop : -3.40 (0.21), residues: 739 Details of bonding type rmsd covalent geometry : bond 0.00670 ( 6614) covalent geometry : angle 0.83013 ( 8713) hydrogen bonds : bond 0.08172 ( 216) hydrogen bonds : angle 6.32894 ( 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 : 0.284 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0323 time to fit residues: 1.1580 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 : 0.272 ------------------------------------------------------------------------------- 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: 0.6980 chunk 33 optimal weight: 50.0000 chunk 5 optimal weight: 0.3980 chunk 19 optimal weight: 40.0000 chunk 9 optimal weight: 40.0000 chunk 53 optimal weight: 5.9990 chunk 94 optimal weight: 20.0000 chunk 114 optimal weight: 0.1980 chunk 123 optimal weight: 5.9990 chunk 39 optimal weight: 40.0000 overall best weight: 2.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.093313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.073454 restraints weight = 35236.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.072815 restraints weight = 34932.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.072839 restraints weight = 31286.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.073110 restraints weight = 25432.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.073313 restraints weight = 21425.696| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6466 moved from start: 0.3937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 6614 Z= 0.136 Angle : 0.540 9.715 8713 Z= 0.298 Chirality : 0.035 0.169 293 Planarity : 0.002 0.009 1330 Dihedral : 21.253 152.387 2095 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.03 % Favored : 86.97 % 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 aren not related in a simple way. whole: -3.31 (0.23), residues: 1259 helix: -0.88 (0.25), residues: 481 sheet: -4.67 (0.75), residues: 30 loop : -3.17 (0.21), residues: 748 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 6614) covalent geometry : angle 0.54045 ( 8713) hydrogen bonds : bond 0.04647 ( 216) hydrogen bonds : angle 4.74577 ( 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 : 0.282 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0341 time to fit residues: 1.1770 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 : 0.224 ------------------------------------------------------------------------------- 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: 40.0000 chunk 39 optimal weight: 40.0000 chunk 51 optimal weight: 20.0000 chunk 117 optimal weight: 0.0020 chunk 36 optimal weight: 6.9990 chunk 14 optimal weight: 7.9990 chunk 3 optimal weight: 10.0000 chunk 68 optimal weight: 8.9990 chunk 91 optimal weight: 10.0000 chunk 17 optimal weight: 0.3980 chunk 6 optimal weight: 20.0000 overall best weight: 4.8794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.091688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.072769 restraints weight = 35534.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.072175 restraints weight = 41089.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.072651 restraints weight = 32840.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.072630 restraints weight = 24428.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.072733 restraints weight = 22458.200| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6489 moved from start: 0.3971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 6614 Z= 0.203 Angle : 0.602 9.915 8713 Z= 0.334 Chirality : 0.044 0.240 293 Planarity : 0.002 0.011 1330 Dihedral : 21.343 149.458 2095 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.08 % Favored : 82.92 % 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 aren not related in a simple way. whole: -3.31 (0.23), residues: 1259 helix: -0.75 (0.25), residues: 476 sheet: -4.83 (0.58), residues: 50 loop : -3.17 (0.22), residues: 733 Details of bonding type rmsd covalent geometry : bond 0.00386 ( 6614) covalent geometry : angle 0.60199 ( 8713) hydrogen bonds : bond 0.05571 ( 216) hydrogen bonds : angle 4.90040 ( 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 : 0.266 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0340 time to fit residues: 1.1317 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 : 0.235 ------------------------------------------------------------------------------- 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: 7.9990 chunk 83 optimal weight: 0.0670 chunk 40 optimal weight: 50.0000 chunk 120 optimal weight: 0.0770 chunk 18 optimal weight: 0.9980 chunk 1 optimal weight: 20.0000 chunk 34 optimal weight: 9.9990 chunk 49 optimal weight: 50.0000 chunk 103 optimal weight: 9.9990 chunk 86 optimal weight: 0.1980 chunk 61 optimal weight: 30.0000 overall best weight: 1.8678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.094412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.071699 restraints weight = 35244.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.072859 restraints weight = 24983.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.074529 restraints weight = 18399.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.074641 restraints weight = 15881.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.074684 restraints weight = 12589.350| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6467 moved from start: 0.4482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 6614 Z= 0.111 Angle : 0.478 10.039 8713 Z= 0.262 Chirality : 0.031 0.156 293 Planarity : 0.001 0.007 1330 Dihedral : 20.965 144.041 2095 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.29 % Favored : 90.71 % 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 aren not related in a simple way. whole: -2.92 (0.24), residues: 1259 helix: -0.36 (0.26), residues: 477 sheet: -4.57 (0.77), residues: 30 loop : -3.09 (0.21), residues: 752 Details of bonding type rmsd covalent geometry : bond 0.00216 ( 6614) covalent geometry : angle 0.47808 ( 8713) hydrogen bonds : bond 0.04226 ( 216) hydrogen bonds : angle 4.06531 ( 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 : 0.237 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0325 time to fit residues: 1.1261 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 : 0.235 ------------------------------------------------------------------------------- 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: 6.9990 chunk 70 optimal weight: 5.9990 chunk 3 optimal weight: 20.0000 chunk 79 optimal weight: 0.0010 chunk 31 optimal weight: 2.9990 chunk 50 optimal weight: 6.9990 chunk 110 optimal weight: 50.0000 chunk 113 optimal weight: 50.0000 chunk 42 optimal weight: 40.0000 chunk 92 optimal weight: 4.9990 overall best weight: 4.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.092374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.071739 restraints weight = 34477.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.071158 restraints weight = 27665.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.071708 restraints weight = 24356.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.071696 restraints weight = 20005.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.071817 restraints weight = 18544.561| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6573 moved from start: 0.4387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 6614 Z= 0.175 Angle : 0.546 9.906 8713 Z= 0.302 Chirality : 0.040 0.228 293 Planarity : 0.002 0.013 1330 Dihedral : 21.135 140.025 2095 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.69 % Favored : 85.31 % 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 aren not related in a simple way. whole: -2.80 (0.24), residues: 1259 helix: -0.21 (0.26), residues: 471 sheet: -4.67 (0.76), residues: 30 loop : -3.02 (0.21), residues: 758 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 6614) covalent geometry : angle 0.54640 ( 8713) hydrogen bonds : bond 0.04916 ( 216) hydrogen bonds : angle 4.37081 ( 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 : 0.226 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0311 time to fit residues: 1.0598 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 : 0.325 ------------------------------------------------------------------------------- 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: 40.0000 chunk 79 optimal weight: 0.0970 chunk 55 optimal weight: 50.0000 chunk 96 optimal weight: 9.9990 chunk 114 optimal weight: 0.0770 chunk 102 optimal weight: 20.0000 chunk 39 optimal weight: 30.0000 chunk 65 optimal weight: 9.9990 chunk 37 optimal weight: 30.0000 chunk 60 optimal weight: 30.0000 overall best weight: 8.0344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.090085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.071610 restraints weight = 36043.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.070828 restraints weight = 44046.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.071339 restraints weight = 33581.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.071308 restraints weight = 26663.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.071432 restraints weight = 24223.273| |-----------------------------------------------------------------------------| r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6551 moved from start: 0.4301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.118 6614 Z= 0.300 Angle : 0.728 9.362 8713 Z= 0.406 Chirality : 0.056 0.323 293 Planarity : 0.003 0.017 1330 Dihedral : 21.600 134.336 2095 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.67 % Favored : 81.33 % 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 aren not related in a simple way. whole: -3.15 (0.24), residues: 1259 helix: -0.56 (0.25), residues: 481 sheet: -4.91 (0.57), residues: 50 loop : -3.12 (0.22), residues: 728 Details of bonding type rmsd covalent geometry : bond 0.00569 ( 6614) covalent geometry : angle 0.72826 ( 8713) hydrogen bonds : bond 0.07036 ( 216) hydrogen bonds : angle 5.39560 ( 580) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1219.05 seconds wall clock time: 21 minutes 28.92 seconds (1288.92 seconds total)