Starting phenix.real_space_refine (version: dev) on Mon Apr 4 14:22:56 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gtd_0062/04_2022/6gtd_0062_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gtd_0062/04_2022/6gtd_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gtd_0062/04_2022/6gtd_0062.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gtd_0062/04_2022/6gtd_0062.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gtd_0062/04_2022/6gtd_0062_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gtd_0062/04_2022/6gtd_0062_neut.pdb" } 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 ------------------------------------------------------------------------------- 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/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: {'PTRANS': 27, 'CIS': 2, '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: {'GLN:plan1': 55, 'HIS:plan': 18, 'TYR:plan': 67, 'ASN:plan1': 97, 'TRP:plan': 8, 'ASP:plan': 97, 'PHE:plan': 83, 'GLU:plan': 93, 'ARG:plan': 33} 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: {'rna3p_pyr': 9, 'rna2p_pur': 4, 'rna3p_pur': 11, 'rna2p_pyr': 4} Link IDs: {'rna3p': 19, 'rna2p': 8} 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: 4.95, per 1000 atoms: 0.77 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 - 3.50 Amino acid : False - 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: 3.28 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 2.21 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: 2.50 Time building geometry restraints manager: 3.46 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: 97.78 - 105.55: 371 105.55 - 113.32: 1986 113.32 - 121.09: 3623 121.09 - 128.87: 2666 128.87 - 136.64: 67 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: 1699 28.96 - 57.92: 232 57.92 - 86.88: 31 86.88 - 115.84: 13 115.84 - 144.80: 1 Dihedral angle restraints: 1976 sinusoidal: 710 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 1973 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 2.520 nonbonded pdb=" O LYS A 613 " pdb=" N ASN A 617 " model vdw 2.306 2.520 nonbonded pdb=" N ARG A 872 " pdb=" OP2 U B -17 " model vdw 2.311 2.520 nonbonded pdb=" O4 U B -15 " pdb=" N6 A B -2 " model vdw 2.319 2.520 nonbonded pdb=" O TRP A 175 " pdb=" N PHE A 179 " model vdw 2.323 2.520 ... (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 ========== 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 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. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.490 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: 3.330 Check model and map are aligned: 0.100 Convert atoms to be neutral: 0.060 Process input model: 25.460 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.470 ------------------------------------------------------------------------------- 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 0.087 6614 Z= 0.556 Angle : 1.263 13.763 8713 Z= 0.790 Chirality : 0.082 0.334 293 Planarity : 0.005 0.028 1330 Dihedral : 21.740 144.798 1974 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 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.49 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.729 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0696 time to fit residues: 2.6650 Evaluate side-chains 13 residues out of total 1155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.680 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 110 optimal weight: 40.0000 chunk 99 optimal weight: 9.9990 chunk 55 optimal weight: 2.9990 chunk 33 optimal weight: 50.0000 chunk 66 optimal weight: 20.0000 chunk 53 optimal weight: 30.0000 chunk 102 optimal weight: 10.0000 chunk 39 optimal weight: 30.0000 chunk 62 optimal weight: 9.9990 chunk 76 optimal weight: 9.9990 chunk 118 optimal weight: 40.0000 overall best weight: 8.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6524 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.110 6614 Z= 0.393 Angle : 0.856 9.147 8713 Z= 0.489 Chirality : 0.065 0.300 293 Planarity : 0.004 0.027 1330 Dihedral : 21.351 152.071 1971 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 20.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.02 % Favored : 79.98 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.99 (0.20), residues: 1259 helix: -3.04 (0.19), residues: 419 sheet: -4.61 (0.58), residues: 50 loop : -3.59 (0.20), residues: 790 *********************** 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 fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.732 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0692 time to fit residues: 2.7385 Evaluate side-chains 13 residues out of total 1155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.740 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 66 optimal weight: 0.1980 chunk 36 optimal weight: 2.9990 chunk 99 optimal weight: 0.4980 chunk 81 optimal weight: 0.7980 chunk 32 optimal weight: 30.0000 chunk 119 optimal weight: 50.0000 chunk 128 optimal weight: 7.9990 chunk 106 optimal weight: 0.9980 chunk 118 optimal weight: 7.9990 chunk 40 optimal weight: 0.7980 chunk 95 optimal weight: 10.0000 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6112 moved from start: 0.3201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.043 6614 Z= 0.126 Angle : 0.525 9.516 8713 Z= 0.290 Chirality : 0.033 0.156 293 Planarity : 0.002 0.013 1330 Dihedral : 19.684 152.690 1971 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.66 % Favored : 91.34 % Rotamer Outliers : 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.18 (0.21), residues: 1259 helix: -2.07 (0.22), residues: 486 sheet: -4.32 (0.72), residues: 30 loop : -3.38 (0.21), residues: 743 *********************** 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 fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.775 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0814 time to fit residues: 3.0619 Evaluate side-chains 13 residues out of total 1155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.773 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 117 optimal weight: 20.0000 chunk 89 optimal weight: 40.0000 chunk 61 optimal weight: 30.0000 chunk 13 optimal weight: 50.0000 chunk 56 optimal weight: 50.0000 chunk 80 optimal weight: 20.0000 chunk 119 optimal weight: 1.9990 chunk 126 optimal weight: 9.9990 chunk 62 optimal weight: 6.9990 chunk 113 optimal weight: 50.0000 chunk 34 optimal weight: 0.0070 overall best weight: 7.8008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6473 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.096 6614 Z= 0.353 Angle : 0.764 9.234 8713 Z= 0.426 Chirality : 0.058 0.275 293 Planarity : 0.003 0.017 1330 Dihedral : 20.736 152.586 1971 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 18.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.41 % Favored : 79.59 % Rotamer Outliers : 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.01 (0.22), residues: 1259 helix: -1.70 (0.23), residues: 475 sheet: -4.66 (0.56), residues: 50 loop : -3.35 (0.21), residues: 734 *********************** 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 fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.719 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0683 time to fit residues: 2.6329 Evaluate side-chains 13 residues out of total 1155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.717 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 105 optimal weight: 0.0570 chunk 71 optimal weight: 30.0000 chunk 1 optimal weight: 10.0000 chunk 94 optimal weight: 20.0000 chunk 52 optimal weight: 50.0000 chunk 108 optimal weight: 30.0000 chunk 87 optimal weight: 10.0000 chunk 0 optimal weight: 30.0000 chunk 64 optimal weight: 40.0000 chunk 113 optimal weight: 50.0000 chunk 31 optimal weight: 0.0370 overall best weight: 8.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6494 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.103 6614 Z= 0.351 Angle : 0.768 9.551 8713 Z= 0.429 Chirality : 0.058 0.306 293 Planarity : 0.003 0.018 1330 Dihedral : 20.842 151.773 1971 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 19.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.54 % Favored : 80.46 % Rotamer Outliers : 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.85 (0.22), residues: 1259 helix: -1.45 (0.24), residues: 459 sheet: -4.65 (0.60), residues: 50 loop : -3.32 (0.21), residues: 750 *********************** 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 fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.725 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0664 time to fit residues: 2.6275 Evaluate side-chains 13 residues out of total 1155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.718 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 42 optimal weight: 50.0000 chunk 114 optimal weight: 0.0000 chunk 25 optimal weight: 50.0000 chunk 74 optimal weight: 10.0000 chunk 31 optimal weight: 0.7980 chunk 126 optimal weight: 7.9990 chunk 105 optimal weight: 0.5980 chunk 58 optimal weight: 9.9990 chunk 10 optimal weight: 2.9990 chunk 41 optimal weight: 20.0000 chunk 66 optimal weight: 0.8980 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6175 moved from start: 0.3772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.046 6614 Z= 0.117 Angle : 0.490 9.678 8713 Z= 0.267 Chirality : 0.030 0.154 293 Planarity : 0.001 0.009 1330 Dihedral : 19.649 153.229 1971 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.13 % Favored : 90.87 % Rotamer Outliers : 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.29 (0.23), residues: 1259 helix: -0.79 (0.25), residues: 481 sheet: -4.55 (0.74), residues: 30 loop : -3.24 (0.21), residues: 748 *********************** 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 fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.802 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0721 time to fit residues: 2.6391 Evaluate side-chains 13 residues out of total 1155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.757 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 122 optimal weight: 20.0000 chunk 14 optimal weight: 10.0000 chunk 72 optimal weight: 0.0010 chunk 92 optimal weight: 5.9990 chunk 71 optimal weight: 0.4980 chunk 106 optimal weight: 0.6980 chunk 70 optimal weight: 6.9990 chunk 126 optimal weight: 10.0000 chunk 79 optimal weight: 2.9990 chunk 76 optimal weight: 30.0000 chunk 58 optimal weight: 10.0000 overall best weight: 2.0390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6262 moved from start: 0.3855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.046 6614 Z= 0.134 Angle : 0.478 9.564 8713 Z= 0.262 Chirality : 0.032 0.169 293 Planarity : 0.001 0.009 1330 Dihedral : 19.555 153.408 1971 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.76 % Favored : 88.24 % Rotamer Outliers : 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.03 (0.24), residues: 1259 helix: -0.46 (0.26), residues: 478 sheet: -4.59 (0.56), residues: 50 loop : -3.08 (0.21), residues: 731 *********************** 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 fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.718 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0697 time to fit residues: 2.6705 Evaluate side-chains 13 residues out of total 1155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.725 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 78 optimal weight: 40.0000 chunk 50 optimal weight: 20.0000 chunk 75 optimal weight: 30.0000 chunk 38 optimal weight: 10.0000 chunk 24 optimal weight: 50.0000 chunk 80 optimal weight: 10.0000 chunk 86 optimal weight: 10.0000 chunk 62 optimal weight: 0.3980 chunk 11 optimal weight: 30.0000 chunk 99 optimal weight: 9.9990 chunk 114 optimal weight: 30.0000 overall best weight: 8.0794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6491 moved from start: 0.3520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.106 6614 Z= 0.361 Angle : 0.735 9.469 8713 Z= 0.410 Chirality : 0.057 0.333 293 Planarity : 0.003 0.016 1330 Dihedral : 20.499 152.001 1971 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 19.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.25 % Favored : 79.75 % Rotamer Outliers : 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.31 (0.23), residues: 1259 helix: -0.74 (0.25), residues: 460 sheet: -4.68 (0.59), residues: 50 loop : -3.16 (0.21), residues: 749 *********************** 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 fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.712 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0682 time to fit residues: 2.6499 Evaluate side-chains 13 residues out of total 1155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.738 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 120 optimal weight: 40.0000 chunk 110 optimal weight: 30.0000 chunk 117 optimal weight: 7.9990 chunk 70 optimal weight: 40.0000 chunk 51 optimal weight: 20.0000 chunk 92 optimal weight: 10.0000 chunk 36 optimal weight: 20.0000 chunk 106 optimal weight: 0.3980 chunk 111 optimal weight: 20.0000 chunk 77 optimal weight: 10.0000 chunk 124 optimal weight: 7.9990 overall best weight: 7.2792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6473 moved from start: 0.3744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.091 6614 Z= 0.318 Angle : 0.696 9.844 8713 Z= 0.387 Chirality : 0.052 0.297 293 Planarity : 0.003 0.017 1330 Dihedral : 20.422 151.667 1971 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 17.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.03 % Favored : 81.97 % Rotamer Outliers : 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.27 (0.23), residues: 1259 helix: -0.81 (0.25), residues: 479 sheet: -4.70 (0.60), residues: 50 loop : -3.09 (0.22), residues: 730 *********************** 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 fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.769 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0695 time to fit residues: 2.7345 Evaluate side-chains 13 residues out of total 1155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.739 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 75 optimal weight: 30.0000 chunk 59 optimal weight: 6.9990 chunk 86 optimal weight: 0.1980 chunk 130 optimal weight: 10.0000 chunk 120 optimal weight: 30.0000 chunk 103 optimal weight: 20.0000 chunk 10 optimal weight: 10.0000 chunk 80 optimal weight: 10.0000 chunk 63 optimal weight: 20.0000 chunk 82 optimal weight: 9.9990 chunk 110 optimal weight: 30.0000 overall best weight: 7.4392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6498 moved from start: 0.4052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.098 6614 Z= 0.328 Angle : 0.726 9.394 8713 Z= 0.404 Chirality : 0.056 0.305 293 Planarity : 0.003 0.016 1330 Dihedral : 20.426 142.333 1971 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 21.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 21.21 % Favored : 78.79 % Rotamer Outliers : 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.33 (0.23), residues: 1259 helix: -0.85 (0.25), residues: 474 sheet: -4.80 (0.59), residues: 50 loop : -3.12 (0.22), residues: 735 ********************** 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 fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.694 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0691 time to fit residues: 2.6877 Evaluate side-chains 13 residues out of total 1155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.787 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 31 optimal weight: 50.0000 chunk 95 optimal weight: 30.0000 chunk 15 optimal weight: 40.0000 chunk 28 optimal weight: 40.0000 chunk 104 optimal weight: 10.0000 chunk 43 optimal weight: 50.0000 chunk 106 optimal weight: 0.0010 chunk 13 optimal weight: 0.0040 chunk 19 optimal weight: 50.0000 chunk 91 optimal weight: 8.9990 chunk 5 optimal weight: 20.0000 overall best weight: 7.8008 ------------------------------------------------------------------------------- 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 = 0.3749 r_free = 0.3749 target = 0.089404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.070634 restraints weight = 35850.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.070078 restraints weight = 38965.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.070321 restraints weight = 35523.591| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6658 moved from start: 0.4207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.101 6614 Z= 0.341 Angle : 0.735 9.358 8713 Z= 0.410 Chirality : 0.057 0.309 293 Planarity : 0.003 0.018 1330 Dihedral : 20.451 136.647 1971 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 20.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.86 % Favored : 80.14 % Rotamer Outliers : 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.31 (0.23), residues: 1259 helix: -0.90 (0.24), residues: 485 sheet: -4.83 (0.59), residues: 50 loop : -3.08 (0.22), residues: 724 =============================================================================== Job complete usr+sys time: 1050.40 seconds wall clock time: 19 minutes 38.74 seconds (1178.74 seconds total)