Starting phenix.real_space_refine (version: dev) on Fri Feb 17 22:08:55 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gtd_0062/02_2023/6gtd_0062_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gtd_0062/02_2023/6gtd_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_0062/02_2023/6gtd_0062.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gtd_0062/02_2023/6gtd_0062.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gtd_0062/02_2023/6gtd_0062_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gtd_0062/02_2023/6gtd_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 Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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: {'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: {'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: {'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: 5.20, per 1000 atoms: 0.81 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: 3.41 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: 1.69 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: 2.84 Time building geometry restraints manager: 3.54 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: 0.720 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: 3.300 Check model and map are aligned: 0.100 Process input model: 24.390 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.070 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.700 ------------------------------------------------------------------------------- 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 : 0.671 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0763 time to fit residues: 2.8669 Evaluate side-chains 13 residues out of total 1155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.671 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8489 ------------------------------------------------------------------------------- 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 : 0.746 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0710 time to fit residues: 2.6767 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: 1.0059 ------------------------------------------------------------------------------- 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: 0.0370 chunk 36 optimal weight: 5.9990 chunk 99 optimal weight: 0.5980 chunk 81 optimal weight: 0.4980 chunk 32 optimal weight: 40.0000 chunk 119 optimal weight: 50.0000 chunk 128 optimal weight: 7.9990 chunk 106 optimal weight: 0.9980 chunk 118 optimal weight: 9.9990 chunk 40 optimal weight: 0.0770 chunk 95 optimal weight: 10.0000 overall best weight: 0.4416 ------------------------------------------------------------------------------- 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: 0.6082 moved from start: 0.3268 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= 0.125 Angle : 0.523 9.783 8713 Z= 0.289 Chirality : 0.032 0.157 293 Planarity : 0.002 0.014 1330 Dihedral : 19.615 153.053 1971 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.34 % Favored : 91.66 % 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: -4.21 (0.21), residues: 1259 helix: -2.08 (0.21), residues: 487 sheet: -4.28 (0.72), residues: 30 loop : -3.40 (0.20), residues: 742 *********************** 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 : 0.746 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.1245 time to fit residues: 3.6300 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 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9331 ------------------------------------------------------------------------------- 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: 20.0000 chunk 56 optimal weight: 50.0000 chunk 80 optimal weight: 20.0000 chunk 119 optimal weight: 0.0060 chunk 126 optimal weight: 9.9990 chunk 62 optimal weight: 7.9990 chunk 113 optimal weight: 50.0000 chunk 34 optimal weight: 1.9990 overall best weight: 8.0006 ------------------------------------------------------------------------------- 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: 0.6474 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.093 6614 Z= 0.354 Angle : 0.759 9.224 8713 Z= 0.424 Chirality : 0.058 0.283 293 Planarity : 0.003 0.017 1330 Dihedral : 20.720 152.619 1971 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 19.10 Ramachandran Plot: Outliers : 0.08 % Allowed : 20.73 % Favored : 79.19 % 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: -1.69 (0.23), residues: 475 sheet: -4.66 (0.56), residues: 50 loop : -3.36 (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: 0.0818 time to fit residues: 2.9067 Evaluate side-chains 13 residues out of total 1155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.683 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9371 ------------------------------------------------------------------------------- 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: 0.9980 chunk 71 optimal weight: 20.0000 chunk 1 optimal weight: 6.9990 chunk 94 optimal weight: 20.0000 chunk 52 optimal weight: 10.0000 chunk 108 optimal weight: 30.0000 chunk 87 optimal weight: 10.0000 chunk 0 optimal weight: 40.0000 chunk 64 optimal weight: 40.0000 chunk 113 optimal weight: 50.0000 chunk 31 optimal weight: 8.9990 overall best weight: 7.3992 ------------------------------------------------------------------------------- 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: 0.6477 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.100 6614 Z= 0.327 Angle : 0.736 9.620 8713 Z= 0.411 Chirality : 0.055 0.295 293 Planarity : 0.003 0.016 1330 Dihedral : 20.756 151.524 1971 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 17.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.35 % Favored : 81.65 % 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: -3.87 (0.22), residues: 1259 helix: -1.41 (0.24), residues: 470 sheet: -4.71 (0.58), residues: 50 loop : -3.38 (0.21), residues: 739 *********************** 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 : 0.708 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0725 time to fit residues: 2.7306 Evaluate side-chains 13 residues out of total 1155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.692 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8918 ------------------------------------------------------------------------------- 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: 0.0170 chunk 25 optimal weight: 40.0000 chunk 74 optimal weight: 6.9990 chunk 31 optimal weight: 40.0000 chunk 126 optimal weight: 7.9990 chunk 105 optimal weight: 8.9990 chunk 58 optimal weight: 10.0000 chunk 10 optimal weight: 0.2980 chunk 41 optimal weight: 9.9990 chunk 66 optimal weight: 0.0000 overall best weight: 3.0626 ------------------------------------------------------------------------------- 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: 0.6327 moved from start: 0.3486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 6614 Z= 0.166 Angle : 0.539 9.693 8713 Z= 0.298 Chirality : 0.035 0.167 293 Planarity : 0.002 0.009 1330 Dihedral : 20.055 152.540 1971 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.69 % Favored : 85.31 % 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: -3.39 (0.23), residues: 1259 helix: -0.88 (0.25), residues: 484 sheet: -4.81 (0.55), residues: 50 loop : -3.20 (0.21), residues: 725 *********************** 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 : 0.756 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0692 time to fit residues: 2.6761 Evaluate side-chains 13 residues out of total 1155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.733 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9787 ------------------------------------------------------------------------------- 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: 40.0000 chunk 92 optimal weight: 9.9990 chunk 71 optimal weight: 9.9990 chunk 106 optimal weight: 0.3980 chunk 70 optimal weight: 10.0000 chunk 126 optimal weight: 10.0000 chunk 79 optimal weight: 0.0170 chunk 76 optimal weight: 30.0000 chunk 58 optimal weight: 10.0000 overall best weight: 6.0826 ------------------------------------------------------------------------------- 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: 0.6448 moved from start: 0.3452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.080 6614 Z= 0.280 Angle : 0.660 9.691 8713 Z= 0.367 Chirality : 0.049 0.274 293 Planarity : 0.003 0.014 1330 Dihedral : 20.381 151.946 1971 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 15.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.46 % Favored : 80.54 % 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: -3.43 (0.23), residues: 1259 helix: -0.83 (0.25), residues: 474 sheet: -4.73 (0.58), residues: 50 loop : -3.27 (0.21), residues: 735 *********************** 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 : 0.650 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0704 time to fit residues: 2.7002 Evaluate side-chains 13 residues out of total 1155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.671 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8499 ------------------------------------------------------------------------------- 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: 20.0000 chunk 50 optimal weight: 40.0000 chunk 75 optimal weight: 30.0000 chunk 38 optimal weight: 50.0000 chunk 24 optimal weight: 50.0000 chunk 80 optimal weight: 9.9990 chunk 86 optimal weight: 7.9990 chunk 62 optimal weight: 0.0670 chunk 11 optimal weight: 30.0000 chunk 99 optimal weight: 10.0000 chunk 114 optimal weight: 0.0060 overall best weight: 5.6142 ------------------------------------------------------------------------------- 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: 0.6432 moved from start: 0.3699 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= 0.254 Angle : 0.628 9.966 8713 Z= 0.348 Chirality : 0.046 0.262 293 Planarity : 0.003 0.014 1330 Dihedral : 20.233 152.219 1971 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.84 % Favored : 83.16 % 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: -3.34 (0.23), residues: 1259 helix: -0.83 (0.25), residues: 482 sheet: -4.84 (0.57), residues: 50 loop : -3.17 (0.22), residues: 727 *********************** 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 : 0.618 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0740 time to fit residues: 2.7742 Evaluate side-chains 13 residues out of total 1155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.733 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9088 ------------------------------------------------------------------------------- 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: 20.0000 chunk 110 optimal weight: 30.0000 chunk 117 optimal weight: 20.0000 chunk 70 optimal weight: 50.0000 chunk 51 optimal weight: 20.0000 chunk 92 optimal weight: 9.9990 chunk 36 optimal weight: 0.3980 chunk 106 optimal weight: 0.1980 chunk 111 optimal weight: 30.0000 chunk 77 optimal weight: 0.0770 chunk 124 optimal weight: 8.9990 overall best weight: 3.9342 ------------------------------------------------------------------------------- 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: 0.6375 moved from start: 0.3996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 6614 Z= 0.193 Angle : 0.557 9.903 8713 Z= 0.308 Chirality : 0.040 0.219 293 Planarity : 0.002 0.010 1330 Dihedral : 19.998 152.537 1971 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.76 % Favored : 83.24 % 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: -3.10 (0.24), residues: 1259 helix: -0.59 (0.26), residues: 488 sheet: -4.82 (0.56), residues: 50 loop : -3.07 (0.22), residues: 721 *********************** 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 : 0.678 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0729 time to fit residues: 2.7429 Evaluate side-chains 13 residues out of total 1155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.713 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8649 ------------------------------------------------------------------------------- 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: 0.9980 chunk 86 optimal weight: 0.0170 chunk 130 optimal weight: 10.0000 chunk 120 optimal weight: 20.0000 chunk 103 optimal weight: 20.0000 chunk 10 optimal weight: 30.0000 chunk 80 optimal weight: 10.0000 chunk 63 optimal weight: 20.0000 chunk 82 optimal weight: 10.0000 chunk 110 optimal weight: 30.0000 overall best weight: 6.2030 ------------------------------------------------------------------------------- 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: 0.6454 moved from start: 0.4020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.084 6614 Z= 0.283 Angle : 0.653 9.876 8713 Z= 0.363 Chirality : 0.049 0.281 293 Planarity : 0.003 0.014 1330 Dihedral : 20.236 152.345 1971 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 16.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.30 % Favored : 80.70 % 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: -3.17 (0.24), residues: 1259 helix: -0.66 (0.25), residues: 483 sheet: -4.82 (0.57), residues: 50 loop : -3.09 (0.22), residues: 726 ********************** 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 : 0.838 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0682 time to fit residues: 2.6563 Evaluate side-chains 13 residues out of total 1155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.650 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8393 ------------------------------------------------------------------------------- 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: 0.0270 chunk 28 optimal weight: 50.0000 chunk 104 optimal weight: 9.9990 chunk 43 optimal weight: 50.0000 chunk 106 optimal weight: 4.9990 chunk 13 optimal weight: 7.9990 chunk 19 optimal weight: 50.0000 chunk 91 optimal weight: 20.0000 chunk 5 optimal weight: 9.9990 overall best weight: 6.6046 ------------------------------------------------------------------------------- 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 = 0.090022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.071682 restraints weight = 35683.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.070434 restraints weight = 40842.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.070911 restraints weight = 35234.435| |-----------------------------------------------------------------------------| r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6667 moved from start: 0.4278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.087 6614 Z= 0.294 Angle : 0.674 9.494 8713 Z= 0.375 Chirality : 0.052 0.287 293 Planarity : 0.003 0.015 1330 Dihedral : 20.335 152.666 1971 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 16.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.46 % Favored : 80.54 % 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: -3.20 (0.24), residues: 1259 helix: -0.73 (0.25), residues: 481 sheet: -4.89 (0.56), residues: 50 loop : -3.06 (0.22), residues: 728 =============================================================================== Job complete usr+sys time: 1059.97 seconds wall clock time: 20 minutes 2.82 seconds (1202.82 seconds total)