Starting phenix.real_space_refine on Sat Nov 16 11:29:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kgf_37219/11_2024/8kgf_37219_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kgf_37219/11_2024/8kgf_37219.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kgf_37219/11_2024/8kgf_37219.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kgf_37219/11_2024/8kgf_37219.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kgf_37219/11_2024/8kgf_37219_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kgf_37219/11_2024/8kgf_37219_neut.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 29 5.49 5 Mg 2 5.21 5 S 35 5.16 5 C 6852 2.51 5 N 1799 2.21 5 O 2155 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 52 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 10872 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 10258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1261, 10258 Classifications: {'peptide': 1261} Link IDs: {'PTRANS': 34, 'TRANS': 1226} Chain breaks: 5 Chain: "G" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 612 Classifications: {'RNA': 29} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 4, 'rna3p_pur': 10, 'rna3p_pyr': 11} Link IDs: {'rna2p': 8, 'rna3p': 20} Chain breaks: 2 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.15, per 1000 atoms: 0.66 Number of scatterers: 10872 At special positions: 0 Unit cell: (100.64, 111.74, 132.46, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 35 16.00 P 29 15.00 Mg 2 11.99 O 2155 8.00 N 1799 7.00 C 6852 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.84 Conformation dependent library (CDL) restraints added in 1.4 seconds 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2378 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 9 sheets defined 54.6% alpha, 10.8% beta 8 base pairs and 13 stacking pairs defined. Time for finding SS restraints: 3.94 Creating SS restraints... Processing helix chain 'A' and resid 6 through 10 Processing helix chain 'A' and resid 29 through 37 Processing helix chain 'A' and resid 38 through 69 removed outlier: 3.798A pdb=" N ASP A 43 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLN A 51 " --> pdb=" O ASN A 47 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS A 52 " --> pdb=" O ASP A 48 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLY A 55 " --> pdb=" O GLN A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 90 removed outlier: 4.303A pdb=" N LEU A 79 " --> pdb=" O ASP A 75 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLU A 84 " --> pdb=" O ALA A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 112 removed outlier: 3.913A pdb=" N LYS A 101 " --> pdb=" O LYS A 97 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL A 102 " --> pdb=" O VAL A 98 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS A 111 " --> pdb=" O LEU A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 131 removed outlier: 4.304A pdb=" N ILE A 130 " --> pdb=" O SER A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 137 Processing helix chain 'A' and resid 144 through 154 removed outlier: 3.909A pdb=" N PHE A 154 " --> pdb=" O ILE A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 160 Processing helix chain 'A' and resid 161 through 173 removed outlier: 3.723A pdb=" N ASN A 170 " --> pdb=" O GLU A 166 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL A 171 " --> pdb=" O ASN A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 187 removed outlier: 3.737A pdb=" N LEU A 185 " --> pdb=" O PHE A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 195 Processing helix chain 'A' and resid 196 through 207 removed outlier: 3.563A pdb=" N MET A 200 " --> pdb=" O ASN A 196 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER A 207 " --> pdb=" O VAL A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 222 removed outlier: 4.826A pdb=" N SER A 213 " --> pdb=" O ASP A 209 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N LEU A 214 " --> pdb=" O MET A 210 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N GLU A 215 " --> pdb=" O ALA A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 234 removed outlier: 3.570A pdb=" N SER A 234 " --> pdb=" O GLU A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 241 Processing helix chain 'A' and resid 243 through 256 Processing helix chain 'A' and resid 268 through 278 removed outlier: 3.577A pdb=" N LEU A 275 " --> pdb=" O GLU A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 288 removed outlier: 4.708A pdb=" N VAL A 286 " --> pdb=" O GLU A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 336 removed outlier: 3.515A pdb=" N VAL A 321 " --> pdb=" O ASP A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 347 Processing helix chain 'A' and resid 348 through 350 No H-bonds generated for 'chain 'A' and resid 348 through 350' Processing helix chain 'A' and resid 362 through 372 Processing helix chain 'A' and resid 375 through 389 removed outlier: 4.195A pdb=" N SER A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LEU A 388 " --> pdb=" O TYR A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 407 Processing helix chain 'A' and resid 410 through 418 removed outlier: 3.781A pdb=" N GLU A 416 " --> pdb=" O GLN A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 444 removed outlier: 4.154A pdb=" N GLU A 426 " --> pdb=" O ASP A 422 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER A 433 " --> pdb=" O LYS A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 475 removed outlier: 3.551A pdb=" N LEU A 469 " --> pdb=" O SER A 465 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR A 475 " --> pdb=" O ARG A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 498 removed outlier: 4.302A pdb=" N CYS A 491 " --> pdb=" O VAL A 487 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR A 494 " --> pdb=" O GLU A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 515 Processing helix chain 'A' and resid 537 through 539 No H-bonds generated for 'chain 'A' and resid 537 through 539' Processing helix chain 'A' and resid 540 through 545 Processing helix chain 'A' and resid 588 through 597 Proline residue: A 594 - end of helix Processing helix chain 'A' and resid 600 through 607 Processing helix chain 'A' and resid 608 through 610 No H-bonds generated for 'chain 'A' and resid 608 through 610' Processing helix chain 'A' and resid 628 through 635 Processing helix chain 'A' and resid 647 through 654 removed outlier: 4.306A pdb=" N ARG A 651 " --> pdb=" O VAL A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 677 removed outlier: 3.521A pdb=" N LYS A 664 " --> pdb=" O ARG A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 684 through 688 removed outlier: 3.749A pdb=" N LEU A 687 " --> pdb=" O ASP A 684 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N PHE A 688 " --> pdb=" O THR A 685 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 684 through 688' Processing helix chain 'A' and resid 690 through 694 removed outlier: 3.732A pdb=" N TYR A 694 " --> pdb=" O SER A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 708 removed outlier: 3.914A pdb=" N PHE A 700 " --> pdb=" O ASP A 696 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 727 removed outlier: 3.599A pdb=" N ILE A 721 " --> pdb=" O PRO A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 741 Processing helix chain 'A' and resid 749 through 758 removed outlier: 3.813A pdb=" N ILE A 758 " --> pdb=" O TYR A 754 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 766 removed outlier: 3.827A pdb=" N ASP A 766 " --> pdb=" O GLU A 762 " (cutoff:3.500A) Processing helix chain 'A' and resid 808 through 818 Processing helix chain 'A' and resid 850 through 855 removed outlier: 4.090A pdb=" N VAL A 855 " --> pdb=" O ARG A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 876 through 888 Processing helix chain 'A' and resid 923 through 927 removed outlier: 3.704A pdb=" N THR A 926 " --> pdb=" O THR A 923 " (cutoff:3.500A) Processing helix chain 'A' and resid 928 through 941 Processing helix chain 'A' and resid 946 through 976 removed outlier: 3.724A pdb=" N VAL A 950 " --> pdb=" O ASP A 946 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR A 951 " --> pdb=" O TRP A 947 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER A 962 " --> pdb=" O LYS A 958 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALA A 963 " --> pdb=" O GLY A 959 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N HIS A 966 " --> pdb=" O SER A 962 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N MET A 971 " --> pdb=" O GLU A 967 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 1013 removed outlier: 3.704A pdb=" N ASN A1013 " --> pdb=" O ILE A1009 " (cutoff:3.500A) Processing helix chain 'A' and resid 1073 through 1077 removed outlier: 3.767A pdb=" N HIS A1076 " --> pdb=" O SER A1073 " (cutoff:3.500A) Processing helix chain 'A' and resid 1079 through 1088 Processing helix chain 'A' and resid 1167 through 1179 Processing helix chain 'A' and resid 1182 through 1186 removed outlier: 4.000A pdb=" N SER A1185 " --> pdb=" O GLU A1182 " (cutoff:3.500A) Processing helix chain 'A' and resid 1189 through 1196 removed outlier: 3.782A pdb=" N PHE A1196 " --> pdb=" O ILE A1192 " (cutoff:3.500A) Processing helix chain 'A' and resid 1198 through 1213 Processing helix chain 'A' and resid 1242 through 1244 No H-bonds generated for 'chain 'A' and resid 1242 through 1244' Processing helix chain 'A' and resid 1251 through 1272 removed outlier: 3.701A pdb=" N GLY A1256 " --> pdb=" O ALA A1252 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA A1257 " --> pdb=" O ASP A1253 " (cutoff:3.500A) Processing helix chain 'A' and resid 1280 through 1291 Processing sheet with id=AA1, first strand: chain 'A' and resid 523 through 524 removed outlier: 4.483A pdb=" N PHE A 858 " --> pdb=" O LEU A 24 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLU A 23 " --> pdb=" O HIS A 736 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N HIS A 736 " --> pdb=" O GLU A 23 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N TYR A 555 " --> pdb=" O LEU A 735 " (cutoff:3.500A) removed outlier: 11.945A pdb=" N ALA A 546 " --> pdb=" O TYR A 583 " (cutoff:3.500A) removed outlier: 9.009A pdb=" N TYR A 583 " --> pdb=" O ALA A 546 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N LEU A 548 " --> pdb=" O MET A 581 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 523 through 524 Processing sheet with id=AA3, first strand: chain 'A' and resid 358 through 359 removed outlier: 3.602A pdb=" N ILE A 358 " --> pdb=" O VAL A 409 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 614 through 616 Processing sheet with id=AA5, first strand: chain 'A' and resid 915 through 920 removed outlier: 3.523A pdb=" N GLU A 917 " --> pdb=" O VAL A 908 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N GLU A 982 " --> pdb=" O ILE A 896 " (cutoff:3.500A) removed outlier: 9.563A pdb=" N ARG A 898 " --> pdb=" O GLU A 982 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N VAL A 979 " --> pdb=" O PHE A1052 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N VAL A1054 " --> pdb=" O VAL A 979 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N LEU A 981 " --> pdb=" O VAL A1054 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1090 through 1095 removed outlier: 6.773A pdb=" N PHE A1090 " --> pdb=" O HIS A1107 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N HIS A1107 " --> pdb=" O PHE A1090 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LYS A1092 " --> pdb=" O ALA A1105 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1135 through 1137 Processing sheet with id=AA8, first strand: chain 'A' and resid 1149 through 1151 Processing sheet with id=AA9, first strand: chain 'A' and resid 1216 through 1218 removed outlier: 4.779A pdb=" N PHE A1239 " --> pdb=" O SER A1229 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N ILE A1231 " --> pdb=" O ILE A1237 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N ILE A1237 " --> pdb=" O ILE A1231 " (cutoff:3.500A) 488 hydrogen bonds defined for protein. 1374 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 18 hydrogen bonds 32 hydrogen bond angles 0 basepair planarities 8 basepair parallelities 13 stacking parallelities Total time for adding SS restraints: 4.31 Time building geometry restraints manager: 3.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2754 1.33 - 1.45: 2208 1.45 - 1.57: 6070 1.57 - 1.70: 55 1.70 - 1.82: 59 Bond restraints: 11146 Sorted by residual: bond pdb=" CA PRO A 353 " pdb=" C PRO A 353 " ideal model delta sigma weight residual 1.520 1.552 -0.031 9.50e-03 1.11e+04 1.08e+01 bond pdb=" CZ ARG A1242 " pdb=" NH2 ARG A1242 " ideal model delta sigma weight residual 1.330 1.294 0.036 1.30e-02 5.92e+03 7.59e+00 bond pdb=" CZ ARG A 851 " pdb=" NH2 ARG A 851 " ideal model delta sigma weight residual 1.330 1.295 0.035 1.30e-02 5.92e+03 7.44e+00 bond pdb=" CZ ARG A1272 " pdb=" NH2 ARG A1272 " ideal model delta sigma weight residual 1.330 1.295 0.035 1.30e-02 5.92e+03 7.21e+00 bond pdb=" CZ ARG A1149 " pdb=" NH2 ARG A1149 " ideal model delta sigma weight residual 1.330 1.296 0.034 1.30e-02 5.92e+03 7.03e+00 ... (remaining 11141 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 11094 1.55 - 3.10: 3326 3.10 - 4.64: 663 4.64 - 6.19: 49 6.19 - 7.74: 6 Bond angle restraints: 15138 Sorted by residual: angle pdb=" N VAL A 232 " pdb=" CA VAL A 232 " pdb=" C VAL A 232 " ideal model delta sigma weight residual 111.44 103.70 7.74 1.34e+00 5.57e-01 3.34e+01 angle pdb=" N PHE A 233 " pdb=" CA PHE A 233 " pdb=" C PHE A 233 " ideal model delta sigma weight residual 111.28 105.48 5.80 1.09e+00 8.42e-01 2.83e+01 angle pdb=" N ILE A 450 " pdb=" CA ILE A 450 " pdb=" C ILE A 450 " ideal model delta sigma weight residual 113.20 108.41 4.79 9.60e-01 1.09e+00 2.49e+01 angle pdb=" N CYS A 197 " pdb=" CA CYS A 197 " pdb=" C CYS A 197 " ideal model delta sigma weight residual 112.38 107.08 5.30 1.22e+00 6.72e-01 1.88e+01 angle pdb=" OE1 GLN A 278 " pdb=" CD GLN A 278 " pdb=" NE2 GLN A 278 " ideal model delta sigma weight residual 122.60 118.60 4.00 1.00e+00 1.00e+00 1.60e+01 ... (remaining 15133 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.68: 6613 35.68 - 71.36: 119 71.36 - 107.04: 13 107.04 - 142.72: 0 142.72 - 178.40: 1 Dihedral angle restraints: 6746 sinusoidal: 3049 harmonic: 3697 Sorted by residual: dihedral pdb=" C5' A G 5 " pdb=" C4' A G 5 " pdb=" C3' A G 5 " pdb=" O3' A G 5 " ideal model delta sinusoidal sigma weight residual 147.00 89.04 57.96 1 8.00e+00 1.56e-02 7.04e+01 dihedral pdb=" O4' U G -7 " pdb=" C1' U G -7 " pdb=" N1 U G -7 " pdb=" C2 U G -7 " ideal model delta sinusoidal sigma weight residual -128.00 50.40 -178.40 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' A G 5 " pdb=" C4' A G 5 " pdb=" C3' A G 5 " pdb=" C2' A G 5 " ideal model delta sinusoidal sigma weight residual 24.00 -31.42 55.42 1 8.00e+00 1.56e-02 6.49e+01 ... (remaining 6743 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 1189 0.075 - 0.150: 386 0.150 - 0.226: 87 0.226 - 0.301: 9 0.301 - 0.376: 3 Chirality restraints: 1674 Sorted by residual: chirality pdb=" CA TYR A1058 " pdb=" N TYR A1058 " pdb=" C TYR A1058 " pdb=" CB TYR A1058 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.54e+00 chirality pdb=" CA HIS A1100 " pdb=" N HIS A1100 " pdb=" C HIS A1100 " pdb=" CB HIS A1100 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.63e+00 chirality pdb=" CA THR A 597 " pdb=" N THR A 597 " pdb=" C THR A 597 " pdb=" CB THR A 597 " both_signs ideal model delta sigma weight residual False 2.53 2.21 0.31 2.00e-01 2.50e+01 2.44e+00 ... (remaining 1671 not shown) Planarity restraints: 1828 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 470 " 0.103 2.00e-02 2.50e+03 5.90e-02 6.96e+01 pdb=" CG TYR A 470 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 TYR A 470 " -0.053 2.00e-02 2.50e+03 pdb=" CD2 TYR A 470 " -0.044 2.00e-02 2.50e+03 pdb=" CE1 TYR A 470 " -0.035 2.00e-02 2.50e+03 pdb=" CE2 TYR A 470 " -0.043 2.00e-02 2.50e+03 pdb=" CZ TYR A 470 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 470 " 0.095 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 694 " -0.103 2.00e-02 2.50e+03 5.69e-02 6.47e+01 pdb=" CG TYR A 694 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 TYR A 694 " 0.046 2.00e-02 2.50e+03 pdb=" CD2 TYR A 694 " 0.042 2.00e-02 2.50e+03 pdb=" CE1 TYR A 694 " 0.035 2.00e-02 2.50e+03 pdb=" CE2 TYR A 694 " 0.035 2.00e-02 2.50e+03 pdb=" CZ TYR A 694 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 694 " -0.089 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 95 " 0.105 2.00e-02 2.50e+03 5.68e-02 6.45e+01 pdb=" CG TYR A 95 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TYR A 95 " -0.035 2.00e-02 2.50e+03 pdb=" CD2 TYR A 95 " -0.048 2.00e-02 2.50e+03 pdb=" CE1 TYR A 95 " -0.038 2.00e-02 2.50e+03 pdb=" CE2 TYR A 95 " -0.026 2.00e-02 2.50e+03 pdb=" CZ TYR A 95 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR A 95 " 0.087 2.00e-02 2.50e+03 ... (remaining 1825 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 19 2.55 - 3.14: 8327 3.14 - 3.72: 16023 3.72 - 4.31: 23251 4.31 - 4.90: 36717 Nonbonded interactions: 84337 Sorted by model distance: nonbonded pdb=" OP2 A G -4 " pdb="MG MG A1401 " model vdw 1.960 2.170 nonbonded pdb=" O LYS A 747 " pdb="MG MG A1401 " model vdw 1.999 2.170 nonbonded pdb=" O SER A 480 " pdb=" OG1 THR A 484 " model vdw 2.424 3.040 nonbonded pdb=" N HIS A1108 " pdb=" O ALA A1124 " model vdw 2.439 3.120 nonbonded pdb=" O2' U G 4 " pdb=" O5' A G 5 " model vdw 2.442 3.040 ... (remaining 84332 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 2.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.450 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 31.250 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 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 : 0.011 0.036 11146 Z= 0.693 Angle : 1.473 7.739 15138 Z= 0.997 Chirality : 0.076 0.376 1674 Planarity : 0.010 0.096 1828 Dihedral : 13.542 178.398 4368 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 0.44 % Allowed : 3.81 % Favored : 95.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.55 (0.21), residues: 1249 helix: -1.16 (0.18), residues: 595 sheet: 0.41 (0.46), residues: 124 loop : -1.05 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.008 TRP A1284 HIS 0.010 0.002 HIS A1100 PHE 0.055 0.008 PHE A 190 TYR 0.109 0.016 TYR A 583 ARG 0.006 0.001 ARG A1242 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 97 time to evaluate : 1.208 Fit side-chains REVERT: A 122 LYS cc_start: 0.8260 (mmpt) cc_final: 0.7716 (mptt) REVERT: A 308 MET cc_start: 0.6517 (mmm) cc_final: 0.6199 (ptm) REVERT: A 344 LEU cc_start: 0.4783 (tp) cc_final: 0.4533 (mt) REVERT: A 422 ASP cc_start: 0.7375 (t0) cc_final: 0.6905 (p0) outliers start: 5 outliers final: 2 residues processed: 102 average time/residue: 1.4101 time to fit residues: 154.3577 Evaluate side-chains 47 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 45 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 384 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 108 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 0.4980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.1980 chunk 74 optimal weight: 2.9990 chunk 116 optimal weight: 10.0000 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 274 ASN A 606 HIS A 941 GLN A1100 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 11146 Z= 0.161 Angle : 0.539 6.294 15138 Z= 0.299 Chirality : 0.040 0.182 1674 Planarity : 0.003 0.040 1828 Dihedral : 11.977 177.330 1794 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.33 % Allowed : 7.79 % Favored : 90.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.21 (0.23), residues: 1249 helix: 0.74 (0.20), residues: 619 sheet: 0.52 (0.46), residues: 120 loop : -0.60 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A1284 HIS 0.007 0.001 HIS A1259 PHE 0.021 0.002 PHE A 121 TYR 0.021 0.002 TYR A 438 ARG 0.006 0.001 ARG A 340 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 50 time to evaluate : 1.272 Fit side-chains REVERT: A 122 LYS cc_start: 0.8151 (mmpt) cc_final: 0.7702 (mptt) REVERT: A 900 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7559 (mm-30) outliers start: 15 outliers final: 2 residues processed: 60 average time/residue: 1.2347 time to fit residues: 82.4413 Evaluate side-chains 43 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 40 time to evaluate : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain A residue 900 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 64 optimal weight: 5.9990 chunk 36 optimal weight: 4.9990 chunk 96 optimal weight: 9.9990 chunk 79 optimal weight: 7.9990 chunk 32 optimal weight: 10.0000 chunk 116 optimal weight: 10.0000 chunk 125 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 39 optimal weight: 6.9990 chunk 93 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.048 11146 Z= 0.485 Angle : 0.645 7.100 15138 Z= 0.351 Chirality : 0.045 0.228 1674 Planarity : 0.004 0.037 1828 Dihedral : 12.177 175.936 1791 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.04 % Allowed : 8.59 % Favored : 89.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.13 (0.24), residues: 1249 helix: 0.73 (0.21), residues: 610 sheet: 0.45 (0.45), residues: 130 loop : -0.70 (0.28), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1284 HIS 0.008 0.002 HIS A 966 PHE 0.021 0.002 PHE A1038 TYR 0.029 0.002 TYR A 583 ARG 0.005 0.001 ARG A 780 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 43 time to evaluate : 1.385 Fit side-chains REVERT: A 122 LYS cc_start: 0.8184 (mmpt) cc_final: 0.7703 (mptt) REVERT: A 356 MET cc_start: 0.4173 (ptm) cc_final: 0.3833 (ptp) REVERT: A 890 ASP cc_start: 0.8351 (t0) cc_final: 0.7949 (p0) REVERT: A 900 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.7752 (mm-30) outliers start: 23 outliers final: 8 residues processed: 63 average time/residue: 1.2015 time to fit residues: 83.4527 Evaluate side-chains 48 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 39 time to evaluate : 1.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 856 ASP Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain A residue 900 GLU Chi-restraints excluded: chain A residue 986 VAL Chi-restraints excluded: chain A residue 1176 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 115 optimal weight: 6.9990 chunk 87 optimal weight: 0.9990 chunk 60 optimal weight: 0.0980 chunk 12 optimal weight: 0.5980 chunk 55 optimal weight: 0.7980 chunk 78 optimal weight: 8.9990 chunk 116 optimal weight: 3.9990 chunk 123 optimal weight: 0.6980 chunk 61 optimal weight: 5.9990 chunk 110 optimal weight: 1.9990 chunk 33 optimal weight: 9.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN A 202 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 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 0.024 11146 Z= 0.125 Angle : 0.455 6.514 15138 Z= 0.250 Chirality : 0.038 0.203 1674 Planarity : 0.003 0.036 1828 Dihedral : 11.884 175.954 1791 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.42 % Allowed : 9.12 % Favored : 89.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.60 (0.24), residues: 1249 helix: 1.33 (0.21), residues: 614 sheet: 0.44 (0.44), residues: 132 loop : -0.74 (0.27), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A1284 HIS 0.007 0.001 HIS A1259 PHE 0.010 0.001 PHE A1038 TYR 0.024 0.001 TYR A 430 ARG 0.003 0.000 ARG A 142 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 45 time to evaluate : 1.252 Fit side-chains revert: symmetry clash REVERT: A 122 LYS cc_start: 0.8169 (mmpt) cc_final: 0.7739 (mptt) REVERT: A 608 GLN cc_start: 0.7902 (OUTLIER) cc_final: 0.7489 (mm-40) REVERT: A 890 ASP cc_start: 0.8372 (t0) cc_final: 0.7880 (p0) REVERT: A 900 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.7610 (mm-30) outliers start: 16 outliers final: 2 residues processed: 57 average time/residue: 1.2606 time to fit residues: 79.0020 Evaluate side-chains 42 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 38 time to evaluate : 1.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 608 GLN Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain A residue 900 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 103 optimal weight: 0.9980 chunk 70 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 92 optimal weight: 7.9990 chunk 51 optimal weight: 6.9990 chunk 105 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 chunk 0 optimal weight: 0.9990 chunk 63 optimal weight: 10.0000 chunk 111 optimal weight: 6.9990 chunk 31 optimal weight: 0.0770 overall best weight: 1.1542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 637 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.3444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11146 Z= 0.162 Angle : 0.465 8.229 15138 Z= 0.251 Chirality : 0.038 0.178 1674 Planarity : 0.003 0.036 1828 Dihedral : 11.715 175.828 1791 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.06 % Allowed : 10.19 % Favored : 88.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.72 (0.24), residues: 1249 helix: 1.44 (0.21), residues: 614 sheet: 0.37 (0.43), residues: 139 loop : -0.69 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1284 HIS 0.006 0.001 HIS A1259 PHE 0.011 0.001 PHE A 523 TYR 0.017 0.001 TYR A 583 ARG 0.007 0.000 ARG A 142 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 43 time to evaluate : 1.203 Fit side-chains revert: symmetry clash REVERT: A 122 LYS cc_start: 0.8177 (mmpt) cc_final: 0.7742 (mptt) REVERT: A 890 ASP cc_start: 0.8367 (t0) cc_final: 0.7852 (p0) REVERT: A 900 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.7659 (mm-30) outliers start: 12 outliers final: 4 residues processed: 51 average time/residue: 1.3723 time to fit residues: 76.5506 Evaluate side-chains 44 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 39 time to evaluate : 1.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 412 GLN Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain A residue 900 GLU Chi-restraints excluded: chain A residue 944 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 41 optimal weight: 0.8980 chunk 111 optimal weight: 7.9990 chunk 24 optimal weight: 0.9980 chunk 72 optimal weight: 4.9990 chunk 30 optimal weight: 0.1980 chunk 123 optimal weight: 5.9990 chunk 102 optimal weight: 0.7980 chunk 57 optimal weight: 6.9990 chunk 10 optimal weight: 9.9990 chunk 40 optimal weight: 20.0000 chunk 65 optimal weight: 5.9990 overall best weight: 1.5782 ------------------------------------------------------------------------------- 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: 0.7657 moved from start: 0.3548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11146 Z= 0.197 Angle : 0.481 9.455 15138 Z= 0.259 Chirality : 0.039 0.173 1674 Planarity : 0.003 0.036 1828 Dihedral : 11.721 175.607 1791 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.13 % Allowed : 9.48 % Favored : 88.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.75 (0.24), residues: 1249 helix: 1.53 (0.21), residues: 604 sheet: 0.37 (0.43), residues: 139 loop : -0.71 (0.27), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1284 HIS 0.006 0.001 HIS A1259 PHE 0.011 0.001 PHE A 523 TYR 0.019 0.001 TYR A 583 ARG 0.002 0.000 ARG A 168 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 42 time to evaluate : 1.305 Fit side-chains REVERT: A 122 LYS cc_start: 0.8183 (mmpt) cc_final: 0.7739 (mptt) REVERT: A 607 PHE cc_start: 0.6666 (OUTLIER) cc_final: 0.6291 (m-80) REVERT: A 608 GLN cc_start: 0.7922 (OUTLIER) cc_final: 0.7465 (mm-40) REVERT: A 890 ASP cc_start: 0.8379 (t0) cc_final: 0.7841 (p0) REVERT: A 900 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.7651 (mm-30) outliers start: 24 outliers final: 7 residues processed: 60 average time/residue: 1.3036 time to fit residues: 85.7837 Evaluate side-chains 50 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 40 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 607 PHE Chi-restraints excluded: chain A residue 608 GLN Chi-restraints excluded: chain A residue 856 ASP Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain A residue 900 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 119 optimal weight: 0.1980 chunk 13 optimal weight: 0.6980 chunk 70 optimal weight: 0.9980 chunk 90 optimal weight: 0.9990 chunk 104 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 123 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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: 0.7620 moved from start: 0.3734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 11146 Z= 0.129 Angle : 0.456 11.025 15138 Z= 0.242 Chirality : 0.038 0.159 1674 Planarity : 0.003 0.038 1828 Dihedral : 11.634 175.705 1791 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.06 % Allowed : 10.45 % Favored : 88.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.88 (0.24), residues: 1249 helix: 1.65 (0.22), residues: 609 sheet: 0.40 (0.43), residues: 139 loop : -0.67 (0.27), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A1284 HIS 0.006 0.001 HIS A1259 PHE 0.010 0.001 PHE A 523 TYR 0.032 0.001 TYR A 95 ARG 0.003 0.000 ARG A 944 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 41 time to evaluate : 1.240 Fit side-chains revert: symmetry clash REVERT: A 122 LYS cc_start: 0.8139 (mmpt) cc_final: 0.7711 (mptt) REVERT: A 607 PHE cc_start: 0.6644 (OUTLIER) cc_final: 0.6261 (m-80) REVERT: A 608 GLN cc_start: 0.7914 (OUTLIER) cc_final: 0.7430 (mm-40) REVERT: A 890 ASP cc_start: 0.8368 (t0) cc_final: 0.7771 (p0) outliers start: 12 outliers final: 3 residues processed: 50 average time/residue: 1.3634 time to fit residues: 74.5940 Evaluate side-chains 44 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 39 time to evaluate : 1.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 607 PHE Chi-restraints excluded: chain A residue 608 GLN Chi-restraints excluded: chain A residue 862 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 49 optimal weight: 10.0000 chunk 73 optimal weight: 1.9990 chunk 37 optimal weight: 10.0000 chunk 24 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 78 optimal weight: 8.9990 chunk 84 optimal weight: 1.9990 chunk 60 optimal weight: 9.9990 chunk 11 optimal weight: 9.9990 chunk 96 optimal weight: 8.9990 chunk 112 optimal weight: 5.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 461 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.3664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 11146 Z= 0.350 Angle : 0.555 9.110 15138 Z= 0.296 Chirality : 0.041 0.180 1674 Planarity : 0.003 0.037 1828 Dihedral : 11.802 175.374 1791 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.15 % Allowed : 10.27 % Favored : 88.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.66 (0.24), residues: 1249 helix: 1.44 (0.21), residues: 603 sheet: 0.38 (0.43), residues: 137 loop : -0.74 (0.27), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1284 HIS 0.008 0.001 HIS A 109 PHE 0.018 0.002 PHE A 233 TYR 0.025 0.002 TYR A 583 ARG 0.003 0.000 ARG A 293 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 41 time to evaluate : 1.161 Fit side-chains revert: symmetry clash REVERT: A 122 LYS cc_start: 0.8181 (mmpt) cc_final: 0.7740 (mptt) REVERT: A 607 PHE cc_start: 0.6746 (OUTLIER) cc_final: 0.6310 (m-80) REVERT: A 608 GLN cc_start: 0.7884 (OUTLIER) cc_final: 0.7399 (mm-40) REVERT: A 890 ASP cc_start: 0.8382 (t0) cc_final: 0.7830 (p0) outliers start: 13 outliers final: 7 residues processed: 53 average time/residue: 1.3159 time to fit residues: 76.6728 Evaluate side-chains 48 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 39 time to evaluate : 1.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 607 PHE Chi-restraints excluded: chain A residue 608 GLN Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain A residue 862 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 118 optimal weight: 0.8980 chunk 107 optimal weight: 4.9990 chunk 114 optimal weight: 0.6980 chunk 69 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 103 optimal weight: 0.7980 chunk 108 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 121 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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: 0.7639 moved from start: 0.3835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 11146 Z= 0.139 Angle : 0.465 8.463 15138 Z= 0.249 Chirality : 0.038 0.167 1674 Planarity : 0.003 0.036 1828 Dihedral : 11.680 175.643 1791 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.06 % Allowed : 10.45 % Favored : 88.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.82 (0.24), residues: 1249 helix: 1.62 (0.21), residues: 608 sheet: 0.44 (0.44), residues: 137 loop : -0.75 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A1284 HIS 0.006 0.001 HIS A1259 PHE 0.011 0.001 PHE A 233 TYR 0.020 0.001 TYR A 384 ARG 0.003 0.000 ARG A1216 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 42 time to evaluate : 1.287 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 308 MET cc_start: 0.6722 (pp-130) cc_final: 0.6130 (ppp) REVERT: A 607 PHE cc_start: 0.6638 (OUTLIER) cc_final: 0.6255 (m-80) REVERT: A 608 GLN cc_start: 0.7898 (OUTLIER) cc_final: 0.7393 (mm-40) REVERT: A 890 ASP cc_start: 0.8361 (t0) cc_final: 0.7750 (p0) outliers start: 12 outliers final: 7 residues processed: 51 average time/residue: 1.2148 time to fit residues: 68.5335 Evaluate side-chains 47 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 38 time to evaluate : 1.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 TYR Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 607 PHE Chi-restraints excluded: chain A residue 608 GLN Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain A residue 862 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 74 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 127 optimal weight: 5.9990 chunk 117 optimal weight: 5.9990 chunk 101 optimal weight: 0.7980 chunk 10 optimal weight: 0.0010 chunk 78 optimal weight: 0.3980 chunk 62 optimal weight: 0.4980 chunk 80 optimal weight: 6.9990 chunk 108 optimal weight: 0.8980 overall best weight: 0.5186 ------------------------------------------------------------------------------- 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: 0.7601 moved from start: 0.4015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 11146 Z= 0.121 Angle : 0.454 8.186 15138 Z= 0.240 Chirality : 0.037 0.144 1674 Planarity : 0.003 0.036 1828 Dihedral : 11.570 175.743 1791 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.62 % Allowed : 11.07 % Favored : 88.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.96 (0.24), residues: 1249 helix: 1.77 (0.22), residues: 608 sheet: 0.69 (0.45), residues: 130 loop : -0.77 (0.27), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1284 HIS 0.006 0.001 HIS A1259 PHE 0.009 0.001 PHE A 523 TYR 0.016 0.001 TYR A 430 ARG 0.003 0.000 ARG A 944 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 1.239 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 308 MET cc_start: 0.6786 (pp-130) cc_final: 0.6225 (ppp) REVERT: A 890 ASP cc_start: 0.8379 (t0) cc_final: 0.7729 (p0) REVERT: A 1153 MET cc_start: 0.8023 (ptp) cc_final: 0.7600 (pmm) outliers start: 7 outliers final: 4 residues processed: 47 average time/residue: 1.3170 time to fit residues: 68.5610 Evaluate side-chains 43 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 39 time to evaluate : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 TYR Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 862 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 31 optimal weight: 10.0000 chunk 93 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 28 optimal weight: 9.9990 chunk 101 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 89 optimal weight: 5.9990 chunk 5 optimal weight: 0.8980 overall best weight: 1.7788 ------------------------------------------------------------------------------- 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 = 0.3891 r_free = 0.3891 target = 0.105773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.069734 restraints weight = 25469.883| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 3.02 r_work: 0.3082 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.3940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 11146 Z= 0.223 Angle : 0.499 9.622 15138 Z= 0.263 Chirality : 0.039 0.202 1674 Planarity : 0.003 0.036 1828 Dihedral : 11.590 175.496 1791 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.80 % Allowed : 11.16 % Favored : 88.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.89 (0.24), residues: 1249 helix: 1.69 (0.22), residues: 608 sheet: 0.48 (0.44), residues: 137 loop : -0.73 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1284 HIS 0.006 0.001 HIS A1259 PHE 0.016 0.001 PHE A 233 TYR 0.022 0.001 TYR A 384 ARG 0.003 0.000 ARG A 944 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3038.13 seconds wall clock time: 60 minutes 52.91 seconds (3652.91 seconds total)