Starting phenix.real_space_refine on Wed Jul 30 12:15:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t6t_41080/07_2025/8t6t_41080.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t6t_41080/07_2025/8t6t_41080.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8t6t_41080/07_2025/8t6t_41080.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t6t_41080/07_2025/8t6t_41080.map" model { file = "/net/cci-nas-00/data/ceres_data/8t6t_41080/07_2025/8t6t_41080.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t6t_41080/07_2025/8t6t_41080.cif" } resolution = 3.04 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= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 126 5.49 5 S 18 5.16 5 C 7378 2.51 5 N 2160 2.21 5 O 2624 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 12306 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1168, 9585 Classifications: {'peptide': 1168} Link IDs: {'PTRANS': 33, 'TRANS': 1134} Chain breaks: 5 Chain: "B" Number of atoms: 2035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 2035 Classifications: {'RNA': 95} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p_pur': 51, 'rna3p_pyr': 33} Link IDs: {'rna2p': 10, 'rna3p': 84} Chain: "C" Number of atoms: 484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 484 Classifications: {'DNA': 24} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 23} Chain: "D" Number of atoms: 202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 202 Classifications: {'DNA': 10} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 9} Time building chain proxies: 9.02, per 1000 atoms: 0.73 Number of scatterers: 12306 At special positions: 0 Unit cell: (87.486, 129.979, 122.48, 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 18 16.00 P 126 15.00 O 2624 8.00 N 2160 7.00 C 7378 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: 3.34 Conformation dependent library (CDL) restraints added in 1.4 seconds 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2230 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 9 sheets defined 52.9% alpha, 8.3% beta 45 base pairs and 78 stacking pairs defined. Time for finding SS restraints: 5.01 Creating SS restraints... Processing helix chain 'A' and resid 59 through 91 removed outlier: 4.859A pdb=" N ASN A 88 " --> pdb=" O GLU A 84 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N GLU A 89 " --> pdb=" O ILE A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 104 Processing helix chain 'A' and resid 121 through 132 Processing helix chain 'A' and resid 134 through 145 removed outlier: 3.910A pdb=" N LEU A 138 " --> pdb=" O THR A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 164 Processing helix chain 'A' and resid 176 through 180 removed outlier: 3.810A pdb=" N ASP A 180 " --> pdb=" O ASP A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 194 Processing helix chain 'A' and resid 208 through 213 removed outlier: 3.603A pdb=" N LEU A 212 " --> pdb=" O ALA A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 229 removed outlier: 5.207A pdb=" N GLU A 223 " --> pdb=" O SER A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 246 removed outlier: 3.659A pdb=" N SER A 245 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 306 removed outlier: 4.139A pdb=" N LEU A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 342 Processing helix chain 'A' and resid 346 through 352 Processing helix chain 'A' and resid 358 through 364 Processing helix chain 'A' and resid 368 through 383 Proline residue: A 378 - end of helix removed outlier: 3.652A pdb=" N MET A 383 " --> pdb=" O ILE A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 395 Processing helix chain 'A' and resid 406 through 410 removed outlier: 4.042A pdb=" N SER A 409 " --> pdb=" O ASP A 406 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE A 410 " --> pdb=" O ASN A 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 406 through 410' Processing helix chain 'A' and resid 411 through 427 removed outlier: 4.057A pdb=" N HIS A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 436 removed outlier: 3.855A pdb=" N LYS A 434 " --> pdb=" O TYR A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 446 Processing helix chain 'A' and resid 483 through 494 removed outlier: 3.686A pdb=" N ILE A 492 " --> pdb=" O ALA A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 526 removed outlier: 3.950A pdb=" N LYS A 526 " --> pdb=" O ASN A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 552 Processing helix chain 'A' and resid 562 through 567 Processing helix chain 'A' and resid 567 through 572 Processing helix chain 'A' and resid 591 through 601 Processing helix chain 'A' and resid 603 through 609 removed outlier: 3.801A pdb=" N LEU A 607 " --> pdb=" O ASP A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 626 Processing helix chain 'A' and resid 628 through 636 Processing helix chain 'A' and resid 637 through 640 Processing helix chain 'A' and resid 644 through 654 removed outlier: 3.513A pdb=" N MET A 648 " --> pdb=" O ASP A 644 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ARG A 653 " --> pdb=" O LYS A 649 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG A 654 " --> pdb=" O GLN A 650 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 669 Processing helix chain 'A' and resid 678 through 685 Processing helix chain 'A' and resid 692 through 699 Processing helix chain 'A' and resid 704 through 712 Processing helix chain 'A' and resid 719 through 724 Processing helix chain 'A' and resid 731 through 751 removed outlier: 4.302A pdb=" N LYS A 735 " --> pdb=" O PRO A 731 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLY A 736 " --> pdb=" O ALA A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 removed outlier: 3.839A pdb=" N HIS A 930 " --> pdb=" O GLN A 926 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N VAL A 931 " --> pdb=" O ILE A 927 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ALA A 932 " --> pdb=" O THR A 928 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N GLN A 933 " --> pdb=" O LYS A 929 " (cutoff:3.500A) Processing helix chain 'A' and resid 959 through 970 removed outlier: 4.182A pdb=" N VAL A 963 " --> pdb=" O LYS A 959 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE A 970 " --> pdb=" O PHE A 966 " (cutoff:3.500A) Processing helix chain 'A' and resid 980 through 1001 removed outlier: 4.450A pdb=" N ALA A 984 " --> pdb=" O ASN A 980 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS A1000 " --> pdb=" O ALA A 996 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1009 removed outlier: 3.843A pdb=" N PHE A1008 " --> pdb=" O LEU A1004 " (cutoff:3.500A) Processing helix chain 'A' and resid 1032 through 1042 Processing helix chain 'A' and resid 1043 through 1047 Processing helix chain 'A' and resid 1077 through 1088 Processing helix chain 'A' and resid 1127 through 1132 Processing helix chain 'A' and resid 1169 through 1177 removed outlier: 4.747A pdb=" N SER A1173 " --> pdb=" O MET A1169 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASN A1177 " --> pdb=" O SER A1173 " (cutoff:3.500A) Processing helix chain 'A' and resid 1177 through 1185 Processing helix chain 'A' and resid 1191 through 1195 Processing helix chain 'A' and resid 1207 through 1209 No H-bonds generated for 'chain 'A' and resid 1207 through 1209' Processing helix chain 'A' and resid 1229 through 1241 Processing helix chain 'A' and resid 1248 through 1262 Processing helix chain 'A' and resid 1264 through 1280 Processing helix chain 'A' and resid 1283 through 1297 removed outlier: 3.501A pdb=" N HIS A1297 " --> pdb=" O ALA A1293 " (cutoff:3.500A) Processing helix chain 'A' and resid 1301 through 1313 removed outlier: 3.568A pdb=" N PHE A1313 " --> pdb=" O ILE A1309 " (cutoff:3.500A) Processing helix chain 'A' and resid 1340 through 1344 removed outlier: 3.680A pdb=" N LEU A1343 " --> pdb=" O LYS A1340 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ASP A1344 " --> pdb=" O GLU A1341 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1340 through 1344' Processing helix chain 'A' and resid 1363 through 1365 No H-bonds generated for 'chain 'A' and resid 1363 through 1365' Processing sheet with id=AA1, first strand: chain 'A' and resid 954 through 958 removed outlier: 6.199A pdb=" N ILE A 759 " --> pdb=" O ILE A 956 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N LEU A 958 " --> pdb=" O ILE A 759 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ILE A 761 " --> pdb=" O LEU A 958 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ASN A 758 " --> pdb=" O TYR A 5 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU A 762 " --> pdb=" O LEU A 9 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N ILE A 11 " --> pdb=" O GLU A 762 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 46 removed outlier: 4.466A pdb=" N GLU A1357 " --> pdb=" O LYS A 33 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N LEU A1203 " --> pdb=" O ILE A1348 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N SER A1202 " --> pdb=" O LEU A1214 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N LEU A1214 " --> pdb=" O GLN A1221 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N GLN A1221 " --> pdb=" O LEU A1214 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 252 through 253 Processing sheet with id=AA4, first strand: chain 'A' and resid 528 through 529 removed outlier: 3.893A pdb=" N ALA A 538 " --> pdb=" O TYR A 529 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1049 through 1051 Processing sheet with id=AA6, first strand: chain 'A' and resid 1063 through 1065 removed outlier: 3.515A pdb=" N TRP A1074 " --> pdb=" O GLU A1064 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1120 through 1121 Processing sheet with id=AA8, first strand: chain 'A' and resid 1156 through 1167 removed outlier: 4.186A pdb=" N LYS A1156 " --> pdb=" O LYS A1151 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N LYS A1151 " --> pdb=" O LYS A1156 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR A1141 " --> pdb=" O ILE A1166 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1324 through 1325 419 hydrogen bonds defined for protein. 1218 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 110 hydrogen bonds 216 hydrogen bond angles 0 basepair planarities 45 basepair parallelities 78 stacking parallelities Total time for adding SS restraints: 7.24 Time building geometry restraints manager: 3.97 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: 2643 1.33 - 1.45: 3315 1.45 - 1.57: 6559 1.57 - 1.69: 255 1.69 - 1.81: 35 Bond restraints: 12807 Sorted by residual: bond pdb=" O3' DA D 38 " pdb=" P DC D 39 " ideal model delta sigma weight residual 1.607 1.639 -0.032 1.50e-02 4.44e+03 4.52e+00 bond pdb=" O3' DA C 14 " pdb=" P DC C 15 " ideal model delta sigma weight residual 1.607 1.639 -0.032 1.50e-02 4.44e+03 4.51e+00 bond pdb=" CB LYS A 942 " pdb=" CG LYS A 942 " ideal model delta sigma weight residual 1.520 1.580 -0.060 3.00e-02 1.11e+03 4.06e+00 bond pdb=" C2' DG D 41 " pdb=" C1' DG D 41 " ideal model delta sigma weight residual 1.525 1.487 0.038 2.00e-02 2.50e+03 3.55e+00 bond pdb=" C1' DA D 40 " pdb=" N9 DA D 40 " ideal model delta sigma weight residual 1.460 1.497 -0.037 2.00e-02 2.50e+03 3.50e+00 ... (remaining 12802 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.16: 17648 5.16 - 10.32: 141 10.32 - 15.48: 46 15.48 - 20.65: 8 20.65 - 25.81: 1 Bond angle restraints: 17844 Sorted by residual: angle pdb=" C2' DC C 15 " pdb=" C1' DC C 15 " pdb=" N1 DC C 15 " ideal model delta sigma weight residual 113.50 130.61 -17.11 1.50e+00 4.44e-01 1.30e+02 angle pdb=" P DC D 44 " pdb=" O5' DC D 44 " pdb=" C5' DC D 44 " ideal model delta sigma weight residual 120.00 135.60 -15.60 1.50e+00 4.44e-01 1.08e+02 angle pdb=" C1' DA D 43 " pdb=" N9 DA D 43 " pdb=" C4 DA D 43 " ideal model delta sigma weight residual 127.05 111.76 15.29 1.50e+00 4.44e-01 1.04e+02 angle pdb=" O4' DA D 40 " pdb=" C1' DA D 40 " pdb=" N9 DA D 40 " ideal model delta sigma weight residual 108.40 123.40 -15.00 1.50e+00 4.44e-01 9.99e+01 angle pdb=" P DA C 14 " pdb=" O5' DA C 14 " pdb=" C5' DA C 14 " ideal model delta sigma weight residual 120.00 134.53 -14.53 1.50e+00 4.44e-01 9.38e+01 ... (remaining 17839 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.38: 7336 33.38 - 66.76: 423 66.76 - 100.14: 36 100.14 - 133.52: 2 133.52 - 166.90: 4 Dihedral angle restraints: 7801 sinusoidal: 4363 harmonic: 3438 Sorted by residual: dihedral pdb=" CA ASN A 726 " pdb=" C ASN A 726 " pdb=" N LEU A 727 " pdb=" CA LEU A 727 " ideal model delta harmonic sigma weight residual 180.00 150.55 29.45 0 5.00e+00 4.00e-02 3.47e+01 dihedral pdb=" CA GLU A1056 " pdb=" C GLU A1056 " pdb=" N ILE A1057 " pdb=" CA ILE A1057 " ideal model delta harmonic sigma weight residual -180.00 -157.89 -22.11 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" CA ILE A1057 " pdb=" C ILE A1057 " pdb=" N ARG A1058 " pdb=" CA ARG A1058 " ideal model delta harmonic sigma weight residual 180.00 158.95 21.05 0 5.00e+00 4.00e-02 1.77e+01 ... (remaining 7798 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.260: 2015 0.260 - 0.520: 24 0.520 - 0.781: 5 0.781 - 1.041: 6 1.041 - 1.301: 5 Chirality restraints: 2055 Sorted by residual: chirality pdb=" C1' DC D 39 " pdb=" O4' DC D 39 " pdb=" C2' DC D 39 " pdb=" N1 DC D 39 " both_signs ideal model delta sigma weight residual False 2.47 1.17 1.30 2.00e-01 2.50e+01 4.23e+01 chirality pdb=" C1' DC C 21 " pdb=" O4' DC C 21 " pdb=" C2' DC C 21 " pdb=" N1 DC C 21 " both_signs ideal model delta sigma weight residual False 2.47 1.21 1.26 2.00e-01 2.50e+01 3.95e+01 chirality pdb=" C1' DC C 15 " pdb=" O4' DC C 15 " pdb=" C2' DC C 15 " pdb=" N1 DC C 15 " both_signs ideal model delta sigma weight residual False 2.47 1.35 1.12 2.00e-01 2.50e+01 3.14e+01 ... (remaining 2052 not shown) Planarity restraints: 1798 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG C 12 " -0.056 2.00e-02 2.50e+03 2.48e-02 1.85e+01 pdb=" N9 DG C 12 " 0.051 2.00e-02 2.50e+03 pdb=" C8 DG C 12 " 0.014 2.00e-02 2.50e+03 pdb=" N7 DG C 12 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DG C 12 " 0.004 2.00e-02 2.50e+03 pdb=" C6 DG C 12 " 0.015 2.00e-02 2.50e+03 pdb=" O6 DG C 12 " -0.034 2.00e-02 2.50e+03 pdb=" N1 DG C 12 " -0.004 2.00e-02 2.50e+03 pdb=" C2 DG C 12 " 0.006 2.00e-02 2.50e+03 pdb=" N2 DG C 12 " 0.006 2.00e-02 2.50e+03 pdb=" N3 DG C 12 " 0.001 2.00e-02 2.50e+03 pdb=" C4 DG C 12 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC C 15 " -0.055 2.00e-02 2.50e+03 2.62e-02 1.55e+01 pdb=" N1 DC C 15 " 0.038 2.00e-02 2.50e+03 pdb=" C2 DC C 15 " 0.008 2.00e-02 2.50e+03 pdb=" O2 DC C 15 " 0.009 2.00e-02 2.50e+03 pdb=" N3 DC C 15 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DC C 15 " -0.007 2.00e-02 2.50e+03 pdb=" N4 DC C 15 " -0.021 2.00e-02 2.50e+03 pdb=" C5 DC C 15 " -0.007 2.00e-02 2.50e+03 pdb=" C6 DC C 15 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG C 17 " -0.048 2.00e-02 2.50e+03 2.06e-02 1.27e+01 pdb=" N9 DG C 17 " 0.047 2.00e-02 2.50e+03 pdb=" C8 DG C 17 " 0.002 2.00e-02 2.50e+03 pdb=" N7 DG C 17 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DG C 17 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DG C 17 " 0.003 2.00e-02 2.50e+03 pdb=" O6 DG C 17 " -0.020 2.00e-02 2.50e+03 pdb=" N1 DG C 17 " -0.005 2.00e-02 2.50e+03 pdb=" C2 DG C 17 " 0.009 2.00e-02 2.50e+03 pdb=" N2 DG C 17 " -0.000 2.00e-02 2.50e+03 pdb=" N3 DG C 17 " 0.006 2.00e-02 2.50e+03 pdb=" C4 DG C 17 " 0.006 2.00e-02 2.50e+03 ... (remaining 1795 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1687 2.76 - 3.29: 11492 3.29 - 3.83: 21918 3.83 - 4.36: 26310 4.36 - 4.90: 40799 Nonbonded interactions: 102206 Sorted by model distance: nonbonded pdb=" O GLN A 83 " pdb=" OG SER A 87 " model vdw 2.222 3.040 nonbonded pdb=" OG1 THR A1167 " pdb=" OE1 GLU A1170 " model vdw 2.252 3.040 nonbonded pdb=" OG1 THR A 404 " pdb=" OD1 ASP A 406 " model vdw 2.259 3.040 nonbonded pdb=" OG1 THR A 474 " pdb=" OD1 ASN A 477 " model vdw 2.261 3.040 nonbonded pdb=" OD1 ASN A 14 " pdb=" OG SER A 55 " model vdw 2.286 3.040 ... (remaining 102201 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=0.00 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: 3.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.590 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 39.640 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 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 : 0.005 0.060 12807 Z= 0.251 Angle : 1.337 25.807 17844 Z= 0.710 Chirality : 0.105 1.301 2055 Planarity : 0.005 0.055 1798 Dihedral : 18.875 166.901 5571 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.48 % Allowed : 9.43 % Favored : 90.10 % 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: -1.61 (0.23), residues: 1156 helix: -0.72 (0.21), residues: 516 sheet: -1.81 (0.45), residues: 110 loop : -1.10 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP A1136 HIS 0.007 0.001 HIS A 329 PHE 0.025 0.003 PHE A 553 TYR 0.025 0.002 TYR A 973 ARG 0.012 0.001 ARG A 635 Details of bonding type rmsd hydrogen bonds : bond 0.13962 ( 529) hydrogen bonds : angle 6.03477 ( 1434) covalent geometry : bond 0.00538 (12807) covalent geometry : angle 1.33670 (17844) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 70 time to evaluate : 1.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 629 ARG cc_start: 0.8636 (tpp80) cc_final: 0.8189 (tpp80) REVERT: A 631 MET cc_start: 0.7538 (mtm) cc_final: 0.7157 (mtm) REVERT: A 1148 LYS cc_start: 0.8914 (mptt) cc_final: 0.8696 (mmtp) REVERT: A 1269 ILE cc_start: 0.9593 (mt) cc_final: 0.9384 (mt) outliers start: 5 outliers final: 1 residues processed: 74 average time/residue: 0.3069 time to fit residues: 32.6681 Evaluate side-chains 57 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 56 time to evaluate : 1.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1241 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 108 optimal weight: 3.9990 chunk 97 optimal weight: 0.6980 chunk 53 optimal weight: 7.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 9.9990 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 74 optimal weight: 6.9990 chunk 116 optimal weight: 10.0000 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 420 HIS A1256 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.118039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.066107 restraints weight = 25319.999| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 2.93 r_work: 0.2778 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.1245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 12807 Z= 0.278 Angle : 0.668 7.278 17844 Z= 0.356 Chirality : 0.043 0.237 2055 Planarity : 0.004 0.052 1798 Dihedral : 20.072 178.179 3076 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.57 % Allowed : 8.67 % Favored : 88.76 % 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: -1.01 (0.23), residues: 1156 helix: -0.02 (0.22), residues: 522 sheet: -1.52 (0.47), residues: 102 loop : -1.05 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A1136 HIS 0.004 0.001 HIS A 930 PHE 0.011 0.001 PHE A1181 TYR 0.019 0.002 TYR A 362 ARG 0.020 0.001 ARG A 654 Details of bonding type rmsd hydrogen bonds : bond 0.05261 ( 529) hydrogen bonds : angle 4.89763 ( 1434) covalent geometry : bond 0.00619 (12807) covalent geometry : angle 0.66807 (17844) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 65 time to evaluate : 1.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 631 MET cc_start: 0.7383 (OUTLIER) cc_final: 0.6993 (ptp) REVERT: A 652 LYS cc_start: 0.8841 (ptmt) cc_final: 0.8351 (pttp) REVERT: A 654 ARG cc_start: 0.8462 (tpp-160) cc_final: 0.8226 (tpp-160) outliers start: 27 outliers final: 14 residues processed: 86 average time/residue: 0.2846 time to fit residues: 34.9297 Evaluate side-chains 70 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 55 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 221 ARG Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 933 GLN Chi-restraints excluded: chain A residue 949 LEU Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1160 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 35 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 17 optimal weight: 7.9990 chunk 126 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 55 optimal weight: 9.9990 chunk 125 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 GLN A 341 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.119346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.067546 restraints weight = 25395.544| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 2.89 r_work: 0.2801 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 12807 Z= 0.164 Angle : 0.572 8.362 17844 Z= 0.306 Chirality : 0.039 0.220 2055 Planarity : 0.003 0.051 1798 Dihedral : 19.925 176.828 3074 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.81 % Allowed : 11.14 % Favored : 87.05 % 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: -0.63 (0.24), residues: 1156 helix: 0.34 (0.22), residues: 534 sheet: -1.47 (0.47), residues: 104 loop : -0.90 (0.26), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 476 HIS 0.003 0.001 HIS A 329 PHE 0.009 0.001 PHE A 432 TYR 0.013 0.001 TYR A1242 ARG 0.004 0.000 ARG A1317 Details of bonding type rmsd hydrogen bonds : bond 0.04299 ( 529) hydrogen bonds : angle 4.56279 ( 1434) covalent geometry : bond 0.00360 (12807) covalent geometry : angle 0.57212 (17844) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 65 time to evaluate : 1.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 341 GLN cc_start: 0.8541 (OUTLIER) cc_final: 0.8297 (pp30) REVERT: A 390 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8731 (mm) REVERT: A 631 MET cc_start: 0.7263 (OUTLIER) cc_final: 0.7027 (ptp) REVERT: A 648 MET cc_start: 0.8711 (mpp) cc_final: 0.8469 (mpp) REVERT: A 649 LYS cc_start: 0.9177 (mmtm) cc_final: 0.8861 (mmmm) REVERT: A 652 LYS cc_start: 0.8827 (ptmt) cc_final: 0.8220 (pttp) outliers start: 19 outliers final: 11 residues processed: 77 average time/residue: 0.2873 time to fit residues: 32.1643 Evaluate side-chains 69 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 55 time to evaluate : 1.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 341 GLN Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 733 ILE Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 933 GLN Chi-restraints excluded: chain A residue 949 LEU Chi-restraints excluded: chain A residue 1146 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 46 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 110 optimal weight: 6.9990 chunk 109 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 24 optimal weight: 0.0470 chunk 117 optimal weight: 3.9990 chunk 59 optimal weight: 7.9990 chunk 64 optimal weight: 5.9990 overall best weight: 2.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1066 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.118470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.066187 restraints weight = 25051.876| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 2.92 r_work: 0.2780 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 12807 Z= 0.258 Angle : 0.601 7.512 17844 Z= 0.319 Chirality : 0.041 0.213 2055 Planarity : 0.004 0.049 1798 Dihedral : 19.898 177.602 3074 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.29 % Allowed : 11.71 % Favored : 86.00 % 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: -0.56 (0.24), residues: 1156 helix: 0.42 (0.22), residues: 538 sheet: -1.48 (0.47), residues: 104 loop : -0.90 (0.26), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 476 HIS 0.006 0.001 HIS A 930 PHE 0.009 0.001 PHE A 97 TYR 0.019 0.001 TYR A1242 ARG 0.004 0.000 ARG A 69 Details of bonding type rmsd hydrogen bonds : bond 0.04479 ( 529) hydrogen bonds : angle 4.51506 ( 1434) covalent geometry : bond 0.00578 (12807) covalent geometry : angle 0.60096 (17844) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 58 time to evaluate : 1.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 649 LYS cc_start: 0.9170 (mmtm) cc_final: 0.8833 (mmmm) REVERT: A 652 LYS cc_start: 0.8846 (ptmt) cc_final: 0.8244 (pttp) REVERT: A 654 ARG cc_start: 0.8131 (tpp-160) cc_final: 0.7706 (tpp-160) REVERT: A 1303 ARG cc_start: 0.8779 (ttm-80) cc_final: 0.8281 (ttm170) outliers start: 24 outliers final: 17 residues processed: 75 average time/residue: 0.2845 time to fit residues: 30.6262 Evaluate side-chains 71 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 54 time to evaluate : 1.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 221 ARG Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 733 ILE Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 933 GLN Chi-restraints excluded: chain A residue 949 LEU Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1148 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 98 optimal weight: 0.4980 chunk 20 optimal weight: 3.9990 chunk 82 optimal weight: 6.9990 chunk 112 optimal weight: 0.9990 chunk 75 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 78 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 81 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 983 HIS A1264 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.119993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.068239 restraints weight = 25210.197| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 2.90 r_work: 0.2813 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12807 Z= 0.132 Angle : 0.541 8.368 17844 Z= 0.287 Chirality : 0.038 0.178 2055 Planarity : 0.003 0.049 1798 Dihedral : 19.843 178.624 3074 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.71 % Allowed : 12.57 % Favored : 85.71 % 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: -0.27 (0.24), residues: 1156 helix: 0.64 (0.22), residues: 538 sheet: -1.33 (0.48), residues: 104 loop : -0.71 (0.27), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 476 HIS 0.003 0.001 HIS A 329 PHE 0.010 0.001 PHE A 518 TYR 0.019 0.001 TYR A1242 ARG 0.002 0.000 ARG A 629 Details of bonding type rmsd hydrogen bonds : bond 0.03865 ( 529) hydrogen bonds : angle 4.34939 ( 1434) covalent geometry : bond 0.00289 (12807) covalent geometry : angle 0.54057 (17844) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 61 time to evaluate : 1.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 GLN cc_start: 0.7245 (OUTLIER) cc_final: 0.5966 (pt0) REVERT: A 390 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8756 (mm) REVERT: A 511 HIS cc_start: 0.8355 (m90) cc_final: 0.7971 (m-70) REVERT: A 649 LYS cc_start: 0.9214 (mmtm) cc_final: 0.8891 (mmmm) REVERT: A 652 LYS cc_start: 0.8815 (ptmt) cc_final: 0.8213 (pttp) REVERT: A 654 ARG cc_start: 0.8150 (tpp-160) cc_final: 0.7725 (tpp-160) REVERT: A 662 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.8021 (pp) REVERT: A 1303 ARG cc_start: 0.8817 (ttm-80) cc_final: 0.8336 (ttm170) outliers start: 18 outliers final: 12 residues processed: 73 average time/residue: 0.2942 time to fit residues: 31.1264 Evaluate side-chains 72 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 57 time to evaluate : 1.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 194 GLN Chi-restraints excluded: chain A residue 221 ARG Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 733 ILE Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 933 GLN Chi-restraints excluded: chain A residue 949 LEU Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1160 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 53 optimal weight: 20.0000 chunk 20 optimal weight: 0.2980 chunk 95 optimal weight: 0.0980 chunk 67 optimal weight: 9.9990 chunk 36 optimal weight: 0.0870 chunk 46 optimal weight: 0.2980 chunk 5 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 overall best weight: 0.3358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 281 GLN A 341 GLN A 413 GLN A 930 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.122123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.070667 restraints weight = 25563.842| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 2.92 r_work: 0.2870 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 12807 Z= 0.104 Angle : 0.514 10.214 17844 Z= 0.271 Chirality : 0.037 0.174 2055 Planarity : 0.003 0.048 1798 Dihedral : 19.706 179.826 3074 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.71 % Allowed : 13.24 % Favored : 85.05 % 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: 0.00 (0.24), residues: 1156 helix: 0.83 (0.22), residues: 546 sheet: -1.07 (0.50), residues: 104 loop : -0.58 (0.27), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 659 HIS 0.002 0.000 HIS A 329 PHE 0.010 0.001 PHE A 518 TYR 0.018 0.001 TYR A1242 ARG 0.003 0.000 ARG A 664 Details of bonding type rmsd hydrogen bonds : bond 0.03408 ( 529) hydrogen bonds : angle 4.18777 ( 1434) covalent geometry : bond 0.00223 (12807) covalent geometry : angle 0.51414 (17844) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 63 time to evaluate : 1.145 Fit side-chains revert: symmetry clash REVERT: A 194 GLN cc_start: 0.7250 (OUTLIER) cc_final: 0.5956 (pt0) REVERT: A 390 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8774 (mm) REVERT: A 637 LYS cc_start: 0.9522 (mmmm) cc_final: 0.9257 (mmmm) REVERT: A 649 LYS cc_start: 0.9249 (mmtm) cc_final: 0.8859 (mmtm) REVERT: A 652 LYS cc_start: 0.8749 (ptmt) cc_final: 0.8235 (pttp) REVERT: A 654 ARG cc_start: 0.8118 (tpp-160) cc_final: 0.7677 (tpp-160) REVERT: A 662 LEU cc_start: 0.8063 (OUTLIER) cc_final: 0.7665 (pp) REVERT: A 1269 ILE cc_start: 0.9482 (mt) cc_final: 0.9206 (mt) REVERT: A 1303 ARG cc_start: 0.8865 (ttm-80) cc_final: 0.8460 (ttm170) outliers start: 18 outliers final: 9 residues processed: 76 average time/residue: 0.2819 time to fit residues: 30.9067 Evaluate side-chains 73 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 61 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 194 GLN Chi-restraints excluded: chain A residue 221 ARG Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 733 ILE Chi-restraints excluded: chain A residue 762 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 52 optimal weight: 0.0970 chunk 46 optimal weight: 0.0040 chunk 69 optimal weight: 0.7980 chunk 79 optimal weight: 3.9990 chunk 66 optimal weight: 9.9990 chunk 39 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 85 optimal weight: 7.9990 chunk 54 optimal weight: 9.9990 chunk 75 optimal weight: 0.8980 chunk 117 optimal weight: 3.9990 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 341 GLN A1297 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.121689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.070127 restraints weight = 25222.262| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 2.88 r_work: 0.2862 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12807 Z= 0.115 Angle : 0.527 9.453 17844 Z= 0.276 Chirality : 0.037 0.176 2055 Planarity : 0.003 0.047 1798 Dihedral : 19.635 178.954 3074 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.52 % Allowed : 13.62 % Favored : 84.86 % 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: 0.10 (0.24), residues: 1156 helix: 0.91 (0.22), residues: 546 sheet: -1.04 (0.50), residues: 104 loop : -0.52 (0.27), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1136 HIS 0.002 0.001 HIS A 982 PHE 0.033 0.001 PHE A 518 TYR 0.013 0.001 TYR A1242 ARG 0.002 0.000 ARG A 152 Details of bonding type rmsd hydrogen bonds : bond 0.03449 ( 529) hydrogen bonds : angle 4.13631 ( 1434) covalent geometry : bond 0.00252 (12807) covalent geometry : angle 0.52676 (17844) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 60 time to evaluate : 1.176 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 194 GLN cc_start: 0.7245 (OUTLIER) cc_final: 0.5942 (pt0) REVERT: A 390 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8782 (mm) REVERT: A 637 LYS cc_start: 0.9515 (mmmm) cc_final: 0.9239 (mmmm) REVERT: A 649 LYS cc_start: 0.9218 (mmtm) cc_final: 0.8959 (mmtm) REVERT: A 654 ARG cc_start: 0.8096 (tpp-160) cc_final: 0.7718 (tpp80) REVERT: A 662 LEU cc_start: 0.7853 (OUTLIER) cc_final: 0.7480 (pp) REVERT: A 933 GLN cc_start: 0.7347 (pt0) cc_final: 0.6707 (pm20) REVERT: A 1269 ILE cc_start: 0.9484 (mt) cc_final: 0.9204 (mt) REVERT: A 1303 ARG cc_start: 0.8862 (ttm-80) cc_final: 0.8440 (ttm170) outliers start: 16 outliers final: 10 residues processed: 71 average time/residue: 0.3011 time to fit residues: 32.1497 Evaluate side-chains 67 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 54 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 194 GLN Chi-restraints excluded: chain A residue 221 ARG Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 733 ILE Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 1160 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 68 optimal weight: 0.1980 chunk 16 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 74 optimal weight: 0.0980 chunk 26 optimal weight: 10.0000 chunk 70 optimal weight: 0.3980 chunk 4 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 55 optimal weight: 0.0980 chunk 0 optimal weight: 3.9990 overall best weight: 0.3180 ------------------------------------------------------------------------------- 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 = 0.3958 r_free = 0.3958 target = 0.122585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.071446 restraints weight = 25347.350| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 2.86 r_work: 0.2888 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 12807 Z= 0.102 Angle : 0.525 8.648 17844 Z= 0.272 Chirality : 0.037 0.176 2055 Planarity : 0.003 0.046 1798 Dihedral : 19.619 178.756 3074 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.43 % Allowed : 14.10 % Favored : 84.48 % 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 (0.24), residues: 1156 helix: 0.99 (0.22), residues: 547 sheet: -0.94 (0.51), residues: 104 loop : -0.47 (0.27), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 659 HIS 0.002 0.001 HIS A 329 PHE 0.034 0.001 PHE A 518 TYR 0.013 0.001 TYR A1242 ARG 0.002 0.000 ARG A1122 Details of bonding type rmsd hydrogen bonds : bond 0.03286 ( 529) hydrogen bonds : angle 4.07948 ( 1434) covalent geometry : bond 0.00221 (12807) covalent geometry : angle 0.52529 (17844) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 60 time to evaluate : 1.186 Fit side-chains revert: symmetry clash REVERT: A 194 GLN cc_start: 0.7272 (OUTLIER) cc_final: 0.5961 (pt0) REVERT: A 307 ARG cc_start: 0.7914 (mmp-170) cc_final: 0.7413 (mmp-170) REVERT: A 390 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8793 (mm) REVERT: A 637 LYS cc_start: 0.9510 (mmmm) cc_final: 0.9224 (mmmm) REVERT: A 649 LYS cc_start: 0.9243 (mmtm) cc_final: 0.8985 (mmtm) REVERT: A 654 ARG cc_start: 0.8045 (tpp-160) cc_final: 0.7656 (tpp80) REVERT: A 661 ARG cc_start: 0.8560 (mmm160) cc_final: 0.8236 (mmm-85) REVERT: A 662 LEU cc_start: 0.7776 (OUTLIER) cc_final: 0.7482 (pp) REVERT: A 933 GLN cc_start: 0.7101 (pt0) cc_final: 0.6559 (pm20) REVERT: A 1269 ILE cc_start: 0.9464 (mt) cc_final: 0.9173 (mt) REVERT: A 1303 ARG cc_start: 0.8851 (ttm-80) cc_final: 0.8428 (ttm170) outliers start: 15 outliers final: 11 residues processed: 72 average time/residue: 0.2945 time to fit residues: 30.2384 Evaluate side-chains 69 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 55 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 194 GLN Chi-restraints excluded: chain A residue 221 ARG Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 733 ILE Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 1160 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 4 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 71 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 23 optimal weight: 6.9990 chunk 125 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 chunk 115 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 = 0.3927 r_free = 0.3927 target = 0.120501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.068933 restraints weight = 25191.664| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 2.89 r_work: 0.2830 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 12807 Z= 0.163 Angle : 0.555 9.699 17844 Z= 0.287 Chirality : 0.038 0.177 2055 Planarity : 0.003 0.046 1798 Dihedral : 19.614 177.666 3074 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.43 % Allowed : 14.29 % Favored : 84.29 % 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: 0.18 (0.24), residues: 1156 helix: 0.98 (0.22), residues: 548 sheet: -1.00 (0.50), residues: 104 loop : -0.50 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 476 HIS 0.005 0.001 HIS A1297 PHE 0.008 0.001 PHE A 168 TYR 0.013 0.001 TYR A 155 ARG 0.007 0.000 ARG A1298 Details of bonding type rmsd hydrogen bonds : bond 0.03655 ( 529) hydrogen bonds : angle 4.10380 ( 1434) covalent geometry : bond 0.00363 (12807) covalent geometry : angle 0.55468 (17844) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 56 time to evaluate : 1.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 GLN cc_start: 0.7273 (OUTLIER) cc_final: 0.5982 (pt0) REVERT: A 307 ARG cc_start: 0.7950 (mmp-170) cc_final: 0.7451 (mmp-170) REVERT: A 390 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8816 (mm) REVERT: A 511 HIS cc_start: 0.8457 (m90) cc_final: 0.8020 (m-70) REVERT: A 637 LYS cc_start: 0.9513 (mmmm) cc_final: 0.9227 (mmmm) REVERT: A 649 LYS cc_start: 0.9266 (mmtm) cc_final: 0.9010 (mmtm) REVERT: A 654 ARG cc_start: 0.8095 (tpp-160) cc_final: 0.7871 (tpp80) REVERT: A 661 ARG cc_start: 0.8665 (mmm160) cc_final: 0.8308 (mmm-85) REVERT: A 662 LEU cc_start: 0.7927 (OUTLIER) cc_final: 0.7599 (pp) REVERT: A 933 GLN cc_start: 0.7233 (pt0) cc_final: 0.6600 (pm20) REVERT: A 1303 ARG cc_start: 0.8839 (ttm-80) cc_final: 0.8407 (ttm170) outliers start: 15 outliers final: 12 residues processed: 68 average time/residue: 0.3318 time to fit residues: 32.2474 Evaluate side-chains 71 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 56 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 194 GLN Chi-restraints excluded: chain A residue 221 ARG Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 733 ILE Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 1148 LYS Chi-restraints excluded: chain A residue 1160 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 52 optimal weight: 8.9990 chunk 73 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 27 optimal weight: 7.9990 chunk 103 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 19 optimal weight: 10.0000 chunk 59 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 116 optimal weight: 10.0000 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.119812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.067880 restraints weight = 25125.822| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 2.87 r_work: 0.2809 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 12807 Z= 0.180 Angle : 0.578 12.857 17844 Z= 0.295 Chirality : 0.039 0.178 2055 Planarity : 0.004 0.064 1798 Dihedral : 19.685 176.639 3074 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.43 % Allowed : 14.29 % Favored : 84.29 % 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: 0.07 (0.24), residues: 1156 helix: 0.91 (0.22), residues: 552 sheet: -1.04 (0.49), residues: 104 loop : -0.59 (0.26), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 476 HIS 0.003 0.001 HIS A1297 PHE 0.028 0.001 PHE A 518 TYR 0.014 0.001 TYR A 362 ARG 0.011 0.000 ARG A1298 Details of bonding type rmsd hydrogen bonds : bond 0.03767 ( 529) hydrogen bonds : angle 4.14699 ( 1434) covalent geometry : bond 0.00402 (12807) covalent geometry : angle 0.57755 (17844) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 58 time to evaluate : 1.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 ARG cc_start: 0.7922 (mmp-170) cc_final: 0.7282 (ppt170) REVERT: A 390 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8800 (mm) REVERT: A 511 HIS cc_start: 0.8455 (m90) cc_final: 0.8013 (m-70) REVERT: A 637 LYS cc_start: 0.9506 (mmmm) cc_final: 0.9219 (mmmm) REVERT: A 649 LYS cc_start: 0.9274 (mmtm) cc_final: 0.9017 (mmtm) REVERT: A 654 ARG cc_start: 0.8129 (tpp-160) cc_final: 0.7727 (tpp80) REVERT: A 661 ARG cc_start: 0.8728 (mmm160) cc_final: 0.8488 (mmm-85) REVERT: A 1303 ARG cc_start: 0.8821 (ttm-80) cc_final: 0.8337 (ttm170) outliers start: 15 outliers final: 11 residues processed: 70 average time/residue: 0.3187 time to fit residues: 32.1476 Evaluate side-chains 70 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 1.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 733 ILE Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 1148 LYS Chi-restraints excluded: chain A residue 1160 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 25 optimal weight: 8.9990 chunk 96 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 95 optimal weight: 0.0010 chunk 52 optimal weight: 20.0000 chunk 80 optimal weight: 0.9990 chunk 127 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 64 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 overall best weight: 0.8590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 933 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.120570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.068943 restraints weight = 25129.330| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 2.85 r_work: 0.2831 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12807 Z= 0.140 Angle : 0.566 13.753 17844 Z= 0.288 Chirality : 0.038 0.178 2055 Planarity : 0.003 0.048 1798 Dihedral : 19.645 176.701 3074 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.14 % Allowed : 14.48 % Favored : 84.38 % 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: 0.12 (0.24), residues: 1156 helix: 0.95 (0.22), residues: 552 sheet: -1.00 (0.49), residues: 104 loop : -0.58 (0.27), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 476 HIS 0.002 0.001 HIS A 116 PHE 0.009 0.001 PHE A 693 TYR 0.014 0.001 TYR A1242 ARG 0.011 0.000 ARG A1298 Details of bonding type rmsd hydrogen bonds : bond 0.03564 ( 529) hydrogen bonds : angle 4.12944 ( 1434) covalent geometry : bond 0.00311 (12807) covalent geometry : angle 0.56616 (17844) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7788.45 seconds wall clock time: 134 minutes 21.47 seconds (8061.47 seconds total)