Starting phenix.real_space_refine on Wed Jul 30 16:10:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9klp_62412/07_2025/9klp_62412.cif Found real_map, /net/cci-nas-00/data/ceres_data/9klp_62412/07_2025/9klp_62412.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9klp_62412/07_2025/9klp_62412.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9klp_62412/07_2025/9klp_62412.map" model { file = "/net/cci-nas-00/data/ceres_data/9klp_62412/07_2025/9klp_62412.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9klp_62412/07_2025/9klp_62412.cif" } resolution = 2.87 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= 0.024 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 Ca 6 9.91 5 P 127 5.49 5 S 32 5.16 5 C 7445 2.51 5 N 2306 2.21 5 O 2653 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 12569 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 9858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1268, 9858 Classifications: {'peptide': 1268} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 55, 'TRANS': 1212} Chain breaks: 10 Unresolved non-hydrogen bonds: 179 Unresolved non-hydrogen angles: 219 Unresolved non-hydrogen dihedrals: 142 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 6, 'GLU:plan': 16, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 127 Chain: "B" Number of atoms: 1878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 1878 Inner-chain residues flagged as termini: ['pdbres=" C B 82 "'] Classifications: {'RNA': 88} Modifications used: {'5*END': 1, 'rna2p_pur': 9, 'rna2p_pyr': 6, 'rna3p_pur': 38, 'rna3p_pyr': 35} Link IDs: {'rna2p': 15, 'rna3p': 72} Chain: "C" Number of atoms: 406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 406 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "D" Number of atoms: 421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 421 Classifications: {'DNA': 21} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 20} Chain breaks: 1 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' CA': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 7.90, per 1000 atoms: 0.63 Number of scatterers: 12569 At special positions: 0 Unit cell: (106.449, 118.916, 131.383, 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) Ca 6 19.99 S 32 16.00 P 127 15.00 O 2653 8.00 N 2306 7.00 C 7445 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: 3.07 Conformation dependent library (CDL) restraints added in 1.2 seconds 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2368 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 7 sheets defined 52.8% alpha, 9.9% beta 27 base pairs and 78 stacking pairs defined. Time for finding SS restraints: 4.19 Creating SS restraints... Processing helix chain 'A' and resid 24 through 52 Processing helix chain 'A' and resid 53 through 54 No H-bonds generated for 'chain 'A' and resid 53 through 54' Processing helix chain 'A' and resid 55 through 59 Processing helix chain 'A' and resid 70 through 85 Processing helix chain 'A' and resid 95 through 97 No H-bonds generated for 'chain 'A' and resid 95 through 97' Processing helix chain 'A' and resid 106 through 125 Processing helix chain 'A' and resid 128 through 144 removed outlier: 5.405A pdb=" N ALA A 141 " --> pdb=" O SER A 137 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N SER A 142 " --> pdb=" O ASP A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 168 Processing helix chain 'A' and resid 174 through 179 removed outlier: 3.599A pdb=" N ASP A 178 " --> pdb=" O ASP A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 185 Processing helix chain 'A' and resid 186 through 192 Processing helix chain 'A' and resid 214 through 228 removed outlier: 3.544A pdb=" N LYS A 218 " --> pdb=" O ASP A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 251 removed outlier: 4.078A pdb=" N THR A 251 " --> pdb=" O GLU A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 269 Processing helix chain 'A' and resid 270 through 273 Processing helix chain 'A' and resid 278 through 286 removed outlier: 3.868A pdb=" N VAL A 282 " --> pdb=" O ASN A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 305 removed outlier: 3.841A pdb=" N ASN A 297 " --> pdb=" O SER A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 330 removed outlier: 3.766A pdb=" N LEU A 313 " --> pdb=" O SER A 309 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLU A 329 " --> pdb=" O VAL A 325 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER A 330 " --> pdb=" O LYS A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 352 removed outlier: 3.565A pdb=" N ARG A 350 " --> pdb=" O ASP A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 372 removed outlier: 3.900A pdb=" N THR A 369 " --> pdb=" O ILE A 366 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N SER A 370 " --> pdb=" O LEU A 367 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU A 371 " --> pdb=" O ASP A 368 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE A 372 " --> pdb=" O THR A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 416 removed outlier: 3.593A pdb=" N PHE A 386 " --> pdb=" O ARG A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 577 removed outlier: 3.505A pdb=" N ARG A 577 " --> pdb=" O ILE A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 622 Processing helix chain 'A' and resid 641 through 647 Processing helix chain 'A' and resid 674 through 686 removed outlier: 3.608A pdb=" N LEU A 678 " --> pdb=" O PRO A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 691 through 703 Processing helix chain 'A' and resid 720 through 726 removed outlier: 3.999A pdb=" N SER A 724 " --> pdb=" O GLY A 720 " (cutoff:3.500A) Processing helix chain 'A' and resid 727 through 730 Processing helix chain 'A' and resid 742 through 746 removed outlier: 4.301A pdb=" N LYS A 746 " --> pdb=" O ILE A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 752 Processing helix chain 'A' and resid 783 through 794 Processing helix chain 'A' and resid 868 through 882 Processing helix chain 'A' and resid 887 through 895 Processing helix chain 'A' and resid 900 through 914 Processing helix chain 'A' and resid 936 through 966 removed outlier: 4.121A pdb=" N LYS A 953 " --> pdb=" O ARG A 949 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N TYR A 954 " --> pdb=" O LEU A 950 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N HIS A 955 " --> pdb=" O ALA A 951 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA A 959 " --> pdb=" O HIS A 955 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N THR A 966 " --> pdb=" O ALA A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 984 through 988 removed outlier: 3.862A pdb=" N SER A 988 " --> pdb=" O ASP A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 1002 through 1015 Processing helix chain 'A' and resid 1021 through 1031 removed outlier: 3.621A pdb=" N LYS A1025 " --> pdb=" O ASP A1021 " (cutoff:3.500A) Processing helix chain 'A' and resid 1032 through 1035 Processing helix chain 'A' and resid 1054 through 1072 Proline residue: A1066 - end of helix Processing helix chain 'A' and resid 1075 through 1108 removed outlier: 4.058A pdb=" N LYS A1098 " --> pdb=" O ALA A1094 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE A1107 " --> pdb=" O MET A1103 " (cutoff:3.500A) Processing helix chain 'A' and resid 1111 through 1115 Processing helix chain 'A' and resid 1116 through 1120 removed outlier: 3.941A pdb=" N ILE A1119 " --> pdb=" O THR A1116 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ARG A1120 " --> pdb=" O PRO A1117 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1116 through 1120' Processing helix chain 'A' and resid 1126 through 1140 removed outlier: 3.700A pdb=" N LEU A1130 " --> pdb=" O SER A1126 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 Processing helix chain 'A' and resid 1162 through 1190 Processing helix chain 'A' and resid 1234 through 1241 removed outlier: 3.913A pdb=" N GLY A1238 " --> pdb=" O ARG A1234 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU A1239 " --> pdb=" O GLU A1235 " (cutoff:3.500A) Processing helix chain 'A' and resid 1242 through 1258 removed outlier: 4.311A pdb=" N LYS A1246 " --> pdb=" O TRP A1242 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LYS A1248 " --> pdb=" O SER A1244 " (cutoff:3.500A) Processing helix chain 'A' and resid 1295 through 1309 Processing helix chain 'A' and resid 1311 through 1326 removed outlier: 3.523A pdb=" N ARG A1315 " --> pdb=" O THR A1311 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N GLN A1326 " --> pdb=" O GLU A1322 " (cutoff:3.500A) Processing helix chain 'A' and resid 1355 through 1360 removed outlier: 3.591A pdb=" N LYS A1359 " --> pdb=" O PRO A1356 " (cutoff:3.500A) Processing helix chain 'A' and resid 1363 through 1374 Processing helix chain 'A' and resid 1457 through 1479 removed outlier: 3.635A pdb=" N ASN A1467 " --> pdb=" O LYS A1463 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ARG A1468 " --> pdb=" O GLU A1464 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL A1469 " --> pdb=" O VAL A1465 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE A1470 " --> pdb=" O GLU A1466 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 560 through 562 Processing sheet with id=AA2, first strand: chain 'A' and resid 86 through 90 removed outlier: 3.746A pdb=" N ALA A 101 " --> pdb=" O TRP A 153 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ASN A 155 " --> pdb=" O ILE A 99 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N ILE A 99 " --> pdb=" O ASN A 155 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 635 through 637 Processing sheet with id=AA4, first strand: chain 'A' and resid 805 through 812 removed outlier: 21.778A pdb=" N GLU A 824 " --> pdb=" O PHE A 854 " (cutoff:3.500A) removed outlier: 17.424A pdb=" N PHE A 854 " --> pdb=" O GLU A 824 " (cutoff:3.500A) removed outlier: 13.618A pdb=" N SER A 826 " --> pdb=" O ARG A 852 " (cutoff:3.500A) removed outlier: 9.248A pdb=" N ARG A 852 " --> pdb=" O SER A 826 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N VAL A 828 " --> pdb=" O LEU A 850 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N ALA A 848 " --> pdb=" O MET A 782 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N MET A 782 " --> pdb=" O ALA A 848 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N LEU A 850 " --> pdb=" O GLU A 780 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N GLU A 780 " --> pdb=" O LEU A 850 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ARG A 852 " --> pdb=" O VAL A 778 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA A 774 " --> pdb=" O ILE A 856 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N ARG A 762 " --> pdb=" O ALA A1216 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N ILE A1218 " --> pdb=" O ARG A 762 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N LEU A 764 " --> pdb=" O ILE A1218 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N GLU A1220 " --> pdb=" O LEU A 764 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N VAL A 766 " --> pdb=" O GLU A1220 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 969 through 972 Processing sheet with id=AA6, first strand: chain 'A' and resid 1338 through 1341 Processing sheet with id=AA7, first strand: chain 'A' and resid 1387 through 1391 504 hydrogen bonds defined for protein. 1437 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 66 hydrogen bonds 124 hydrogen bond angles 0 basepair planarities 27 basepair parallelities 78 stacking parallelities Total time for adding SS restraints: 5.79 Time building geometry restraints manager: 3.62 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: 2398 1.33 - 1.45: 3721 1.45 - 1.57: 6665 1.57 - 1.68: 251 1.68 - 1.80: 51 Bond restraints: 13086 Sorted by residual: bond pdb=" P DT D 24 " pdb=" OP2 DT D 24 " ideal model delta sigma weight residual 1.480 1.520 -0.040 2.00e-02 2.50e+03 4.05e+00 bond pdb=" P DT D 16 " pdb=" OP2 DT D 16 " ideal model delta sigma weight residual 1.480 1.520 -0.040 2.00e-02 2.50e+03 3.94e+00 bond pdb=" C ASP A1380 " pdb=" N TRP A1381 " ideal model delta sigma weight residual 1.331 1.292 0.039 2.07e-02 2.33e+03 3.62e+00 bond pdb=" P DT D 24 " pdb=" OP1 DT D 24 " ideal model delta sigma weight residual 1.480 1.515 -0.035 2.00e-02 2.50e+03 3.14e+00 bond pdb=" P DT D 26 " pdb=" OP1 DT D 26 " ideal model delta sigma weight residual 1.480 1.515 -0.035 2.00e-02 2.50e+03 3.06e+00 ... (remaining 13081 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.83: 17873 1.83 - 3.66: 375 3.66 - 5.49: 34 5.49 - 7.32: 12 7.32 - 9.15: 2 Bond angle restraints: 18296 Sorted by residual: angle pdb=" CA ARG A 74 " pdb=" CB ARG A 74 " pdb=" CG ARG A 74 " ideal model delta sigma weight residual 114.10 121.08 -6.98 2.00e+00 2.50e-01 1.22e+01 angle pdb=" N GLU A 322 " pdb=" CA GLU A 322 " pdb=" CB GLU A 322 " ideal model delta sigma weight residual 110.12 114.52 -4.40 1.47e+00 4.63e-01 8.95e+00 angle pdb=" O3' DT D 24 " pdb=" P DT D 25 " pdb=" O5' DT D 25 " ideal model delta sigma weight residual 104.00 108.36 -4.36 1.50e+00 4.44e-01 8.46e+00 angle pdb=" O3' DT D 15 " pdb=" P DT D 16 " pdb=" OP2 DT D 16 " ideal model delta sigma weight residual 108.00 116.21 -8.21 3.00e+00 1.11e-01 7.50e+00 angle pdb=" C GLU A 322 " pdb=" N ASP A 323 " pdb=" CA ASP A 323 " ideal model delta sigma weight residual 120.31 116.26 4.05 1.52e+00 4.33e-01 7.09e+00 ... (remaining 18291 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.91: 7176 27.91 - 55.81: 548 55.81 - 83.72: 150 83.72 - 111.62: 4 111.62 - 139.53: 1 Dihedral angle restraints: 7879 sinusoidal: 4225 harmonic: 3654 Sorted by residual: dihedral pdb=" CA GLN A1362 " pdb=" C GLN A1362 " pdb=" N ALA A1363 " pdb=" CA ALA A1363 " ideal model delta harmonic sigma weight residual -180.00 -158.73 -21.27 0 5.00e+00 4.00e-02 1.81e+01 dihedral pdb=" CA PRO A 973 " pdb=" C PRO A 973 " pdb=" N GLY A 974 " pdb=" CA GLY A 974 " ideal model delta harmonic sigma weight residual 180.00 -160.15 -19.85 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA THR A 380 " pdb=" C THR A 380 " pdb=" N ALA A 381 " pdb=" CA ALA A 381 " ideal model delta harmonic sigma weight residual -180.00 -161.21 -18.79 0 5.00e+00 4.00e-02 1.41e+01 ... (remaining 7876 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.121: 2053 0.121 - 0.242: 17 0.242 - 0.363: 0 0.363 - 0.484: 1 0.484 - 0.605: 3 Chirality restraints: 2074 Sorted by residual: chirality pdb=" P DT D 24 " pdb=" OP1 DT D 24 " pdb=" OP2 DT D 24 " pdb=" O5' DT D 24 " both_signs ideal model delta sigma weight residual True 2.35 -2.95 -0.61 2.00e-01 2.50e+01 9.16e+00 chirality pdb=" P DT D 16 " pdb=" OP1 DT D 16 " pdb=" OP2 DT D 16 " pdb=" O5' DT D 16 " both_signs ideal model delta sigma weight residual True 2.35 -2.93 -0.58 2.00e-01 2.50e+01 8.54e+00 chirality pdb=" P DT D 26 " pdb=" OP1 DT D 26 " pdb=" OP2 DT D 26 " pdb=" O5' DT D 26 " both_signs ideal model delta sigma weight residual True 2.35 -2.92 -0.57 2.00e-01 2.50e+01 8.24e+00 ... (remaining 2071 not shown) Planarity restraints: 1893 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR A1002 " -0.019 2.00e-02 2.50e+03 3.71e-02 1.37e+01 pdb=" C TYR A1002 " 0.064 2.00e-02 2.50e+03 pdb=" O TYR A1002 " -0.024 2.00e-02 2.50e+03 pdb=" N LEU A1003 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A1458 " -0.026 2.00e-02 2.50e+03 2.55e-02 1.30e+01 pdb=" CG TYR A1458 " 0.063 2.00e-02 2.50e+03 pdb=" CD1 TYR A1458 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR A1458 " -0.021 2.00e-02 2.50e+03 pdb=" CE1 TYR A1458 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR A1458 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR A1458 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR A1458 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 845 " -0.032 5.00e-02 4.00e+02 4.78e-02 3.65e+00 pdb=" N PRO A 846 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO A 846 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 846 " -0.026 5.00e-02 4.00e+02 ... (remaining 1890 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.44: 32 2.44 - 3.06: 7608 3.06 - 3.67: 18329 3.67 - 4.29: 27554 4.29 - 4.90: 45142 Nonbonded interactions: 98665 Sorted by model distance: nonbonded pdb="CA CA B 202 " pdb="CA CA B 204 " model vdw 1.830 1.980 nonbonded pdb="CA CA B 201 " pdb="CA CA B 203 " model vdw 1.854 1.980 nonbonded pdb="CA CA A1501 " pdb="CA CA A1502 " model vdw 1.984 1.980 nonbonded pdb=" OE1 GLU A1228 " pdb=" OG SER A1271 " model vdw 2.189 3.040 nonbonded pdb=" OG SER A 276 " pdb=" OD1 ASN A 278 " model vdw 2.199 3.040 ... (remaining 98660 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: 1.980 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: 0.530 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 34.010 Find NCS groups from input model: 0.120 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:11.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 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 : 0.007 0.040 13086 Z= 0.307 Angle : 0.639 9.152 18296 Z= 0.340 Chirality : 0.047 0.605 2074 Planarity : 0.005 0.051 1893 Dihedral : 18.916 139.530 5511 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.41 % Favored : 95.51 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % 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: 0.59 (0.24), residues: 1246 helix: 1.57 (0.22), residues: 601 sheet: 0.05 (0.42), residues: 133 loop : -0.93 (0.26), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 30 HIS 0.006 0.001 HIS A 33 PHE 0.018 0.002 PHE A 43 TYR 0.063 0.002 TYR A1458 ARG 0.015 0.001 ARG A 74 Details of bonding type rmsd hydrogen bonds : bond 0.18323 ( 570) hydrogen bonds : angle 5.88184 ( 1561) covalent geometry : bond 0.00687 (13086) covalent geometry : angle 0.63865 (18296) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 1.428 Fit side-chains REVERT: A 1006 MET cc_start: 0.8533 (tmm) cc_final: 0.8201 (tmm) REVERT: A 1064 MET cc_start: 0.8636 (mmp) cc_final: 0.8203 (mpm) REVERT: A 1159 GLU cc_start: 0.8363 (tp30) cc_final: 0.8136 (pm20) REVERT: A 1322 GLU cc_start: 0.8975 (tp30) cc_final: 0.8406 (tp30) REVERT: A 1326 GLN cc_start: 0.7365 (pm20) cc_final: 0.6831 (pm20) REVERT: A 1335 MET cc_start: 0.6497 (tpp) cc_final: 0.6289 (tpp) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 2.1824 time to fit residues: 169.6174 Evaluate side-chains 47 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 1.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 116 optimal weight: 1.9990 chunk 104 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 70 optimal weight: 7.9990 chunk 55 optimal weight: 0.7980 chunk 108 optimal weight: 0.8980 chunk 41 optimal weight: 0.6980 chunk 65 optimal weight: 0.8980 chunk 80 optimal weight: 10.0000 chunk 125 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 813 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 = 0.3677 r_free = 0.3677 target = 0.113411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.078604 restraints weight = 22207.270| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 2.47 r_work: 0.2977 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.1241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13086 Z= 0.123 Angle : 0.527 8.970 18296 Z= 0.277 Chirality : 0.037 0.383 2074 Planarity : 0.004 0.037 1893 Dihedral : 19.755 144.577 3201 Min Nonbonded Distance : 1.692 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.13 % Favored : 96.79 % Rotamer: Outliers : 0.20 % Allowed : 7.46 % Favored : 92.34 % 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: 1.04 (0.24), residues: 1246 helix: 2.16 (0.22), residues: 601 sheet: 0.18 (0.41), residues: 143 loop : -1.02 (0.26), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 30 HIS 0.003 0.001 HIS A 33 PHE 0.009 0.001 PHE A 43 TYR 0.018 0.001 TYR A1038 ARG 0.007 0.000 ARG A 362 Details of bonding type rmsd hydrogen bonds : bond 0.05350 ( 570) hydrogen bonds : angle 3.87086 ( 1561) covalent geometry : bond 0.00254 (13086) covalent geometry : angle 0.52726 (18296) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 53 time to evaluate : 1.244 Fit side-chains REVERT: A 960 ARG cc_start: 0.7731 (ttp80) cc_final: 0.7423 (tmt90) REVERT: A 1038 TYR cc_start: 0.7657 (t80) cc_final: 0.7362 (t80) REVERT: A 1064 MET cc_start: 0.8620 (mmp) cc_final: 0.8098 (mpm) REVERT: A 1135 GLU cc_start: 0.8675 (tp30) cc_final: 0.8376 (tp30) REVERT: A 1159 GLU cc_start: 0.8270 (tp30) cc_final: 0.8022 (pm20) outliers start: 2 outliers final: 2 residues processed: 55 average time/residue: 2.1921 time to fit residues: 130.9927 Evaluate side-chains 50 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 48 time to evaluate : 1.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 170 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 137 optimal weight: 7.9990 chunk 81 optimal weight: 10.0000 chunk 42 optimal weight: 6.9990 chunk 106 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 36 optimal weight: 0.5980 chunk 100 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 63 optimal weight: 5.9990 chunk 12 optimal weight: 9.9990 chunk 62 optimal weight: 4.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 813 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 = 0.3560 r_free = 0.3560 target = 0.107467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.073053 restraints weight = 22826.624| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 2.43 r_work: 0.2848 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.1141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.040 13086 Z= 0.306 Angle : 0.622 9.118 18296 Z= 0.328 Chirality : 0.042 0.425 2074 Planarity : 0.005 0.050 1893 Dihedral : 19.823 146.714 3201 Min Nonbonded Distance : 1.551 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.41 % Favored : 95.51 % Rotamer: Outliers : 0.92 % Allowed : 10.01 % Favored : 89.07 % 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: 0.73 (0.23), residues: 1246 helix: 1.92 (0.21), residues: 595 sheet: 0.07 (0.42), residues: 134 loop : -1.15 (0.25), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 779 HIS 0.005 0.001 HIS A 33 PHE 0.013 0.002 PHE A1292 TYR 0.016 0.002 TYR A1458 ARG 0.006 0.001 ARG A1276 Details of bonding type rmsd hydrogen bonds : bond 0.06381 ( 570) hydrogen bonds : angle 4.07151 ( 1561) covalent geometry : bond 0.00695 (13086) covalent geometry : angle 0.62249 (18296) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 1.264 Fit side-chains REVERT: A 179 MET cc_start: 0.8858 (OUTLIER) cc_final: 0.7946 (ttt) REVERT: A 625 ASP cc_start: 0.8424 (t0) cc_final: 0.8166 (t0) REVERT: A 960 ARG cc_start: 0.7672 (ttp80) cc_final: 0.7202 (ttp80) REVERT: A 1020 ARG cc_start: 0.8182 (mtm110) cc_final: 0.7907 (ptp-110) REVERT: A 1038 TYR cc_start: 0.7677 (t80) cc_final: 0.7400 (t80) REVERT: A 1064 MET cc_start: 0.8580 (mmp) cc_final: 0.8164 (mpm) REVERT: A 1135 GLU cc_start: 0.8652 (tp30) cc_final: 0.8400 (tp30) outliers start: 9 outliers final: 4 residues processed: 59 average time/residue: 1.9379 time to fit residues: 122.9618 Evaluate side-chains 53 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 48 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 1402 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 136 optimal weight: 4.9990 chunk 128 optimal weight: 6.9990 chunk 36 optimal weight: 0.6980 chunk 97 optimal weight: 0.6980 chunk 29 optimal weight: 9.9990 chunk 69 optimal weight: 0.8980 chunk 86 optimal weight: 20.0000 chunk 126 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 92 optimal weight: 0.9990 chunk 12 optimal weight: 0.0370 overall best weight: 0.6660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.112759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.078407 restraints weight = 22524.610| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 2.44 r_work: 0.2941 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 13086 Z= 0.107 Angle : 0.491 9.041 18296 Z= 0.256 Chirality : 0.034 0.305 2074 Planarity : 0.004 0.041 1893 Dihedral : 19.668 146.523 3201 Min Nonbonded Distance : 1.701 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.92 % Allowed : 12.56 % Favored : 86.52 % 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: 1.14 (0.24), residues: 1246 helix: 2.29 (0.22), residues: 599 sheet: 0.11 (0.41), residues: 143 loop : -1.00 (0.26), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 30 HIS 0.003 0.001 HIS A 33 PHE 0.006 0.001 PHE A 272 TYR 0.017 0.001 TYR A1002 ARG 0.005 0.000 ARG A 362 Details of bonding type rmsd hydrogen bonds : bond 0.04475 ( 570) hydrogen bonds : angle 3.57820 ( 1561) covalent geometry : bond 0.00223 (13086) covalent geometry : angle 0.49112 (18296) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 1.121 Fit side-chains REVERT: A 322 GLU cc_start: 0.8763 (OUTLIER) cc_final: 0.8553 (mp0) REVERT: A 625 ASP cc_start: 0.8433 (t0) cc_final: 0.8195 (t0) REVERT: A 960 ARG cc_start: 0.7545 (ttp80) cc_final: 0.7179 (tmt90) REVERT: A 1020 ARG cc_start: 0.8053 (mtm110) cc_final: 0.7835 (ptp-110) REVERT: A 1038 TYR cc_start: 0.7836 (t80) cc_final: 0.7552 (t80) REVERT: A 1063 LYS cc_start: 0.7759 (mmpt) cc_final: 0.7538 (mtpp) REVERT: A 1064 MET cc_start: 0.8531 (mmp) cc_final: 0.8088 (mpm) REVERT: A 1135 GLU cc_start: 0.8673 (tp30) cc_final: 0.8440 (tp30) REVERT: A 1159 GLU cc_start: 0.8148 (tp30) cc_final: 0.7686 (pm20) outliers start: 9 outliers final: 1 residues processed: 61 average time/residue: 1.7660 time to fit residues: 116.0072 Evaluate side-chains 49 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 47 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 322 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 87 optimal weight: 9.9990 chunk 82 optimal weight: 5.9990 chunk 113 optimal weight: 0.0270 chunk 8 optimal weight: 7.9990 chunk 1 optimal weight: 2.9990 chunk 38 optimal weight: 9.9990 chunk 67 optimal weight: 3.9990 chunk 39 optimal weight: 0.5980 chunk 42 optimal weight: 6.9990 chunk 25 optimal weight: 9.9990 chunk 132 optimal weight: 10.0000 overall best weight: 2.7244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 813 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 = 0.3580 r_free = 0.3580 target = 0.108737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.074127 restraints weight = 22660.553| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 2.44 r_work: 0.2860 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.1446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 13086 Z= 0.241 Angle : 0.571 9.900 18296 Z= 0.297 Chirality : 0.039 0.364 2074 Planarity : 0.004 0.047 1893 Dihedral : 19.714 147.611 3201 Min Nonbonded Distance : 1.576 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.09 % Favored : 95.83 % Rotamer: Outliers : 0.92 % Allowed : 14.10 % Favored : 84.98 % 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: 0.92 (0.24), residues: 1246 helix: 2.17 (0.21), residues: 592 sheet: 0.05 (0.42), residues: 137 loop : -1.12 (0.25), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 30 HIS 0.005 0.001 HIS A 33 PHE 0.013 0.002 PHE A1416 TYR 0.016 0.002 TYR A1002 ARG 0.005 0.000 ARG A 977 Details of bonding type rmsd hydrogen bonds : bond 0.05679 ( 570) hydrogen bonds : angle 3.82431 ( 1561) covalent geometry : bond 0.00546 (13086) covalent geometry : angle 0.57091 (18296) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 52 time to evaluate : 1.309 Fit side-chains REVERT: A 625 ASP cc_start: 0.8542 (t0) cc_final: 0.8205 (t0) REVERT: A 960 ARG cc_start: 0.7709 (ttp80) cc_final: 0.7148 (tpp80) REVERT: A 1038 TYR cc_start: 0.7798 (t80) cc_final: 0.7511 (t80) REVERT: A 1063 LYS cc_start: 0.7805 (mmpt) cc_final: 0.7530 (mtpp) REVERT: A 1064 MET cc_start: 0.8527 (mmp) cc_final: 0.8234 (mpm) REVERT: A 1135 GLU cc_start: 0.8651 (tp30) cc_final: 0.8395 (tp30) outliers start: 9 outliers final: 4 residues processed: 61 average time/residue: 1.6400 time to fit residues: 108.5295 Evaluate side-chains 54 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 50 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 812 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 107 optimal weight: 2.9990 chunk 38 optimal weight: 10.0000 chunk 94 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 103 optimal weight: 9.9990 chunk 121 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 chunk 25 optimal weight: 10.0000 chunk 61 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 813 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 = 0.3586 r_free = 0.3586 target = 0.109517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.075056 restraints weight = 22898.924| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 2.44 r_work: 0.2882 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 13086 Z= 0.180 Angle : 0.538 10.443 18296 Z= 0.278 Chirality : 0.036 0.318 2074 Planarity : 0.004 0.040 1893 Dihedral : 19.732 147.826 3201 Min Nonbonded Distance : 1.610 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.61 % Favored : 96.31 % Rotamer: Outliers : 0.82 % Allowed : 14.50 % Favored : 84.68 % 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: 0.99 (0.24), residues: 1246 helix: 2.22 (0.22), residues: 593 sheet: 0.05 (0.41), residues: 142 loop : -1.10 (0.26), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 30 HIS 0.005 0.001 HIS A 33 PHE 0.009 0.001 PHE A 712 TYR 0.016 0.001 TYR A1002 ARG 0.006 0.000 ARG A1020 Details of bonding type rmsd hydrogen bonds : bond 0.05167 ( 570) hydrogen bonds : angle 3.70835 ( 1561) covalent geometry : bond 0.00403 (13086) covalent geometry : angle 0.53760 (18296) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 2.430 Fit side-chains REVERT: A 625 ASP cc_start: 0.8561 (t0) cc_final: 0.8217 (t0) REVERT: A 960 ARG cc_start: 0.7654 (ttp80) cc_final: 0.7083 (tpp80) REVERT: A 1038 TYR cc_start: 0.7816 (t80) cc_final: 0.7558 (t80) REVERT: A 1064 MET cc_start: 0.8437 (mmp) cc_final: 0.8166 (mpm) REVERT: A 1135 GLU cc_start: 0.8665 (tp30) cc_final: 0.8417 (tp30) REVERT: A 1159 GLU cc_start: 0.8128 (tp30) cc_final: 0.7555 (pm20) REVERT: A 1462 ARG cc_start: 0.8884 (OUTLIER) cc_final: 0.8393 (ttp-170) outliers start: 8 outliers final: 3 residues processed: 61 average time/residue: 2.7559 time to fit residues: 181.8535 Evaluate side-chains 53 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 49 time to evaluate : 1.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain A residue 1462 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 19 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 chunk 22 optimal weight: 7.9990 chunk 44 optimal weight: 0.4980 chunk 37 optimal weight: 3.9990 chunk 35 optimal weight: 6.9990 chunk 123 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 50 optimal weight: 0.4980 chunk 73 optimal weight: 3.9990 chunk 119 optimal weight: 6.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 813 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 = 0.3600 r_free = 0.3600 target = 0.110104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.075525 restraints weight = 22704.677| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 2.44 r_work: 0.2887 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 13086 Z= 0.171 Angle : 0.527 10.832 18296 Z= 0.272 Chirality : 0.036 0.301 2074 Planarity : 0.004 0.040 1893 Dihedral : 19.737 147.831 3201 Min Nonbonded Distance : 1.615 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.93 % Favored : 95.99 % Rotamer: Outliers : 1.23 % Allowed : 14.81 % Favored : 83.96 % 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: 1.03 (0.24), residues: 1246 helix: 2.26 (0.22), residues: 596 sheet: 0.05 (0.41), residues: 142 loop : -1.11 (0.26), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 30 HIS 0.005 0.001 HIS A 33 PHE 0.009 0.001 PHE A 712 TYR 0.016 0.001 TYR A1002 ARG 0.008 0.000 ARG A 946 Details of bonding type rmsd hydrogen bonds : bond 0.05010 ( 570) hydrogen bonds : angle 3.65248 ( 1561) covalent geometry : bond 0.00383 (13086) covalent geometry : angle 0.52687 (18296) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 55 time to evaluate : 1.312 Fit side-chains REVERT: A 322 GLU cc_start: 0.8796 (OUTLIER) cc_final: 0.8319 (mp0) REVERT: A 624 LEU cc_start: 0.9383 (OUTLIER) cc_final: 0.9109 (mp) REVERT: A 625 ASP cc_start: 0.8570 (t0) cc_final: 0.8202 (t0) REVERT: A 960 ARG cc_start: 0.7648 (ttp80) cc_final: 0.7074 (tpp80) REVERT: A 1038 TYR cc_start: 0.7834 (t80) cc_final: 0.7550 (t80) REVERT: A 1135 GLU cc_start: 0.8674 (tp30) cc_final: 0.8430 (tp30) REVERT: A 1391 ASP cc_start: 0.8084 (t0) cc_final: 0.7763 (OUTLIER) REVERT: A 1462 ARG cc_start: 0.8914 (OUTLIER) cc_final: 0.8404 (ttp-170) outliers start: 12 outliers final: 4 residues processed: 66 average time/residue: 1.6834 time to fit residues: 120.5983 Evaluate side-chains 57 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 51 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain A residue 1462 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 32 optimal weight: 5.9990 chunk 110 optimal weight: 9.9990 chunk 23 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 77 optimal weight: 7.9990 chunk 40 optimal weight: 3.9990 chunk 44 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 chunk 133 optimal weight: 5.9990 chunk 109 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 813 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 = 0.3587 r_free = 0.3587 target = 0.109231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.074523 restraints weight = 22863.378| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 2.45 r_work: 0.2870 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 13086 Z= 0.211 Angle : 0.570 12.205 18296 Z= 0.291 Chirality : 0.038 0.323 2074 Planarity : 0.004 0.040 1893 Dihedral : 19.761 148.345 3201 Min Nonbonded Distance : 1.580 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.01 % Favored : 95.91 % Rotamer: Outliers : 1.02 % Allowed : 15.83 % Favored : 83.15 % 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: 0.91 (0.24), residues: 1246 helix: 2.14 (0.21), residues: 595 sheet: 0.14 (0.42), residues: 133 loop : -1.15 (0.25), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 30 HIS 0.005 0.001 HIS A 33 PHE 0.011 0.001 PHE A 712 TYR 0.015 0.001 TYR A1002 ARG 0.007 0.000 ARG A1020 Details of bonding type rmsd hydrogen bonds : bond 0.05368 ( 570) hydrogen bonds : angle 3.75125 ( 1561) covalent geometry : bond 0.00476 (13086) covalent geometry : angle 0.57019 (18296) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 51 time to evaluate : 1.126 Fit side-chains REVERT: A 322 GLU cc_start: 0.8784 (OUTLIER) cc_final: 0.8323 (mp0) REVERT: A 624 LEU cc_start: 0.9387 (OUTLIER) cc_final: 0.9121 (mp) REVERT: A 625 ASP cc_start: 0.8602 (t0) cc_final: 0.8225 (t0) REVERT: A 960 ARG cc_start: 0.7683 (ttp80) cc_final: 0.7131 (tpp80) REVERT: A 1038 TYR cc_start: 0.7849 (t80) cc_final: 0.7594 (t80) REVERT: A 1084 LEU cc_start: 0.7699 (mp) cc_final: 0.7098 (pp) REVERT: A 1135 GLU cc_start: 0.8642 (tp30) cc_final: 0.8414 (tp30) REVERT: A 1391 ASP cc_start: 0.8106 (t0) cc_final: 0.7795 (OUTLIER) REVERT: A 1462 ARG cc_start: 0.8925 (OUTLIER) cc_final: 0.8397 (ttp-170) outliers start: 10 outliers final: 6 residues processed: 60 average time/residue: 1.6989 time to fit residues: 109.9039 Evaluate side-chains 58 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 50 time to evaluate : 1.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain A residue 1462 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 33 optimal weight: 6.9990 chunk 9 optimal weight: 0.5980 chunk 99 optimal weight: 5.9990 chunk 130 optimal weight: 5.9990 chunk 129 optimal weight: 4.9990 chunk 123 optimal weight: 5.9990 chunk 54 optimal weight: 0.0870 chunk 100 optimal weight: 0.6980 chunk 70 optimal weight: 7.9990 chunk 116 optimal weight: 0.9990 chunk 133 optimal weight: 4.9990 overall best weight: 1.4762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 813 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 = 0.3598 r_free = 0.3598 target = 0.110181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.075851 restraints weight = 22745.004| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 2.42 r_work: 0.2900 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13086 Z= 0.151 Angle : 0.538 13.970 18296 Z= 0.274 Chirality : 0.036 0.300 2074 Planarity : 0.004 0.038 1893 Dihedral : 19.759 148.106 3201 Min Nonbonded Distance : 1.625 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.61 % Favored : 96.31 % Rotamer: Outliers : 0.92 % Allowed : 15.83 % Favored : 83.25 % 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: 1.05 (0.24), residues: 1246 helix: 2.29 (0.22), residues: 596 sheet: 0.05 (0.41), residues: 142 loop : -1.10 (0.26), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 30 HIS 0.004 0.001 HIS A 33 PHE 0.018 0.001 PHE A1416 TYR 0.016 0.001 TYR A1002 ARG 0.007 0.000 ARG A 946 Details of bonding type rmsd hydrogen bonds : bond 0.04869 ( 570) hydrogen bonds : angle 3.64158 ( 1561) covalent geometry : bond 0.00336 (13086) covalent geometry : angle 0.53800 (18296) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 54 time to evaluate : 1.109 Fit side-chains REVERT: A 322 GLU cc_start: 0.8764 (OUTLIER) cc_final: 0.8279 (mp0) REVERT: A 624 LEU cc_start: 0.9383 (OUTLIER) cc_final: 0.9116 (mp) REVERT: A 625 ASP cc_start: 0.8596 (t0) cc_final: 0.8201 (t0) REVERT: A 960 ARG cc_start: 0.7636 (ttp80) cc_final: 0.7062 (tpp80) REVERT: A 1038 TYR cc_start: 0.7781 (t80) cc_final: 0.7484 (t80) REVERT: A 1084 LEU cc_start: 0.7670 (mp) cc_final: 0.7092 (pp) REVERT: A 1135 GLU cc_start: 0.8683 (tp30) cc_final: 0.8439 (tp30) REVERT: A 1159 GLU cc_start: 0.8074 (tp30) cc_final: 0.7610 (pm20) REVERT: A 1391 ASP cc_start: 0.8092 (t0) cc_final: 0.7762 (OUTLIER) REVERT: A 1462 ARG cc_start: 0.8894 (OUTLIER) cc_final: 0.8380 (ttp-170) outliers start: 9 outliers final: 5 residues processed: 62 average time/residue: 1.6462 time to fit residues: 110.0618 Evaluate side-chains 59 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain A residue 1462 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 57 optimal weight: 5.9990 chunk 76 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 chunk 78 optimal weight: 8.9990 chunk 60 optimal weight: 5.9990 chunk 69 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 118 optimal weight: 0.9980 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 813 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 = 0.3559 r_free = 0.3559 target = 0.107486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.073074 restraints weight = 22688.598| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 2.42 r_work: 0.2851 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.039 13086 Z= 0.294 Angle : 0.632 14.417 18296 Z= 0.323 Chirality : 0.041 0.366 2074 Planarity : 0.005 0.047 1893 Dihedral : 19.863 148.849 3201 Min Nonbonded Distance : 1.546 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.49 % Favored : 95.43 % Rotamer: Outliers : 0.92 % Allowed : 15.83 % Favored : 83.25 % 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: 0.71 (0.24), residues: 1246 helix: 1.97 (0.21), residues: 593 sheet: -0.06 (0.42), residues: 137 loop : -1.22 (0.25), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 30 HIS 0.006 0.001 HIS A 33 PHE 0.011 0.002 PHE A1292 TYR 0.014 0.002 TYR A 969 ARG 0.008 0.001 ARG A1020 Details of bonding type rmsd hydrogen bonds : bond 0.05989 ( 570) hydrogen bonds : angle 3.91242 ( 1561) covalent geometry : bond 0.00669 (13086) covalent geometry : angle 0.63199 (18296) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 1.121 Fit side-chains REVERT: A 624 LEU cc_start: 0.9395 (OUTLIER) cc_final: 0.9174 (mp) REVERT: A 625 ASP cc_start: 0.8695 (t0) cc_final: 0.8211 (t0) REVERT: A 960 ARG cc_start: 0.7666 (ttp80) cc_final: 0.7157 (tpp80) REVERT: A 1038 TYR cc_start: 0.7795 (t80) cc_final: 0.7538 (t80) REVERT: A 1084 LEU cc_start: 0.7671 (mp) cc_final: 0.6978 (pp) REVERT: A 1135 GLU cc_start: 0.8632 (tp30) cc_final: 0.8389 (tp30) REVERT: A 1153 GLU cc_start: 0.7106 (tm-30) cc_final: 0.6734 (tm-30) REVERT: A 1391 ASP cc_start: 0.8225 (t0) cc_final: 0.7889 (t70) REVERT: A 1462 ARG cc_start: 0.8910 (OUTLIER) cc_final: 0.8358 (ttp-170) outliers start: 9 outliers final: 4 residues processed: 61 average time/residue: 1.6564 time to fit residues: 108.7452 Evaluate side-chains 57 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 51 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain A residue 1462 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 4 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 24 optimal weight: 10.0000 chunk 47 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 8 optimal weight: 0.4980 chunk 31 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 84 optimal weight: 6.9990 chunk 64 optimal weight: 8.9990 chunk 52 optimal weight: 3.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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 = 0.3606 r_free = 0.3606 target = 0.110781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.076426 restraints weight = 22626.892| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 2.43 r_work: 0.2911 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13086 Z= 0.139 Angle : 0.532 14.649 18296 Z= 0.270 Chirality : 0.035 0.285 2074 Planarity : 0.004 0.040 1893 Dihedral : 19.777 148.229 3201 Min Nonbonded Distance : 1.664 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.37 % Favored : 96.55 % Rotamer: Outliers : 0.82 % Allowed : 15.93 % Favored : 83.25 % 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: 1.06 (0.24), residues: 1246 helix: 2.30 (0.22), residues: 596 sheet: 0.02 (0.41), residues: 142 loop : -1.10 (0.26), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 30 HIS 0.004 0.001 HIS A 33 PHE 0.007 0.001 PHE A 712 TYR 0.017 0.001 TYR A1002 ARG 0.008 0.000 ARG A1020 Details of bonding type rmsd hydrogen bonds : bond 0.04615 ( 570) hydrogen bonds : angle 3.60945 ( 1561) covalent geometry : bond 0.00309 (13086) covalent geometry : angle 0.53188 (18296) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7404.90 seconds wall clock time: 134 minutes 18.84 seconds (8058.84 seconds total)