Starting phenix.real_space_refine on Wed Jul 30 06:05:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6o0y_0584/07_2025/6o0y_0584.cif Found real_map, /net/cci-nas-00/data/ceres_data/6o0y_0584/07_2025/6o0y_0584.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6o0y_0584/07_2025/6o0y_0584.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6o0y_0584/07_2025/6o0y_0584.map" model { file = "/net/cci-nas-00/data/ceres_data/6o0y_0584/07_2025/6o0y_0584.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6o0y_0584/07_2025/6o0y_0584.cif" } resolution = 3.37 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= -0.001 sd= 0.044 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 149 5.49 5 S 15 5.16 5 C 7059 2.51 5 N 2092 2.21 5 O 2513 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 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: 11828 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 8669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1146, 8669 Classifications: {'peptide': 1146} Incomplete info: {'truncation_to_alanine': 158} Link IDs: {'PTRANS': 29, 'TRANS': 1116} Chain breaks: 4 Unresolved non-hydrogen bonds: 761 Unresolved non-hydrogen angles: 916 Unresolved non-hydrogen dihedrals: 609 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 10, 'TYR:plan': 1, 'ASN:plan1': 9, 'ASP:plan': 37, 'GLU:plan': 63, 'ARG:plan': 19} Unresolved non-hydrogen planarities: 490 Chain: "B" Number of atoms: 2104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 2104 Classifications: {'RNA': 98} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p_pur': 53, 'rna3p_pyr': 34} Link IDs: {'rna2p': 11, 'rna3p': 86} Chain: "C" Number of atoms: 261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 261 Classifications: {'DNA': 13} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 12} Chain: "D" Number of atoms: 331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 331 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain breaks: 1 Chain: "c" Number of atoms: 463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 463 Classifications: {'DNA': 23} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 22} Time building chain proxies: 8.63, per 1000 atoms: 0.73 Number of scatterers: 11828 At special positions: 0 Unit cell: (137.104, 126.236, 88.616, 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 15 16.00 P 149 15.00 O 2513 8.00 N 2092 7.00 C 7059 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: 3.33 Conformation dependent library (CDL) restraints added in 1.3 seconds 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2182 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 7 sheets defined 51.7% alpha, 7.6% beta 52 base pairs and 95 stacking pairs defined. Time for finding SS restraints: 4.48 Creating SS restraints... Processing helix chain 'A' and resid 59 through 92 removed outlier: 3.720A pdb=" N ARG A 70 " --> pdb=" O ARG A 66 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ARG A 71 " --> pdb=" O THR A 67 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N TYR A 72 " --> pdb=" O ALA A 68 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N THR A 73 " --> pdb=" O ARG A 69 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N ASN A 88 " --> pdb=" O GLU A 84 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N GLU A 89 " --> pdb=" O ILE A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 103 Processing helix chain 'A' and resid 121 through 132 removed outlier: 4.005A pdb=" N GLU A 125 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 145 Processing helix chain 'A' and resid 150 through 164 removed outlier: 3.590A pdb=" N PHE A 164 " --> pdb=" O HIS A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 343 Processing helix chain 'A' and resid 346 through 352 removed outlier: 3.737A pdb=" N ILE A 350 " --> pdb=" O LYS A 346 " (cutoff:3.500A) 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: 3.600A pdb=" N MET A 383 " --> pdb=" O ILE A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 394 Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.756A pdb=" N ASN A 407 " --> pdb=" O THR A 404 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLY A 408 " --> pdb=" O PHE A 405 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N SER A 409 " --> pdb=" O ASP A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 427 removed outlier: 4.411A pdb=" N HIS A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 436 removed outlier: 3.943A pdb=" N LYS A 434 " --> pdb=" O TYR A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 446 removed outlier: 3.527A pdb=" N ILE A 440 " --> pdb=" O ASN A 436 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU A 444 " --> pdb=" O ILE A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 494 removed outlier: 3.779A pdb=" N ILE A 492 " --> pdb=" O ALA A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 525 Processing helix chain 'A' and resid 541 through 552 Processing helix chain 'A' and resid 560 through 567 Processing helix chain 'A' and resid 591 through 602 Processing helix chain 'A' and resid 604 through 609 Processing helix chain 'A' and resid 612 through 626 Processing helix chain 'A' and resid 631 through 637 Processing helix chain 'A' and resid 638 through 640 No H-bonds generated for 'chain 'A' and resid 638 through 640' Processing helix chain 'A' and resid 644 through 652 removed outlier: 3.559A pdb=" N LYS A 652 " --> pdb=" O MET A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 668 removed outlier: 3.520A pdb=" N ILE A 667 " --> pdb=" O SER A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 685 Processing helix chain 'A' and resid 692 through 698 Processing helix chain 'A' and resid 704 through 712 Processing helix chain 'A' and resid 719 through 726 Processing helix chain 'A' and resid 730 through 751 removed outlier: 3.530A pdb=" N LYS A 734 " --> pdb=" O SER A 730 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 776 Processing helix chain 'A' and resid 779 through 791 removed outlier: 4.053A pdb=" N ARG A 783 " --> pdb=" O GLU A 779 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU A 785 " --> pdb=" O MET A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 794 through 798 removed outlier: 3.983A pdb=" N GLU A 798 " --> pdb=" O ILE A 795 " (cutoff:3.500A) Processing helix chain 'A' and resid 808 through 817 removed outlier: 3.755A pdb=" N LEU A 813 " --> pdb=" O GLU A 809 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N TYR A 814 " --> pdb=" O LYS A 810 " (cutoff:3.500A) Processing helix chain 'A' and resid 859 through 866 removed outlier: 3.649A pdb=" N ASN A 863 " --> pdb=" O ARG A 859 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LYS A 866 " --> pdb=" O LYS A 862 " (cutoff:3.500A) Processing helix chain 'A' and resid 872 through 889 removed outlier: 6.169A pdb=" N ASN A 881 " --> pdb=" O LYS A 877 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N TYR A 882 " --> pdb=" O LYS A 878 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASN A 888 " --> pdb=" O ARG A 884 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ALA A 889 " --> pdb=" O GLN A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 893 through 901 Processing helix chain 'A' and resid 902 through 905 Processing helix chain 'A' and resid 917 through 940 removed outlier: 4.035A pdb=" N LEU A 921 " --> pdb=" O ILE A 917 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG A 925 " --> pdb=" O LEU A 921 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASN A 940 " --> pdb=" O ASP A 936 " (cutoff:3.500A) Processing helix chain 'A' and resid 960 through 970 removed outlier: 3.647A pdb=" N PHE A 970 " --> pdb=" O PHE A 966 " (cutoff:3.500A) Processing helix chain 'A' and resid 981 through 1000 Processing helix chain 'A' and resid 1080 through 1087 Processing helix chain 'A' and resid 1127 through 1132 Processing helix chain 'A' and resid 1170 through 1177 removed outlier: 4.102A pdb=" N ASN A1177 " --> pdb=" O SER A1173 " (cutoff:3.500A) Processing helix chain 'A' and resid 1177 through 1185 removed outlier: 3.632A pdb=" N PHE A1181 " --> pdb=" O ASN A1177 " (cutoff:3.500A) Processing helix chain 'A' and resid 1191 through 1195 removed outlier: 3.836A pdb=" N ILE A1195 " --> pdb=" O LYS A1192 " (cutoff:3.500A) 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 1240 removed outlier: 3.508A pdb=" N VAL A1233 " --> pdb=" O PRO A1229 " (cutoff:3.500A) Processing helix chain 'A' and resid 1252 through 1261 Processing helix chain 'A' and resid 1263 through 1278 removed outlier: 3.825A pdb=" N ASP A1267 " --> pdb=" O LYS A1263 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N PHE A1276 " --> pdb=" O GLN A1272 " (cutoff:3.500A) Processing helix chain 'A' and resid 1283 through 1296 Processing helix chain 'A' and resid 1301 through 1313 removed outlier: 3.808A pdb=" N HIS A1311 " --> pdb=" O GLU A1307 " (cutoff:3.500A) Processing helix chain 'A' and resid 1314 through 1317 removed outlier: 4.072A pdb=" N ASN A1317 " --> pdb=" O THR A1314 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1314 through 1317' Processing helix chain 'A' and resid 1341 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 959 removed outlier: 4.459A pdb=" N GLU A 762 " --> pdb=" O LEU A 9 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N ILE A 11 " --> pdb=" O GLU A 762 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL A1095 " --> pdb=" O ALA A 50 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 29 through 33 Processing sheet with id=AA3, first strand: chain 'A' and resid 35 through 36 removed outlier: 6.827A pdb=" N LEU A 35 " --> pdb=" O ARG A1359 " (cutoff:3.500A) removed outlier: 8.218A pdb=" N ASP A1361 " --> pdb=" O LEU A 35 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N LEU A1203 " --> pdb=" O ILE A1348 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 528 through 530 removed outlier: 3.694A pdb=" N LYS A 528 " --> pdb=" O SER A 581 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 837 through 840 Processing sheet with id=AA6, first strand: chain 'A' and resid 1157 through 1167 removed outlier: 3.545A pdb=" N TYR A1141 " --> pdb=" O ILE A1166 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ILE A1196 " --> pdb=" O LEU A1144 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1324 through 1325 392 hydrogen bonds defined for protein. 1143 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 130 hydrogen bonds 252 hydrogen bond angles 0 basepair planarities 52 basepair parallelities 95 stacking parallelities Total time for adding SS restraints: 7.40 Time building geometry restraints manager: 3.76 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: 1912 1.33 - 1.44: 3845 1.44 - 1.56: 6290 1.56 - 1.68: 294 1.68 - 1.80: 28 Bond restraints: 12369 Sorted by residual: bond pdb=" C3' DC C 1 " pdb=" O3' DC C 1 " ideal model delta sigma weight residual 1.422 1.463 -0.041 3.00e-02 1.11e+03 1.87e+00 bond pdb=" C3' A B 38 " pdb=" O3' A B 38 " ideal model delta sigma weight residual 1.417 1.436 -0.019 1.50e-02 4.44e+03 1.67e+00 bond pdb=" C3' A B 8 " pdb=" O3' A B 8 " ideal model delta sigma weight residual 1.417 1.436 -0.019 1.50e-02 4.44e+03 1.64e+00 bond pdb=" O5' DT c 21 " pdb=" C5' DT c 21 " ideal model delta sigma weight residual 1.423 1.385 0.038 3.00e-02 1.11e+03 1.62e+00 bond pdb=" CB ILE A 733 " pdb=" CG2 ILE A 733 " ideal model delta sigma weight residual 1.521 1.479 0.042 3.30e-02 9.18e+02 1.58e+00 ... (remaining 12364 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 17050 2.10 - 4.19: 337 4.19 - 6.29: 39 6.29 - 8.38: 13 8.38 - 10.48: 1 Bond angle restraints: 17440 Sorted by residual: angle pdb=" O3' A B 42 " pdb=" C3' A B 42 " pdb=" C2' A B 42 " ideal model delta sigma weight residual 113.70 119.97 -6.27 1.50e+00 4.44e-01 1.75e+01 angle pdb=" C3' A B 8 " pdb=" O3' A B 8 " pdb=" P A B 9 " ideal model delta sigma weight residual 120.20 126.00 -5.80 1.50e+00 4.44e-01 1.49e+01 angle pdb=" C3' A B 38 " pdb=" O3' A B 38 " pdb=" P G B 39 " ideal model delta sigma weight residual 120.20 125.78 -5.58 1.50e+00 4.44e-01 1.39e+01 angle pdb=" O3' A B 38 " pdb=" C3' A B 38 " pdb=" C2' A B 38 " ideal model delta sigma weight residual 113.70 119.06 -5.36 1.50e+00 4.44e-01 1.27e+01 angle pdb=" C3' A B 42 " pdb=" O3' A B 42 " pdb=" P G B 43 " ideal model delta sigma weight residual 120.20 125.54 -5.34 1.50e+00 4.44e-01 1.27e+01 ... (remaining 17435 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.17: 6817 31.17 - 62.34: 437 62.34 - 93.51: 82 93.51 - 124.68: 0 124.68 - 155.86: 5 Dihedral angle restraints: 7341 sinusoidal: 3972 harmonic: 3369 Sorted by residual: dihedral pdb=" O4' C B 70 " pdb=" C1' C B 70 " pdb=" N1 C B 70 " pdb=" C2 C B 70 " ideal model delta sinusoidal sigma weight residual 200.00 57.44 142.56 1 1.50e+01 4.44e-03 7.65e+01 dihedral pdb=" O4' U B 97 " pdb=" C1' U B 97 " pdb=" N1 U B 97 " pdb=" C2 U B 97 " ideal model delta sinusoidal sigma weight residual -160.00 -73.39 -86.61 1 1.50e+01 4.44e-03 4.01e+01 dihedral pdb=" CA ASN A 612 " pdb=" C ASN A 612 " pdb=" N GLU A 613 " pdb=" CA GLU A 613 " ideal model delta harmonic sigma weight residual -180.00 -155.40 -24.60 0 5.00e+00 4.00e-02 2.42e+01 ... (remaining 7338 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 1810 0.067 - 0.133: 246 0.133 - 0.200: 28 0.200 - 0.266: 4 0.266 - 0.333: 3 Chirality restraints: 2091 Sorted by residual: chirality pdb=" C3' A B 42 " pdb=" C4' A B 42 " pdb=" O3' A B 42 " pdb=" C2' A B 42 " both_signs ideal model delta sigma weight residual False -2.48 -2.14 -0.33 2.00e-01 2.50e+01 2.77e+00 chirality pdb=" C3' A B 8 " pdb=" C4' A B 8 " pdb=" O3' A B 8 " pdb=" C2' A B 8 " both_signs ideal model delta sigma weight residual False -2.48 -2.17 -0.31 2.00e-01 2.50e+01 2.43e+00 chirality pdb=" C3' A B 38 " pdb=" C4' A B 38 " pdb=" O3' A B 38 " pdb=" C2' A B 38 " both_signs ideal model delta sigma weight residual False -2.48 -2.17 -0.31 2.00e-01 2.50e+01 2.42e+00 ... (remaining 2088 not shown) Planarity restraints: 1656 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 622 " -0.015 2.00e-02 2.50e+03 3.06e-02 9.35e+00 pdb=" C THR A 622 " 0.053 2.00e-02 2.50e+03 pdb=" O THR A 622 " -0.020 2.00e-02 2.50e+03 pdb=" N LEU A 623 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 617 " 0.015 2.00e-02 2.50e+03 2.96e-02 8.74e+00 pdb=" C GLU A 617 " -0.051 2.00e-02 2.50e+03 pdb=" O GLU A 617 " 0.019 2.00e-02 2.50e+03 pdb=" N ASP A 618 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 619 " -0.015 2.00e-02 2.50e+03 2.90e-02 8.43e+00 pdb=" C ILE A 619 " 0.050 2.00e-02 2.50e+03 pdb=" O ILE A 619 " -0.019 2.00e-02 2.50e+03 pdb=" N VAL A 620 " -0.017 2.00e-02 2.50e+03 ... (remaining 1653 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 3093 2.80 - 3.32: 9597 3.32 - 3.85: 20409 3.85 - 4.37: 22751 4.37 - 4.90: 35911 Nonbonded interactions: 91761 Sorted by model distance: nonbonded pdb=" O2 DC C 1 " pdb=" N2 DG D 40 " model vdw 2.272 2.496 nonbonded pdb=" O TYR A 521 " pdb=" OG1 THR A 525 " model vdw 2.306 3.040 nonbonded pdb=" OG SER A 512 " pdb=" OE2 GLU A 617 " model vdw 2.317 3.040 nonbonded pdb=" O TYR A 25 " pdb=" OH TYR A 988 " model vdw 2.330 3.040 nonbonded pdb=" OH TYR A 373 " pdb=" O LEU A 398 " model vdw 2.352 3.040 ... (remaining 91756 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=0.49 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: 1.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.570 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 38.020 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.050 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 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 0.047 12369 Z= 0.257 Angle : 0.737 10.478 17440 Z= 0.406 Chirality : 0.048 0.333 2091 Planarity : 0.005 0.055 1656 Dihedral : 19.216 155.856 5159 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 0.37 % Allowed : 6.94 % Favored : 92.69 % 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: -4.11 (0.19), residues: 1136 helix: -2.75 (0.15), residues: 537 sheet: -1.14 (0.48), residues: 117 loop : -3.01 (0.22), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 476 HIS 0.007 0.001 HIS A 328 PHE 0.015 0.001 PHE A1327 TYR 0.014 0.002 TYR A 155 ARG 0.002 0.000 ARG A 71 Details of bonding type rmsd hydrogen bonds : bond 0.15367 ( 522) hydrogen bonds : angle 6.25252 ( 1395) covalent geometry : bond 0.00542 (12369) covalent geometry : angle 0.73667 (17440) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 72 time to evaluate : 1.251 Fit side-chains REVERT: A 465 MET cc_start: 0.8497 (tmm) cc_final: 0.8126 (tmm) REVERT: A 733 ILE cc_start: 0.8269 (pt) cc_final: 0.8044 (mm) REVERT: A 746 GLU cc_start: 0.8814 (tm-30) cc_final: 0.8535 (tm-30) outliers start: 3 outliers final: 2 residues processed: 75 average time/residue: 0.2697 time to fit residues: 29.6791 Evaluate side-chains 52 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 50 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 1190 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 107 optimal weight: 0.9990 chunk 96 optimal weight: 8.9990 chunk 53 optimal weight: 9.9990 chunk 32 optimal weight: 7.9990 chunk 64 optimal weight: 10.0000 chunk 51 optimal weight: 7.9990 chunk 99 optimal weight: 7.9990 chunk 38 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 chunk 74 optimal weight: 6.9990 chunk 115 optimal weight: 6.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN A 41 HIS A 113 HIS A 402 GLN A 899 ASN A1177 ASN A1252 ASN A1295 ASN A1308 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.075446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.054646 restraints weight = 39399.190| |-----------------------------------------------------------------------------| r_work (start): 0.2798 rms_B_bonded: 2.96 r_work: 0.2666 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2665 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2665 r_free = 0.2665 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2665 r_free = 0.2665 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2665 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.1020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 12369 Z= 0.264 Angle : 0.588 6.396 17440 Z= 0.322 Chirality : 0.040 0.228 2091 Planarity : 0.004 0.043 1656 Dihedral : 20.108 162.418 3268 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 1.49 % Allowed : 11.40 % Favored : 87.11 % 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: -2.27 (0.22), residues: 1136 helix: -0.80 (0.20), residues: 560 sheet: -0.61 (0.51), residues: 99 loop : -2.54 (0.25), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 476 HIS 0.003 0.001 HIS A 160 PHE 0.014 0.001 PHE A1327 TYR 0.023 0.001 TYR A 594 ARG 0.003 0.000 ARG A1333 Details of bonding type rmsd hydrogen bonds : bond 0.05666 ( 522) hydrogen bonds : angle 4.37144 ( 1395) covalent geometry : bond 0.00566 (12369) covalent geometry : angle 0.58810 (17440) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 51 time to evaluate : 1.282 Fit side-chains REVERT: A 733 ILE cc_start: 0.8262 (pt) cc_final: 0.7978 (mm) REVERT: A 746 GLU cc_start: 0.9200 (tm-30) cc_final: 0.8755 (tm-30) outliers start: 12 outliers final: 10 residues processed: 60 average time/residue: 0.2520 time to fit residues: 24.0324 Evaluate side-chains 55 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 45 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 927 ILE Chi-restraints excluded: chain A residue 995 THR Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1313 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 79 optimal weight: 5.9990 chunk 30 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 86 optimal weight: 6.9990 chunk 42 optimal weight: 5.9990 chunk 102 optimal weight: 20.0000 chunk 118 optimal weight: 7.9990 chunk 87 optimal weight: 0.7980 chunk 109 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 107 optimal weight: 9.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 817 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.077498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.056737 restraints weight = 39257.534| |-----------------------------------------------------------------------------| r_work (start): 0.2850 rms_B_bonded: 2.99 r_work: 0.2718 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12369 Z= 0.137 Angle : 0.486 7.500 17440 Z= 0.268 Chirality : 0.037 0.218 2091 Planarity : 0.003 0.031 1656 Dihedral : 19.894 156.917 3268 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.73 % Allowed : 12.02 % Favored : 86.25 % 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: -1.31 (0.24), residues: 1136 helix: 0.18 (0.22), residues: 560 sheet: -0.71 (0.48), residues: 115 loop : -2.23 (0.26), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 476 HIS 0.003 0.001 HIS A 328 PHE 0.009 0.001 PHE A 432 TYR 0.017 0.001 TYR A 594 ARG 0.002 0.000 ARG A1333 Details of bonding type rmsd hydrogen bonds : bond 0.04374 ( 522) hydrogen bonds : angle 3.81542 ( 1395) covalent geometry : bond 0.00289 (12369) covalent geometry : angle 0.48615 (17440) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 1.067 Fit side-chains REVERT: A 733 ILE cc_start: 0.8256 (pt) cc_final: 0.7979 (mm) REVERT: A 746 GLU cc_start: 0.9158 (tm-30) cc_final: 0.8666 (tm-30) outliers start: 14 outliers final: 10 residues processed: 69 average time/residue: 0.1993 time to fit residues: 21.9837 Evaluate side-chains 61 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 51 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 525 THR Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 943 TYR Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1313 PHE Chi-restraints excluded: chain A residue 1337 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 110 optimal weight: 10.0000 chunk 121 optimal weight: 10.0000 chunk 29 optimal weight: 0.8980 chunk 25 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 chunk 93 optimal weight: 8.9990 chunk 118 optimal weight: 7.9990 chunk 120 optimal weight: 8.9990 chunk 34 optimal weight: 7.9990 chunk 84 optimal weight: 4.9990 chunk 99 optimal weight: 9.9990 overall best weight: 3.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 721 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.076129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.055316 restraints weight = 39175.423| |-----------------------------------------------------------------------------| r_work (start): 0.2817 rms_B_bonded: 2.97 r_work: 0.2685 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12369 Z= 0.205 Angle : 0.532 7.580 17440 Z= 0.288 Chirality : 0.038 0.220 2091 Planarity : 0.003 0.031 1656 Dihedral : 19.923 159.047 3268 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 2.11 % Allowed : 13.01 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.24), residues: 1136 helix: 0.56 (0.22), residues: 563 sheet: -0.50 (0.49), residues: 105 loop : -2.17 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 476 HIS 0.003 0.001 HIS A 160 PHE 0.017 0.001 PHE A1258 TYR 0.013 0.001 TYR A 594 ARG 0.001 0.000 ARG A1333 Details of bonding type rmsd hydrogen bonds : bond 0.04851 ( 522) hydrogen bonds : angle 3.84214 ( 1395) covalent geometry : bond 0.00441 (12369) covalent geometry : angle 0.53157 (17440) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 51 time to evaluate : 1.298 Fit side-chains REVERT: A 733 ILE cc_start: 0.8241 (pt) cc_final: 0.7931 (mm) REVERT: A 746 GLU cc_start: 0.9191 (tm-30) cc_final: 0.8685 (tm-30) outliers start: 17 outliers final: 13 residues processed: 64 average time/residue: 0.2765 time to fit residues: 28.9127 Evaluate side-chains 63 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 50 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 525 THR Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 927 ILE Chi-restraints excluded: chain A residue 943 TYR Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1179 ILE Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1313 PHE Chi-restraints excluded: chain A residue 1337 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 8 optimal weight: 3.9990 chunk 21 optimal weight: 0.0470 chunk 124 optimal weight: 8.9990 chunk 22 optimal weight: 6.9990 chunk 14 optimal weight: 4.9990 chunk 114 optimal weight: 10.0000 chunk 55 optimal weight: 6.9990 chunk 67 optimal weight: 9.9990 chunk 4 optimal weight: 7.9990 chunk 7 optimal weight: 2.9990 chunk 66 optimal weight: 10.0000 overall best weight: 3.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 721 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.075402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.054602 restraints weight = 39358.342| |-----------------------------------------------------------------------------| r_work (start): 0.2799 rms_B_bonded: 2.93 r_work: 0.2668 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 12369 Z= 0.248 Angle : 0.564 8.223 17440 Z= 0.303 Chirality : 0.040 0.224 2091 Planarity : 0.003 0.033 1656 Dihedral : 19.967 159.947 3268 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 2.48 % Allowed : 14.50 % Favored : 83.02 % 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: -0.79 (0.25), residues: 1136 helix: 0.69 (0.22), residues: 563 sheet: -0.33 (0.50), residues: 99 loop : -2.11 (0.26), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 476 HIS 0.003 0.001 HIS A 328 PHE 0.012 0.001 PHE A1327 TYR 0.011 0.001 TYR A 155 ARG 0.002 0.000 ARG A1333 Details of bonding type rmsd hydrogen bonds : bond 0.05187 ( 522) hydrogen bonds : angle 3.91174 ( 1395) covalent geometry : bond 0.00536 (12369) covalent geometry : angle 0.56393 (17440) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 48 time to evaluate : 2.201 Fit side-chains REVERT: A 733 ILE cc_start: 0.8305 (pt) cc_final: 0.7982 (mm) REVERT: A 746 GLU cc_start: 0.9232 (tm-30) cc_final: 0.8729 (tm-30) outliers start: 20 outliers final: 17 residues processed: 64 average time/residue: 0.2796 time to fit residues: 28.9274 Evaluate side-chains 65 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 48 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 525 THR Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 927 ILE Chi-restraints excluded: chain A residue 943 TYR Chi-restraints excluded: chain A residue 995 THR Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1164 LEU Chi-restraints excluded: chain A residue 1179 ILE Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1313 PHE Chi-restraints excluded: chain A residue 1330 THR Chi-restraints excluded: chain A residue 1337 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 79 optimal weight: 10.0000 chunk 9 optimal weight: 0.8980 chunk 97 optimal weight: 4.9990 chunk 90 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 69 optimal weight: 20.0000 chunk 115 optimal weight: 6.9990 chunk 109 optimal weight: 0.9990 chunk 18 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 chunk 84 optimal weight: 0.8980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 721 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.077897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.057168 restraints weight = 39362.945| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 2.98 r_work: 0.2725 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12369 Z= 0.120 Angle : 0.478 8.499 17440 Z= 0.260 Chirality : 0.036 0.211 2091 Planarity : 0.003 0.028 1656 Dihedral : 19.805 156.351 3268 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.48 % Allowed : 15.12 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.25), residues: 1136 helix: 1.02 (0.23), residues: 563 sheet: -0.49 (0.48), residues: 115 loop : -1.89 (0.27), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 476 HIS 0.003 0.000 HIS A 160 PHE 0.014 0.001 PHE A1258 TYR 0.012 0.001 TYR A 594 ARG 0.001 0.000 ARG A1333 Details of bonding type rmsd hydrogen bonds : bond 0.04097 ( 522) hydrogen bonds : angle 3.60819 ( 1395) covalent geometry : bond 0.00252 (12369) covalent geometry : angle 0.47813 (17440) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 55 time to evaluate : 1.247 Fit side-chains REVERT: A 733 ILE cc_start: 0.8225 (pt) cc_final: 0.7922 (mm) REVERT: A 746 GLU cc_start: 0.9247 (tm-30) cc_final: 0.8689 (tm-30) REVERT: A 1266 LEU cc_start: 0.8812 (tt) cc_final: 0.8596 (mp) outliers start: 20 outliers final: 14 residues processed: 72 average time/residue: 0.2036 time to fit residues: 23.4068 Evaluate side-chains 66 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 52 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 525 THR Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain A residue 927 ILE Chi-restraints excluded: chain A residue 943 TYR Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1160 VAL Chi-restraints excluded: chain A residue 1164 LEU Chi-restraints excluded: chain A residue 1179 ILE Chi-restraints excluded: chain A residue 1313 PHE Chi-restraints excluded: chain A residue 1337 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 106 optimal weight: 6.9990 chunk 125 optimal weight: 5.9990 chunk 94 optimal weight: 2.9990 chunk 61 optimal weight: 7.9990 chunk 20 optimal weight: 5.9990 chunk 122 optimal weight: 10.0000 chunk 71 optimal weight: 9.9990 chunk 54 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 48 optimal weight: 0.4980 chunk 40 optimal weight: 5.9990 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 721 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.076441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.055608 restraints weight = 39631.030| |-----------------------------------------------------------------------------| r_work (start): 0.2821 rms_B_bonded: 2.96 r_work: 0.2689 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 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 0.038 12369 Z= 0.197 Angle : 0.542 13.859 17440 Z= 0.287 Chirality : 0.038 0.216 2091 Planarity : 0.003 0.031 1656 Dihedral : 19.863 158.693 3267 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 2.35 % Allowed : 15.99 % Favored : 81.66 % 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: -0.40 (0.25), residues: 1136 helix: 0.99 (0.23), residues: 563 sheet: -0.28 (0.49), residues: 105 loop : -1.87 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 476 HIS 0.003 0.001 HIS A 160 PHE 0.011 0.001 PHE A 432 TYR 0.022 0.001 TYR A 988 ARG 0.001 0.000 ARG A 71 Details of bonding type rmsd hydrogen bonds : bond 0.04683 ( 522) hydrogen bonds : angle 3.77839 ( 1395) covalent geometry : bond 0.00425 (12369) covalent geometry : angle 0.54191 (17440) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 50 time to evaluate : 1.216 Fit side-chains REVERT: A 733 ILE cc_start: 0.8255 (pt) cc_final: 0.7936 (mm) REVERT: A 746 GLU cc_start: 0.9243 (tm-30) cc_final: 0.8682 (tm-30) outliers start: 19 outliers final: 15 residues processed: 65 average time/residue: 0.2723 time to fit residues: 28.2435 Evaluate side-chains 65 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 50 time to evaluate : 1.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 525 THR Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 927 ILE Chi-restraints excluded: chain A residue 943 TYR Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1160 VAL Chi-restraints excluded: chain A residue 1164 LEU Chi-restraints excluded: chain A residue 1179 ILE Chi-restraints excluded: chain A residue 1270 ILE Chi-restraints excluded: chain A residue 1313 PHE Chi-restraints excluded: chain A residue 1337 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 30 optimal weight: 3.9990 chunk 81 optimal weight: 8.9990 chunk 119 optimal weight: 6.9990 chunk 73 optimal weight: 9.9990 chunk 94 optimal weight: 1.9990 chunk 110 optimal weight: 10.0000 chunk 125 optimal weight: 4.9990 chunk 115 optimal weight: 6.9990 chunk 121 optimal weight: 10.0000 chunk 13 optimal weight: 0.9990 chunk 69 optimal weight: 20.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 721 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.075665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.054823 restraints weight = 39656.967| |-----------------------------------------------------------------------------| r_work (start): 0.2804 rms_B_bonded: 2.96 r_work: 0.2673 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 12369 Z= 0.245 Angle : 0.574 13.136 17440 Z= 0.305 Chirality : 0.040 0.221 2091 Planarity : 0.003 0.033 1656 Dihedral : 19.922 159.737 3267 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 2.60 % Allowed : 15.61 % Favored : 81.78 % 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: -0.47 (0.25), residues: 1136 helix: 0.92 (0.23), residues: 563 sheet: -0.26 (0.49), residues: 105 loop : -1.89 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 476 HIS 0.003 0.001 HIS A 160 PHE 0.012 0.001 PHE A1327 TYR 0.019 0.001 TYR A 988 ARG 0.002 0.000 ARG A 967 Details of bonding type rmsd hydrogen bonds : bond 0.05101 ( 522) hydrogen bonds : angle 3.89318 ( 1395) covalent geometry : bond 0.00530 (12369) covalent geometry : angle 0.57390 (17440) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 48 time to evaluate : 1.246 Fit side-chains REVERT: A 733 ILE cc_start: 0.8301 (pt) cc_final: 0.7955 (mm) REVERT: A 746 GLU cc_start: 0.9268 (tm-30) cc_final: 0.8744 (tm-30) outliers start: 21 outliers final: 18 residues processed: 65 average time/residue: 0.2003 time to fit residues: 21.0335 Evaluate side-chains 65 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 47 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 525 THR Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 622 THR Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 927 ILE Chi-restraints excluded: chain A residue 943 TYR Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1102 THR Chi-restraints excluded: chain A residue 1160 VAL Chi-restraints excluded: chain A residue 1164 LEU Chi-restraints excluded: chain A residue 1179 ILE Chi-restraints excluded: chain A residue 1270 ILE Chi-restraints excluded: chain A residue 1313 PHE Chi-restraints excluded: chain A residue 1330 THR Chi-restraints excluded: chain A residue 1337 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 11 optimal weight: 0.0060 chunk 118 optimal weight: 7.9990 chunk 106 optimal weight: 2.9990 chunk 62 optimal weight: 30.0000 chunk 95 optimal weight: 1.9990 chunk 47 optimal weight: 7.9990 chunk 102 optimal weight: 0.0170 chunk 91 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 chunk 122 optimal weight: 10.0000 chunk 52 optimal weight: 0.9980 overall best weight: 0.6038 ------------------------------------------------------------------------------- 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 = 0.3376 r_free = 0.3376 target = 0.079270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.058308 restraints weight = 38728.189| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 3.04 r_work: 0.2742 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 12369 Z= 0.099 Angle : 0.493 12.544 17440 Z= 0.260 Chirality : 0.036 0.203 2091 Planarity : 0.003 0.027 1656 Dihedral : 19.708 154.179 3267 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.98 % Allowed : 16.48 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.25), residues: 1136 helix: 1.21 (0.23), residues: 561 sheet: -0.19 (0.49), residues: 115 loop : -1.74 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 18 HIS 0.003 0.001 HIS A 983 PHE 0.009 0.001 PHE A 432 TYR 0.018 0.001 TYR A 988 ARG 0.001 0.000 ARG A 661 Details of bonding type rmsd hydrogen bonds : bond 0.03745 ( 522) hydrogen bonds : angle 3.60303 ( 1395) covalent geometry : bond 0.00201 (12369) covalent geometry : angle 0.49265 (17440) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 53 time to evaluate : 1.218 Fit side-chains REVERT: A 746 GLU cc_start: 0.9246 (tm-30) cc_final: 0.8669 (tm-30) outliers start: 16 outliers final: 14 residues processed: 66 average time/residue: 0.2016 time to fit residues: 21.6221 Evaluate side-chains 64 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 50 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 525 THR Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 943 TYR Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1102 THR Chi-restraints excluded: chain A residue 1160 VAL Chi-restraints excluded: chain A residue 1164 LEU Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1313 PHE Chi-restraints excluded: chain A residue 1337 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 75 optimal weight: 10.0000 chunk 55 optimal weight: 1.9990 chunk 119 optimal weight: 7.9990 chunk 91 optimal weight: 6.9990 chunk 45 optimal weight: 5.9990 chunk 17 optimal weight: 7.9990 chunk 116 optimal weight: 7.9990 chunk 32 optimal weight: 5.9990 chunk 52 optimal weight: 0.9980 chunk 11 optimal weight: 0.0570 chunk 84 optimal weight: 0.9980 overall best weight: 2.0102 ------------------------------------------------------------------------------- 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 = 0.3341 r_free = 0.3341 target = 0.077499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.056524 restraints weight = 38805.456| |-----------------------------------------------------------------------------| r_work (start): 0.2835 rms_B_bonded: 3.01 r_work: 0.2699 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12369 Z= 0.149 Angle : 0.508 12.468 17440 Z= 0.270 Chirality : 0.037 0.208 2091 Planarity : 0.003 0.030 1656 Dihedral : 19.766 157.531 3267 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.73 % Allowed : 16.98 % Favored : 81.29 % 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: -0.06 (0.26), residues: 1136 helix: 1.26 (0.23), residues: 563 sheet: -0.06 (0.49), residues: 114 loop : -1.73 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 476 HIS 0.003 0.001 HIS A1264 PHE 0.013 0.001 PHE A1258 TYR 0.017 0.001 TYR A 988 ARG 0.001 0.000 ARG A 71 Details of bonding type rmsd hydrogen bonds : bond 0.04244 ( 522) hydrogen bonds : angle 3.63964 ( 1395) covalent geometry : bond 0.00319 (12369) covalent geometry : angle 0.50774 (17440) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 51 time to evaluate : 1.249 Fit side-chains REVERT: A 746 GLU cc_start: 0.9248 (tm-30) cc_final: 0.8687 (tm-30) outliers start: 14 outliers final: 13 residues processed: 62 average time/residue: 0.2311 time to fit residues: 22.8736 Evaluate side-chains 64 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 51 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 525 THR Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 943 TYR Chi-restraints excluded: chain A residue 1102 THR Chi-restraints excluded: chain A residue 1160 VAL Chi-restraints excluded: chain A residue 1164 LEU Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1313 PHE Chi-restraints excluded: chain A residue 1337 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 44 optimal weight: 10.0000 chunk 103 optimal weight: 10.0000 chunk 47 optimal weight: 6.9990 chunk 112 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 105 optimal weight: 0.9980 chunk 116 optimal weight: 7.9990 chunk 117 optimal weight: 10.0000 chunk 10 optimal weight: 0.7980 chunk 63 optimal weight: 6.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- 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 = 0.3346 r_free = 0.3346 target = 0.077802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.056800 restraints weight = 38829.205| |-----------------------------------------------------------------------------| r_work (start): 0.2842 rms_B_bonded: 3.01 r_work: 0.2706 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12369 Z= 0.132 Angle : 0.501 12.383 17440 Z= 0.267 Chirality : 0.037 0.207 2091 Planarity : 0.003 0.030 1656 Dihedral : 19.756 157.098 3267 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.86 % Allowed : 17.22 % Favored : 80.92 % 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: -0.01 (0.26), residues: 1136 helix: 1.29 (0.23), residues: 563 sheet: 0.02 (0.49), residues: 114 loop : -1.71 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 476 HIS 0.002 0.001 HIS A 160 PHE 0.010 0.001 PHE A 432 TYR 0.015 0.001 TYR A 988 ARG 0.001 0.000 ARG A 71 Details of bonding type rmsd hydrogen bonds : bond 0.04155 ( 522) hydrogen bonds : angle 3.59170 ( 1395) covalent geometry : bond 0.00281 (12369) covalent geometry : angle 0.50058 (17440) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6578.66 seconds wall clock time: 118 minutes 6.17 seconds (7086.17 seconds total)