Starting phenix.real_space_refine on Thu Aug 6 10:24:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8pjj_17711/08_2026/8pjj_17711.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pjj_17711/08_2026/8pjj_17711.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8pjj_17711/08_2026/8pjj_17711.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8pjj_17711/08_2026/8pjj_17711.cif" model { file = "/net/cci-nas-00/data/ceres_data/8pjj_17711/08_2026/8pjj_17711.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pjj_17711/08_2026/8pjj_17711.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8pjj_17711/08_2026/8pjj_17711.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pjj_17711/08_2026/8pjj_17711.map" } resolution = 4.24 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 7392 atoms to isotropic. 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 42 5.49 5 S 47 5.16 5 C 5137 2.51 5 N 1438 2.21 5 O 1684 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8348 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7474 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 946, 7463 Classifications: {'peptide': 946} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 46, 'TRANS': 898} Chain breaks: 2 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 17 Conformer: "B" Number of residues, atoms: 946, 7463 Classifications: {'peptide': 946} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 46, 'TRANS': 898} Chain breaks: 2 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 17 bond proxies already assigned to first conformer: 7593 Chain: "B" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 847 Classifications: {'RNAv2': 40} Modifications used: {'rna2p_pyr': 3, 'rna3p_pur': 19, 'rna3p_pyr': 18} Link IDs: {'rna2p': 2, 'rna3p': 37} Chain breaks: 1 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.05, per 1000 atoms: 0.37 Number of scatterers: 8348 At special positions: 0 Unit cell: (74.56, 102.52, 137.004, 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 47 16.00 P 42 15.00 O 1684 8.00 N 1438 7.00 C 5137 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: 0.69 Conformation dependent library (CDL) restraints added in 501.0 milliseconds 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1810 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 7 sheets defined 47.1% alpha, 10.8% beta 10 base pairs and 15 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'A' and resid 171 through 181 Processing helix chain 'A' and resid 223 through 242 Processing helix chain 'A' and resid 268 through 283 Processing helix chain 'A' and resid 347 through 351 Processing helix chain 'A' and resid 352 through 371 Processing helix chain 'A' and resid 371 through 384 Processing helix chain 'A' and resid 385 through 388 Processing helix chain 'A' and resid 389 through 400 removed outlier: 3.741A pdb=" N ASN A 398 " --> pdb=" O LEU A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 415 removed outlier: 3.601A pdb=" N THR A 415 " --> pdb=" O GLY A 412 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 412 through 415' Processing helix chain 'A' and resid 416 through 428 removed outlier: 3.564A pdb=" N SER A 428 " --> pdb=" O ASP A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 458 Processing helix chain 'A' and resid 486 through 494 Processing helix chain 'A' and resid 513 through 530 removed outlier: 3.585A pdb=" N ASP A 525 " --> pdb=" O VAL A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 551 Processing helix chain 'A' and resid 570 through 578 Processing helix chain 'A' and resid 621 through 629 Processing helix chain 'A' and resid 636 through 651 removed outlier: 3.737A pdb=" N LEU A 640 " --> pdb=" O SER A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 676 Processing helix chain 'A' and resid 695 through 703 removed outlier: 3.785A pdb=" N GLN A 699 " --> pdb=" O PRO A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 722 removed outlier: 3.554A pdb=" N GLU A 721 " --> pdb=" O THR A 717 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N THR A 722 " --> pdb=" O ASN A 718 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 717 through 722' Processing helix chain 'A' and resid 758 through 767 Processing helix chain 'A' and resid 782 through 789 removed outlier: 3.584A pdb=" N LEU A 789 " --> pdb=" O ARG A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 812 Processing helix chain 'A' and resid 816 through 823 Processing helix chain 'A' and resid 829 through 842 removed outlier: 3.620A pdb=" N VAL A 833 " --> pdb=" O PRO A 829 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 862 removed outlier: 3.739A pdb=" N ARG A 861 " --> pdb=" O ARG A 857 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 878 removed outlier: 5.040A pdb=" N MET A 871 " --> pdb=" O ARG A 867 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LEU A 874 " --> pdb=" O LYS A 870 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA A 876 " --> pdb=" O MET A 872 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL A 877 " --> pdb=" O VAL A 873 " (cutoff:3.500A) Processing helix chain 'A' and resid 880 through 893 Processing helix chain 'A' and resid 908 through 914 Processing helix chain 'A' and resid 920 through 937 Processing helix chain 'A' and resid 940 through 950 removed outlier: 3.923A pdb=" N ARG A 945 " --> pdb=" O HIS A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 954 through 975 Processing helix chain 'A' and resid 977 through 981 removed outlier: 3.821A pdb=" N CYS A 980 " --> pdb=" O PRO A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 994 through 1008 Processing helix chain 'A' and resid 1101 through 1110 removed outlier: 3.573A pdb=" N ALA A1105 " --> pdb=" O GLU A1101 " (cutoff:3.500A) Processing helix chain 'A' and resid 1111 through 1125 Processing helix chain 'A' and resid 1126 through 1129 removed outlier: 3.678A pdb=" N ILE A1129 " --> pdb=" O PRO A1126 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1126 through 1129' Processing helix chain 'A' and resid 1133 through 1147 Processing sheet with id=AA1, first strand: chain 'A' and resid 188 through 192 removed outlier: 3.689A pdb=" N LEU A 204 " --> pdb=" O ALA A 217 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 188 through 192 Processing sheet with id=AA3, first strand: chain 'A' and resid 465 through 468 removed outlier: 7.478A pdb=" N ILE A 436 " --> pdb=" O LEU A 483 " (cutoff:3.500A) removed outlier: 9.157A pdb=" N CYS A 485 " --> pdb=" O ILE A 436 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ILE A 504 " --> pdb=" O ILE A 536 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N MET A 538 " --> pdb=" O ILE A 504 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N VAL A 403 " --> pdb=" O LEU A 537 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N SER A 539 " --> pdb=" O VAL A 403 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ILE A 405 " --> pdb=" O SER A 539 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N LEU A 557 " --> pdb=" O VAL A 402 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N ILE A 404 " --> pdb=" O LEU A 557 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N VAL A 559 " --> pdb=" O ILE A 404 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ARG A 406 " --> pdb=" O VAL A 559 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 568 through 569 removed outlier: 5.252A pdb=" N PHE A 569 " --> pdb=" O THR A 779 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL A 730 " --> pdb=" O PHE A 776 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N PHE A 778 " --> pdb=" O VAL A 730 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N VAL A 732 " --> pdb=" O PHE A 778 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N ALA A 655 " --> pdb=" O ILE A 729 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N ILE A 656 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N SER A 716 " --> pdb=" O ILE A 656 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N VAL A 658 " --> pdb=" O SER A 716 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N GLN A 686 " --> pdb=" O ILE A 713 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N LEU A 715 " --> pdb=" O GLN A 686 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N LEU A 688 " --> pdb=" O LEU A 715 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 737 through 744 removed outlier: 3.861A pdb=" N ALA A 738 " --> pdb=" O VAL A 755 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N VAL A 755 " --> pdb=" O ALA A 738 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA A 753 " --> pdb=" O MET A 740 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1055 through 1056 removed outlier: 3.880A pdb=" N SER A1062 " --> pdb=" O ILE A1056 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N CYS A1063 " --> pdb=" O ALA A1028 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N LEU A1030 " --> pdb=" O CYS A1063 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LYS A1027 " --> pdb=" O THR A1023 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N LYS A1020 " --> pdb=" O LYS A1016 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1090 through 1092 325 hydrogen bonds defined for protein. 933 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 25 hydrogen bonds 50 hydrogen bond angles 0 basepair planarities 10 basepair parallelities 15 stacking parallelities Total time for adding SS restraints: 1.54 Time building geometry restraints manager: 0.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2475 1.34 - 1.46: 1525 1.46 - 1.58: 4440 1.58 - 1.70: 81 1.70 - 1.82: 71 Bond restraints: 8592 Sorted by residual: bond pdb=" N ASP A 605 " pdb=" CA ASP A 605 " ideal model delta sigma weight residual 1.460 1.489 -0.029 1.02e-02 9.61e+03 8.03e+00 bond pdb=" N ASP A 603 " pdb=" CA ASP A 603 " ideal model delta sigma weight residual 1.455 1.487 -0.032 1.23e-02 6.61e+03 6.80e+00 bond pdb=" N LYS A 604 " pdb=" CA LYS A 604 " ideal model delta sigma weight residual 1.457 1.490 -0.032 1.29e-02 6.01e+03 6.27e+00 bond pdb=" N GLU A 608 " pdb=" CA GLU A 608 " ideal model delta sigma weight residual 1.456 1.485 -0.029 1.23e-02 6.61e+03 5.46e+00 bond pdb=" N GLU A 602 " pdb=" CA GLU A 602 " ideal model delta sigma weight residual 1.457 1.486 -0.029 1.29e-02 6.01e+03 5.17e+00 ... (remaining 8587 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 11431 2.05 - 4.09: 331 4.09 - 6.14: 58 6.14 - 8.19: 12 8.19 - 10.23: 3 Bond angle restraints: 11835 Sorted by residual: angle pdb=" N GLU A 379 " pdb=" CA GLU A 379 " pdb=" CB GLU A 379 " ideal model delta sigma weight residual 110.39 117.65 -7.26 1.66e+00 3.63e-01 1.91e+01 angle pdb=" N LEU A 630 " pdb=" CA LEU A 630 " pdb=" CB LEU A 630 " ideal model delta sigma weight residual 110.49 116.86 -6.37 1.69e+00 3.50e-01 1.42e+01 angle pdb=" C MET A 629 " pdb=" N LEU A 630 " pdb=" CA LEU A 630 " ideal model delta sigma weight residual 121.54 128.60 -7.06 1.91e+00 2.74e-01 1.37e+01 angle pdb=" C GLU A 608 " pdb=" N ILE A 609 " pdb=" CA ILE A 609 " ideal model delta sigma weight residual 123.14 118.37 4.77 1.31e+00 5.83e-01 1.33e+01 angle pdb=" C LEU A 378 " pdb=" N GLU A 379 " pdb=" CA GLU A 379 " ideal model delta sigma weight residual 120.72 114.76 5.96 1.67e+00 3.59e-01 1.27e+01 ... (remaining 11830 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.64: 5011 34.64 - 69.27: 140 69.27 - 103.91: 17 103.91 - 138.55: 1 138.55 - 173.18: 1 Dihedral angle restraints: 5170 sinusoidal: 2390 harmonic: 2780 Sorted by residual: dihedral pdb=" C4' C B 45 " pdb=" C3' C B 45 " pdb=" C2' C B 45 " pdb=" C1' C B 45 " ideal model delta sinusoidal sigma weight residual 36.35 -35.38 71.73 1 3.10e+00 1.04e-01 6.86e+02 dihedral pdb=" C4' C B 46 " pdb=" C3' C B 46 " pdb=" C2' C B 46 " pdb=" C1' C B 46 " ideal model delta sinusoidal sigma weight residual 36.34 -35.22 71.57 1 3.10e+00 1.04e-01 6.83e+02 dihedral pdb=" C4' C B 44 " pdb=" C3' C B 44 " pdb=" C2' C B 44 " pdb=" C1' C B 44 " ideal model delta sinusoidal sigma weight residual 36.35 -33.03 69.38 1 3.10e+00 1.04e-01 6.47e+02 ... (remaining 5167 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1159 0.063 - 0.126: 177 0.126 - 0.189: 9 0.189 - 0.253: 39 0.253 - 0.316: 7 Chirality restraints: 1391 Sorted by residual: chirality pdb=" P C B 35 " pdb=" OP1 C B 35 " pdb=" OP2 C B 35 " pdb=" O5' C B 35 " both_signs ideal model delta sigma weight residual True 2.17 -2.49 -0.32 2.00e-01 2.50e+01 2.49e+00 chirality pdb=" P G B 31 " pdb=" OP1 G B 31 " pdb=" OP2 G B 31 " pdb=" O5' G B 31 " both_signs ideal model delta sigma weight residual True 2.17 -2.45 -0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" C2' C B 46 " pdb=" C3' C B 46 " pdb=" O2' C B 46 " pdb=" C1' C B 46 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 1.90e+00 ... (remaining 1388 not shown) Planarity restraints: 1374 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A1134 " -0.030 5.00e-02 4.00e+02 4.60e-02 3.38e+00 pdb=" N PRO A1135 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO A1135 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A1135 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' U B 9 " -0.024 2.00e-02 2.50e+03 1.20e-02 3.22e+00 pdb=" N1 U B 9 " 0.025 2.00e-02 2.50e+03 pdb=" C2 U B 9 " 0.001 2.00e-02 2.50e+03 pdb=" O2 U B 9 " 0.003 2.00e-02 2.50e+03 pdb=" N3 U B 9 " -0.001 2.00e-02 2.50e+03 pdb=" C4 U B 9 " -0.003 2.00e-02 2.50e+03 pdb=" O4 U B 9 " -0.007 2.00e-02 2.50e+03 pdb=" C5 U B 9 " -0.002 2.00e-02 2.50e+03 pdb=" C6 U B 9 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A B 8 " -0.018 2.00e-02 2.50e+03 8.11e-03 1.81e+00 pdb=" N9 A B 8 " 0.017 2.00e-02 2.50e+03 pdb=" C8 A B 8 " 0.002 2.00e-02 2.50e+03 pdb=" N7 A B 8 " -0.002 2.00e-02 2.50e+03 pdb=" C5 A B 8 " -0.001 2.00e-02 2.50e+03 pdb=" C6 A B 8 " 0.000 2.00e-02 2.50e+03 pdb=" N6 A B 8 " -0.006 2.00e-02 2.50e+03 pdb=" N1 A B 8 " 0.002 2.00e-02 2.50e+03 pdb=" C2 A B 8 " -0.003 2.00e-02 2.50e+03 pdb=" N3 A B 8 " 0.004 2.00e-02 2.50e+03 pdb=" C4 A B 8 " 0.005 2.00e-02 2.50e+03 ... (remaining 1371 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 289 2.68 - 3.23: 8761 3.23 - 3.79: 14214 3.79 - 4.34: 18337 4.34 - 4.90: 27342 Nonbonded interactions: 68943 Sorted by model distance: nonbonded pdb=" O GLN A 332 " pdb=" OH TYR A 479 " model vdw 2.120 3.040 nonbonded pdb=" NH1 ARG A 198 " pdb=" O2 U B 29 " model vdw 2.171 3.120 nonbonded pdb=" OG BSER A1070 " pdb=" OE1 GLN A1073 " model vdw 2.189 3.040 nonbonded pdb=" OG1 THR A 744 " pdb=" OD1 ASN A 747 " model vdw 2.212 3.040 nonbonded pdb=" OG SER A 548 " pdb=" O CYS A 554 " model vdw 2.226 3.040 ... (remaining 68938 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.330 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 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 : 0.003 0.032 8592 Z= 0.156 Angle : 0.803 10.234 11835 Z= 0.391 Chirality : 0.061 0.316 1391 Planarity : 0.004 0.046 1374 Dihedral : 16.002 173.184 3360 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 19.29 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.57 % Favored : 90.11 % Rotamer: Outliers : 0.72 % Allowed : 0.24 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.28), residues: 942 helix: -0.09 (0.26), residues: 415 sheet: -1.24 (0.51), residues: 113 loop : -1.20 (0.32), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 375 TYR 0.009 0.001 TYR A 530 PHE 0.009 0.001 PHE A 518 TRP 0.018 0.001 TRP A 328 HIS 0.003 0.001 HIS A1032 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.16 ( 8592) covalent geometry : angle 0.80303 / 0.39 (11835) hydrogen bonds : bond 0.17642 / 12.32 ( 344) hydrogen bonds : angle 6.84802 / 4.68 ( 983) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 63 time to evaluate : 0.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 358 MET cc_start: 0.9628 (mmp) cc_final: 0.9366 (mmm) REVERT: A 389 MET cc_start: 0.8688 (pmm) cc_final: 0.8300 (pmm) REVERT: A 483 LEU cc_start: 0.9233 (tp) cc_final: 0.9002 (tp) REVERT: A 538 MET cc_start: 0.4037 (ttt) cc_final: 0.3357 (ttt) REVERT: A 670 MET cc_start: 0.9229 (mmp) cc_final: 0.8980 (mmm) REVERT: A 797 MET cc_start: 0.8448 (ppp) cc_final: 0.7691 (ppp) REVERT: A 872 MET cc_start: 0.9050 (mmp) cc_final: 0.8832 (mmm) REVERT: A 966 GLN cc_start: 0.9527 (tt0) cc_final: 0.9254 (mp10) REVERT: A 1001 LEU cc_start: 0.9395 (tt) cc_final: 0.9191 (pp) outliers start: 4 outliers final: 1 residues processed: 67 average time/residue: 0.0751 time to fit residues: 7.9409 Evaluate side-chains 53 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 52 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 10.0000 chunk 97 optimal weight: 10.0000 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 20.0000 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 0.0170 chunk 45 optimal weight: 6.9990 overall best weight: 2.5824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 684 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.065529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.046655 restraints weight = 251460.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.048659 restraints weight = 124655.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.049989 restraints weight = 75274.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.051112 restraints weight = 49590.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.051435 restraints weight = 36686.469| |-----------------------------------------------------------------------------| r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3161 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3161 r_free = 0.3161 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3161 r_free = 0.3161 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3161 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.1058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 8592 Z= 0.177 Angle : 0.868 11.786 11835 Z= 0.394 Chirality : 0.057 0.584 1391 Planarity : 0.004 0.046 1374 Dihedral : 14.278 173.828 1511 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 18.43 Ramachandran Plot: Outliers : 0.43 % Allowed : 8.30 % Favored : 91.28 % Rotamer: Outliers : 0.24 % Allowed : 2.88 % Favored : 96.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.27), residues: 942 helix: -0.16 (0.24), residues: 422 sheet: -1.47 (0.52), residues: 98 loop : -1.34 (0.32), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 198 TYR 0.014 0.002 TYR A 550 PHE 0.020 0.002 PHE A 200 TRP 0.019 0.001 TRP A 328 HIS 0.009 0.001 HIS A 503 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.18 ( 8592) covalent geometry : angle 0.86806 / 0.39 (11835) hydrogen bonds : bond 0.05877 / 4.10 ( 344) hydrogen bonds : angle 5.43936 / 3.72 ( 983) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.299 Fit side-chains revert: symmetry clash REVERT: A 358 MET cc_start: 0.9654 (mmp) cc_final: 0.9391 (mmm) REVERT: A 389 MET cc_start: 0.8537 (pmm) cc_final: 0.8078 (pmm) REVERT: A 440 GLN cc_start: 0.8766 (tt0) cc_final: 0.8449 (tt0) REVERT: A 483 LEU cc_start: 0.9386 (tp) cc_final: 0.9101 (tp) REVERT: A 484 PHE cc_start: 0.9610 (m-10) cc_final: 0.9409 (m-10) REVERT: A 538 MET cc_start: 0.4142 (ttt) cc_final: 0.3895 (ttt) REVERT: A 629 MET cc_start: 0.6907 (tmm) cc_final: 0.6601 (tpp) REVERT: A 797 MET cc_start: 0.8742 (ppp) cc_final: 0.8123 (ppp) REVERT: A 807 LEU cc_start: 0.9562 (mt) cc_final: 0.9192 (tt) outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 0.0662 time to fit residues: 6.6759 Evaluate side-chains 45 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 89 optimal weight: 7.9990 chunk 38 optimal weight: 50.0000 chunk 29 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 93 optimal weight: 0.9980 chunk 59 optimal weight: 8.9990 chunk 53 optimal weight: 10.0000 chunk 79 optimal weight: 10.0000 chunk 34 optimal weight: 8.9990 chunk 40 optimal weight: 9.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 430 GLN A 684 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.062034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.042462 restraints weight = 197409.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.044362 restraints weight = 102237.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 64)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.046078 restraints weight = 69212.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 64)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.047100 restraints weight = 52654.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 60)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.047810 restraints weight = 43389.937| |-----------------------------------------------------------------------------| r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3070 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3070 r_free = 0.3070 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3070 r_free = 0.3070 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3070 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 8592 Z= 0.203 Angle : 0.857 12.426 11835 Z= 0.395 Chirality : 0.056 0.521 1391 Planarity : 0.005 0.047 1374 Dihedral : 14.157 174.046 1511 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 22.66 Ramachandran Plot: Outliers : 0.43 % Allowed : 9.26 % Favored : 90.32 % Rotamer: Outliers : 0.48 % Allowed : 2.64 % Favored : 96.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.27), residues: 942 helix: -0.16 (0.24), residues: 421 sheet: -1.51 (0.49), residues: 110 loop : -1.46 (0.32), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 198 TYR 0.012 0.002 TYR A 550 PHE 0.023 0.002 PHE A 200 TRP 0.024 0.002 TRP A 328 HIS 0.006 0.002 HIS A 503 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.20 ( 8592) covalent geometry : angle 0.85737 / 0.39 (11835) hydrogen bonds : bond 0.05322 / 3.73 ( 344) hydrogen bonds : angle 5.36709 / 3.70 ( 983) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 58 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 358 MET cc_start: 0.9638 (mmp) cc_final: 0.9368 (mmm) REVERT: A 389 MET cc_start: 0.8765 (pmm) cc_final: 0.8366 (pmm) REVERT: A 440 GLN cc_start: 0.8908 (tt0) cc_final: 0.8487 (tt0) REVERT: A 483 LEU cc_start: 0.9392 (tp) cc_final: 0.9173 (tp) REVERT: A 629 MET cc_start: 0.6703 (tmm) cc_final: 0.6494 (tpp) REVERT: A 670 MET cc_start: 0.9222 (mmp) cc_final: 0.9020 (mmm) REVERT: A 872 MET cc_start: 0.9049 (mmp) cc_final: 0.8769 (mmp) REVERT: A 1004 LEU cc_start: 0.8988 (mm) cc_final: 0.8733 (mm) outliers start: 2 outliers final: 1 residues processed: 60 average time/residue: 0.0819 time to fit residues: 7.4340 Evaluate side-chains 45 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 44 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 94 optimal weight: 10.0000 chunk 40 optimal weight: 6.9990 chunk 96 optimal weight: 10.0000 chunk 11 optimal weight: 0.7980 chunk 31 optimal weight: 5.9990 chunk 33 optimal weight: 9.9990 chunk 44 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 21 optimal weight: 0.8980 chunk 81 optimal weight: 0.9980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 510 HIS A 684 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.065063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.045099 restraints weight = 217613.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.047171 restraints weight = 105961.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.048992 restraints weight = 68931.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.049898 restraints weight = 51188.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 64)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.050921 restraints weight = 41886.574| |-----------------------------------------------------------------------------| r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3142 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3142 r_free = 0.3142 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3142 r_free = 0.3142 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3142 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 8592 Z= 0.137 Angle : 0.817 12.449 11835 Z= 0.371 Chirality : 0.054 0.518 1391 Planarity : 0.005 0.070 1374 Dihedral : 13.942 175.282 1511 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 17.27 Ramachandran Plot: Outliers : 0.43 % Allowed : 8.72 % Favored : 90.85 % Rotamer: Outliers : 0.24 % Allowed : 2.52 % Favored : 97.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.27), residues: 942 helix: -0.09 (0.24), residues: 428 sheet: -1.49 (0.51), residues: 96 loop : -1.45 (0.32), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 198 TYR 0.008 0.001 TYR A 425 PHE 0.017 0.001 PHE A 200 TRP 0.018 0.001 TRP A 328 HIS 0.006 0.001 HIS A 503 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 ( 8592) covalent geometry : angle 0.81658 / 0.37 (11835) hydrogen bonds : bond 0.04456 / 3.07 ( 344) hydrogen bonds : angle 5.05537 / 3.49 ( 983) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 358 MET cc_start: 0.9658 (mmp) cc_final: 0.9397 (mmm) REVERT: A 389 MET cc_start: 0.8772 (pmm) cc_final: 0.8369 (pmm) REVERT: A 440 GLN cc_start: 0.8949 (tt0) cc_final: 0.8573 (tt0) REVERT: A 483 LEU cc_start: 0.9409 (tp) cc_final: 0.9134 (tp) REVERT: A 538 MET cc_start: 0.2638 (ttt) cc_final: 0.1742 (ttt) REVERT: A 670 MET cc_start: 0.9212 (mmp) cc_final: 0.8960 (mmm) REVERT: A 807 LEU cc_start: 0.9582 (mt) cc_final: 0.9251 (tt) REVERT: A 872 MET cc_start: 0.8986 (mmp) cc_final: 0.8727 (mmm) REVERT: A 1001 LEU cc_start: 0.9452 (tt) cc_final: 0.9234 (pp) REVERT: A 1004 LEU cc_start: 0.8946 (mm) cc_final: 0.8729 (mm) outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.0723 time to fit residues: 6.9955 Evaluate side-chains 47 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 5 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 73 optimal weight: 6.9990 chunk 6 optimal weight: 10.0000 chunk 16 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 9 optimal weight: 20.0000 chunk 80 optimal weight: 7.9990 chunk 58 optimal weight: 0.7980 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 169 ASN A 684 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.065153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.048477 restraints weight = 246284.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.050052 restraints weight = 117687.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.051375 restraints weight = 67209.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.051611 restraints weight = 45323.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.051922 restraints weight = 42288.684| |-----------------------------------------------------------------------------| r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3150 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3150 r_free = 0.3150 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3150 r_free = 0.3150 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3150 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 8592 Z= 0.133 Angle : 0.804 12.335 11835 Z= 0.365 Chirality : 0.054 0.542 1391 Planarity : 0.005 0.062 1374 Dihedral : 13.796 176.517 1511 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 16.72 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.04 % Favored : 90.64 % Rotamer: Outliers : 0.24 % Allowed : 2.04 % Favored : 97.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.28), residues: 942 helix: -0.00 (0.24), residues: 426 sheet: -1.34 (0.53), residues: 96 loop : -1.47 (0.32), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 173 TYR 0.009 0.001 TYR A 550 PHE 0.014 0.001 PHE A 200 TRP 0.017 0.001 TRP A 328 HIS 0.007 0.001 HIS A 510 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 ( 8592) covalent geometry : angle 0.80382 / 0.37 (11835) hydrogen bonds : bond 0.04332 / 3.01 ( 344) hydrogen bonds : angle 5.03981 / 3.49 ( 983) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 358 MET cc_start: 0.9685 (mmp) cc_final: 0.9410 (mmm) REVERT: A 389 MET cc_start: 0.8819 (pmm) cc_final: 0.8417 (pmm) REVERT: A 440 GLN cc_start: 0.8925 (tt0) cc_final: 0.8441 (tt0) REVERT: A 483 LEU cc_start: 0.9404 (tp) cc_final: 0.9122 (tp) REVERT: A 538 MET cc_start: 0.2211 (ttt) cc_final: 0.1740 (ttt) REVERT: A 670 MET cc_start: 0.9154 (mmp) cc_final: 0.8899 (mmm) REVERT: A 797 MET cc_start: 0.8684 (ppp) cc_final: 0.7987 (ppp) REVERT: A 807 LEU cc_start: 0.9584 (mt) cc_final: 0.9237 (tt) REVERT: A 872 MET cc_start: 0.8960 (mmp) cc_final: 0.8656 (mmm) REVERT: A 1001 LEU cc_start: 0.9455 (tt) cc_final: 0.9231 (pp) outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.0701 time to fit residues: 6.8097 Evaluate side-chains 44 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 2 optimal weight: 40.0000 chunk 22 optimal weight: 6.9990 chunk 37 optimal weight: 0.7980 chunk 38 optimal weight: 5.9990 chunk 52 optimal weight: 8.9990 chunk 54 optimal weight: 3.9990 chunk 68 optimal weight: 6.9990 chunk 47 optimal weight: 10.0000 chunk 8 optimal weight: 6.9990 chunk 55 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 684 GLN ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1032 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.061494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.044420 restraints weight = 242163.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.046331 restraints weight = 107038.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.047029 restraints weight = 71816.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.047919 restraints weight = 48397.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.048119 restraints weight = 38277.481| |-----------------------------------------------------------------------------| r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3069 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3069 r_free = 0.3069 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3069 r_free = 0.3069 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3069 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.2717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 8592 Z= 0.188 Angle : 0.832 12.991 11835 Z= 0.382 Chirality : 0.056 0.624 1391 Planarity : 0.005 0.087 1374 Dihedral : 13.907 177.890 1511 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 21.98 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.72 % Favored : 90.96 % Rotamer: Outliers : 0.24 % Allowed : 1.68 % Favored : 98.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.28), residues: 942 helix: -0.14 (0.24), residues: 427 sheet: -1.03 (0.55), residues: 91 loop : -1.39 (0.32), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 198 TYR 0.011 0.002 TYR A 420 PHE 0.021 0.002 PHE A 200 TRP 0.020 0.002 TRP A 328 HIS 0.007 0.002 HIS A 510 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.19 ( 8592) covalent geometry : angle 0.83183 / 0.38 (11835) hydrogen bonds : bond 0.04847 / 3.41 ( 344) hydrogen bonds : angle 5.16054 / 3.56 ( 983) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.276 Fit side-chains REVERT: A 358 MET cc_start: 0.9630 (mmp) cc_final: 0.9352 (mmm) REVERT: A 389 MET cc_start: 0.8772 (pmm) cc_final: 0.8372 (pmm) REVERT: A 440 GLN cc_start: 0.9038 (tt0) cc_final: 0.8646 (tt0) REVERT: A 483 LEU cc_start: 0.9389 (tp) cc_final: 0.9181 (tp) REVERT: A 538 MET cc_start: 0.1680 (ttt) cc_final: 0.1402 (ttt) REVERT: A 577 MET cc_start: 0.7969 (pmm) cc_final: 0.7277 (pmm) REVERT: A 629 MET cc_start: 0.6620 (tmm) cc_final: 0.5977 (tpp) REVERT: A 670 MET cc_start: 0.9159 (mmp) cc_final: 0.8934 (mmm) REVERT: A 797 MET cc_start: 0.8759 (ppp) cc_final: 0.8061 (ppp) REVERT: A 872 MET cc_start: 0.9084 (mmp) cc_final: 0.8785 (mmm) REVERT: A 1004 LEU cc_start: 0.8929 (mm) cc_final: 0.8692 (mm) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.0640 time to fit residues: 5.7929 Evaluate side-chains 41 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 33 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 28 optimal weight: 6.9990 chunk 42 optimal weight: 2.9990 chunk 95 optimal weight: 10.0000 chunk 10 optimal weight: 0.7980 chunk 63 optimal weight: 0.0030 chunk 69 optimal weight: 0.7980 chunk 12 optimal weight: 0.0070 chunk 37 optimal weight: 0.8980 overall best weight: 0.5008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 684 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.065867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.049074 restraints weight = 249076.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.051583 restraints weight = 113039.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.052986 restraints weight = 56847.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.053301 restraints weight = 37446.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.053542 restraints weight = 34767.919| |-----------------------------------------------------------------------------| r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3188 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3188 r_free = 0.3188 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3188 r_free = 0.3188 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.3188 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 8592 Z= 0.130 Angle : 0.802 12.736 11835 Z= 0.366 Chirality : 0.055 0.563 1391 Planarity : 0.005 0.081 1374 Dihedral : 13.705 178.202 1511 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 15.43 Ramachandran Plot: Outliers : 0.43 % Allowed : 8.83 % Favored : 90.74 % Rotamer: Outliers : 0.24 % Allowed : 1.08 % Favored : 98.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.28), residues: 942 helix: 0.01 (0.25), residues: 426 sheet: -1.43 (0.50), residues: 103 loop : -1.30 (0.33), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 938 TYR 0.008 0.001 TYR A 177 PHE 0.014 0.001 PHE A 518 TRP 0.016 0.001 TRP A 328 HIS 0.010 0.001 HIS A1032 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 ( 8592) covalent geometry : angle 0.80166 / 0.37 (11835) hydrogen bonds : bond 0.04179 / 2.90 ( 344) hydrogen bonds : angle 4.93391 / 3.42 ( 983) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.256 Fit side-chains REVERT: A 358 MET cc_start: 0.9671 (mmp) cc_final: 0.9399 (mmm) REVERT: A 389 MET cc_start: 0.8903 (pmm) cc_final: 0.8539 (pmm) REVERT: A 440 GLN cc_start: 0.8970 (tt0) cc_final: 0.8603 (tt0) REVERT: A 483 LEU cc_start: 0.9372 (tp) cc_final: 0.9090 (tp) REVERT: A 538 MET cc_start: 0.2604 (ttt) cc_final: 0.2274 (ttt) REVERT: A 577 MET cc_start: 0.7823 (pmm) cc_final: 0.7520 (pmm) REVERT: A 629 MET cc_start: 0.6422 (tmm) cc_final: 0.5777 (tpp) REVERT: A 637 PHE cc_start: 0.8693 (m-80) cc_final: 0.8436 (m-80) REVERT: A 670 MET cc_start: 0.9147 (mmp) cc_final: 0.8931 (mmm) REVERT: A 807 LEU cc_start: 0.9614 (mt) cc_final: 0.9249 (pp) REVERT: A 872 MET cc_start: 0.9020 (mmp) cc_final: 0.8607 (mmm) REVERT: A 1003 LEU cc_start: 0.9431 (tt) cc_final: 0.9212 (tt) REVERT: A 1004 LEU cc_start: 0.8903 (mm) cc_final: 0.8677 (mm) outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 0.0730 time to fit residues: 7.0895 Evaluate side-chains 44 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 97 optimal weight: 10.0000 chunk 36 optimal weight: 2.9990 chunk 18 optimal weight: 0.0570 chunk 77 optimal weight: 0.1980 chunk 50 optimal weight: 9.9990 chunk 79 optimal weight: 2.9990 chunk 74 optimal weight: 7.9990 chunk 12 optimal weight: 7.9990 chunk 71 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 overall best weight: 2.0504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 684 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.063383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.044805 restraints weight = 160614.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.046568 restraints weight = 89671.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.047710 restraints weight = 61924.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 62)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.049095 restraints weight = 48778.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.049641 restraints weight = 40105.560| |-----------------------------------------------------------------------------| r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3110 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3110 r_free = 0.3110 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3110 r_free = 0.3110 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3110 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.2928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 8592 Z= 0.151 Angle : 0.809 12.671 11835 Z= 0.370 Chirality : 0.055 0.608 1391 Planarity : 0.004 0.071 1374 Dihedral : 13.634 175.580 1511 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 18.13 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.83 % Favored : 90.85 % Rotamer: Outliers : 0.24 % Allowed : 0.60 % Favored : 99.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.21 (0.28), residues: 942 helix: -0.05 (0.25), residues: 417 sheet: -1.49 (0.50), residues: 103 loop : -1.32 (0.32), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 173 TYR 0.010 0.001 TYR A 890 PHE 0.015 0.001 PHE A 200 TRP 0.016 0.001 TRP A 328 HIS 0.005 0.001 HIS A 510 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 ( 8592) covalent geometry : angle 0.80884 / 0.37 (11835) hydrogen bonds : bond 0.04413 / 3.12 ( 344) hydrogen bonds : angle 4.91103 / 3.40 ( 983) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.301 Fit side-chains revert: symmetry clash REVERT: A 358 MET cc_start: 0.9627 (mmp) cc_final: 0.9343 (mmm) REVERT: A 389 MET cc_start: 0.8827 (pmm) cc_final: 0.8436 (pmm) REVERT: A 440 GLN cc_start: 0.8979 (tt0) cc_final: 0.8547 (tt0) REVERT: A 483 LEU cc_start: 0.9374 (tp) cc_final: 0.9125 (tp) REVERT: A 577 MET cc_start: 0.7927 (pmm) cc_final: 0.7520 (pmm) REVERT: A 629 MET cc_start: 0.6241 (tmm) cc_final: 0.5541 (tpp) REVERT: A 637 PHE cc_start: 0.8639 (m-80) cc_final: 0.8405 (m-80) REVERT: A 670 MET cc_start: 0.9142 (mmp) cc_final: 0.8917 (mmm) REVERT: A 797 MET cc_start: 0.8674 (ppp) cc_final: 0.7956 (ppp) REVERT: A 807 LEU cc_start: 0.9640 (mt) cc_final: 0.9349 (pp) REVERT: A 872 MET cc_start: 0.9028 (mmp) cc_final: 0.8751 (mmm) REVERT: A 1004 LEU cc_start: 0.8894 (mm) cc_final: 0.8606 (mm) outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.0746 time to fit residues: 6.8648 Evaluate side-chains 44 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 48 optimal weight: 7.9990 chunk 46 optimal weight: 0.2980 chunk 79 optimal weight: 4.9990 chunk 4 optimal weight: 6.9990 chunk 15 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 chunk 45 optimal weight: 5.9990 chunk 90 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 chunk 78 optimal weight: 6.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 684 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.062906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.046469 restraints weight = 234852.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.048275 restraints weight = 113643.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.049589 restraints weight = 61939.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.049658 restraints weight = 46886.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.049908 restraints weight = 40765.372| |-----------------------------------------------------------------------------| r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3155 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3155 r_free = 0.3155 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3155 r_free = 0.3155 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3155 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.3096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 8592 Z= 0.156 Angle : 0.810 12.949 11835 Z= 0.372 Chirality : 0.055 0.623 1391 Planarity : 0.005 0.076 1374 Dihedral : 13.674 172.987 1511 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 19.53 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.47 % Favored : 90.21 % Rotamer: Outliers : 0.24 % Allowed : 0.48 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.28), residues: 942 helix: -0.07 (0.25), residues: 425 sheet: -1.58 (0.50), residues: 103 loop : -1.32 (0.32), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 173 TYR 0.009 0.001 TYR A 420 PHE 0.016 0.001 PHE A 200 TRP 0.017 0.001 TRP A 328 HIS 0.004 0.001 HIS A 503 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.16 ( 8592) covalent geometry : angle 0.80951 / 0.37 (11835) hydrogen bonds : bond 0.04449 / 3.11 ( 344) hydrogen bonds : angle 4.95502 / 3.42 ( 983) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.190 Fit side-chains revert: symmetry clash REVERT: A 358 MET cc_start: 0.9687 (mmp) cc_final: 0.9445 (mmm) REVERT: A 389 MET cc_start: 0.9017 (pmm) cc_final: 0.8684 (pmm) REVERT: A 440 GLN cc_start: 0.8852 (tt0) cc_final: 0.8417 (tt0) REVERT: A 483 LEU cc_start: 0.9427 (tp) cc_final: 0.9175 (tp) REVERT: A 577 MET cc_start: 0.8244 (pmm) cc_final: 0.7864 (pmm) REVERT: A 637 PHE cc_start: 0.8809 (m-80) cc_final: 0.8523 (m-80) REVERT: A 670 MET cc_start: 0.9176 (mmp) cc_final: 0.8959 (mmm) REVERT: A 797 MET cc_start: 0.8819 (ppp) cc_final: 0.8137 (ppp) REVERT: A 872 MET cc_start: 0.8919 (mmp) cc_final: 0.8562 (mmm) REVERT: A 1004 LEU cc_start: 0.8956 (mm) cc_final: 0.8728 (mm) outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.0678 time to fit residues: 6.2437 Evaluate side-chains 41 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 66 optimal weight: 8.9990 chunk 85 optimal weight: 0.0470 chunk 58 optimal weight: 40.0000 chunk 42 optimal weight: 2.9990 chunk 18 optimal weight: 6.9990 chunk 27 optimal weight: 0.6980 chunk 39 optimal weight: 8.9990 chunk 38 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 9 optimal weight: 0.0980 overall best weight: 0.7480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 684 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.065551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.045311 restraints weight = 262994.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.047647 restraints weight = 116769.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.049452 restraints weight = 72817.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 64)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.050858 restraints weight = 52881.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 70)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.051729 restraints weight = 41937.695| |-----------------------------------------------------------------------------| r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3156 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3156 r_free = 0.3156 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3156 r_free = 0.3156 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3156 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.3212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 8592 Z= 0.128 Angle : 0.804 12.604 11835 Z= 0.367 Chirality : 0.054 0.583 1391 Planarity : 0.005 0.077 1374 Dihedral : 13.502 168.602 1511 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.94 % Favored : 90.74 % Rotamer: Outliers : 0.24 % Allowed : 0.24 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.21 (0.28), residues: 942 helix: -0.05 (0.25), residues: 425 sheet: -1.46 (0.51), residues: 103 loop : -1.34 (0.32), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 173 TYR 0.008 0.001 TYR A 177 PHE 0.012 0.001 PHE A 518 TRP 0.015 0.001 TRP A 328 HIS 0.004 0.001 HIS A 510 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 ( 8592) covalent geometry : angle 0.80377 / 0.37 (11835) hydrogen bonds : bond 0.04159 / 2.91 ( 344) hydrogen bonds : angle 4.88170 / 3.39 ( 983) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 358 MET cc_start: 0.9632 (mmp) cc_final: 0.9350 (mmm) REVERT: A 389 MET cc_start: 0.8879 (pmm) cc_final: 0.8515 (pmm) REVERT: A 440 GLN cc_start: 0.8968 (tt0) cc_final: 0.8504 (tt0) REVERT: A 483 LEU cc_start: 0.9386 (tp) cc_final: 0.9105 (tp) REVERT: A 577 MET cc_start: 0.8149 (pmm) cc_final: 0.7727 (pmm) REVERT: A 629 MET cc_start: 0.6247 (tmm) cc_final: 0.5535 (tpp) REVERT: A 670 MET cc_start: 0.9128 (mmp) cc_final: 0.8899 (mmm) REVERT: A 797 MET cc_start: 0.8716 (ppp) cc_final: 0.8069 (ppp) REVERT: A 807 LEU cc_start: 0.9667 (mt) cc_final: 0.9399 (pp) REVERT: A 872 MET cc_start: 0.8978 (mmp) cc_final: 0.8658 (mmm) REVERT: A 1003 LEU cc_start: 0.9442 (tt) cc_final: 0.9232 (tt) REVERT: A 1004 LEU cc_start: 0.8910 (mm) cc_final: 0.8649 (mm) outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.0743 time to fit residues: 7.2507 Evaluate side-chains 46 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 71 optimal weight: 0.9990 chunk 60 optimal weight: 7.9990 chunk 63 optimal weight: 6.9990 chunk 73 optimal weight: 9.9990 chunk 29 optimal weight: 4.9990 chunk 83 optimal weight: 0.0470 chunk 3 optimal weight: 10.0000 chunk 27 optimal weight: 0.9990 chunk 39 optimal weight: 0.0970 chunk 18 optimal weight: 4.9990 chunk 80 optimal weight: 0.8980 overall best weight: 0.6080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 684 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.066175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.046392 restraints weight = 210177.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.048416 restraints weight = 104749.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.050265 restraints weight = 69009.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.051492 restraints weight = 50900.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 58)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.052354 restraints weight = 40897.896| |-----------------------------------------------------------------------------| r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3178 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3178 r_free = 0.3178 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3178 r_free = 0.3178 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3178 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.3339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 8592 Z= 0.126 Angle : 0.801 12.403 11835 Z= 0.365 Chirality : 0.053 0.584 1391 Planarity : 0.004 0.071 1374 Dihedral : 13.306 167.090 1511 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.15 % Favored : 90.53 % Rotamer: Outliers : 0.24 % Allowed : 0.48 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.28), residues: 942 helix: 0.04 (0.25), residues: 425 sheet: -1.39 (0.52), residues: 103 loop : -1.37 (0.32), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 173 TYR 0.008 0.001 TYR A 177 PHE 0.011 0.001 PHE A 200 TRP 0.014 0.001 TRP A 328 HIS 0.004 0.001 HIS A1032 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 ( 8592) covalent geometry : angle 0.80067 / 0.37 (11835) hydrogen bonds : bond 0.04093 / 2.87 ( 344) hydrogen bonds : angle 4.78720 / 3.32 ( 983) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2016.60 seconds wall clock time: 35 minutes 26.15 seconds (2126.15 seconds total)