Starting phenix.real_space_refine on Tue Apr 9 07:11:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pjj_17711/04_2024/8pjj_17711_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pjj_17711/04_2024/8pjj_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pjj_17711/04_2024/8pjj_17711.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pjj_17711/04_2024/8pjj_17711.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pjj_17711/04_2024/8pjj_17711_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pjj_17711/04_2024/8pjj_17711_updated.pdb" } resolution = 4.24 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.010 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 Residue "A PHE 551": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 603": "OD1" <-> "OD2" Residue "A ASP 605": "OD1" <-> "OD2" Residue "A ASP 882": "OD1" <-> "OD2" Residue "A GLU 896": "OE1" <-> "OE2" Residue "A GLU 1025": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/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: {'RNA': 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: 8.77, per 1000 atoms: 1.05 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 - 3.50 Amino acid : False - 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: 3.90 Conformation dependent library (CDL) restraints added in 3.0 seconds 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... running ksdssp... Secondary structure from input PDB file: 37 helices and 8 sheets defined 40.1% alpha, 9.2% beta 10 base pairs and 15 stacking pairs defined. Time for finding SS restraints: 4.32 Creating SS restraints... Processing helix chain 'A' and resid 172 through 180 Processing helix chain 'A' and resid 224 through 241 Processing helix chain 'A' and resid 269 through 282 Processing helix chain 'A' and resid 348 through 350 No H-bonds generated for 'chain 'A' and resid 348 through 350' Processing helix chain 'A' and resid 353 through 370 Processing helix chain 'A' and resid 372 through 383 Processing helix chain 'A' and resid 385 through 399 removed outlier: 3.687A pdb=" N MET A 389 " --> pdb=" O ILE A 386 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N SER A 391 " --> pdb=" O ALA A 388 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ILE A 397 " --> pdb=" O LEU A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 415 No H-bonds generated for 'chain 'A' and resid 413 through 415' Processing helix chain 'A' and resid 417 through 427 Processing helix chain 'A' and resid 443 through 457 Processing helix chain 'A' and resid 487 through 495 removed outlier: 4.243A pdb=" N GLU A 495 " --> pdb=" O LEU A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 529 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 550 Processing helix chain 'A' and resid 571 through 577 Processing helix chain 'A' and resid 622 through 628 Processing helix chain 'A' and resid 637 through 650 Processing helix chain 'A' and resid 663 through 675 Processing helix chain 'A' and resid 696 through 703 Processing helix chain 'A' and resid 718 through 721 No H-bonds generated for 'chain 'A' and resid 718 through 721' Processing helix chain 'A' and resid 759 through 766 Processing helix chain 'A' and resid 783 through 786 No H-bonds generated for 'chain 'A' and resid 783 through 786' Processing helix chain 'A' and resid 803 through 811 Processing helix chain 'A' and resid 817 through 822 Processing helix chain 'A' and resid 830 through 841 Processing helix chain 'A' and resid 854 through 861 removed outlier: 3.739A pdb=" N ARG A 861 " --> pdb=" O ARG A 857 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 877 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 881 through 892 Processing helix chain 'A' and resid 909 through 915 removed outlier: 4.685A pdb=" N SER A 915 " --> pdb=" O GLN A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 921 through 936 Processing helix chain 'A' and resid 941 through 949 removed outlier: 3.923A pdb=" N ARG A 945 " --> pdb=" O HIS A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 955 through 974 Processing helix chain 'A' and resid 978 through 980 No H-bonds generated for 'chain 'A' and resid 978 through 980' Processing helix chain 'A' and resid 995 through 1007 Processing helix chain 'A' and resid 1102 through 1109 Processing helix chain 'A' and resid 1112 through 1124 Processing helix chain 'A' and resid 1126 through 1128 No H-bonds generated for 'chain 'A' and resid 1126 through 1128' Processing helix chain 'A' and resid 1134 through 1146 Processing sheet with id= A, first strand: chain 'A' and resid 188 through 192 removed outlier: 4.154A pdb=" N ALA A 202 " --> pdb=" O GLU A 219 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N GLU A 219 " --> pdb=" O ALA A 202 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU A 204 " --> pdb=" O ALA A 217 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 535 through 539 Processing sheet with id= C, first strand: chain 'A' and resid 465 through 468 removed outlier: 6.204A pdb=" N ILE A 482 " --> pdb=" O GLY A 466 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N SER A 468 " --> pdb=" O ILE A 482 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N PHE A 484 " --> pdb=" O SER A 468 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 685 through 689 removed outlier: 5.998A pdb=" N THR A 711 " --> pdb=" O GLN A 686 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N LEU A 688 " --> pdb=" O THR A 711 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ILE A 713 " --> pdb=" O LEU A 688 " (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: 7.193A pdb=" N LEU A 657 " --> pdb=" O VAL A 730 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N VAL A 732 " --> pdb=" O LEU A 657 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N PHE A 659 " --> pdb=" O VAL A 732 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N ASP A 734 " --> pdb=" O PHE A 659 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N PHE A 776 " --> pdb=" O VAL A 732 " (cutoff:3.500A) removed outlier: 8.730A pdb=" N ASP A 734 " --> pdb=" O PHE A 776 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N PHE A 778 " --> pdb=" O ASP A 734 " (cutoff:3.500A) Processing sheet with id= E, 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= F, first strand: chain 'A' and resid 1027 through 1029 removed outlier: 4.130A pdb=" N LYS A1027 " --> pdb=" O THR A1023 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N LEU A1022 " --> pdb=" O HIS A1015 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N HIS A1015 " --> pdb=" O LEU A1022 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 1054 through 1056 removed outlier: 3.880A pdb=" N SER A1062 " --> pdb=" O ILE A1056 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 1090 through 1092 261 hydrogen bonds defined for protein. 732 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: 2.72 Time building geometry restraints manager: 4.19 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: 98.58 - 106.11: 425 106.11 - 113.63: 4874 113.63 - 121.15: 4228 121.15 - 128.67: 2227 128.67 - 136.20: 81 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 - 35.95: 5117 35.95 - 71.89: 165 71.89 - 107.84: 21 107.84 - 143.79: 3 143.79 - 179.73: 2 Dihedral angle restraints: 5308 sinusoidal: 2528 harmonic: 2780 Sorted by residual: dihedral pdb=" O4' C B 45 " pdb=" C1' C B 45 " pdb=" N1 C B 45 " pdb=" C2 C B 45 " ideal model delta sinusoidal sigma weight residual -128.00 51.73 -179.73 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O1B ADP A1201 " pdb=" O3A ADP A1201 " pdb=" PB ADP A1201 " pdb=" PA ADP A1201 " ideal model delta sinusoidal sigma weight residual 300.00 170.25 129.75 1 2.00e+01 2.50e-03 3.93e+01 dihedral pdb=" O4' U B 4 " pdb=" C1' U B 4 " pdb=" N1 U B 4 " pdb=" C2 U B 4 " ideal model delta sinusoidal sigma weight residual -160.00 -77.44 -82.56 1 1.50e+01 4.44e-03 3.71e+01 ... (remaining 5305 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 950 0.035 - 0.071: 289 0.071 - 0.106: 113 0.106 - 0.142: 35 0.142 - 0.177: 4 Chirality restraints: 1391 Sorted by residual: chirality pdb=" C1' U B 9 " pdb=" O4' U B 9 " pdb=" C2' U B 9 " pdb=" N1 U B 9 " both_signs ideal model delta sigma weight residual False 2.47 2.29 0.18 2.00e-01 2.50e+01 7.86e-01 chirality pdb=" CA GLU A 608 " pdb=" N GLU A 608 " pdb=" C GLU A 608 " pdb=" CB GLU A 608 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.54e-01 chirality pdb=" CB ILE A 735 " pdb=" CA ILE A 735 " pdb=" CG1 ILE A 735 " pdb=" CG2 ILE A 735 " both_signs ideal model delta sigma weight residual False 2.64 2.80 -0.15 2.00e-01 2.50e+01 5.85e-01 ... (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: 293 2.68 - 3.23: 8808 3.23 - 3.79: 14283 3.79 - 4.34: 18431 4.34 - 4.90: 27360 Nonbonded interactions: 69175 Sorted by model distance: nonbonded pdb=" O GLN A 332 " pdb=" OH TYR A 479 " model vdw 2.120 2.440 nonbonded pdb=" NH1 ARG A 198 " pdb=" O2 U B 29 " model vdw 2.171 2.520 nonbonded pdb=" OG BSER A1070 " pdb=" OE1 GLN A1073 " model vdw 2.189 2.440 nonbonded pdb=" OG1 THR A 744 " pdb=" OD1 ASN A 747 " model vdw 2.212 2.440 nonbonded pdb=" OG SER A 548 " pdb=" O CYS A 554 " model vdw 2.226 2.440 ... (remaining 69170 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 0.870 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.010 Extract box with map and model: 3.930 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 34.940 Find NCS groups from input model: 0.210 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: 0.000 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 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= 0.181 Angle : 0.755 10.234 11835 Z= 0.384 Chirality : 0.042 0.177 1391 Planarity : 0.004 0.046 1374 Dihedral : 17.529 179.735 3498 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 19.23 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.28), 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 TRP 0.018 0.001 TRP A 328 HIS 0.003 0.001 HIS A1032 PHE 0.009 0.001 PHE A 518 TYR 0.009 0.001 TYR A 530 ARG 0.008 0.000 ARG A 375 *********************** 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 fitting. rotamer outliers: 4 poor density : 63 time to evaluate : 0.967 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: 0.8301 (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: 0.3358 (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: 0.8831 (mmm) REVERT: A 966 GLN cc_start: 0.9527 (tt0) cc_final: 0.9254 (mp10) outliers start: 4 outliers final: 1 residues processed: 67 average time/residue: 0.1700 time to fit residues: 17.3637 Evaluate side-chains 53 residues out of total 833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 52 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 0.9990 chunk 74 optimal weight: 10.0000 chunk 41 optimal weight: 4.9990 chunk 25 optimal weight: 0.6980 chunk 50 optimal weight: 7.9990 chunk 39 optimal weight: 8.9990 chunk 76 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 chunk 46 optimal weight: 8.9990 chunk 57 optimal weight: 0.0030 chunk 88 optimal weight: 0.8980 overall best weight: 1.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 684 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.0737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 8592 Z= 0.171 Angle : 0.676 8.174 11835 Z= 0.329 Chirality : 0.041 0.189 1391 Planarity : 0.004 0.044 1374 Dihedral : 18.586 178.372 1649 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 22.47 Ramachandran Plot: Outliers : 0.43 % Allowed : 9.15 % Favored : 90.43 % Rotamer: Outliers : 0.24 % Allowed : 3.25 % Favored : 96.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: -1.08 (0.28), residues: 942 helix: -0.01 (0.26), residues: 415 sheet: -1.43 (0.51), residues: 105 loop : -1.13 (0.33), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 328 HIS 0.003 0.001 HIS A 510 PHE 0.019 0.001 PHE A 200 TYR 0.008 0.001 TYR A 550 ARG 0.007 0.000 ARG A 198 *********************** 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 fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 1.195 Fit side-chains revert: symmetry clash REVERT: A 169 ASN cc_start: 0.8736 (p0) cc_final: 0.8534 (t0) REVERT: A 358 MET cc_start: 0.9632 (mmp) cc_final: 0.9376 (mmm) REVERT: A 389 MET cc_start: 0.8985 (pmm) cc_final: 0.8677 (pmm) REVERT: A 440 GLN cc_start: 0.8758 (tt0) cc_final: 0.8437 (tt0) REVERT: A 483 LEU cc_start: 0.9249 (tp) cc_final: 0.9026 (tp) REVERT: A 629 MET cc_start: 0.7019 (tmm) cc_final: 0.6641 (tpp) REVERT: A 797 MET cc_start: 0.8647 (ppp) cc_final: 0.8016 (ppp) outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 0.1808 time to fit residues: 17.4184 Evaluate side-chains 49 residues out of total 833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 8.9990 chunk 27 optimal weight: 6.9990 chunk 74 optimal weight: 9.9990 chunk 60 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 96 optimal weight: 10.0000 chunk 79 optimal weight: 0.8980 chunk 88 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 684 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.1119 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= 0.168 Angle : 0.663 7.599 11835 Z= 0.322 Chirality : 0.041 0.193 1391 Planarity : 0.004 0.052 1374 Dihedral : 18.443 178.229 1649 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 21.00 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.36 % Favored : 90.32 % Rotamer: Outliers : 0.36 % Allowed : 1.80 % Favored : 97.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.28), residues: 942 helix: 0.13 (0.26), residues: 413 sheet: -1.61 (0.50), residues: 103 loop : -1.18 (0.33), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 328 HIS 0.002 0.001 HIS A 503 PHE 0.017 0.001 PHE A 200 TYR 0.008 0.001 TYR A 550 ARG 0.007 0.000 ARG A 198 *********************** 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 fitting. rotamer outliers: 1 poor density : 59 time to evaluate : 0.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 358 MET cc_start: 0.9644 (mmp) cc_final: 0.9388 (mmm) REVERT: A 389 MET cc_start: 0.9016 (pmm) cc_final: 0.8740 (pmm) REVERT: A 483 LEU cc_start: 0.9244 (tp) cc_final: 0.9013 (tp) REVERT: A 629 MET cc_start: 0.7188 (tmm) cc_final: 0.6854 (tpp) REVERT: A 1004 LEU cc_start: 0.8917 (mm) cc_final: 0.8660 (mm) outliers start: 1 outliers final: 1 residues processed: 60 average time/residue: 0.1735 time to fit residues: 15.8786 Evaluate side-chains 47 residues out of total 833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 46 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 88 optimal weight: 1.9990 chunk 67 optimal weight: 10.0000 chunk 46 optimal weight: 10.0000 chunk 9 optimal weight: 20.0000 chunk 42 optimal weight: 6.9990 chunk 59 optimal weight: 6.9990 chunk 89 optimal weight: 0.9980 chunk 94 optimal weight: 10.0000 chunk 84 optimal weight: 7.9990 chunk 25 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 ASN A 179 GLN ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 430 GLN A 684 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.1725 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= 0.222 Angle : 0.696 7.706 11835 Z= 0.341 Chirality : 0.042 0.213 1391 Planarity : 0.004 0.055 1374 Dihedral : 18.456 177.820 1649 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 26.45 Ramachandran Plot: Outliers : 0.43 % Allowed : 10.00 % Favored : 89.57 % Rotamer: Outliers : 0.36 % Allowed : 2.40 % 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 (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: -1.10 (0.28), residues: 942 helix: 0.06 (0.26), residues: 420 sheet: -1.61 (0.50), residues: 102 loop : -1.23 (0.33), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 328 HIS 0.005 0.001 HIS A 922 PHE 0.023 0.002 PHE A 200 TYR 0.011 0.001 TYR A 420 ARG 0.006 0.001 ARG A 198 *********************** 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 59 residues out of total 833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 58 time to evaluate : 0.736 Fit side-chains revert: symmetry clash REVERT: A 358 MET cc_start: 0.9606 (mmp) cc_final: 0.9346 (mmm) REVERT: A 389 MET cc_start: 0.9115 (pmm) cc_final: 0.8842 (pmm) REVERT: A 440 GLN cc_start: 0.8945 (tt0) cc_final: 0.8482 (tt0) REVERT: A 629 MET cc_start: 0.7256 (tmm) cc_final: 0.6978 (tpp) REVERT: A 670 MET cc_start: 0.9247 (mmp) cc_final: 0.9030 (mmm) REVERT: A 797 MET cc_start: 0.8674 (ppp) cc_final: 0.7950 (ppp) REVERT: A 1004 LEU cc_start: 0.9014 (mm) cc_final: 0.8811 (mm) outliers start: 1 outliers final: 0 residues processed: 59 average time/residue: 0.1915 time to fit residues: 16.6079 Evaluate side-chains 41 residues out of total 833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 53 optimal weight: 10.0000 chunk 1 optimal weight: 7.9990 chunk 70 optimal weight: 10.0000 chunk 39 optimal weight: 5.9990 chunk 80 optimal weight: 10.0000 chunk 65 optimal weight: 1.9990 chunk 0 optimal weight: 30.0000 chunk 48 optimal weight: 0.0970 chunk 85 optimal weight: 9.9990 chunk 23 optimal weight: 0.0070 chunk 31 optimal weight: 9.9990 overall best weight: 3.2202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 684 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 8592 Z= 0.236 Angle : 0.708 8.284 11835 Z= 0.349 Chirality : 0.043 0.224 1391 Planarity : 0.005 0.098 1374 Dihedral : 18.546 179.188 1649 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 28.47 Ramachandran Plot: Outliers : 0.43 % Allowed : 10.21 % Favored : 89.36 % Rotamer: Outliers : 0.24 % Allowed : 2.16 % Favored : 97.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: -1.17 (0.28), residues: 942 helix: -0.01 (0.25), residues: 420 sheet: -1.43 (0.51), residues: 97 loop : -1.33 (0.33), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 328 HIS 0.003 0.001 HIS A 922 PHE 0.022 0.002 PHE A 200 TYR 0.011 0.002 TYR A 420 ARG 0.011 0.001 ARG A1158 *********************** 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 56 residues out of total 833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 358 MET cc_start: 0.9592 (mmp) cc_final: 0.9332 (mmm) REVERT: A 389 MET cc_start: 0.9176 (pmm) cc_final: 0.8907 (pmm) REVERT: A 440 GLN cc_start: 0.9051 (tt0) cc_final: 0.8518 (tt0) REVERT: A 629 MET cc_start: 0.7327 (tmm) cc_final: 0.7047 (tpp) REVERT: A 670 MET cc_start: 0.9260 (mmp) cc_final: 0.9004 (mmm) REVERT: A 871 MET cc_start: 0.8758 (ptp) cc_final: 0.8341 (pmm) REVERT: A 1004 LEU cc_start: 0.9074 (mm) cc_final: 0.8771 (mm) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.1669 time to fit residues: 14.3885 Evaluate side-chains 39 residues out of total 833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 85 optimal weight: 6.9990 chunk 18 optimal weight: 0.0170 chunk 55 optimal weight: 3.9990 chunk 23 optimal weight: 8.9990 chunk 94 optimal weight: 9.9990 chunk 78 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 7 optimal weight: 0.0570 chunk 31 optimal weight: 5.9990 chunk 49 optimal weight: 0.0470 chunk 91 optimal weight: 3.9990 overall best weight: 1.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 684 GLN ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 8592 Z= 0.175 Angle : 0.687 8.705 11835 Z= 0.332 Chirality : 0.042 0.220 1391 Planarity : 0.004 0.056 1374 Dihedral : 18.443 179.266 1649 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 24.19 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.79 % Favored : 89.89 % Rotamer: Outliers : 0.24 % Allowed : 1.56 % Favored : 98.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: -1.12 (0.29), residues: 942 helix: 0.06 (0.26), residues: 417 sheet: -1.51 (0.51), residues: 102 loop : -1.28 (0.33), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 328 HIS 0.004 0.001 HIS A 510 PHE 0.018 0.001 PHE A 200 TYR 0.007 0.001 TYR A 550 ARG 0.004 0.000 ARG A1158 *********************** 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 56 residues out of total 833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 358 MET cc_start: 0.9590 (mmp) cc_final: 0.9330 (mmm) REVERT: A 440 GLN cc_start: 0.9051 (tt0) cc_final: 0.8512 (tt0) REVERT: A 483 LEU cc_start: 0.9255 (tp) cc_final: 0.9044 (tp) REVERT: A 538 MET cc_start: 0.3473 (ttt) cc_final: 0.3144 (ttt) REVERT: A 629 MET cc_start: 0.7266 (tmm) cc_final: 0.6987 (tpp) REVERT: A 670 MET cc_start: 0.9233 (mmp) cc_final: 0.8997 (mmm) REVERT: A 797 MET cc_start: 0.8677 (ppp) cc_final: 0.7955 (ppp) REVERT: A 807 LEU cc_start: 0.9624 (mt) cc_final: 0.9297 (tt) REVERT: A 872 MET cc_start: 0.9027 (mmp) cc_final: 0.8793 (mmm) REVERT: A 1004 LEU cc_start: 0.9021 (mm) cc_final: 0.8769 (mm) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.1526 time to fit residues: 13.6649 Evaluate side-chains 44 residues out of total 833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 10 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 chunk 69 optimal weight: 10.0000 chunk 53 optimal weight: 4.9990 chunk 79 optimal weight: 0.3980 chunk 52 optimal weight: 3.9990 chunk 94 optimal weight: 10.0000 chunk 59 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 43 optimal weight: 8.9990 chunk 58 optimal weight: 2.9990 overall best weight: 2.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 419 GLN ** A 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 684 GLN ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.2583 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= 0.198 Angle : 0.683 8.314 11835 Z= 0.332 Chirality : 0.042 0.228 1391 Planarity : 0.005 0.076 1374 Dihedral : 18.462 179.589 1649 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 25.84 Ramachandran Plot: Outliers : 0.32 % Allowed : 10.00 % Favored : 89.68 % Rotamer: Outliers : 0.24 % Allowed : 1.32 % Favored : 98.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.28), residues: 942 helix: 0.08 (0.26), residues: 419 sheet: -1.53 (0.50), residues: 102 loop : -1.35 (0.33), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 328 HIS 0.005 0.001 HIS A 510 PHE 0.020 0.002 PHE A 200 TYR 0.011 0.001 TYR A 420 ARG 0.005 0.000 ARG A 844 *********************** 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 58 residues out of total 833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 358 MET cc_start: 0.9580 (mmp) cc_final: 0.9321 (mmm) REVERT: A 389 MET cc_start: 0.9193 (pmm) cc_final: 0.8855 (pmm) REVERT: A 440 GLN cc_start: 0.9064 (tt0) cc_final: 0.8616 (tt0) REVERT: A 483 LEU cc_start: 0.9275 (tp) cc_final: 0.9072 (tp) REVERT: A 538 MET cc_start: 0.3703 (ttt) cc_final: 0.3325 (ttt) REVERT: A 629 MET cc_start: 0.7284 (tmm) cc_final: 0.6993 (tpp) REVERT: A 670 MET cc_start: 0.9209 (mmp) cc_final: 0.8980 (mmm) REVERT: A 797 MET cc_start: 0.8687 (ppp) cc_final: 0.7996 (ppp) REVERT: A 872 MET cc_start: 0.9004 (mmp) cc_final: 0.8801 (mmm) REVERT: A 1004 LEU cc_start: 0.9012 (mm) cc_final: 0.8759 (mm) outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.1811 time to fit residues: 16.0761 Evaluate side-chains 40 residues out of total 833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 37 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 chunk 28 optimal weight: 10.0000 chunk 18 optimal weight: 0.0010 chunk 60 optimal weight: 0.0980 chunk 64 optimal weight: 0.0870 chunk 46 optimal weight: 0.0040 chunk 8 optimal weight: 0.9990 chunk 74 optimal weight: 7.9990 chunk 85 optimal weight: 5.9990 chunk 90 optimal weight: 0.7980 overall best weight: 0.1976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 419 GLN A 510 HIS A 958 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 8592 Z= 0.158 Angle : 0.705 9.162 11835 Z= 0.338 Chirality : 0.043 0.215 1391 Planarity : 0.004 0.068 1374 Dihedral : 18.266 179.953 1649 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 19.84 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.36 % Favored : 90.32 % Rotamer: Outliers : 0.24 % Allowed : 0.36 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.28), residues: 942 helix: 0.02 (0.26), residues: 415 sheet: -1.50 (0.50), residues: 103 loop : -1.26 (0.33), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 328 HIS 0.002 0.001 HIS A 984 PHE 0.013 0.001 PHE A 200 TYR 0.009 0.001 TYR A 467 ARG 0.009 0.000 ARG A 173 *********************** 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 fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 0.940 Fit side-chains revert: symmetry clash REVERT: A 358 MET cc_start: 0.9580 (mmp) cc_final: 0.9322 (mmm) REVERT: A 389 MET cc_start: 0.9151 (pmm) cc_final: 0.8871 (pmm) REVERT: A 440 GLN cc_start: 0.9128 (tt0) cc_final: 0.8600 (tt0) REVERT: A 483 LEU cc_start: 0.9287 (tp) cc_final: 0.8994 (tp) REVERT: A 538 MET cc_start: 0.3324 (ttt) cc_final: 0.2667 (ttt) REVERT: A 629 MET cc_start: 0.7168 (tmm) cc_final: 0.6892 (tpp) REVERT: A 670 MET cc_start: 0.9181 (mmp) cc_final: 0.8948 (mmm) REVERT: A 797 MET cc_start: 0.8640 (ppp) cc_final: 0.7968 (ppp) REVERT: A 807 LEU cc_start: 0.9628 (mt) cc_final: 0.9276 (tt) REVERT: A 872 MET cc_start: 0.9025 (mmp) cc_final: 0.8792 (mmm) REVERT: A 1004 LEU cc_start: 0.8943 (mm) cc_final: 0.8688 (mm) outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.1618 time to fit residues: 15.4869 Evaluate side-chains 46 residues out of total 833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 6.9990 chunk 88 optimal weight: 10.0000 chunk 90 optimal weight: 4.9990 chunk 52 optimal weight: 7.9990 chunk 38 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 79 optimal weight: 3.9990 chunk 83 optimal weight: 8.9990 chunk 87 optimal weight: 0.7980 chunk 57 optimal weight: 0.6980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 419 GLN A 684 GLN A 958 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 8592 Z= 0.165 Angle : 0.669 8.309 11835 Z= 0.323 Chirality : 0.042 0.220 1391 Planarity : 0.004 0.060 1374 Dihedral : 18.250 179.301 1649 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 23.02 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.36 % Favored : 90.32 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.29), residues: 942 helix: 0.20 (0.26), residues: 417 sheet: -1.48 (0.51), residues: 103 loop : -1.25 (0.33), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 328 HIS 0.002 0.001 HIS A 510 PHE 0.015 0.001 PHE A 200 TYR 0.010 0.001 TYR A 467 ARG 0.003 0.000 ARG A1158 *********************** 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 60 residues out of total 833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 0.951 Fit side-chains REVERT: A 358 MET cc_start: 0.9570 (mmp) cc_final: 0.9286 (mmm) REVERT: A 389 MET cc_start: 0.9165 (pmm) cc_final: 0.8897 (pmm) REVERT: A 440 GLN cc_start: 0.9110 (tt0) cc_final: 0.8652 (tt0) REVERT: A 483 LEU cc_start: 0.9254 (tp) cc_final: 0.8996 (tp) REVERT: A 538 MET cc_start: 0.3061 (ttt) cc_final: 0.2744 (ttt) REVERT: A 670 MET cc_start: 0.9176 (mmp) cc_final: 0.8953 (mmm) REVERT: A 797 MET cc_start: 0.8689 (ppp) cc_final: 0.8117 (ppp) REVERT: A 872 MET cc_start: 0.9027 (mmp) cc_final: 0.8812 (mmm) REVERT: A 966 GLN cc_start: 0.9564 (tt0) cc_final: 0.9201 (mt0) REVERT: A 1004 LEU cc_start: 0.8923 (mm) cc_final: 0.8668 (mm) outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.1541 time to fit residues: 14.7909 Evaluate side-chains 43 residues out of total 833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 93 optimal weight: 10.0000 chunk 56 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 64 optimal weight: 0.0050 chunk 97 optimal weight: 9.9990 chunk 89 optimal weight: 0.8980 chunk 77 optimal weight: 5.9990 chunk 8 optimal weight: 0.0980 chunk 60 optimal weight: 0.0060 chunk 47 optimal weight: 8.9990 chunk 61 optimal weight: 0.0030 overall best weight: 0.1820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 ASN A 179 GLN ** A 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.082 8592 Z= 0.147 Angle : 0.685 8.292 11835 Z= 0.327 Chirality : 0.042 0.206 1391 Planarity : 0.004 0.055 1374 Dihedral : 17.993 178.101 1649 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 17.88 Ramachandran Plot: Outliers : 0.43 % Allowed : 8.62 % Favored : 90.96 % Rotamer: Outliers : 0.24 % Allowed : 0.00 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: -1.12 (0.28), residues: 942 helix: 0.06 (0.26), residues: 417 sheet: -1.39 (0.47), residues: 117 loop : -1.30 (0.33), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 328 HIS 0.002 0.001 HIS A 510 PHE 0.010 0.001 PHE A 200 TYR 0.007 0.001 TYR A 550 ARG 0.010 0.000 ARG A1158 ********************** 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 64 residues out of total 833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 1.000 Fit side-chains REVERT: A 358 MET cc_start: 0.9582 (mmp) cc_final: 0.9306 (mmm) REVERT: A 389 MET cc_start: 0.9096 (pmm) cc_final: 0.8890 (pmm) REVERT: A 440 GLN cc_start: 0.9035 (tt0) cc_final: 0.8522 (tt0) REVERT: A 483 LEU cc_start: 0.9241 (tp) cc_final: 0.8908 (tp) REVERT: A 629 MET cc_start: 0.6854 (tmm) cc_final: 0.6085 (tpp) REVERT: A 670 MET cc_start: 0.9154 (mmp) cc_final: 0.8933 (mmm) REVERT: A 797 MET cc_start: 0.8656 (ppp) cc_final: 0.8080 (ppp) REVERT: A 807 LEU cc_start: 0.9630 (mt) cc_final: 0.9250 (tt) REVERT: A 872 MET cc_start: 0.8972 (mmp) cc_final: 0.8748 (mmm) REVERT: A 954 MET cc_start: 0.8793 (mmt) cc_final: 0.8540 (mmp) REVERT: A 966 GLN cc_start: 0.9560 (tt0) cc_final: 0.9190 (mt0) REVERT: A 1004 LEU cc_start: 0.8820 (mm) cc_final: 0.8571 (mm) outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.1563 time to fit residues: 15.8909 Evaluate side-chains 48 residues out of total 833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 0.0010 chunk 23 optimal weight: 7.9990 chunk 71 optimal weight: 3.9990 chunk 11 optimal weight: 6.9990 chunk 21 optimal weight: 10.0000 chunk 77 optimal weight: 6.9990 chunk 32 optimal weight: 0.9980 chunk 79 optimal weight: 0.6980 chunk 9 optimal weight: 7.9990 chunk 14 optimal weight: 0.4980 chunk 68 optimal weight: 7.9990 overall best weight: 1.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 419 GLN ** A 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.064934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.046840 restraints weight = 244131.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.048996 restraints weight = 119018.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.049889 restraints weight = 75232.160| |-----------------------------------------------------------------------------| r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3128 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3128 r_free = 0.3128 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 = 0.3128 r_free = 0.3128 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3128 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 8592 Z= 0.154 Angle : 0.659 8.085 11835 Z= 0.316 Chirality : 0.041 0.209 1391 Planarity : 0.004 0.054 1374 Dihedral : 18.021 179.750 1649 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 20.70 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.15 % Favored : 90.53 % 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 (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: -1.00 (0.29), residues: 942 helix: 0.22 (0.26), residues: 416 sheet: -1.39 (0.48), residues: 117 loop : -1.29 (0.33), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 328 HIS 0.002 0.001 HIS A 922 PHE 0.014 0.001 PHE A 200 TYR 0.009 0.001 TYR A 420 ARG 0.003 0.000 ARG A1158 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1813.89 seconds wall clock time: 34 minutes 14.12 seconds (2054.12 seconds total)