Starting phenix.real_space_refine on Thu Jan 16 15:32:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b5v_44226/01_2025/9b5v_44226.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b5v_44226/01_2025/9b5v_44226.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b5v_44226/01_2025/9b5v_44226.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b5v_44226/01_2025/9b5v_44226.map" model { file = "/net/cci-nas-00/data/ceres_data/9b5v_44226/01_2025/9b5v_44226.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b5v_44226/01_2025/9b5v_44226.cif" } resolution = 3.94 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= 0.040 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 3 5.49 5 Mg 2 5.21 5 S 42 5.16 5 C 6074 2.51 5 N 1573 2.21 5 O 1833 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 9527 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 985, 7734 Classifications: {'peptide': 985} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 55, 'TRANS': 928} Chain breaks: 1 Chain: "C" Number of atoms: 1158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1158 Classifications: {'peptide': 147} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 131} Chain: "D" Number of atoms: 596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 596 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 6 Unusual residues: {'A1AIV': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.06, per 1000 atoms: 0.64 Number of scatterers: 9527 At special positions: 0 Unit cell: (91.504, 100.016, 121.296, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 42 16.00 P 3 15.00 Mg 2 11.99 O 1833 8.00 N 1573 7.00 C 6074 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 593 " - pdb=" SG CYS C 85 " distance=2.93 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.45 Conformation dependent library (CDL) restraints added in 1.2 seconds 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2264 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 11 sheets defined 46.8% alpha, 16.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.39 Creating SS restraints... Processing helix chain 'A' and resid 20 through 25 removed outlier: 4.063A pdb=" N TYR A 25 " --> pdb=" O SER A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 36 Processing helix chain 'A' and resid 46 through 60 Processing helix chain 'A' and resid 74 through 79 removed outlier: 3.936A pdb=" N SER A 79 " --> pdb=" O ASP A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 88 removed outlier: 3.887A pdb=" N ILE A 88 " --> pdb=" O GLU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 101 removed outlier: 4.510A pdb=" N SER A 98 " --> pdb=" O LYS A 94 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N LYS A 99 " --> pdb=" O VAL A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 123 Processing helix chain 'A' and resid 132 through 146 removed outlier: 3.707A pdb=" N PHE A 142 " --> pdb=" O GLU A 138 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N LYS A 145 " --> pdb=" O ASP A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 224 removed outlier: 3.796A pdb=" N GLY A 224 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 274 removed outlier: 4.428A pdb=" N LYS A 273 " --> pdb=" O ARG A 269 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ASP A 274 " --> pdb=" O GLU A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 305 removed outlier: 3.727A pdb=" N ILE A 293 " --> pdb=" O PRO A 289 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLN A 296 " --> pdb=" O HIS A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 332 Processing helix chain 'A' and resid 339 through 349 Processing helix chain 'A' and resid 354 through 375 Processing helix chain 'A' and resid 389 through 392 Processing helix chain 'A' and resid 410 through 418 removed outlier: 4.565A pdb=" N VAL A 416 " --> pdb=" O GLY A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 427 Processing helix chain 'A' and resid 436 through 450 Processing helix chain 'A' and resid 468 through 474 removed outlier: 3.875A pdb=" N ASN A 473 " --> pdb=" O SER A 470 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG A 474 " --> pdb=" O ASN A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 483 Processing helix chain 'A' and resid 486 through 499 removed outlier: 3.627A pdb=" N CYS A 490 " --> pdb=" O LEU A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 503 Processing helix chain 'A' and resid 514 through 518 removed outlier: 3.625A pdb=" N GLU A 518 " --> pdb=" O PRO A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 527 Processing helix chain 'A' and resid 538 through 553 removed outlier: 3.562A pdb=" N ARG A 542 " --> pdb=" O ASN A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 583 Processing helix chain 'A' and resid 591 through 597 Processing helix chain 'A' and resid 601 through 618 Processing helix chain 'A' and resid 618 through 628 Processing helix chain 'A' and resid 632 through 641 removed outlier: 3.515A pdb=" N LYS A 639 " --> pdb=" O GLU A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 643 through 656 Processing helix chain 'A' and resid 662 through 679 Processing helix chain 'A' and resid 679 through 689 removed outlier: 3.521A pdb=" N GLN A 683 " --> pdb=" O ASN A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 737 Processing helix chain 'A' and resid 743 through 753 removed outlier: 3.996A pdb=" N TYR A 747 " --> pdb=" O ASP A 743 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLY A 753 " --> pdb=" O ARG A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 781 through 794 Processing helix chain 'A' and resid 796 through 800 Processing helix chain 'A' and resid 818 through 834 Processing helix chain 'A' and resid 840 through 849 Processing helix chain 'A' and resid 855 through 876 removed outlier: 3.626A pdb=" N VAL A 871 " --> pdb=" O CYS A 867 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LYS A 872 " --> pdb=" O LEU A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 883 removed outlier: 3.671A pdb=" N TYR A 883 " --> pdb=" O ILE A 880 " (cutoff:3.500A) Processing helix chain 'A' and resid 926 through 937 Processing helix chain 'A' and resid 958 through 966 Processing helix chain 'A' and resid 969 through 979 Processing helix chain 'C' and resid 3 through 16 Processing helix chain 'C' and resid 98 through 112 Processing helix chain 'C' and resid 120 through 130 Processing helix chain 'C' and resid 130 through 145 Processing helix chain 'D' and resid 22 through 35 Processing helix chain 'D' and resid 37 through 41 Processing helix chain 'D' and resid 56 through 60 Processing sheet with id=AA1, first strand: chain 'A' and resid 109 through 111 removed outlier: 6.939A pdb=" N VAL A 64 " --> pdb=" O SER A 110 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N VAL A 126 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N ALA A 153 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N VAL A 128 " --> pdb=" O ALA A 153 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N SER A 155 " --> pdb=" O VAL A 128 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N TYR A 385 " --> pdb=" O VAL A 278 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 170 through 172 Processing sheet with id=AA3, first strand: chain 'A' and resid 227 through 228 removed outlier: 4.046A pdb=" N PHE A 209 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N THR A 195 " --> pdb=" O ALA A 186 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ILE A 188 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VAL A 193 " --> pdb=" O ILE A 188 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 227 through 228 removed outlier: 4.046A pdb=" N PHE A 209 " --> pdb=" O VAL A 257 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 506 through 509 removed outlier: 6.518A pdb=" N ILE A 459 " --> pdb=" O THR A 507 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N TYR A 509 " --> pdb=" O ILE A 459 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N VAL A 461 " --> pdb=" O TYR A 509 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU A 531 " --> pdb=" O SER A 429 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N SER A 559 " --> pdb=" O ASN A 534 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 905 through 907 Processing sheet with id=AA7, first strand: chain 'A' and resid 920 through 923 removed outlier: 6.321A pdb=" N TYR A 920 " --> pdb=" O CYS A1009 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LYS A1011 " --> pdb=" O TYR A 920 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N LEU A 922 " --> pdb=" O LYS A1011 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ASP A 996 " --> pdb=" O VAL A 942 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N VAL A 942 " --> pdb=" O ASP A 996 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N SER A 947 " --> pdb=" O LEU A 951 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N LEU A 951 " --> pdb=" O SER A 947 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 920 through 923 removed outlier: 6.321A pdb=" N TYR A 920 " --> pdb=" O CYS A1009 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LYS A1011 " --> pdb=" O TYR A 920 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N LEU A 922 " --> pdb=" O LYS A1011 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N CYS A 995 " --> pdb=" O VAL A1003 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 21 through 22 removed outlier: 6.332A pdb=" N HIS C 32 " --> pdb=" O VAL C 26 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 21 through 22 Processing sheet with id=AB2, first strand: chain 'D' and resid 12 through 16 removed outlier: 8.804A pdb=" N LEU D 67 " --> pdb=" O GLN D 2 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N PHE D 4 " --> pdb=" O LEU D 67 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N LEU D 69 " --> pdb=" O PHE D 4 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N LYS D 6 " --> pdb=" O LEU D 69 " (cutoff:3.500A) 469 hydrogen bonds defined for protein. 1272 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.33 Time building geometry restraints manager: 2.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 1616 1.27 - 1.40: 2291 1.40 - 1.54: 5657 1.54 - 1.67: 110 1.67 - 1.81: 64 Bond restraints: 9738 Sorted by residual: bond pdb=" C04 A1AIV D 101 " pdb=" C05 A1AIV D 101 " ideal model delta sigma weight residual 1.453 1.525 -0.072 2.00e-02 2.50e+03 1.29e+01 bond pdb=" N MET D 1 " pdb=" CA MET D 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.76e+00 bond pdb=" C SER A 589 " pdb=" N PHE A 590 " ideal model delta sigma weight residual 1.339 1.277 0.062 5.57e-02 3.22e+02 1.25e+00 bond pdb=" C1' ATP A1103 " pdb=" C2' ATP A1103 " ideal model delta sigma weight residual 1.531 1.519 0.012 1.20e-02 6.94e+03 9.88e-01 bond pdb=" C05 A1AIV D 101 " pdb=" N06 A1AIV D 101 " ideal model delta sigma weight residual 1.151 1.132 0.019 2.00e-02 2.50e+03 8.68e-01 ... (remaining 9733 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.35: 12916 1.35 - 2.70: 192 2.70 - 4.05: 76 4.05 - 5.40: 9 5.40 - 6.74: 2 Bond angle restraints: 13195 Sorted by residual: angle pdb=" C LYS A 381 " pdb=" N GLN A 382 " pdb=" CA GLN A 382 " ideal model delta sigma weight residual 121.70 127.93 -6.23 1.80e+00 3.09e-01 1.20e+01 angle pdb=" C2' ATP A1103 " pdb=" C1' ATP A1103 " pdb=" O4' ATP A1103 " ideal model delta sigma weight residual 106.53 103.32 3.21 1.18e+00 7.24e-01 7.47e+00 angle pdb=" C3' ATP A1103 " pdb=" C4' ATP A1103 " pdb=" C5' ATP A1103 " ideal model delta sigma weight residual 115.19 110.91 4.28 1.76e+00 3.23e-01 5.92e+00 angle pdb=" C1' ATP A1103 " pdb=" C2' ATP A1103 " pdb=" O2' ATP A1103 " ideal model delta sigma weight residual 110.58 103.84 6.74 2.79e+00 1.28e-01 5.83e+00 angle pdb=" C4' ATP A1103 " pdb=" C3' ATP A1103 " pdb=" O3' ATP A1103 " ideal model delta sigma weight residual 111.06 106.03 5.03 2.50e+00 1.60e-01 4.05e+00 ... (remaining 13190 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.05: 5695 18.05 - 36.10: 188 36.10 - 54.15: 42 54.15 - 72.21: 1 72.21 - 90.26: 3 Dihedral angle restraints: 5929 sinusoidal: 2424 harmonic: 3505 Sorted by residual: dihedral pdb=" CB CYS A 593 " pdb=" SG CYS A 593 " pdb=" SG CYS C 85 " pdb=" CB CYS C 85 " ideal model delta sinusoidal sigma weight residual -86.00 -176.26 90.26 1 1.00e+01 1.00e-02 9.64e+01 dihedral pdb=" CB ARG D 74 " pdb=" CG ARG D 74 " pdb=" CD ARG D 74 " pdb=" NE ARG D 74 " ideal model delta sinusoidal sigma weight residual -60.00 -114.00 54.00 3 1.50e+01 4.44e-03 9.25e+00 dihedral pdb=" N GLU A 869 " pdb=" CA GLU A 869 " pdb=" CB GLU A 869 " pdb=" CG GLU A 869 " ideal model delta sinusoidal sigma weight residual -60.00 -113.49 53.49 3 1.50e+01 4.44e-03 9.21e+00 ... (remaining 5926 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1274 0.054 - 0.108: 160 0.108 - 0.161: 34 0.161 - 0.215: 1 0.215 - 0.269: 2 Chirality restraints: 1471 Sorted by residual: chirality pdb=" C2' ATP A1103 " pdb=" C1' ATP A1103 " pdb=" C3' ATP A1103 " pdb=" O2' ATP A1103 " both_signs ideal model delta sigma weight residual False -2.68 -2.95 0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" C3' ATP A1103 " pdb=" C2' ATP A1103 " pdb=" C4' ATP A1103 " pdb=" O3' ATP A1103 " both_signs ideal model delta sigma weight residual False -2.63 -2.88 0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" C4' ATP A1103 " pdb=" C3' ATP A1103 " pdb=" C5' ATP A1103 " pdb=" O4' ATP A1103 " both_signs ideal model delta sigma weight residual False -2.49 -2.71 0.21 2.00e-01 2.50e+01 1.14e+00 ... (remaining 1468 not shown) Planarity restraints: 1707 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU D 67 " -0.007 2.00e-02 2.50e+03 1.44e-02 2.06e+00 pdb=" C LEU D 67 " 0.025 2.00e-02 2.50e+03 pdb=" O LEU D 67 " -0.009 2.00e-02 2.50e+03 pdb=" N HIS D 68 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL C 120 " -0.018 5.00e-02 4.00e+02 2.67e-02 1.14e+00 pdb=" N PRO C 121 " 0.046 5.00e-02 4.00e+02 pdb=" CA PRO C 121 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO C 121 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR C 60 " -0.015 5.00e-02 4.00e+02 2.33e-02 8.69e-01 pdb=" N PRO C 61 " 0.040 5.00e-02 4.00e+02 pdb=" CA PRO C 61 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO C 61 " -0.012 5.00e-02 4.00e+02 ... (remaining 1704 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 108 2.56 - 3.14: 7921 3.14 - 3.73: 14486 3.73 - 4.31: 20176 4.31 - 4.90: 34385 Nonbonded interactions: 77076 Sorted by model distance: nonbonded pdb="MG MG A1101 " pdb=" O2A ATP A1103 " model vdw 1.969 2.170 nonbonded pdb="MG MG A1102 " pdb=" O1B ATP A1103 " model vdw 2.020 2.170 nonbonded pdb="MG MG A1101 " pdb=" O3G ATP A1103 " model vdw 2.020 2.170 nonbonded pdb=" OD2 ASP A 465 " pdb="MG MG A1102 " model vdw 2.102 2.170 nonbonded pdb=" OE2 GLU A 468 " pdb="MG MG A1102 " model vdw 2.137 2.170 ... (remaining 77071 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 24.390 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 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 0.072 9738 Z= 0.204 Angle : 0.511 6.744 13195 Z= 0.268 Chirality : 0.040 0.269 1471 Planarity : 0.003 0.027 1707 Dihedral : 9.567 80.529 3662 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.83 % Favored : 98.00 % Rotamer: Outliers : 2.36 % Allowed : 2.54 % Favored : 95.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % 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: 1.41 (0.25), residues: 1199 helix: 1.95 (0.25), residues: 476 sheet: 0.28 (0.37), residues: 217 loop : 0.37 (0.29), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 702 HIS 0.004 0.001 HIS D 68 PHE 0.009 0.001 PHE A 842 TYR 0.009 0.001 TYR C 134 ARG 0.002 0.000 ARG C 133 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 177 time to evaluate : 1.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 CYS cc_start: 0.9489 (m) cc_final: 0.9288 (m) REVERT: A 162 ILE cc_start: 0.9638 (mt) cc_final: 0.9426 (mm) REVERT: A 235 TYR cc_start: 0.8418 (m-80) cc_final: 0.8048 (m-10) REVERT: A 345 GLU cc_start: 0.9319 (mm-30) cc_final: 0.8892 (mm-30) REVERT: A 353 ASP cc_start: 0.8282 (t0) cc_final: 0.7796 (m-30) REVERT: A 357 MET cc_start: 0.8930 (mmm) cc_final: 0.8714 (mmm) REVERT: A 445 ASN cc_start: 0.9149 (m-40) cc_final: 0.8497 (m-40) REVERT: A 448 MET cc_start: 0.9487 (mmp) cc_final: 0.9212 (mmm) REVERT: A 526 PHE cc_start: 0.9415 (OUTLIER) cc_final: 0.8668 (t80) REVERT: A 557 LEU cc_start: 0.9055 (mt) cc_final: 0.8851 (mp) REVERT: A 562 LEU cc_start: 0.9130 (tp) cc_final: 0.8729 (pp) REVERT: A 606 ILE cc_start: 0.9407 (mt) cc_final: 0.9140 (mm) REVERT: A 622 ASP cc_start: 0.9196 (m-30) cc_final: 0.8778 (t0) REVERT: A 919 ARG cc_start: 0.7144 (OUTLIER) cc_final: 0.6914 (ptp-170) REVERT: A 955 ASN cc_start: 0.9305 (OUTLIER) cc_final: 0.8897 (m-40) REVERT: C 28 ASP cc_start: 0.8386 (m-30) cc_final: 0.8174 (t70) REVERT: C 67 VAL cc_start: 0.9346 (t) cc_final: 0.9115 (t) REVERT: C 88 ILE cc_start: 0.9083 (pt) cc_final: 0.8615 (mp) REVERT: D 50 LEU cc_start: 0.8222 (mt) cc_final: 0.7606 (mt) outliers start: 25 outliers final: 6 residues processed: 197 average time/residue: 0.2643 time to fit residues: 69.0974 Evaluate side-chains 87 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 78 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 526 PHE Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain A residue 919 ARG Chi-restraints excluded: chain A residue 955 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 100 optimal weight: 0.7980 chunk 90 optimal weight: 1.9990 chunk 50 optimal weight: 0.3980 chunk 30 optimal weight: 3.9990 chunk 60 optimal weight: 0.5980 chunk 48 optimal weight: 0.9990 chunk 93 optimal weight: 0.4980 chunk 36 optimal weight: 0.1980 chunk 56 optimal weight: 3.9990 chunk 69 optimal weight: 6.9990 chunk 108 optimal weight: 1.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.051094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.039512 restraints weight = 58992.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.040840 restraints weight = 34191.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.041758 restraints weight = 23262.278| |-----------------------------------------------------------------------------| r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 9738 Z= 0.200 Angle : 0.604 9.309 13195 Z= 0.309 Chirality : 0.044 0.207 1471 Planarity : 0.004 0.055 1707 Dihedral : 5.716 60.553 1341 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.51 % Allowed : 8.01 % Favored : 90.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % 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: 1.50 (0.25), residues: 1199 helix: 1.87 (0.24), residues: 497 sheet: 0.75 (0.39), residues: 194 loop : 0.33 (0.29), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 33 HIS 0.004 0.001 HIS D 68 PHE 0.013 0.001 PHE A 237 TYR 0.020 0.001 TYR A 25 ARG 0.006 0.001 ARG A 406 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 91 time to evaluate : 1.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 MET cc_start: 0.8949 (OUTLIER) cc_final: 0.8662 (ppp) REVERT: A 235 TYR cc_start: 0.8284 (m-80) cc_final: 0.7994 (m-10) REVERT: A 253 VAL cc_start: 0.8289 (OUTLIER) cc_final: 0.8055 (p) REVERT: A 285 MET cc_start: 0.8670 (pmm) cc_final: 0.8063 (mpp) REVERT: A 345 GLU cc_start: 0.9235 (mm-30) cc_final: 0.8878 (mm-30) REVERT: A 353 ASP cc_start: 0.8096 (t0) cc_final: 0.7819 (m-30) REVERT: A 445 ASN cc_start: 0.9117 (m-40) cc_final: 0.8602 (m-40) REVERT: A 464 MET cc_start: 0.8875 (pmt) cc_final: 0.8270 (pmt) REVERT: A 526 PHE cc_start: 0.9350 (OUTLIER) cc_final: 0.8525 (t80) REVERT: A 562 LEU cc_start: 0.9116 (tp) cc_final: 0.8886 (tp) REVERT: A 622 ASP cc_start: 0.9517 (m-30) cc_final: 0.8788 (t0) REVERT: A 626 MET cc_start: 0.9234 (mmp) cc_final: 0.8838 (mmp) REVERT: A 707 ARG cc_start: 0.7876 (mtp85) cc_final: 0.7635 (mtt180) REVERT: A 809 GLU cc_start: 0.8567 (mp0) cc_final: 0.8251 (tp30) REVERT: A 906 MET cc_start: 0.7595 (tmm) cc_final: 0.7359 (tmm) REVERT: C 38 MET cc_start: 0.7591 (mmm) cc_final: 0.6733 (mmm) REVERT: C 63 LYS cc_start: 0.9761 (OUTLIER) cc_final: 0.9559 (tppt) REVERT: C 130 ASP cc_start: 0.8783 (t0) cc_final: 0.8305 (p0) REVERT: D 73 LEU cc_start: 0.9291 (pt) cc_final: 0.9041 (mt) outliers start: 16 outliers final: 5 residues processed: 100 average time/residue: 0.2331 time to fit residues: 32.9417 Evaluate side-chains 79 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 70 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 MET Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 526 PHE Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain C residue 63 LYS Chi-restraints excluded: chain D residue 31 GLN Chi-restraints excluded: chain D residue 44 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 61 optimal weight: 7.9990 chunk 70 optimal weight: 0.0770 chunk 60 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 chunk 85 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 18 optimal weight: 0.7980 overall best weight: 1.3742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.050151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.038671 restraints weight = 61377.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.039973 restraints weight = 35344.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.040870 restraints weight = 24121.383| |-----------------------------------------------------------------------------| r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.2631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9738 Z= 0.216 Angle : 0.571 8.715 13195 Z= 0.287 Chirality : 0.042 0.169 1471 Planarity : 0.004 0.045 1707 Dihedral : 5.398 59.246 1330 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.07 % Allowed : 8.48 % Favored : 89.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % 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: 1.57 (0.25), residues: 1199 helix: 1.89 (0.24), residues: 500 sheet: 0.68 (0.38), residues: 206 loop : 0.44 (0.30), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 33 HIS 0.003 0.001 HIS D 68 PHE 0.013 0.001 PHE A 934 TYR 0.010 0.001 TYR A 25 ARG 0.009 0.001 ARG C 5 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 70 time to evaluate : 1.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 MET cc_start: 0.9453 (ttm) cc_final: 0.9121 (ttp) REVERT: A 184 MET cc_start: 0.8679 (OUTLIER) cc_final: 0.8092 (tpt) REVERT: A 235 TYR cc_start: 0.8335 (m-80) cc_final: 0.8056 (m-10) REVERT: A 285 MET cc_start: 0.8695 (pmm) cc_final: 0.8129 (mpp) REVERT: A 353 ASP cc_start: 0.8200 (t0) cc_final: 0.7811 (m-30) REVERT: A 445 ASN cc_start: 0.9085 (m-40) cc_final: 0.8611 (m-40) REVERT: A 464 MET cc_start: 0.8920 (pmt) cc_final: 0.8376 (pmt) REVERT: A 526 PHE cc_start: 0.9343 (OUTLIER) cc_final: 0.8438 (t80) REVERT: A 562 LEU cc_start: 0.9133 (tp) cc_final: 0.8906 (tp) REVERT: A 606 ILE cc_start: 0.9445 (mt) cc_final: 0.9244 (mp) REVERT: A 622 ASP cc_start: 0.9499 (m-30) cc_final: 0.8788 (t0) REVERT: A 626 MET cc_start: 0.9351 (mmp) cc_final: 0.8808 (mmp) REVERT: A 707 ARG cc_start: 0.7959 (mtp85) cc_final: 0.7733 (mtt180) REVERT: A 906 MET cc_start: 0.7592 (tmm) cc_final: 0.7241 (tmm) REVERT: A 945 LEU cc_start: 0.9492 (mt) cc_final: 0.9197 (mt) REVERT: C 52 LEU cc_start: 0.9160 (mp) cc_final: 0.8911 (mt) REVERT: C 63 LYS cc_start: 0.9763 (OUTLIER) cc_final: 0.9556 (tppt) REVERT: C 130 ASP cc_start: 0.8784 (t0) cc_final: 0.8405 (p0) REVERT: D 1 MET cc_start: 0.4765 (tmm) cc_final: 0.3963 (tmm) REVERT: D 50 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8655 (mp) REVERT: D 73 LEU cc_start: 0.9266 (pt) cc_final: 0.9047 (mt) outliers start: 22 outliers final: 11 residues processed: 86 average time/residue: 0.2199 time to fit residues: 27.4419 Evaluate side-chains 79 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 64 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 526 PHE Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 723 ASP Chi-restraints excluded: chain A residue 927 LEU Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain C residue 63 LYS Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain D residue 31 GLN Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 50 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 53 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 84 optimal weight: 0.6980 chunk 16 optimal weight: 0.4980 chunk 65 optimal weight: 5.9990 chunk 82 optimal weight: 7.9990 chunk 69 optimal weight: 0.4980 chunk 35 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 79 optimal weight: 0.7980 chunk 95 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.050531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.039121 restraints weight = 60057.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.040420 restraints weight = 34852.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.041325 restraints weight = 23638.965| |-----------------------------------------------------------------------------| r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9738 Z= 0.155 Angle : 0.534 9.108 13195 Z= 0.269 Chirality : 0.041 0.166 1471 Planarity : 0.004 0.051 1707 Dihedral : 5.196 59.112 1329 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.26 % Allowed : 8.77 % Favored : 88.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % 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: 1.56 (0.25), residues: 1199 helix: 1.85 (0.24), residues: 499 sheet: 0.65 (0.36), residues: 219 loop : 0.50 (0.31), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 33 HIS 0.002 0.001 HIS D 68 PHE 0.011 0.001 PHE A 934 TYR 0.009 0.001 TYR A 25 ARG 0.015 0.001 ARG C 5 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 75 time to evaluate : 1.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 MET cc_start: 0.8964 (ptp) cc_final: 0.8562 (ppp) REVERT: A 112 VAL cc_start: 0.8986 (OUTLIER) cc_final: 0.8778 (p) REVERT: A 218 MET cc_start: 0.4816 (mmm) cc_final: 0.4212 (mmm) REVERT: A 235 TYR cc_start: 0.8311 (m-80) cc_final: 0.7990 (m-10) REVERT: A 285 MET cc_start: 0.8730 (pmm) cc_final: 0.8120 (mpp) REVERT: A 345 GLU cc_start: 0.9142 (mm-30) cc_final: 0.8835 (mm-30) REVERT: A 353 ASP cc_start: 0.8223 (t0) cc_final: 0.7795 (m-30) REVERT: A 370 LEU cc_start: 0.9368 (OUTLIER) cc_final: 0.8960 (pp) REVERT: A 445 ASN cc_start: 0.9093 (m-40) cc_final: 0.8611 (m-40) REVERT: A 464 MET cc_start: 0.8833 (pmt) cc_final: 0.8288 (pmt) REVERT: A 526 PHE cc_start: 0.9329 (OUTLIER) cc_final: 0.8407 (t80) REVERT: A 562 LEU cc_start: 0.9120 (tp) cc_final: 0.8893 (tp) REVERT: A 606 ILE cc_start: 0.9353 (mt) cc_final: 0.9113 (mp) REVERT: A 622 ASP cc_start: 0.9490 (m-30) cc_final: 0.8775 (t0) REVERT: A 626 MET cc_start: 0.9351 (mmp) cc_final: 0.8816 (mmp) REVERT: A 707 ARG cc_start: 0.7965 (mtp85) cc_final: 0.7755 (mtt180) REVERT: A 906 MET cc_start: 0.7490 (tmm) cc_final: 0.7142 (tmm) REVERT: C 52 LEU cc_start: 0.9197 (mp) cc_final: 0.8967 (mt) REVERT: C 63 LYS cc_start: 0.9763 (OUTLIER) cc_final: 0.9562 (tppt) REVERT: C 130 ASP cc_start: 0.8757 (t0) cc_final: 0.8497 (p0) REVERT: D 1 MET cc_start: 0.4756 (tmm) cc_final: 0.4463 (tmm) outliers start: 24 outliers final: 9 residues processed: 91 average time/residue: 0.1894 time to fit residues: 26.0083 Evaluate side-chains 79 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 526 PHE Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain C residue 63 LYS Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain D residue 31 GLN Chi-restraints excluded: chain D residue 44 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 85 optimal weight: 0.0010 chunk 33 optimal weight: 6.9990 chunk 43 optimal weight: 0.9980 chunk 76 optimal weight: 0.6980 chunk 89 optimal weight: 8.9990 chunk 17 optimal weight: 10.0000 chunk 104 optimal weight: 7.9990 chunk 59 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 54 optimal weight: 0.6980 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.050385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.039073 restraints weight = 60161.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.040383 restraints weight = 34637.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.041277 restraints weight = 23551.580| |-----------------------------------------------------------------------------| r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.3007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9738 Z= 0.152 Angle : 0.550 13.047 13195 Z= 0.270 Chirality : 0.043 0.314 1471 Planarity : 0.003 0.050 1707 Dihedral : 5.107 59.790 1329 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.98 % Allowed : 9.43 % Favored : 88.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % 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: 1.62 (0.26), residues: 1199 helix: 1.89 (0.24), residues: 500 sheet: 0.68 (0.37), residues: 219 loop : 0.55 (0.31), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 33 HIS 0.001 0.000 HIS D 68 PHE 0.012 0.001 PHE A 934 TYR 0.008 0.001 TYR A 627 ARG 0.003 0.000 ARG A 406 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 73 time to evaluate : 1.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 MET cc_start: 0.9004 (ptp) cc_final: 0.8541 (ppp) REVERT: A 112 VAL cc_start: 0.9026 (OUTLIER) cc_final: 0.8814 (p) REVERT: A 218 MET cc_start: 0.4408 (mmm) cc_final: 0.3806 (mmm) REVERT: A 235 TYR cc_start: 0.8308 (m-80) cc_final: 0.8011 (m-10) REVERT: A 285 MET cc_start: 0.8716 (pmm) cc_final: 0.8383 (pmm) REVERT: A 345 GLU cc_start: 0.9101 (mm-30) cc_final: 0.8797 (mm-30) REVERT: A 353 ASP cc_start: 0.8197 (t0) cc_final: 0.7757 (m-30) REVERT: A 370 LEU cc_start: 0.9355 (OUTLIER) cc_final: 0.8957 (pp) REVERT: A 445 ASN cc_start: 0.9107 (m-40) cc_final: 0.8619 (m-40) REVERT: A 464 MET cc_start: 0.8852 (pmt) cc_final: 0.8321 (pmt) REVERT: A 526 PHE cc_start: 0.9300 (OUTLIER) cc_final: 0.8321 (t80) REVERT: A 562 LEU cc_start: 0.9125 (tp) cc_final: 0.8903 (tp) REVERT: A 606 ILE cc_start: 0.9307 (OUTLIER) cc_final: 0.9071 (mp) REVERT: A 622 ASP cc_start: 0.9489 (m-30) cc_final: 0.8773 (t0) REVERT: A 626 MET cc_start: 0.9368 (mmp) cc_final: 0.8885 (mmp) REVERT: A 906 MET cc_start: 0.7447 (tmm) cc_final: 0.7241 (tmm) REVERT: A 908 VAL cc_start: 0.8428 (OUTLIER) cc_final: 0.8148 (p) REVERT: C 13 LEU cc_start: 0.9563 (pp) cc_final: 0.9335 (mm) REVERT: D 1 MET cc_start: 0.5031 (tmm) cc_final: 0.4741 (tmm) outliers start: 21 outliers final: 8 residues processed: 87 average time/residue: 0.1955 time to fit residues: 25.5321 Evaluate side-chains 82 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 69 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 526 PHE Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain A residue 606 ILE Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 723 ASP Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain D residue 31 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 84 optimal weight: 2.9990 chunk 7 optimal weight: 0.0270 chunk 90 optimal weight: 4.9990 chunk 99 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 17 optimal weight: 10.0000 chunk 37 optimal weight: 5.9990 chunk 89 optimal weight: 7.9990 chunk 102 optimal weight: 7.9990 overall best weight: 2.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.048821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.037613 restraints weight = 62677.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.038821 restraints weight = 37115.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.039635 restraints weight = 25768.200| |-----------------------------------------------------------------------------| r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 9738 Z= 0.296 Angle : 0.611 9.635 13195 Z= 0.307 Chirality : 0.043 0.201 1471 Planarity : 0.004 0.051 1707 Dihedral : 5.236 56.534 1329 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.36 % Allowed : 9.80 % Favored : 87.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % 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: 1.56 (0.26), residues: 1199 helix: 1.89 (0.24), residues: 501 sheet: 0.55 (0.37), residues: 216 loop : 0.50 (0.31), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 33 HIS 0.003 0.001 HIS A 458 PHE 0.012 0.002 PHE A 617 TYR 0.012 0.001 TYR D 59 ARG 0.004 0.000 ARG D 72 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 66 time to evaluate : 1.162 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 218 MET cc_start: 0.4467 (mmm) cc_final: 0.3875 (mmm) REVERT: A 235 TYR cc_start: 0.8399 (m-80) cc_final: 0.8068 (m-10) REVERT: A 285 MET cc_start: 0.8663 (pmm) cc_final: 0.8324 (pmm) REVERT: A 345 GLU cc_start: 0.9063 (mm-30) cc_final: 0.8793 (mm-30) REVERT: A 445 ASN cc_start: 0.9070 (m-40) cc_final: 0.8574 (m-40) REVERT: A 464 MET cc_start: 0.8984 (pmt) cc_final: 0.8364 (pmt) REVERT: A 526 PHE cc_start: 0.9263 (OUTLIER) cc_final: 0.8299 (t80) REVERT: A 562 LEU cc_start: 0.9053 (tp) cc_final: 0.8798 (tp) REVERT: A 606 ILE cc_start: 0.9367 (OUTLIER) cc_final: 0.9126 (mp) REVERT: A 618 LYS cc_start: 0.8475 (ttmt) cc_final: 0.8009 (tppt) REVERT: A 622 ASP cc_start: 0.9484 (m-30) cc_final: 0.8807 (t0) REVERT: A 626 MET cc_start: 0.9312 (mmp) cc_final: 0.8876 (mmp) REVERT: A 906 MET cc_start: 0.7488 (tmm) cc_final: 0.7200 (tmm) REVERT: C 13 LEU cc_start: 0.9534 (pp) cc_final: 0.9330 (mm) REVERT: C 38 MET cc_start: 0.8194 (mmm) cc_final: 0.7514 (mmm) REVERT: D 1 MET cc_start: 0.5243 (tmm) cc_final: 0.4224 (tmm) outliers start: 25 outliers final: 14 residues processed: 85 average time/residue: 0.2034 time to fit residues: 25.9345 Evaluate side-chains 74 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 58 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 526 PHE Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain A residue 606 ILE Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 723 ASP Chi-restraints excluded: chain A residue 927 LEU Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain D residue 25 ASN Chi-restraints excluded: chain D residue 31 GLN Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 44 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 79 optimal weight: 0.5980 chunk 69 optimal weight: 4.9990 chunk 43 optimal weight: 0.6980 chunk 61 optimal weight: 4.9990 chunk 85 optimal weight: 0.0980 chunk 33 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 104 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.049971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.038716 restraints weight = 60777.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.039969 restraints weight = 35880.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.040847 restraints weight = 24720.548| |-----------------------------------------------------------------------------| r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.3332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9738 Z= 0.156 Angle : 0.562 9.620 13195 Z= 0.279 Chirality : 0.042 0.261 1471 Planarity : 0.004 0.051 1707 Dihedral : 5.109 59.681 1329 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.51 % Allowed : 10.84 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % 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: 1.59 (0.26), residues: 1199 helix: 1.90 (0.24), residues: 502 sheet: 0.57 (0.37), residues: 216 loop : 0.52 (0.31), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 33 HIS 0.002 0.000 HIS C 125 PHE 0.032 0.001 PHE D 4 TYR 0.008 0.001 TYR A 627 ARG 0.003 0.000 ARG A 406 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 70 time to evaluate : 1.122 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 218 MET cc_start: 0.4254 (mmm) cc_final: 0.3484 (mmm) REVERT: A 235 TYR cc_start: 0.8282 (m-80) cc_final: 0.7937 (m-10) REVERT: A 285 MET cc_start: 0.8637 (pmm) cc_final: 0.8304 (pmm) REVERT: A 345 GLU cc_start: 0.9020 (mm-30) cc_final: 0.8779 (mm-30) REVERT: A 353 ASP cc_start: 0.8021 (t0) cc_final: 0.7716 (m-30) REVERT: A 445 ASN cc_start: 0.9103 (m-40) cc_final: 0.8630 (m-40) REVERT: A 464 MET cc_start: 0.8946 (pmt) cc_final: 0.8485 (pmt) REVERT: A 562 LEU cc_start: 0.9109 (tp) cc_final: 0.8888 (tp) REVERT: A 606 ILE cc_start: 0.9322 (OUTLIER) cc_final: 0.9083 (mp) REVERT: A 618 LYS cc_start: 0.8482 (ttmt) cc_final: 0.8059 (tppt) REVERT: A 622 ASP cc_start: 0.9475 (m-30) cc_final: 0.8779 (t0) REVERT: A 626 MET cc_start: 0.9322 (mmp) cc_final: 0.8882 (mmp) REVERT: A 707 ARG cc_start: 0.8618 (mtt180) cc_final: 0.7999 (tmt170) REVERT: A 908 VAL cc_start: 0.8506 (OUTLIER) cc_final: 0.8183 (p) REVERT: C 38 MET cc_start: 0.8337 (mmm) cc_final: 0.7741 (mmm) REVERT: D 1 MET cc_start: 0.5421 (tmm) cc_final: 0.5161 (tmm) REVERT: D 43 LEU cc_start: 0.9187 (tp) cc_final: 0.8904 (tp) outliers start: 16 outliers final: 11 residues processed: 80 average time/residue: 0.2205 time to fit residues: 25.4960 Evaluate side-chains 73 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 60 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain A residue 606 ILE Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 723 ASP Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain D residue 31 GLN Chi-restraints excluded: chain D residue 39 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 82 optimal weight: 5.9990 chunk 40 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 55 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 chunk 118 optimal weight: 5.9990 chunk 52 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.049786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.038625 restraints weight = 61863.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.039868 restraints weight = 36519.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.040716 restraints weight = 25205.513| |-----------------------------------------------------------------------------| r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.3445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9738 Z= 0.178 Angle : 0.576 9.901 13195 Z= 0.285 Chirality : 0.043 0.305 1471 Planarity : 0.004 0.050 1707 Dihedral : 4.847 58.909 1327 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.70 % Allowed : 11.12 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % 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: 1.55 (0.25), residues: 1199 helix: 1.90 (0.24), residues: 502 sheet: 0.51 (0.37), residues: 210 loop : 0.48 (0.30), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 33 HIS 0.002 0.000 HIS A 305 PHE 0.027 0.001 PHE D 4 TYR 0.009 0.001 TYR A 627 ARG 0.002 0.000 ARG D 74 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 63 time to evaluate : 1.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 MET cc_start: 0.4104 (mmm) cc_final: 0.3294 (mmm) REVERT: A 235 TYR cc_start: 0.8338 (m-80) cc_final: 0.7992 (m-10) REVERT: A 285 MET cc_start: 0.8624 (pmm) cc_final: 0.8271 (pmm) REVERT: A 345 GLU cc_start: 0.9010 (mm-30) cc_final: 0.8771 (mm-30) REVERT: A 353 ASP cc_start: 0.8024 (t0) cc_final: 0.7707 (m-30) REVERT: A 445 ASN cc_start: 0.9084 (m-40) cc_final: 0.8600 (m-40) REVERT: A 464 MET cc_start: 0.8939 (pmt) cc_final: 0.8433 (pmt) REVERT: A 562 LEU cc_start: 0.9074 (tp) cc_final: 0.8837 (tp) REVERT: A 606 ILE cc_start: 0.9315 (OUTLIER) cc_final: 0.9077 (mp) REVERT: A 618 LYS cc_start: 0.8444 (ttmt) cc_final: 0.8088 (tppt) REVERT: A 622 ASP cc_start: 0.9471 (m-30) cc_final: 0.8782 (t0) REVERT: A 626 MET cc_start: 0.9337 (mmp) cc_final: 0.8885 (mmp) REVERT: D 1 MET cc_start: 0.5408 (tmm) cc_final: 0.4612 (tmm) outliers start: 18 outliers final: 15 residues processed: 74 average time/residue: 0.2125 time to fit residues: 23.4697 Evaluate side-chains 77 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 61 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 449 MET Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain A residue 606 ILE Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 723 ASP Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain D residue 31 GLN Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 67 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 19 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 105 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.048915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.037877 restraints weight = 61553.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.039085 restraints weight = 36439.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.039914 restraints weight = 25239.983| |-----------------------------------------------------------------------------| r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.3518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9738 Z= 0.269 Angle : 0.608 10.305 13195 Z= 0.301 Chirality : 0.042 0.277 1471 Planarity : 0.004 0.048 1707 Dihedral : 4.944 59.939 1327 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.17 % Allowed : 10.74 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % 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: 1.49 (0.25), residues: 1199 helix: 1.91 (0.24), residues: 502 sheet: 0.35 (0.36), residues: 214 loop : 0.45 (0.30), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 33 HIS 0.003 0.001 HIS A 458 PHE 0.023 0.001 PHE D 4 TYR 0.011 0.001 TYR A 627 ARG 0.003 0.000 ARG D 74 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 56 time to evaluate : 1.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 MET cc_start: 0.4195 (mmm) cc_final: 0.3363 (mmm) REVERT: A 235 TYR cc_start: 0.8364 (m-80) cc_final: 0.8019 (m-10) REVERT: A 285 MET cc_start: 0.8647 (pmm) cc_final: 0.8278 (pmm) REVERT: A 345 GLU cc_start: 0.9008 (mm-30) cc_final: 0.8772 (mm-30) REVERT: A 445 ASN cc_start: 0.9085 (m-40) cc_final: 0.8591 (m-40) REVERT: A 464 MET cc_start: 0.8937 (pmt) cc_final: 0.8427 (pmt) REVERT: A 562 LEU cc_start: 0.9049 (tp) cc_final: 0.8797 (tp) REVERT: A 606 ILE cc_start: 0.9341 (OUTLIER) cc_final: 0.9101 (mp) REVERT: A 618 LYS cc_start: 0.8488 (ttmt) cc_final: 0.8147 (tppt) REVERT: A 622 ASP cc_start: 0.9474 (m-30) cc_final: 0.8761 (t0) REVERT: A 626 MET cc_start: 0.9322 (mmp) cc_final: 0.8875 (mmp) REVERT: D 1 MET cc_start: 0.5358 (tmm) cc_final: 0.4544 (tmm) outliers start: 23 outliers final: 20 residues processed: 73 average time/residue: 0.2128 time to fit residues: 23.1600 Evaluate side-chains 76 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 55 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain A residue 606 ILE Chi-restraints excluded: chain A residue 614 GLU Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 723 ASP Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 927 LEU Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain D residue 25 ASN Chi-restraints excluded: chain D residue 31 GLN Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 67 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 13 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 chunk 61 optimal weight: 0.7980 chunk 17 optimal weight: 6.9990 chunk 46 optimal weight: 0.9990 chunk 100 optimal weight: 6.9990 chunk 79 optimal weight: 0.9980 chunk 94 optimal weight: 0.0060 chunk 33 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.049800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.038714 restraints weight = 62075.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.039952 restraints weight = 36513.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.040816 restraints weight = 25152.180| |-----------------------------------------------------------------------------| r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.3613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9738 Z= 0.163 Angle : 0.580 9.738 13195 Z= 0.283 Chirality : 0.042 0.288 1471 Planarity : 0.004 0.048 1707 Dihedral : 4.796 57.361 1327 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.60 % Allowed : 11.40 % Favored : 86.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % 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: 1.48 (0.25), residues: 1199 helix: 1.91 (0.24), residues: 502 sheet: 0.32 (0.37), residues: 203 loop : 0.44 (0.30), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 33 HIS 0.001 0.000 HIS A 818 PHE 0.021 0.001 PHE D 4 TYR 0.008 0.001 TYR A 81 ARG 0.003 0.000 ARG A 406 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 64 time to evaluate : 1.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 TYR cc_start: 0.8347 (m-80) cc_final: 0.7973 (m-10) REVERT: A 285 MET cc_start: 0.8618 (pmm) cc_final: 0.8239 (pmm) REVERT: A 345 GLU cc_start: 0.8991 (mm-30) cc_final: 0.8751 (mm-30) REVERT: A 349 GLN cc_start: 0.8572 (mm-40) cc_final: 0.8366 (mm-40) REVERT: A 445 ASN cc_start: 0.9086 (m-40) cc_final: 0.8563 (m-40) REVERT: A 464 MET cc_start: 0.8934 (pmt) cc_final: 0.8462 (pmt) REVERT: A 562 LEU cc_start: 0.9119 (tp) cc_final: 0.8891 (tp) REVERT: A 606 ILE cc_start: 0.9309 (OUTLIER) cc_final: 0.9070 (mp) REVERT: A 622 ASP cc_start: 0.9455 (m-30) cc_final: 0.8769 (t0) REVERT: A 626 MET cc_start: 0.9312 (mmp) cc_final: 0.8884 (mmp) outliers start: 17 outliers final: 13 residues processed: 74 average time/residue: 0.2129 time to fit residues: 23.3327 Evaluate side-chains 74 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 60 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain A residue 606 ILE Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain D residue 31 GLN Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 67 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 44 optimal weight: 5.9990 chunk 89 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 112 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 chunk 93 optimal weight: 0.7980 chunk 60 optimal weight: 0.3980 chunk 39 optimal weight: 0.8980 chunk 80 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.049763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.038619 restraints weight = 61225.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.039870 restraints weight = 35843.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.040711 restraints weight = 24715.970| |-----------------------------------------------------------------------------| r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.3693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9738 Z= 0.170 Angle : 0.600 9.960 13195 Z= 0.292 Chirality : 0.042 0.298 1471 Planarity : 0.004 0.047 1707 Dihedral : 4.750 56.158 1327 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.60 % Allowed : 11.78 % Favored : 86.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % 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: 1.47 (0.25), residues: 1199 helix: 1.87 (0.24), residues: 502 sheet: 0.25 (0.37), residues: 204 loop : 0.51 (0.30), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 669 HIS 0.001 0.000 HIS A 305 PHE 0.019 0.001 PHE D 4 TYR 0.010 0.001 TYR A 627 ARG 0.003 0.000 ARG D 74 Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 2657.90 seconds wall clock time: 48 minutes 41.90 seconds (2921.90 seconds total)