Starting phenix.real_space_refine on Fri Mar 14 06:33:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b5u_44225/03_2025/9b5u_44225.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b5u_44225/03_2025/9b5u_44225.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b5u_44225/03_2025/9b5u_44225.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b5u_44225/03_2025/9b5u_44225.map" model { file = "/net/cci-nas-00/data/ceres_data/9b5u_44225/03_2025/9b5u_44225.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b5u_44225/03_2025/9b5u_44225.cif" } resolution = 3.67 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= 0.046 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 8 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 6.91, per 1000 atoms: 0.73 Number of scatterers: 9527 At special positions: 0 Unit cell: (100.016, 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=2.92 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: 2.58 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 46.6% alpha, 16.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.47 Creating SS restraints... Processing helix chain 'A' and resid 20 through 25 removed outlier: 3.968A 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 73 through 79 removed outlier: 3.842A pdb=" N SER A 79 " --> pdb=" O ASP A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 88 removed outlier: 3.911A pdb=" N ILE A 88 " --> pdb=" O GLU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 101 removed outlier: 3.552A pdb=" N VAL A 95 " --> pdb=" O PRO A 91 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N SER A 98 " --> pdb=" O LYS A 94 " (cutoff:3.500A) removed outlier: 4.616A 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 144 removed outlier: 3.751A pdb=" N PHE A 142 " --> pdb=" O GLU A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 224 removed outlier: 3.844A pdb=" N GLY A 224 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 274 removed outlier: 4.412A pdb=" N LYS A 273 " --> pdb=" O ARG A 269 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASP A 274 " --> pdb=" O GLU A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 305 removed outlier: 3.671A pdb=" N ILE A 293 " --> pdb=" O PRO A 289 " (cutoff:3.500A) removed outlier: 3.679A 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: 4.619A 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: 3.786A pdb=" N ASN A 473 " --> pdb=" O SER A 470 " (cutoff:3.500A) removed outlier: 3.574A 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: 3.537A 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: 3.662A 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 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: 3.578A pdb=" N THR A 636 " --> pdb=" O ASN A 632 " (cutoff:3.500A) removed outlier: 3.544A 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 Processing helix chain 'A' and resid 718 through 737 Processing helix chain 'A' and resid 743 through 753 removed outlier: 4.045A pdb=" N TYR A 747 " --> pdb=" O ASP A 743 " (cutoff:3.500A) removed outlier: 3.909A 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: 3.546A pdb=" N VAL A 871 " --> pdb=" O CYS A 867 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LYS A 872 " --> pdb=" O LEU A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 883 removed outlier: 3.705A 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 39 No H-bonds generated for 'chain 'D' and resid 37 through 39' 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: 6.774A pdb=" N VAL A 64 " --> pdb=" O SER A 110 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ASN A 39 " --> pdb=" O CYS A 125 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N VAL A 127 " --> pdb=" O ASN A 39 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N LEU A 41 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N THR A 129 " --> pdb=" O LEU A 41 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N ILE A 43 " --> pdb=" O THR A 129 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N VAL A 126 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N ALA A 153 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N VAL A 128 " --> pdb=" O ALA A 153 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N SER A 155 " --> pdb=" O VAL A 128 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N VAL A 278 " --> pdb=" O TYR A 385 " (cutoff:3.500A) removed outlier: 8.977A pdb=" N ASP A 387 " --> 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: 3.525A pdb=" N VAL A 210 " --> pdb=" O ARG A 227 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N PHE A 209 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N THR A 195 " --> pdb=" O ALA A 186 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N ILE A 188 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 6.635A 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: 3.525A pdb=" N VAL A 210 " --> pdb=" O ARG A 227 " (cutoff:3.500A) removed outlier: 3.942A 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: 6.544A pdb=" N ILE A 459 " --> pdb=" O THR A 507 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N TYR A 509 " --> pdb=" O ILE A 459 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N VAL A 461 " --> pdb=" O TYR A 509 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LEU A 531 " --> pdb=" O SER A 429 " (cutoff:3.500A) removed outlier: 4.155A 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 908 Processing sheet with id=AA7, first strand: chain 'A' and resid 920 through 922 removed outlier: 6.407A pdb=" N TYR A 920 " --> pdb=" O CYS A1009 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N VAL A 990 " --> pdb=" O SER A 947 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N SER A 947 " --> pdb=" O VAL A 990 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N GLU A 992 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N LEU A 945 " --> pdb=" O GLU A 992 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N CYS A 994 " --> pdb=" O THR A 943 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N SER A 947 " --> pdb=" O LEU A 951 " (cutoff:3.500A) removed outlier: 6.090A 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 922 removed outlier: 6.407A pdb=" N TYR A 920 " --> pdb=" O CYS A1009 " (cutoff:3.500A) removed outlier: 4.323A 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: 6.153A 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 16 464 hydrogen bonds defined for protein. 1254 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: 3.67 Time building geometry restraints manager: 3.03 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 1.528 -0.075 2.00e-02 2.50e+03 1.41e+01 bond pdb=" N MET D 1 " pdb=" CA MET D 1 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.65e+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 9.25e-01 bond pdb=" C1' ATP A1103 " pdb=" O4' ATP A1103 " ideal model delta sigma weight residual 1.416 1.404 0.012 1.30e-02 5.92e+03 8.07e-01 bond pdb=" C05 A1AIV D 101 " pdb=" N06 A1AIV D 101 " ideal model delta sigma weight residual 1.151 1.133 0.018 2.00e-02 2.50e+03 7.82e-01 ... (remaining 9733 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.32: 12988 1.32 - 2.64: 127 2.64 - 3.97: 68 3.97 - 5.29: 7 5.29 - 6.61: 5 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 121.70 128.31 -6.61 1.80e+00 3.09e-01 1.35e+01 angle pdb=" C2' ATP A1103 " pdb=" C1' ATP A1103 " pdb=" O4' ATP A1103 " ideal model delta sigma weight residual 106.53 103.26 3.27 1.18e+00 7.24e-01 7.76e+00 angle pdb=" C3' ATP A1103 " pdb=" C4' ATP A1103 " pdb=" C5' ATP A1103 " ideal model delta sigma weight residual 115.19 110.64 4.55 1.76e+00 3.23e-01 6.68e+00 angle pdb=" C1' ATP A1103 " pdb=" C2' ATP A1103 " pdb=" O2' ATP A1103 " ideal model delta sigma weight residual 110.58 104.17 6.41 2.79e+00 1.28e-01 5.26e+00 angle pdb=" C2' ATP A1103 " pdb=" C3' ATP A1103 " pdb=" O3' ATP A1103 " ideal model delta sigma weight residual 111.83 106.44 5.39 2.67e+00 1.40e-01 4.08e+00 ... (remaining 13190 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.86: 5580 13.86 - 27.72: 266 27.72 - 41.57: 60 41.57 - 55.43: 17 55.43 - 69.29: 6 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 -148.51 62.51 1 1.00e+01 1.00e-02 5.17e+01 dihedral pdb=" N GLU A 587 " pdb=" CA GLU A 587 " pdb=" CB GLU A 587 " pdb=" CG GLU A 587 " ideal model delta sinusoidal sigma weight residual -60.00 -119.20 59.20 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA ARG D 74 " pdb=" CB ARG D 74 " pdb=" CG ARG D 74 " pdb=" CD ARG D 74 " ideal model delta sinusoidal sigma weight residual -60.00 -116.13 56.13 3 1.50e+01 4.44e-03 9.38e+00 ... (remaining 5926 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1277 0.055 - 0.110: 166 0.110 - 0.165: 25 0.165 - 0.220: 0 0.220 - 0.275: 3 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 -2.96 0.28 2.00e-01 2.50e+01 1.89e+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 0.24 2.00e-01 2.50e+01 1.46e+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 0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 1468 not shown) Planarity restraints: 1707 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY C 39 " -0.024 5.00e-02 4.00e+02 3.68e-02 2.17e+00 pdb=" N PRO C 40 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO C 40 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 40 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG D 42 " -0.005 2.00e-02 2.50e+03 1.06e-02 1.13e+00 pdb=" C ARG D 42 " 0.018 2.00e-02 2.50e+03 pdb=" O ARG D 42 " -0.007 2.00e-02 2.50e+03 pdb=" N LEU D 43 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 922 " 0.017 5.00e-02 4.00e+02 2.54e-02 1.04e+00 pdb=" N PRO A 923 " -0.044 5.00e-02 4.00e+02 pdb=" CA PRO A 923 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 923 " 0.014 5.00e-02 4.00e+02 ... (remaining 1704 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 86 2.57 - 3.15: 7939 3.15 - 3.74: 14087 3.74 - 4.32: 19920 4.32 - 4.90: 34050 Nonbonded interactions: 76082 Sorted by model distance: nonbonded pdb=" O SER A 589 " pdb=" NH2 ARG C 90 " model vdw 1.989 3.120 nonbonded pdb="MG MG A1102 " pdb=" O1B ATP A1103 " model vdw 2.001 2.170 nonbonded pdb="MG MG A1101 " pdb=" O2A ATP A1103 " model vdw 2.006 2.170 nonbonded pdb=" OD2 ASP A 463 " pdb=" O3' ATP A1103 " model vdw 2.075 3.040 nonbonded pdb="MG MG A1101 " pdb=" O3G ATP A1103 " model vdw 2.095 2.170 ... (remaining 76077 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: 3.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 27.480 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 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 : 0.004 0.075 9738 Z= 0.224 Angle : 0.472 6.611 13195 Z= 0.242 Chirality : 0.041 0.275 1471 Planarity : 0.003 0.037 1707 Dihedral : 9.224 69.288 3662 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.70 % Allowed : 2.83 % Favored : 95.48 % 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: 1.42 (0.25), residues: 1199 helix: 1.82 (0.25), residues: 492 sheet: 0.50 (0.37), residues: 203 loop : 0.37 (0.29), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 93 HIS 0.002 0.001 HIS C 75 PHE 0.008 0.001 PHE A 842 TYR 0.010 0.001 TYR A 732 ARG 0.002 0.000 ARG C 131 *********************** 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: 18 poor density : 184 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 MET cc_start: 0.9041 (mtp) cc_final: 0.8702 (mmm) REVERT: A 442 MET cc_start: 0.9481 (tpp) cc_final: 0.9080 (mmm) REVERT: A 510 GLN cc_start: 0.8583 (pt0) cc_final: 0.8306 (pp30) REVERT: A 650 ASN cc_start: 0.9079 (m-40) cc_final: 0.8652 (t0) REVERT: A 669 TRP cc_start: 0.9314 (t60) cc_final: 0.9039 (t60) REVERT: A 675 ASP cc_start: 0.9263 (OUTLIER) cc_final: 0.8967 (m-30) REVERT: A 676 LYS cc_start: 0.9187 (ttpp) cc_final: 0.8690 (tppt) REVERT: A 811 GLU cc_start: 0.8348 (tp30) cc_final: 0.8059 (tp30) REVERT: A 936 LYS cc_start: 0.9439 (OUTLIER) cc_final: 0.8784 (ptpp) REVERT: A 937 GLU cc_start: 0.9077 (OUTLIER) cc_final: 0.8847 (mm-30) REVERT: A 992 GLU cc_start: 0.8781 (mm-30) cc_final: 0.8505 (mm-30) REVERT: D 24 ASP cc_start: 0.7949 (m-30) cc_final: 0.7499 (t0) outliers start: 18 outliers final: 7 residues processed: 198 average time/residue: 0.2977 time to fit residues: 76.7065 Evaluate side-chains 100 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 90 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 317 ASP Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 675 ASP Chi-restraints excluded: chain A residue 919 ARG Chi-restraints excluded: chain A residue 936 LYS Chi-restraints excluded: chain A residue 937 GLU Chi-restraints excluded: chain D residue 74 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 100 optimal weight: 10.0000 chunk 90 optimal weight: 0.8980 chunk 50 optimal weight: 0.3980 chunk 30 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 48 optimal weight: 0.8980 chunk 93 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 108 optimal weight: 0.9980 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 = 0.3487 r_free = 0.3487 target = 0.071735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.054458 restraints weight = 37094.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.056429 restraints weight = 19135.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.057764 restraints weight = 12405.128| |-----------------------------------------------------------------------------| r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9738 Z= 0.203 Angle : 0.606 10.014 13195 Z= 0.307 Chirality : 0.043 0.274 1471 Planarity : 0.004 0.044 1707 Dihedral : 6.101 64.960 1349 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.70 % Allowed : 8.58 % Favored : 89.73 % 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 (0.25), residues: 1199 helix: 1.80 (0.24), residues: 501 sheet: 1.08 (0.39), residues: 193 loop : 0.46 (0.30), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 141 HIS 0.004 0.001 HIS C 32 PHE 0.017 0.001 PHE A 633 TYR 0.010 0.001 TYR C 145 ARG 0.005 0.001 ARG D 54 *********************** 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 121 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 103 time to evaluate : 1.154 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 MET cc_start: 0.9134 (mtp) cc_final: 0.8873 (mmm) REVERT: A 154 ASP cc_start: 0.7646 (t0) cc_final: 0.6863 (m-30) REVERT: A 196 MET cc_start: 0.8713 (mmm) cc_final: 0.8384 (mmm) REVERT: A 286 MET cc_start: 0.6704 (tmm) cc_final: 0.6448 (tmm) REVERT: A 442 MET cc_start: 0.9415 (tpp) cc_final: 0.9011 (mmm) REVERT: A 669 TRP cc_start: 0.9364 (t60) cc_final: 0.9058 (t60) REVERT: A 675 ASP cc_start: 0.9031 (OUTLIER) cc_final: 0.8573 (t0) REVERT: A 676 LYS cc_start: 0.9083 (ttpp) cc_final: 0.8763 (tppt) REVERT: A 811 GLU cc_start: 0.8319 (tp30) cc_final: 0.8007 (tp30) REVERT: A 937 GLU cc_start: 0.9021 (OUTLIER) cc_final: 0.8787 (mm-30) REVERT: C 38 MET cc_start: 0.8400 (mpp) cc_final: 0.7293 (mpp) REVERT: C 122 GLU cc_start: 0.8560 (tm-30) cc_final: 0.8239 (tm-30) REVERT: C 130 ASP cc_start: 0.8607 (t0) cc_final: 0.8137 (t0) REVERT: D 1 MET cc_start: 0.5068 (ppp) cc_final: 0.3781 (pmm) REVERT: D 2 GLN cc_start: 0.8441 (pm20) cc_final: 0.8190 (pm20) REVERT: D 43 LEU cc_start: 0.8150 (mm) cc_final: 0.7508 (mm) REVERT: D 71 LEU cc_start: 0.8025 (mp) cc_final: 0.7240 (tp) outliers start: 18 outliers final: 11 residues processed: 116 average time/residue: 0.2827 time to fit residues: 44.8929 Evaluate side-chains 92 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 79 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 ARG Chi-restraints excluded: chain A residue 250 TYR Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 526 PHE Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 675 ASP Chi-restraints excluded: chain A residue 937 GLU Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 107 SER Chi-restraints excluded: chain D residue 48 LYS Chi-restraints excluded: chain D residue 74 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 61 optimal weight: 4.9990 chunk 70 optimal weight: 0.9980 chunk 60 optimal weight: 0.5980 chunk 27 optimal weight: 0.2980 chunk 85 optimal weight: 0.0070 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: 3.9990 chunk 18 optimal weight: 0.9980 overall best weight: 0.5798 ------------------------------------------------------------------------------- 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 = 0.3483 r_free = 0.3483 target = 0.070699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.053965 restraints weight = 37760.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.055911 restraints weight = 19193.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.057224 restraints weight = 12378.334| |-----------------------------------------------------------------------------| r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9738 Z= 0.169 Angle : 0.540 8.314 13195 Z= 0.272 Chirality : 0.042 0.228 1471 Planarity : 0.004 0.045 1707 Dihedral : 5.823 60.891 1337 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 1.41 % Allowed : 9.99 % 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: 1.58 (0.25), residues: 1199 helix: 1.80 (0.24), residues: 502 sheet: 0.91 (0.37), residues: 211 loop : 0.43 (0.30), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 93 HIS 0.002 0.000 HIS C 32 PHE 0.014 0.001 PHE A 633 TYR 0.018 0.001 TYR C 134 ARG 0.012 0.001 ARG C 143 *********************** 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 104 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 89 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 MET cc_start: 0.9076 (mtp) cc_final: 0.8855 (mmm) REVERT: A 154 ASP cc_start: 0.7647 (t0) cc_final: 0.6820 (m-30) REVERT: A 196 MET cc_start: 0.8689 (mmm) cc_final: 0.8284 (mmm) REVERT: A 442 MET cc_start: 0.9344 (tpp) cc_final: 0.9066 (mmm) REVERT: A 669 TRP cc_start: 0.9340 (t60) cc_final: 0.9047 (t60) REVERT: A 675 ASP cc_start: 0.8992 (OUTLIER) cc_final: 0.8549 (t0) REVERT: A 676 LYS cc_start: 0.9054 (ttpp) cc_final: 0.8756 (tppt) REVERT: A 811 GLU cc_start: 0.8212 (tp30) cc_final: 0.7997 (tp30) REVERT: A 937 GLU cc_start: 0.8933 (OUTLIER) cc_final: 0.8718 (mp0) REVERT: A 944 MET cc_start: 0.7687 (tmm) cc_final: 0.7461 (tmm) REVERT: C 38 MET cc_start: 0.8416 (mpp) cc_final: 0.7277 (mpp) REVERT: C 122 GLU cc_start: 0.8669 (tm-30) cc_final: 0.8356 (tm-30) REVERT: D 1 MET cc_start: 0.5405 (ppp) cc_final: 0.4898 (pmm) REVERT: D 42 ARG cc_start: 0.8797 (mtm180) cc_final: 0.8312 (mmt-90) REVERT: D 71 LEU cc_start: 0.8164 (mp) cc_final: 0.7479 (tp) outliers start: 15 outliers final: 9 residues processed: 100 average time/residue: 0.2236 time to fit residues: 31.5940 Evaluate side-chains 90 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 79 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 TYR Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 675 ASP Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 937 GLU Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 74 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 53 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 65 optimal weight: 0.8980 chunk 82 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 95 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3472 r_free = 0.3472 target = 0.070127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.053359 restraints weight = 37500.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.055282 restraints weight = 19281.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.056550 restraints weight = 12484.937| |-----------------------------------------------------------------------------| r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.2509 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= 0.182 Angle : 0.517 10.629 13195 Z= 0.260 Chirality : 0.041 0.213 1471 Planarity : 0.004 0.045 1707 Dihedral : 5.690 59.575 1337 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.32 % Allowed : 10.08 % 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: 1.63 (0.25), residues: 1199 helix: 1.82 (0.24), residues: 503 sheet: 0.96 (0.38), residues: 203 loop : 0.49 (0.30), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 93 HIS 0.002 0.001 HIS A 305 PHE 0.015 0.001 PHE A 633 TYR 0.023 0.001 TYR C 134 ARG 0.006 0.000 ARG A 919 *********************** 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 101 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 87 time to evaluate : 1.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 ASP cc_start: 0.7805 (t0) cc_final: 0.6849 (m-30) REVERT: A 196 MET cc_start: 0.8677 (mmm) cc_final: 0.8315 (mmm) REVERT: A 357 MET cc_start: 0.8225 (tpt) cc_final: 0.7988 (tpt) REVERT: A 442 MET cc_start: 0.9315 (tpp) cc_final: 0.9081 (mmm) REVERT: A 669 TRP cc_start: 0.9354 (t60) cc_final: 0.9130 (t60) REVERT: A 675 ASP cc_start: 0.8975 (OUTLIER) cc_final: 0.8712 (m-30) REVERT: A 676 LYS cc_start: 0.9084 (ttpp) cc_final: 0.8660 (tppt) REVERT: A 937 GLU cc_start: 0.8964 (OUTLIER) cc_final: 0.8736 (mp0) REVERT: A 944 MET cc_start: 0.7969 (tmm) cc_final: 0.7756 (tmm) REVERT: C 38 MET cc_start: 0.8451 (mpp) cc_final: 0.7356 (mpp) REVERT: C 122 GLU cc_start: 0.8731 (tm-30) cc_final: 0.8449 (tm-30) REVERT: D 1 MET cc_start: 0.5301 (ppp) cc_final: 0.5027 (pmm) REVERT: D 42 ARG cc_start: 0.8832 (mtm180) cc_final: 0.8256 (mmt-90) REVERT: D 71 LEU cc_start: 0.8190 (mp) cc_final: 0.7549 (tp) outliers start: 14 outliers final: 8 residues processed: 98 average time/residue: 0.2363 time to fit residues: 32.6964 Evaluate side-chains 86 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 76 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 TYR Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 675 ASP Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 937 GLU Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 74 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 85 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 chunk 76 optimal weight: 0.0000 chunk 89 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 104 optimal weight: 0.0980 chunk 59 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 13 optimal weight: 4.9990 chunk 54 optimal weight: 0.8980 overall best weight: 0.5184 ------------------------------------------------------------------------------- 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 = 0.3484 r_free = 0.3484 target = 0.071405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.053892 restraints weight = 37420.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.055874 restraints weight = 19252.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.057191 restraints weight = 12486.899| |-----------------------------------------------------------------------------| r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9738 Z= 0.144 Angle : 0.507 12.310 13195 Z= 0.252 Chirality : 0.041 0.209 1471 Planarity : 0.003 0.044 1707 Dihedral : 5.562 59.838 1337 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.23 % Allowed : 11.31 % Favored : 87.46 % 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: 1.70 (0.25), residues: 1199 helix: 1.87 (0.24), residues: 505 sheet: 0.90 (0.38), residues: 205 loop : 0.58 (0.30), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP C 93 HIS 0.001 0.000 HIS A 305 PHE 0.017 0.001 PHE A 633 TYR 0.024 0.001 TYR C 134 ARG 0.005 0.000 ARG A 919 *********************** 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 96 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 154 ASP cc_start: 0.7796 (t0) cc_final: 0.6788 (m-30) REVERT: A 196 MET cc_start: 0.8713 (mmm) cc_final: 0.8316 (mmm) REVERT: A 442 MET cc_start: 0.9307 (tpp) cc_final: 0.9053 (mmm) REVERT: A 669 TRP cc_start: 0.9357 (t60) cc_final: 0.9139 (t60) REVERT: A 869 GLU cc_start: 0.8535 (mm-30) cc_final: 0.8277 (mm-30) REVERT: A 937 GLU cc_start: 0.9039 (OUTLIER) cc_final: 0.8742 (mp0) REVERT: A 944 MET cc_start: 0.7879 (tmm) cc_final: 0.7634 (tmm) REVERT: C 38 MET cc_start: 0.8484 (mpp) cc_final: 0.7457 (mpp) REVERT: C 122 GLU cc_start: 0.8764 (tm-30) cc_final: 0.8461 (tm-30) REVERT: D 1 MET cc_start: 0.5367 (ppp) cc_final: 0.5113 (pmm) REVERT: D 40 GLN cc_start: 0.8140 (mt0) cc_final: 0.7912 (mm-40) REVERT: D 42 ARG cc_start: 0.8881 (mtm180) cc_final: 0.8319 (mmt-90) REVERT: D 71 LEU cc_start: 0.8235 (mp) cc_final: 0.7582 (tp) outliers start: 13 outliers final: 10 residues processed: 92 average time/residue: 0.2504 time to fit residues: 32.7456 Evaluate side-chains 85 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 74 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 TYR Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 526 PHE Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 937 GLU Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 74 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 84 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 90 optimal weight: 0.8980 chunk 99 optimal weight: 9.9990 chunk 61 optimal weight: 0.0070 chunk 100 optimal weight: 0.5980 chunk 73 optimal weight: 0.3980 chunk 17 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 chunk 102 optimal weight: 5.9990 overall best weight: 0.5798 ------------------------------------------------------------------------------- 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 = 0.3483 r_free = 0.3483 target = 0.070533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.053915 restraints weight = 37526.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.055808 restraints weight = 19005.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.057074 restraints weight = 12263.343| |-----------------------------------------------------------------------------| r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.2789 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= 0.151 Angle : 0.499 12.043 13195 Z= 0.249 Chirality : 0.041 0.202 1471 Planarity : 0.003 0.042 1707 Dihedral : 5.294 59.370 1335 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.51 % Allowed : 11.03 % Favored : 87.46 % 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: 1.77 (0.25), residues: 1199 helix: 1.92 (0.24), residues: 504 sheet: 1.01 (0.38), residues: 202 loop : 0.59 (0.30), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 93 HIS 0.001 0.000 HIS A 305 PHE 0.018 0.001 PHE A 633 TYR 0.023 0.001 TYR C 134 ARG 0.004 0.000 ARG A 919 *********************** 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 95 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 79 time to evaluate : 1.410 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 80 GLN cc_start: 0.8609 (OUTLIER) cc_final: 0.8045 (tm-30) REVERT: A 154 ASP cc_start: 0.7719 (t0) cc_final: 0.6758 (m-30) REVERT: A 196 MET cc_start: 0.8637 (mmm) cc_final: 0.7190 (mmm) REVERT: A 218 MET cc_start: 0.7136 (mmt) cc_final: 0.6751 (mmt) REVERT: A 442 MET cc_start: 0.9294 (tpp) cc_final: 0.9057 (mmm) REVERT: A 668 MET cc_start: 0.8323 (tmm) cc_final: 0.8050 (tmm) REVERT: A 669 TRP cc_start: 0.9372 (t60) cc_final: 0.9110 (t60) REVERT: A 869 GLU cc_start: 0.8476 (mm-30) cc_final: 0.8270 (mm-30) REVERT: C 38 MET cc_start: 0.8530 (mpp) cc_final: 0.7482 (mpp) REVERT: C 122 GLU cc_start: 0.8720 (tm-30) cc_final: 0.8427 (tm-30) REVERT: D 42 ARG cc_start: 0.8842 (mtm180) cc_final: 0.8313 (mmt-90) REVERT: D 71 LEU cc_start: 0.8274 (mp) cc_final: 0.7621 (tp) outliers start: 16 outliers final: 9 residues processed: 91 average time/residue: 0.2204 time to fit residues: 29.1010 Evaluate side-chains 84 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 74 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 250 TYR Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 74 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 79 optimal weight: 0.9980 chunk 69 optimal weight: 0.0010 chunk 43 optimal weight: 0.7980 chunk 61 optimal weight: 0.9990 chunk 85 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 104 optimal weight: 0.0970 chunk 20 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 overall best weight: 0.5786 ------------------------------------------------------------------------------- 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 = 0.3485 r_free = 0.3485 target = 0.070720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.053848 restraints weight = 37743.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.055760 restraints weight = 19188.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.057070 restraints weight = 12440.244| |-----------------------------------------------------------------------------| r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9738 Z= 0.152 Angle : 0.513 12.007 13195 Z= 0.255 Chirality : 0.041 0.197 1471 Planarity : 0.003 0.039 1707 Dihedral : 5.026 58.554 1332 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.51 % Allowed : 11.59 % Favored : 86.90 % 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: 1.79 (0.26), residues: 1199 helix: 1.97 (0.24), residues: 503 sheet: 0.98 (0.38), residues: 212 loop : 0.58 (0.30), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP C 93 HIS 0.002 0.000 HIS A 305 PHE 0.038 0.001 PHE A 254 TYR 0.026 0.001 TYR C 134 ARG 0.004 0.000 ARG A 919 *********************** 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 91 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 75 time to evaluate : 1.235 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 80 GLN cc_start: 0.8615 (OUTLIER) cc_final: 0.8064 (tm-30) REVERT: A 154 ASP cc_start: 0.7805 (t0) cc_final: 0.6801 (m-30) REVERT: A 196 MET cc_start: 0.8861 (mmm) cc_final: 0.8462 (mmm) REVERT: A 218 MET cc_start: 0.7024 (mmt) cc_final: 0.6658 (mmt) REVERT: A 668 MET cc_start: 0.8305 (tmm) cc_final: 0.8050 (tmm) REVERT: A 669 TRP cc_start: 0.9369 (t60) cc_final: 0.9118 (t60) REVERT: C 38 MET cc_start: 0.8565 (mpp) cc_final: 0.7599 (mpp) REVERT: C 122 GLU cc_start: 0.8750 (tm-30) cc_final: 0.8461 (tm-30) REVERT: D 1 MET cc_start: 0.4819 (pmm) cc_final: 0.2846 (ppp) REVERT: D 42 ARG cc_start: 0.8807 (mtm180) cc_final: 0.8400 (mmt-90) REVERT: D 71 LEU cc_start: 0.8265 (mp) cc_final: 0.7743 (tp) outliers start: 16 outliers final: 10 residues processed: 86 average time/residue: 0.2446 time to fit residues: 30.1618 Evaluate side-chains 80 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 69 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 250 TYR Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 74 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 82 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 31 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 118 optimal weight: 10.0000 chunk 52 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 = 0.3467 r_free = 0.3467 target = 0.069898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.053043 restraints weight = 38425.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.054934 restraints weight = 19677.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.056205 restraints weight = 12797.145| |-----------------------------------------------------------------------------| r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9738 Z= 0.203 Angle : 0.540 11.182 13195 Z= 0.267 Chirality : 0.041 0.191 1471 Planarity : 0.003 0.042 1707 Dihedral : 5.049 57.347 1332 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.32 % Allowed : 11.78 % Favored : 86.90 % 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: 1.79 (0.25), residues: 1199 helix: 1.99 (0.24), residues: 502 sheet: 0.98 (0.38), residues: 212 loop : 0.56 (0.30), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 446 HIS 0.002 0.001 HIS A 458 PHE 0.032 0.001 PHE A 254 TYR 0.023 0.001 TYR C 134 ARG 0.004 0.000 ARG A 919 *********************** 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 86 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 72 time to evaluate : 0.968 Fit side-chains revert: symmetry clash REVERT: A 80 GLN cc_start: 0.8643 (OUTLIER) cc_final: 0.8104 (tm-30) REVERT: A 196 MET cc_start: 0.8886 (mmm) cc_final: 0.8435 (mmm) REVERT: A 218 MET cc_start: 0.7042 (mmt) cc_final: 0.6685 (mmt) REVERT: A 442 MET cc_start: 0.9285 (mmm) cc_final: 0.9071 (mmm) REVERT: A 668 MET cc_start: 0.8307 (tmm) cc_final: 0.8053 (tmm) REVERT: A 669 TRP cc_start: 0.9397 (t60) cc_final: 0.9142 (t60) REVERT: C 38 MET cc_start: 0.8539 (mpp) cc_final: 0.7611 (mpp) REVERT: C 122 GLU cc_start: 0.8767 (tm-30) cc_final: 0.8473 (tm-30) REVERT: C 135 GLU cc_start: 0.8855 (mm-30) cc_final: 0.8625 (mm-30) REVERT: D 1 MET cc_start: 0.4853 (pmm) cc_final: 0.2597 (ppp) REVERT: D 42 ARG cc_start: 0.8524 (mtm180) cc_final: 0.8218 (mmt-90) REVERT: D 71 LEU cc_start: 0.8372 (mp) cc_final: 0.7716 (tp) REVERT: D 74 ARG cc_start: 0.6505 (OUTLIER) cc_final: 0.6243 (ptp-170) outliers start: 14 outliers final: 10 residues processed: 83 average time/residue: 0.2278 time to fit residues: 27.5481 Evaluate side-chains 80 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 68 time to evaluate : 1.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 250 TYR Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 74 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 19 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 17 optimal weight: 9.9990 chunk 15 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- 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 = 0.3471 r_free = 0.3471 target = 0.070030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.053286 restraints weight = 37784.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.055138 restraints weight = 19396.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.056430 restraints weight = 12672.675| |-----------------------------------------------------------------------------| r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.3011 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= 0.181 Angle : 0.529 11.109 13195 Z= 0.262 Chirality : 0.041 0.188 1471 Planarity : 0.003 0.042 1707 Dihedral : 5.054 57.597 1332 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.60 % Allowed : 11.50 % Favored : 86.90 % 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: 1.80 (0.25), residues: 1199 helix: 1.98 (0.24), residues: 503 sheet: 1.01 (0.38), residues: 212 loop : 0.57 (0.30), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 446 HIS 0.002 0.001 HIS A 458 PHE 0.031 0.001 PHE A 254 TYR 0.028 0.001 TYR C 134 ARG 0.009 0.000 ARG D 54 *********************** 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 90 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 73 time to evaluate : 1.221 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 80 GLN cc_start: 0.8629 (OUTLIER) cc_final: 0.8094 (tm-30) REVERT: A 196 MET cc_start: 0.8957 (mmm) cc_final: 0.8496 (mmm) REVERT: A 218 MET cc_start: 0.7002 (mmt) cc_final: 0.6737 (mmt) REVERT: A 442 MET cc_start: 0.9253 (mmm) cc_final: 0.8988 (mmm) REVERT: A 668 MET cc_start: 0.8308 (tmm) cc_final: 0.8056 (tmm) REVERT: A 669 TRP cc_start: 0.9388 (t60) cc_final: 0.9148 (t60) REVERT: C 38 MET cc_start: 0.8546 (mpp) cc_final: 0.7623 (mpp) REVERT: C 122 GLU cc_start: 0.8792 (tm-30) cc_final: 0.8502 (tm-30) REVERT: C 135 GLU cc_start: 0.8875 (mm-30) cc_final: 0.8630 (mm-30) REVERT: D 1 MET cc_start: 0.4842 (pmm) cc_final: 0.2713 (ppp) REVERT: D 71 LEU cc_start: 0.8335 (mp) cc_final: 0.7895 (tp) REVERT: D 74 ARG cc_start: 0.6462 (OUTLIER) cc_final: 0.6135 (ptp-170) outliers start: 17 outliers final: 11 residues processed: 86 average time/residue: 0.2338 time to fit residues: 28.6128 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 : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 250 TYR Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 116 ASP Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 74 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 13 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 chunk 17 optimal weight: 10.0000 chunk 46 optimal weight: 2.9990 chunk 100 optimal weight: 8.9990 chunk 79 optimal weight: 0.7980 chunk 94 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 90 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.3470 r_free = 0.3470 target = 0.070042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.053087 restraints weight = 38599.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.055017 restraints weight = 19611.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.056285 restraints weight = 12702.746| |-----------------------------------------------------------------------------| r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.3071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9738 Z= 0.183 Angle : 0.542 10.973 13195 Z= 0.267 Chirality : 0.041 0.201 1471 Planarity : 0.003 0.043 1707 Dihedral : 5.055 57.659 1332 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.23 % Allowed : 11.69 % 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: 1.84 (0.26), residues: 1199 helix: 1.99 (0.24), residues: 503 sheet: 1.14 (0.38), residues: 218 loop : 0.55 (0.30), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 446 HIS 0.002 0.001 HIS A 458 PHE 0.030 0.001 PHE A 254 TYR 0.028 0.001 TYR C 134 ARG 0.018 0.001 ARG D 42 ********************** 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: 13 poor density : 68 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 80 GLN cc_start: 0.8648 (OUTLIER) cc_final: 0.8092 (tm-30) REVERT: A 218 MET cc_start: 0.6989 (mmt) cc_final: 0.6737 (mmt) REVERT: A 442 MET cc_start: 0.9272 (mmm) cc_final: 0.8994 (mmm) REVERT: C 38 MET cc_start: 0.8556 (mpp) cc_final: 0.7631 (mpp) REVERT: C 122 GLU cc_start: 0.8795 (tm-30) cc_final: 0.8502 (tm-30) REVERT: C 135 GLU cc_start: 0.8893 (mm-30) cc_final: 0.8644 (mm-30) REVERT: D 1 MET cc_start: 0.4861 (pmm) cc_final: 0.2633 (ppp) outliers start: 13 outliers final: 10 residues processed: 77 average time/residue: 0.2065 time to fit residues: 23.5133 Evaluate side-chains 78 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 67 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 250 TYR Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain D residue 44 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 44 optimal weight: 6.9990 chunk 89 optimal weight: 6.9990 chunk 78 optimal weight: 4.9990 chunk 112 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 93 optimal weight: 0.0170 chunk 60 optimal weight: 0.8980 chunk 39 optimal weight: 0.0870 chunk 80 optimal weight: 0.0980 chunk 34 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 overall best weight: 0.3596 ------------------------------------------------------------------------------- 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 = 0.3488 r_free = 0.3488 target = 0.070904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.054035 restraints weight = 38007.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.055988 restraints weight = 19321.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.057281 restraints weight = 12476.323| |-----------------------------------------------------------------------------| r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.3169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9738 Z= 0.144 Angle : 0.548 14.795 13195 Z= 0.265 Chirality : 0.041 0.189 1471 Planarity : 0.003 0.044 1707 Dihedral : 4.685 59.456 1328 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.13 % Allowed : 11.97 % Favored : 86.90 % 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: 1.89 (0.26), residues: 1199 helix: 2.05 (0.24), residues: 495 sheet: 1.16 (0.38), residues: 218 loop : 0.59 (0.30), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 669 HIS 0.001 0.000 HIS A 721 PHE 0.032 0.001 PHE A 254 TYR 0.029 0.001 TYR C 134 ARG 0.012 0.000 ARG D 42 Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 2888.64 seconds wall clock time: 51 minutes 58.76 seconds (3118.76 seconds total)