Starting phenix.real_space_refine on Fri Mar 14 04:36:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b5o_44219/03_2025/9b5o_44219.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b5o_44219/03_2025/9b5o_44219.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b5o_44219/03_2025/9b5o_44219.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b5o_44219/03_2025/9b5o_44219.map" model { file = "/net/cci-nas-00/data/ceres_data/9b5o_44219/03_2025/9b5o_44219.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b5o_44219/03_2025/9b5o_44219.cif" } resolution = 3.19 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= 0.059 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 5 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: 7.29, per 1000 atoms: 0.77 Number of scatterers: 9527 At special positions: 0 Unit cell: (91.504, 100.016, 120.232, 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=2.89 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: 2.49 Conformation dependent library (CDL) restraints added in 1.1 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: 52 helices and 10 sheets defined 47.6% alpha, 15.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.38 Creating SS restraints... Processing helix chain 'A' and resid 20 through 25 removed outlier: 3.839A 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: 3.685A pdb=" N SER A 79 " --> pdb=" O ASP A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 88 removed outlier: 3.880A pdb=" N ILE A 88 " --> pdb=" O GLU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 101 removed outlier: 4.297A pdb=" N SER A 98 " --> pdb=" O LYS A 94 " (cutoff:3.500A) removed outlier: 4.560A 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: 3.738A pdb=" N PHE A 142 " --> pdb=" O GLU A 138 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N LYS A 145 " --> pdb=" O ASP A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 223 removed outlier: 3.573A pdb=" N ASP A 223 " --> pdb=" O GLY A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 274 removed outlier: 4.353A pdb=" N LYS A 273 " --> pdb=" O ARG A 269 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASP A 274 " --> pdb=" O GLU A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 305 removed outlier: 3.629A pdb=" N ILE A 293 " --> pdb=" O PRO A 289 " (cutoff:3.500A) removed outlier: 3.622A 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 399 through 404 Processing helix chain 'A' and resid 410 through 418 removed outlier: 4.391A 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: 3.682A pdb=" N ASN A 473 " --> pdb=" O SER A 470 " (cutoff:3.500A) removed outlier: 3.509A 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 Processing helix chain 'A' and resid 500 through 503 Processing helix chain 'A' and resid 514 through 518 removed outlier: 3.763A pdb=" N GLU A 518 " --> pdb=" O PRO A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 528 removed outlier: 3.847A pdb=" N LYS A 528 " --> pdb=" O GLU A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 553 removed outlier: 3.523A pdb=" N ARG A 542 " --> pdb=" O ASN A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 582 removed outlier: 3.518A pdb=" N SER A 581 " --> pdb=" O SER A 578 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER A 582 " --> pdb=" O TYR A 579 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 578 through 582' 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 630 Processing helix chain 'A' and resid 632 through 641 removed outlier: 3.680A 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 removed outlier: 3.509A pdb=" N CYS A 666 " --> pdb=" O SER A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 689 removed outlier: 3.580A 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: 4.002A pdb=" N TYR A 747 " --> pdb=" O ASP A 743 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLY A 753 " --> pdb=" O ARG A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 781 through 794 removed outlier: 3.862A pdb=" N GLN A 785 " --> pdb=" O ASN A 781 " (cutoff:3.500A) 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: 3.625A pdb=" N VAL A 871 " --> pdb=" O CYS A 867 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LYS A 872 " --> pdb=" O LEU A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 883 removed outlier: 3.557A pdb=" N GLU A 882 " --> pdb=" O LYS A 879 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N TYR A 883 " --> pdb=" O ILE A 880 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 879 through 883' 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: 6.850A pdb=" N VAL A 64 " --> pdb=" O SER A 110 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ASN A 39 " --> pdb=" O CYS A 125 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N VAL A 127 " --> pdb=" O ASN A 39 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N LEU A 41 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N VAL A 126 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N ALA A 153 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N VAL A 128 " --> pdb=" O ALA A 153 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N SER A 155 " --> pdb=" O VAL A 128 " (cutoff:3.500A) removed outlier: 4.398A 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: 4.211A pdb=" N PHE A 209 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N THR A 195 " --> pdb=" O ALA A 186 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ILE A 188 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 6.227A 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: 4.211A 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: 6.511A pdb=" N ILE A 459 " --> pdb=" O THR A 507 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N TYR A 509 " --> pdb=" O ILE A 459 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N VAL A 461 " --> pdb=" O TYR A 509 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU A 531 " --> pdb=" O SER A 429 " (cutoff:3.500A) removed outlier: 4.275A 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: 6.406A pdb=" N TYR A 920 " --> pdb=" O CYS A1009 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N LYS A1011 " --> pdb=" O TYR A 920 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N LEU A 922 " --> pdb=" O LYS A1011 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N VAL A 990 " --> pdb=" O SER A 947 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N SER A 947 " --> pdb=" O VAL A 990 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N GLU A 992 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N LEU A 945 " --> pdb=" O GLU A 992 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N CYS A 994 " --> pdb=" O THR A 943 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N SER A 947 " --> pdb=" O LEU A 951 " (cutoff:3.500A) removed outlier: 5.515A 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: 6.406A pdb=" N TYR A 920 " --> pdb=" O CYS A1009 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N LYS A1011 " --> pdb=" O TYR A 920 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N LEU A 922 " --> pdb=" O LYS A1011 " (cutoff:3.500A) removed outlier: 4.442A 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 26 removed outlier: 3.653A pdb=" N GLY C 24 " --> pdb=" O GLN C 34 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N HIS C 32 " --> pdb=" O VAL C 26 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 12 through 16 468 hydrogen bonds defined for protein. 1275 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: 3.60 Time building geometry restraints manager: 2.97 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: 5650 1.54 - 1.67: 117 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 1.30e+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 2.81e+00 bond pdb=" C1' ATP A1103 " pdb=" C2' ATP A1103 " ideal model delta sigma weight residual 1.531 1.520 0.011 1.20e-02 6.94e+03 8.69e-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 8.35e-01 bond pdb=" C1' ATP A1103 " pdb=" O4' ATP A1103 " ideal model delta sigma weight residual 1.416 1.406 0.010 1.30e-02 5.92e+03 5.66e-01 ... (remaining 9733 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.30: 13037 1.30 - 2.60: 79 2.60 - 3.90: 69 3.90 - 5.20: 7 5.20 - 6.51: 3 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 121.70 128.21 -6.51 1.80e+00 3.09e-01 1.31e+01 angle pdb=" C2' ATP A1103 " pdb=" C1' ATP A1103 " pdb=" O4' ATP A1103 " ideal model delta sigma weight residual 106.53 103.20 3.33 1.18e+00 7.24e-01 8.02e+00 angle pdb=" C3' ATP A1103 " pdb=" C4' ATP A1103 " pdb=" C5' ATP A1103 " ideal model delta sigma weight residual 115.19 110.74 4.45 1.76e+00 3.23e-01 6.39e+00 angle pdb=" C2' ATP A1103 " pdb=" C3' ATP A1103 " pdb=" O3' ATP A1103 " ideal model delta sigma weight residual 111.83 105.67 6.16 2.67e+00 1.40e-01 5.32e+00 angle pdb=" C3' ATP A1103 " pdb=" C2' ATP A1103 " pdb=" O2' ATP A1103 " ideal model delta sigma weight residual 111.83 106.25 5.58 2.67e+00 1.40e-01 4.37e+00 ... (remaining 13190 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 5722 17.98 - 35.95: 166 35.95 - 53.92: 31 53.92 - 71.90: 8 71.90 - 89.87: 2 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 -146.74 60.74 1 1.00e+01 1.00e-02 4.91e+01 dihedral pdb=" CA LYS A 884 " pdb=" C LYS A 884 " pdb=" N ASN A 885 " pdb=" CA ASN A 885 " ideal model delta harmonic sigma weight residual 180.00 164.17 15.83 0 5.00e+00 4.00e-02 1.00e+01 dihedral pdb=" CA LEU A 870 " pdb=" CB LEU A 870 " pdb=" CG LEU A 870 " pdb=" CD1 LEU A 870 " ideal model delta sinusoidal sigma weight residual 60.00 119.22 -59.22 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 5926 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1268 0.052 - 0.104: 145 0.104 - 0.156: 55 0.156 - 0.208: 0 0.208 - 0.260: 3 Chirality restraints: 1471 Sorted by residual: 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 -2.89 0.26 2.00e-01 2.50e+01 1.69e+00 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 -2.94 0.26 2.00e-01 2.50e+01 1.66e+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 -2.72 0.23 2.00e-01 2.50e+01 1.27e+00 ... (remaining 1468 not shown) Planarity restraints: 1707 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER C 94 " 0.021 5.00e-02 4.00e+02 3.11e-02 1.55e+00 pdb=" N PRO C 95 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO C 95 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 95 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 17 " 0.018 5.00e-02 4.00e+02 2.70e-02 1.17e+00 pdb=" N PRO C 18 " -0.047 5.00e-02 4.00e+02 pdb=" CA PRO C 18 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO C 18 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 259 " 0.015 5.00e-02 4.00e+02 2.29e-02 8.42e-01 pdb=" N PRO A 260 " -0.040 5.00e-02 4.00e+02 pdb=" CA PRO A 260 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 260 " 0.013 5.00e-02 4.00e+02 ... (remaining 1704 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 67 2.60 - 3.17: 8137 3.17 - 3.75: 13881 3.75 - 4.32: 20449 4.32 - 4.90: 34623 Nonbonded interactions: 77157 Sorted by model distance: nonbonded pdb=" OD2 ASP A 465 " pdb="MG MG A1102 " model vdw 2.022 2.170 nonbonded pdb="MG MG A1101 " pdb=" O2B ATP A1103 " model vdw 2.039 2.170 nonbonded pdb="MG MG A1102 " pdb=" O1B ATP A1103 " model vdw 2.053 2.170 nonbonded pdb="MG MG A1101 " pdb=" O3G ATP A1103 " model vdw 2.077 2.170 nonbonded pdb=" OD2 ASP A 463 " pdb=" O3' ATP A1103 " model vdw 2.172 3.040 ... (remaining 77152 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.600 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: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 27.280 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 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= 0.187 Angle : 0.438 6.505 13195 Z= 0.220 Chirality : 0.041 0.260 1471 Planarity : 0.003 0.031 1707 Dihedral : 9.279 89.875 3662 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 1.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.85 % Allowed : 2.17 % Favored : 96.98 % 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: 1.91 (0.25), residues: 493 sheet: 0.36 (0.36), residues: 196 loop : 0.43 (0.28), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 608 HIS 0.002 0.000 HIS A 988 PHE 0.009 0.001 PHE A 842 TYR 0.006 0.001 TYR A 81 ARG 0.001 0.000 ARG A 409 *********************** 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 183 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 174 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 MET cc_start: 0.5436 (mtt) cc_final: 0.5196 (mmt) REVERT: A 227 ARG cc_start: 0.7642 (mtt-85) cc_final: 0.7401 (mmt90) REVERT: A 562 LEU cc_start: 0.8946 (tp) cc_final: 0.8711 (tp) REVERT: A 567 ASN cc_start: 0.8789 (p0) cc_final: 0.8580 (p0) REVERT: A 643 ASN cc_start: 0.8425 (m-40) cc_final: 0.8200 (t0) REVERT: A 649 GLU cc_start: 0.8461 (mt-10) cc_final: 0.8103 (mm-30) REVERT: A 937 GLU cc_start: 0.8721 (OUTLIER) cc_final: 0.8107 (mp0) REVERT: A 994 CYS cc_start: 0.7878 (m) cc_final: 0.7428 (m) REVERT: C 59 ASP cc_start: 0.7994 (m-30) cc_final: 0.7578 (t0) REVERT: C 116 ASP cc_start: 0.8084 (m-30) cc_final: 0.7498 (t0) REVERT: C 117 ASP cc_start: 0.8755 (t0) cc_final: 0.8494 (t70) REVERT: C 130 ASP cc_start: 0.6472 (t0) cc_final: 0.5956 (t0) outliers start: 9 outliers final: 3 residues processed: 180 average time/residue: 0.3158 time to fit residues: 73.1814 Evaluate side-chains 102 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 98 time to evaluate : 1.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain A residue 937 GLU Chi-restraints excluded: chain C residue 85 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 100 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 60 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 chunk 93 optimal weight: 0.0000 chunk 36 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 108 optimal weight: 0.7980 overall best weight: 0.6984 ------------------------------------------------------------------------------- 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 = 0.3785 r_free = 0.3785 target = 0.137168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.086568 restraints weight = 13607.117| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 3.06 r_work: 0.2930 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9738 Z= 0.231 Angle : 0.535 7.224 13195 Z= 0.272 Chirality : 0.044 0.263 1471 Planarity : 0.004 0.043 1707 Dihedral : 6.186 85.806 1333 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.70 % Allowed : 6.69 % Favored : 91.61 % 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: 1.85 (0.24), residues: 503 sheet: 0.51 (0.36), residues: 201 loop : 0.41 (0.29), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 917 HIS 0.008 0.001 HIS D 68 PHE 0.018 0.001 PHE A 956 TYR 0.012 0.001 TYR C 74 ARG 0.008 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 121 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 103 time to evaluate : 1.128 Fit side-chains revert: symmetry clash REVERT: A 80 GLN cc_start: 0.8928 (OUTLIER) cc_final: 0.7389 (tm-30) REVERT: A 154 ASP cc_start: 0.7684 (m-30) cc_final: 0.7424 (m-30) REVERT: A 197 LEU cc_start: 0.6249 (mp) cc_final: 0.5311 (mp) REVERT: A 464 MET cc_start: 0.8767 (OUTLIER) cc_final: 0.7507 (pmt) REVERT: A 562 LEU cc_start: 0.8417 (tp) cc_final: 0.8205 (tp) REVERT: A 567 ASN cc_start: 0.8552 (p0) cc_final: 0.8320 (p0) REVERT: A 603 GLU cc_start: 0.8692 (mp0) cc_final: 0.8324 (mp0) REVERT: A 649 GLU cc_start: 0.8765 (mt-10) cc_final: 0.8436 (mm-30) REVERT: A 739 LYS cc_start: 0.8971 (tppt) cc_final: 0.8455 (ttpp) REVERT: A 937 GLU cc_start: 0.8953 (OUTLIER) cc_final: 0.8743 (mm-30) REVERT: C 7 ASN cc_start: 0.8888 (t0) cc_final: 0.8464 (p0) REVERT: C 59 ASP cc_start: 0.8131 (m-30) cc_final: 0.7596 (t0) REVERT: C 116 ASP cc_start: 0.7998 (m-30) cc_final: 0.7584 (t0) REVERT: D 42 ARG cc_start: 0.7627 (mtm180) cc_final: 0.7293 (mtp180) outliers start: 18 outliers final: 8 residues processed: 117 average time/residue: 0.2884 time to fit residues: 44.6109 Evaluate side-chains 99 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 898 SER Chi-restraints excluded: chain A residue 937 GLU Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain D residue 69 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 61 optimal weight: 0.8980 chunk 70 optimal weight: 0.3980 chunk 60 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 67 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 18 optimal weight: 7.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3775 r_free = 0.3775 target = 0.136169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.085478 restraints weight = 13843.477| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 3.07 r_work: 0.2913 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9738 Z= 0.242 Angle : 0.508 7.627 13195 Z= 0.262 Chirality : 0.043 0.156 1471 Planarity : 0.004 0.051 1707 Dihedral : 6.040 74.186 1332 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.32 % Allowed : 7.73 % Favored : 90.95 % 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: 1.44 (0.25), residues: 1199 helix: 1.77 (0.24), residues: 498 sheet: 0.58 (0.36), residues: 201 loop : 0.42 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 93 HIS 0.003 0.001 HIS D 68 PHE 0.014 0.001 PHE A 956 TYR 0.011 0.001 TYR C 134 ARG 0.009 0.001 ARG A 841 *********************** 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 110 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 96 time to evaluate : 1.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLN cc_start: 0.8946 (OUTLIER) cc_final: 0.7406 (tm-30) REVERT: A 218 MET cc_start: 0.4418 (mmt) cc_final: 0.3934 (mmt) REVERT: A 464 MET cc_start: 0.8751 (OUTLIER) cc_final: 0.7501 (pmt) REVERT: A 562 LEU cc_start: 0.8417 (tp) cc_final: 0.8215 (tp) REVERT: A 567 ASN cc_start: 0.8659 (p0) cc_final: 0.8388 (p0) REVERT: A 603 GLU cc_start: 0.8665 (mp0) cc_final: 0.8246 (mp0) REVERT: A 649 GLU cc_start: 0.8749 (mt-10) cc_final: 0.8412 (mm-30) REVERT: A 739 LYS cc_start: 0.9008 (tppt) cc_final: 0.8538 (ttpp) REVERT: A 937 GLU cc_start: 0.8940 (OUTLIER) cc_final: 0.8726 (mm-30) REVERT: C 59 ASP cc_start: 0.8096 (m-30) cc_final: 0.7571 (t0) REVERT: C 92 GLN cc_start: 0.6784 (tm-30) cc_final: 0.6325 (tm-30) REVERT: C 116 ASP cc_start: 0.7966 (m-30) cc_final: 0.7583 (t0) REVERT: D 42 ARG cc_start: 0.7610 (mtm180) cc_final: 0.7249 (mtp180) outliers start: 14 outliers final: 9 residues processed: 107 average time/residue: 0.2945 time to fit residues: 41.2763 Evaluate side-chains 103 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 91 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 879 LYS Chi-restraints excluded: chain A residue 898 SER Chi-restraints excluded: chain A residue 937 GLU Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 85 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 53 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 82 optimal weight: 0.0170 chunk 69 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 62 optimal weight: 7.9990 chunk 79 optimal weight: 0.4980 chunk 95 optimal weight: 3.9990 overall best weight: 0.5618 ------------------------------------------------------------------------------- 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 = 0.3780 r_free = 0.3780 target = 0.136559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.086124 restraints weight = 13687.731| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 3.06 r_work: 0.2925 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9738 Z= 0.187 Angle : 0.484 7.124 13195 Z= 0.249 Chirality : 0.042 0.199 1471 Planarity : 0.004 0.049 1707 Dihedral : 5.946 78.102 1332 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.41 % Allowed : 7.35 % Favored : 91.23 % 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: 1.39 (0.25), residues: 1199 helix: 1.76 (0.24), residues: 499 sheet: 0.58 (0.35), residues: 207 loop : 0.34 (0.28), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 93 HIS 0.002 0.000 HIS D 68 PHE 0.012 0.001 PHE D 4 TYR 0.011 0.001 TYR C 134 ARG 0.008 0.001 ARG C 143 *********************** 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 111 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 96 time to evaluate : 1.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLN cc_start: 0.8939 (OUTLIER) cc_final: 0.7424 (tm-30) REVERT: A 154 ASP cc_start: 0.7703 (m-30) cc_final: 0.7471 (m-30) REVERT: A 218 MET cc_start: 0.4485 (mmt) cc_final: 0.4049 (mmt) REVERT: A 227 ARG cc_start: 0.6684 (mmm-85) cc_final: 0.6204 (mmt90) REVERT: A 333 GLN cc_start: 0.8563 (mp10) cc_final: 0.7417 (tm-30) REVERT: A 464 MET cc_start: 0.8728 (OUTLIER) cc_final: 0.7585 (pmt) REVERT: A 562 LEU cc_start: 0.8419 (tp) cc_final: 0.8206 (tp) REVERT: A 567 ASN cc_start: 0.8649 (p0) cc_final: 0.8391 (p0) REVERT: A 603 GLU cc_start: 0.8660 (mp0) cc_final: 0.8227 (mp0) REVERT: A 649 GLU cc_start: 0.8738 (mt-10) cc_final: 0.8239 (mm-30) REVERT: A 739 LYS cc_start: 0.9055 (tppt) cc_final: 0.8625 (ttpp) REVERT: C 7 ASN cc_start: 0.8906 (t0) cc_final: 0.8549 (p0) REVERT: C 38 MET cc_start: 0.8336 (mmm) cc_final: 0.7924 (mmm) REVERT: C 59 ASP cc_start: 0.8016 (m-30) cc_final: 0.7426 (t70) REVERT: C 92 GLN cc_start: 0.6915 (tm-30) cc_final: 0.6432 (tm-30) REVERT: C 116 ASP cc_start: 0.7935 (m-30) cc_final: 0.7580 (t0) REVERT: C 131 ARG cc_start: 0.7479 (tpt170) cc_final: 0.6866 (tpt90) REVERT: D 42 ARG cc_start: 0.7571 (mtm180) cc_final: 0.7215 (mtp180) outliers start: 15 outliers final: 7 residues processed: 105 average time/residue: 0.2802 time to fit residues: 39.2460 Evaluate side-chains 103 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 94 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 646 GLU Chi-restraints excluded: chain A residue 879 LYS Chi-restraints excluded: chain A residue 898 SER Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 85 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 85 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 chunk 43 optimal weight: 0.0870 chunk 76 optimal weight: 5.9990 chunk 89 optimal weight: 4.9990 chunk 17 optimal weight: 0.0370 chunk 104 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 overall best weight: 0.5238 ------------------------------------------------------------------------------- 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 = 0.3777 r_free = 0.3777 target = 0.135726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.085969 restraints weight = 13634.885| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 2.99 r_work: 0.2953 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9738 Z= 0.178 Angle : 0.480 8.142 13195 Z= 0.247 Chirality : 0.042 0.184 1471 Planarity : 0.004 0.058 1707 Dihedral : 5.634 76.891 1329 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.23 % Allowed : 7.82 % Favored : 90.95 % 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: 1.46 (0.25), residues: 1199 helix: 1.82 (0.24), residues: 499 sheet: 0.64 (0.35), residues: 210 loop : 0.35 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 93 HIS 0.003 0.000 HIS A 305 PHE 0.011 0.001 PHE D 4 TYR 0.010 0.001 TYR C 134 ARG 0.007 0.000 ARG C 143 *********************** 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 111 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 98 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 ASP cc_start: 0.7670 (m-30) cc_final: 0.7443 (m-30) REVERT: A 333 GLN cc_start: 0.8550 (mp10) cc_final: 0.7429 (tm-30) REVERT: A 464 MET cc_start: 0.8721 (OUTLIER) cc_final: 0.7514 (pmt) REVERT: A 562 LEU cc_start: 0.8486 (tp) cc_final: 0.8275 (tp) REVERT: A 567 ASN cc_start: 0.8679 (p0) cc_final: 0.8428 (p0) REVERT: A 603 GLU cc_start: 0.8666 (mp0) cc_final: 0.8404 (mp0) REVERT: A 649 GLU cc_start: 0.8736 (mt-10) cc_final: 0.8232 (mm-30) REVERT: A 739 LYS cc_start: 0.9070 (tppt) cc_final: 0.8647 (ttpp) REVERT: C 38 MET cc_start: 0.8325 (mmm) cc_final: 0.7867 (mmm) REVERT: C 59 ASP cc_start: 0.7982 (m-30) cc_final: 0.7442 (t70) REVERT: C 92 GLN cc_start: 0.7044 (tm-30) cc_final: 0.6536 (tm-30) REVERT: C 116 ASP cc_start: 0.7925 (m-30) cc_final: 0.7597 (t0) REVERT: D 42 ARG cc_start: 0.7599 (mtm180) cc_final: 0.7229 (mtp180) REVERT: D 56 LEU cc_start: 0.8716 (mt) cc_final: 0.8497 (pp) outliers start: 13 outliers final: 9 residues processed: 107 average time/residue: 0.3029 time to fit residues: 42.7566 Evaluate side-chains 101 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 91 time to evaluate : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 646 GLU Chi-restraints excluded: chain A residue 879 LYS Chi-restraints excluded: chain A residue 898 SER Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 85 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 84 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 99 optimal weight: 6.9990 chunk 61 optimal weight: 0.0970 chunk 100 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 17 optimal weight: 0.0970 chunk 37 optimal weight: 0.5980 chunk 89 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- 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 = 0.3762 r_free = 0.3762 target = 0.134912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.084480 restraints weight = 13743.610| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 3.05 r_work: 0.2900 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9738 Z= 0.277 Angle : 0.512 6.845 13195 Z= 0.264 Chirality : 0.043 0.190 1471 Planarity : 0.004 0.058 1707 Dihedral : 5.726 74.642 1329 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.13 % Allowed : 8.67 % Favored : 90.20 % 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: 1.39 (0.25), residues: 1199 helix: 1.73 (0.24), residues: 498 sheet: 0.53 (0.36), residues: 201 loop : 0.39 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 93 HIS 0.003 0.001 HIS D 68 PHE 0.011 0.001 PHE A 842 TYR 0.011 0.001 TYR A 81 ARG 0.011 0.001 ARG A 841 *********************** 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 103 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 91 time to evaluate : 1.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLN cc_start: 0.8999 (OUTLIER) cc_final: 0.7510 (tm-30) REVERT: A 218 MET cc_start: 0.4189 (mmt) cc_final: 0.3973 (mmt) REVERT: A 333 GLN cc_start: 0.8564 (mp10) cc_final: 0.7453 (tm-30) REVERT: A 464 MET cc_start: 0.8727 (OUTLIER) cc_final: 0.7431 (pmt) REVERT: A 567 ASN cc_start: 0.8687 (p0) cc_final: 0.8399 (p0) REVERT: A 649 GLU cc_start: 0.8764 (mt-10) cc_final: 0.8446 (mm-30) REVERT: A 739 LYS cc_start: 0.9136 (tppt) cc_final: 0.8710 (ttpp) REVERT: C 7 ASN cc_start: 0.8837 (t0) cc_final: 0.8302 (t0) REVERT: C 38 MET cc_start: 0.8332 (mmm) cc_final: 0.7879 (mmm) REVERT: C 59 ASP cc_start: 0.8076 (m-30) cc_final: 0.7576 (t70) REVERT: C 92 GLN cc_start: 0.6921 (tm-30) cc_final: 0.6451 (tm-30) REVERT: C 116 ASP cc_start: 0.7895 (m-30) cc_final: 0.7586 (t0) REVERT: D 42 ARG cc_start: 0.7539 (mtm180) cc_final: 0.7211 (mtp180) outliers start: 12 outliers final: 10 residues processed: 100 average time/residue: 0.3321 time to fit residues: 44.2206 Evaluate side-chains 100 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 1.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 646 GLU Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 879 LYS Chi-restraints excluded: chain A residue 898 SER Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 100 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 79 optimal weight: 0.6980 chunk 69 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 85 optimal weight: 0.0370 chunk 33 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 20 optimal weight: 0.3980 chunk 30 optimal weight: 0.6980 chunk 78 optimal weight: 0.7980 overall best weight: 0.5258 ------------------------------------------------------------------------------- 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 = 0.3777 r_free = 0.3777 target = 0.136108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.085911 restraints weight = 13648.939| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 3.03 r_work: 0.2924 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9738 Z= 0.177 Angle : 0.494 8.637 13195 Z= 0.250 Chirality : 0.041 0.171 1471 Planarity : 0.004 0.055 1707 Dihedral : 5.702 76.690 1329 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.04 % Allowed : 9.43 % Favored : 89.54 % 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: 1.38 (0.25), residues: 1199 helix: 1.78 (0.24), residues: 499 sheet: 0.55 (0.35), residues: 209 loop : 0.31 (0.28), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 669 HIS 0.002 0.000 HIS A 604 PHE 0.008 0.001 PHE D 4 TYR 0.010 0.001 TYR C 134 ARG 0.011 0.001 ARG C 143 *********************** 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 104 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 93 time to evaluate : 1.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 MET cc_start: 0.4112 (mmt) cc_final: 0.3859 (mmt) REVERT: A 333 GLN cc_start: 0.8621 (mp10) cc_final: 0.7529 (tm-30) REVERT: A 464 MET cc_start: 0.8681 (OUTLIER) cc_final: 0.7438 (pmt) REVERT: A 567 ASN cc_start: 0.8646 (p0) cc_final: 0.8373 (p0) REVERT: A 649 GLU cc_start: 0.8749 (mt-10) cc_final: 0.8434 (mm-30) REVERT: A 739 LYS cc_start: 0.9139 (tppt) cc_final: 0.8713 (ttpp) REVERT: C 38 MET cc_start: 0.8295 (mmm) cc_final: 0.7812 (mmm) REVERT: C 59 ASP cc_start: 0.7984 (m-30) cc_final: 0.7392 (t0) REVERT: C 92 GLN cc_start: 0.7114 (tm-30) cc_final: 0.6632 (tm-30) REVERT: C 116 ASP cc_start: 0.7862 (m-30) cc_final: 0.7556 (t0) REVERT: C 144 LYS cc_start: 0.8612 (ttpp) cc_final: 0.8131 (mtmm) REVERT: D 6 LYS cc_start: 0.6568 (mmmm) cc_final: 0.6365 (mmtm) REVERT: D 42 ARG cc_start: 0.7529 (mtm180) cc_final: 0.7196 (mtp180) REVERT: D 56 LEU cc_start: 0.8813 (mt) cc_final: 0.8562 (pp) outliers start: 11 outliers final: 9 residues processed: 101 average time/residue: 0.3897 time to fit residues: 51.9800 Evaluate side-chains 98 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 88 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 646 GLU Chi-restraints excluded: chain A residue 879 LYS Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 100 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 82 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 71 optimal weight: 0.7980 chunk 55 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 118 optimal weight: 9.9990 chunk 52 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.3773 r_free = 0.3773 target = 0.135557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.083885 restraints weight = 13848.600| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 3.13 r_work: 0.2885 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9738 Z= 0.263 Angle : 0.515 7.625 13195 Z= 0.263 Chirality : 0.043 0.159 1471 Planarity : 0.004 0.053 1707 Dihedral : 5.728 73.359 1329 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.32 % Allowed : 9.43 % Favored : 89.26 % 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: 1.34 (0.25), residues: 1199 helix: 1.68 (0.24), residues: 499 sheet: 0.54 (0.36), residues: 201 loop : 0.35 (0.28), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 93 HIS 0.002 0.001 HIS A 305 PHE 0.011 0.001 PHE A 431 TYR 0.010 0.001 TYR A 81 ARG 0.009 0.001 ARG A 841 *********************** 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 100 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 86 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLN cc_start: 0.8998 (OUTLIER) cc_final: 0.7435 (tm-30) REVERT: A 218 MET cc_start: 0.4159 (mmt) cc_final: 0.3862 (mmt) REVERT: A 333 GLN cc_start: 0.8629 (mp10) cc_final: 0.7443 (tm-30) REVERT: A 464 MET cc_start: 0.8716 (OUTLIER) cc_final: 0.7447 (pmt) REVERT: A 567 ASN cc_start: 0.8711 (p0) cc_final: 0.8404 (p0) REVERT: A 739 LYS cc_start: 0.9140 (tppt) cc_final: 0.8734 (ttpp) REVERT: C 38 MET cc_start: 0.8262 (mmm) cc_final: 0.7787 (mmm) REVERT: C 59 ASP cc_start: 0.8070 (m-30) cc_final: 0.7553 (t0) REVERT: C 92 GLN cc_start: 0.7188 (tm-30) cc_final: 0.6739 (tm-30) REVERT: C 101 LYS cc_start: 0.8245 (mmtt) cc_final: 0.7957 (mmmt) REVERT: C 116 ASP cc_start: 0.7884 (m-30) cc_final: 0.7618 (t0) REVERT: C 144 LYS cc_start: 0.8347 (ttpp) cc_final: 0.8041 (mtmm) REVERT: D 6 LYS cc_start: 0.6770 (mmmm) cc_final: 0.6527 (mmtm) REVERT: D 42 ARG cc_start: 0.7557 (mtm180) cc_final: 0.7098 (mtm180) REVERT: D 56 LEU cc_start: 0.8822 (mt) cc_final: 0.8574 (pp) outliers start: 14 outliers final: 9 residues processed: 97 average time/residue: 0.5002 time to fit residues: 69.9892 Evaluate side-chains 94 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 83 time to evaluate : 3.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 646 GLU Chi-restraints excluded: chain A residue 879 LYS Chi-restraints excluded: chain A residue 898 SER Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 100 SER 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: 0.6980 chunk 105 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 17 optimal weight: 0.3980 chunk 15 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 31 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 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 = 0.3771 r_free = 0.3771 target = 0.135487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.086594 restraints weight = 13692.371| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 3.21 r_work: 0.2920 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.2782 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= 0.209 Angle : 0.514 13.732 13195 Z= 0.257 Chirality : 0.042 0.153 1471 Planarity : 0.004 0.050 1707 Dihedral : 5.700 74.799 1329 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.13 % Allowed : 9.80 % Favored : 89.07 % 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: 1.36 (0.25), residues: 1199 helix: 1.70 (0.24), residues: 499 sheet: 0.54 (0.36), residues: 201 loop : 0.37 (0.28), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 93 HIS 0.002 0.001 HIS C 32 PHE 0.009 0.001 PHE D 4 TYR 0.009 0.001 TYR C 134 ARG 0.007 0.001 ARG A 841 *********************** 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 99 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 87 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLN cc_start: 0.8980 (OUTLIER) cc_final: 0.7489 (tm-30) REVERT: A 218 MET cc_start: 0.4126 (mmt) cc_final: 0.3809 (mmt) REVERT: A 333 GLN cc_start: 0.8636 (mp10) cc_final: 0.7470 (tm-30) REVERT: A 464 MET cc_start: 0.8660 (OUTLIER) cc_final: 0.7414 (pmt) REVERT: A 567 ASN cc_start: 0.8710 (p0) cc_final: 0.8408 (p0) REVERT: A 739 LYS cc_start: 0.9141 (tppt) cc_final: 0.8735 (ttpp) REVERT: C 38 MET cc_start: 0.8258 (mmm) cc_final: 0.7782 (mmm) REVERT: C 59 ASP cc_start: 0.8084 (m-30) cc_final: 0.7453 (t0) REVERT: C 92 GLN cc_start: 0.7169 (tm-30) cc_final: 0.6752 (tm-30) REVERT: C 101 LYS cc_start: 0.8258 (mmtt) cc_final: 0.7967 (mmmt) REVERT: C 116 ASP cc_start: 0.7869 (m-30) cc_final: 0.7617 (t0) REVERT: C 144 LYS cc_start: 0.8400 (ttpp) cc_final: 0.8076 (mtmm) REVERT: D 6 LYS cc_start: 0.7171 (mmmm) cc_final: 0.6889 (mmtm) REVERT: D 42 ARG cc_start: 0.7570 (mtm180) cc_final: 0.7166 (mtp180) REVERT: D 56 LEU cc_start: 0.8825 (mt) cc_final: 0.8586 (pp) outliers start: 12 outliers final: 9 residues processed: 95 average time/residue: 0.2905 time to fit residues: 36.6574 Evaluate side-chains 96 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 646 GLU Chi-restraints excluded: chain A residue 879 LYS Chi-restraints excluded: chain A residue 898 SER Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 100 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 13 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 chunk 61 optimal weight: 0.6980 chunk 17 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 79 optimal weight: 0.7980 chunk 94 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 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 = 0.3764 r_free = 0.3764 target = 0.134892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.084659 restraints weight = 13924.757| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 3.05 r_work: 0.2901 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9738 Z= 0.243 Angle : 0.521 12.973 13195 Z= 0.262 Chirality : 0.043 0.290 1471 Planarity : 0.004 0.050 1707 Dihedral : 5.724 73.882 1329 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.13 % Allowed : 9.61 % Favored : 89.26 % 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: 1.32 (0.25), residues: 1199 helix: 1.68 (0.24), residues: 499 sheet: 0.49 (0.36), residues: 201 loop : 0.35 (0.28), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 93 HIS 0.002 0.001 HIS A 305 PHE 0.009 0.001 PHE D 4 TYR 0.010 0.001 TYR C 134 ARG 0.006 0.000 ARG A 841 ********************** 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 98 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 86 time to evaluate : 1.035 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 80 GLN cc_start: 0.8985 (OUTLIER) cc_final: 0.7500 (tm-30) REVERT: A 184 MET cc_start: 0.7765 (mtt) cc_final: 0.7526 (tpp) REVERT: A 218 MET cc_start: 0.4156 (mmt) cc_final: 0.3843 (mmt) REVERT: A 333 GLN cc_start: 0.8637 (mp10) cc_final: 0.7471 (tm-30) REVERT: A 464 MET cc_start: 0.8639 (OUTLIER) cc_final: 0.7411 (pmt) REVERT: A 567 ASN cc_start: 0.8699 (p0) cc_final: 0.8395 (p0) REVERT: A 739 LYS cc_start: 0.9124 (tppt) cc_final: 0.8738 (ttpp) REVERT: A 804 ARG cc_start: 0.7448 (mpt180) cc_final: 0.7034 (mpt180) REVERT: C 38 MET cc_start: 0.8238 (mmm) cc_final: 0.7757 (mmm) REVERT: C 59 ASP cc_start: 0.8068 (m-30) cc_final: 0.7443 (t0) REVERT: C 92 GLN cc_start: 0.7248 (tm-30) cc_final: 0.6832 (tm-30) REVERT: C 101 LYS cc_start: 0.8260 (mmtt) cc_final: 0.7959 (mmmt) REVERT: C 116 ASP cc_start: 0.7857 (m-30) cc_final: 0.7610 (t0) REVERT: C 144 LYS cc_start: 0.8462 (ttpp) cc_final: 0.8201 (mtmm) REVERT: D 6 LYS cc_start: 0.7192 (mmmm) cc_final: 0.6900 (mmtm) REVERT: D 42 ARG cc_start: 0.7352 (mtm180) cc_final: 0.6964 (mtp180) REVERT: D 56 LEU cc_start: 0.8825 (mt) cc_final: 0.8585 (pp) outliers start: 12 outliers final: 10 residues processed: 94 average time/residue: 0.3256 time to fit residues: 40.6864 Evaluate side-chains 97 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 85 time to evaluate : 1.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 646 GLU Chi-restraints excluded: chain A residue 879 LYS Chi-restraints excluded: chain A residue 898 SER Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 100 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 44 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 112 optimal weight: 10.0000 chunk 48 optimal weight: 0.4980 chunk 93 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 chunk 39 optimal weight: 0.9990 chunk 80 optimal weight: 0.5980 chunk 34 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.3766 r_free = 0.3766 target = 0.134956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.084812 restraints weight = 13806.280| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 3.03 r_work: 0.2904 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9738 Z= 0.232 Angle : 0.524 14.241 13195 Z= 0.263 Chirality : 0.042 0.193 1471 Planarity : 0.004 0.048 1707 Dihedral : 5.723 73.306 1329 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.13 % Allowed : 9.52 % Favored : 89.35 % 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: 1.27 (0.25), residues: 1199 helix: 1.66 (0.24), residues: 499 sheet: 0.58 (0.37), residues: 198 loop : 0.23 (0.28), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 93 HIS 0.002 0.000 HIS C 32 PHE 0.009 0.001 PHE A 842 TYR 0.010 0.001 TYR C 134 ARG 0.007 0.001 ARG C 8 Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 5185.84 seconds wall clock time: 90 minutes 57.02 seconds (5457.02 seconds total)