Starting phenix.real_space_refine on Tue Nov 18 00:36:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b5o_44219/11_2025/9b5o_44219.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b5o_44219/11_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_44219/11_2025/9b5o_44219.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b5o_44219/11_2025/9b5o_44219.map" model { file = "/net/cci-nas-00/data/ceres_data/9b5o_44219/11_2025/9b5o_44219.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b5o_44219/11_2025/9b5o_44219.cif" } resolution = 3.19 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.059 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/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: 2.42, per 1000 atoms: 0.25 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: 0.99 Conformation dependent library (CDL) restraints added in 366.9 milliseconds 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: 0.43 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: 1.90 Time building geometry restraints manager: 1.26 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: 4.790 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.970 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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:1.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.610 ------------------------------------------------------------------------------- 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 : 0.009 0.859 9741 Z= 0.466 Angle : 0.602 45.159 13197 Z= 0.295 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (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 ARG 0.001 0.000 ARG A 409 TYR 0.006 0.001 TYR A 81 PHE 0.009 0.001 PHE A 842 TRP 0.004 0.001 TRP A 608 HIS 0.002 0.000 HIS A 988 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 9738) covalent geometry : angle 0.43838 (13195) SS BOND : bond 0.85909 ( 1) SS BOND : angle 33.48973 ( 2) hydrogen bonds : bond 0.14200 ( 455) hydrogen bonds : angle 5.73942 ( 1275) Misc. bond : bond 0.07835 ( 2) *********************** 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 : 0.384 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: 0.1501 time to fit residues: 34.5347 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 : 0.412 ------------------------------------------------------------------------------- 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 108 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.0040 chunk 113 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 117 optimal weight: 5.9990 overall best weight: 0.9996 ------------------------------------------------------------------------------- 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 = 0.3767 r_free = 0.3767 target = 0.135656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.085042 restraints weight = 13724.712| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 3.07 r_work: 0.2905 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 9741 Z= 0.189 Angle : 0.563 8.734 13197 Z= 0.287 Chirality : 0.044 0.243 1471 Planarity : 0.004 0.047 1707 Dihedral : 6.320 84.840 1333 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.60 % Allowed : 6.88 % Favored : 91.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.25), residues: 1199 helix: 1.76 (0.24), residues: 503 sheet: 0.46 (0.36), residues: 201 loop : 0.38 (0.29), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 406 TYR 0.011 0.002 TYR C 74 PHE 0.017 0.001 PHE A 956 TRP 0.005 0.001 TRP A 669 HIS 0.008 0.001 HIS D 68 Details of bonding type rmsd covalent geometry : bond 0.00465 ( 9738) covalent geometry : angle 0.55704 (13195) SS BOND : bond 0.00033 ( 1) SS BOND : angle 6.46840 ( 2) hydrogen bonds : bond 0.04451 ( 455) hydrogen bonds : angle 4.62042 ( 1275) Misc. bond : bond 0.00582 ( 2) *********************** 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: 17 poor density : 104 time to evaluate : 0.406 Fit side-chains revert: symmetry clash REVERT: A 80 GLN cc_start: 0.8970 (OUTLIER) cc_final: 0.7448 (tm-30) REVERT: A 197 LEU cc_start: 0.6283 (mp) cc_final: 0.5712 (mt) REVERT: A 464 MET cc_start: 0.8790 (OUTLIER) cc_final: 0.7570 (pmt) REVERT: A 567 ASN cc_start: 0.8689 (p0) cc_final: 0.8400 (p0) REVERT: A 603 GLU cc_start: 0.8705 (mp0) cc_final: 0.8277 (mp0) REVERT: A 649 GLU cc_start: 0.8780 (mt-10) cc_final: 0.8450 (mm-30) REVERT: A 739 LYS cc_start: 0.8979 (tppt) cc_final: 0.8475 (ttpp) REVERT: A 937 GLU cc_start: 0.8949 (OUTLIER) cc_final: 0.8738 (mm-30) REVERT: C 7 ASN cc_start: 0.8875 (t0) cc_final: 0.8458 (p0) REVERT: C 59 ASP cc_start: 0.8152 (m-30) cc_final: 0.7629 (t0) REVERT: C 116 ASP cc_start: 0.8028 (m-30) cc_final: 0.7634 (t0) REVERT: D 42 ARG cc_start: 0.7617 (mtm180) cc_final: 0.7195 (mtp180) outliers start: 17 outliers final: 9 residues processed: 117 average time/residue: 0.1414 time to fit residues: 21.8069 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 : 0.402 ------------------------------------------------------------------------------- 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 A residue 1003 VAL 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 17 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 34 optimal weight: 0.9990 chunk 104 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 84 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.135321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.084803 restraints weight = 13645.267| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 3.06 r_work: 0.2902 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9741 Z= 0.162 Angle : 0.520 8.033 13197 Z= 0.268 Chirality : 0.043 0.146 1471 Planarity : 0.004 0.046 1707 Dihedral : 6.235 76.672 1332 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.41 % Allowed : 8.01 % Favored : 90.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.25), residues: 1199 helix: 1.69 (0.24), residues: 498 sheet: 0.50 (0.36), residues: 201 loop : 0.37 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 841 TYR 0.011 0.001 TYR C 134 PHE 0.014 0.001 PHE A 956 TRP 0.006 0.001 TRP C 93 HIS 0.004 0.001 HIS D 68 Details of bonding type rmsd covalent geometry : bond 0.00398 ( 9738) covalent geometry : angle 0.51560 (13195) SS BOND : bond 0.01056 ( 1) SS BOND : angle 5.18975 ( 2) hydrogen bonds : bond 0.04135 ( 455) hydrogen bonds : angle 4.48362 ( 1275) Misc. bond : bond 0.00122 ( 2) *********************** 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 113 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 98 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLN cc_start: 0.8970 (OUTLIER) cc_final: 0.7447 (tm-30) REVERT: A 218 MET cc_start: 0.4389 (mmt) cc_final: 0.3904 (mmt) REVERT: A 464 MET cc_start: 0.8683 (OUTLIER) cc_final: 0.7428 (pmt) REVERT: A 567 ASN cc_start: 0.8677 (p0) cc_final: 0.8386 (p0) REVERT: A 603 GLU cc_start: 0.8676 (mp0) cc_final: 0.8219 (mp0) REVERT: A 649 GLU cc_start: 0.8754 (mt-10) cc_final: 0.8416 (mm-30) REVERT: A 739 LYS cc_start: 0.9011 (tppt) cc_final: 0.8595 (ttpp) REVERT: C 59 ASP cc_start: 0.8122 (m-30) cc_final: 0.7600 (t0) REVERT: C 92 GLN cc_start: 0.6861 (tm-30) cc_final: 0.6389 (tm-30) REVERT: C 116 ASP cc_start: 0.7995 (m-30) cc_final: 0.7617 (t0) REVERT: D 42 ARG cc_start: 0.7563 (mtm180) cc_final: 0.7196 (mtp180) outliers start: 15 outliers final: 9 residues processed: 111 average time/residue: 0.1396 time to fit residues: 20.4196 Evaluate side-chains 101 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 90 time to evaluate : 0.377 ------------------------------------------------------------------------------- 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 462 THR Chi-restraints excluded: chain A residue 464 MET 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 A residue 1003 VAL 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 44 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 46 optimal weight: 0.6980 chunk 49 optimal weight: 0.6980 chunk 117 optimal weight: 0.9980 chunk 100 optimal weight: 4.9990 chunk 70 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 88 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 = 0.3762 r_free = 0.3762 target = 0.135111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.084741 restraints weight = 13852.963| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 3.06 r_work: 0.2901 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9741 Z= 0.149 Angle : 0.503 7.123 13197 Z= 0.259 Chirality : 0.043 0.226 1471 Planarity : 0.004 0.050 1707 Dihedral : 5.827 77.846 1329 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.79 % Allowed : 7.82 % Favored : 90.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.25), residues: 1199 helix: 1.70 (0.24), residues: 497 sheet: 0.42 (0.35), residues: 209 loop : 0.30 (0.28), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 143 TYR 0.010 0.001 TYR C 134 PHE 0.012 0.001 PHE A 956 TRP 0.006 0.001 TRP C 93 HIS 0.003 0.001 HIS D 68 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 9738) covalent geometry : angle 0.50037 (13195) SS BOND : bond 0.00019 ( 1) SS BOND : angle 4.56085 ( 2) hydrogen bonds : bond 0.03890 ( 455) hydrogen bonds : angle 4.39785 ( 1275) Misc. bond : bond 0.00158 ( 2) *********************** 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 114 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 95 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLN cc_start: 0.8971 (OUTLIER) cc_final: 0.7481 (tm-30) REVERT: A 218 MET cc_start: 0.4493 (mmt) cc_final: 0.4109 (mmt) REVERT: A 227 ARG cc_start: 0.6724 (mmm-85) cc_final: 0.6223 (mmt90) REVERT: A 333 GLN cc_start: 0.8580 (mp10) cc_final: 0.7333 (tm-30) REVERT: A 464 MET cc_start: 0.8730 (OUTLIER) cc_final: 0.7484 (pmt) REVERT: A 567 ASN cc_start: 0.8687 (p0) cc_final: 0.8395 (p0) REVERT: A 603 GLU cc_start: 0.8738 (mp0) cc_final: 0.8260 (mp0) REVERT: A 649 GLU cc_start: 0.8756 (mt-10) cc_final: 0.8426 (mm-30) REVERT: A 723 ASP cc_start: 0.7677 (t0) cc_final: 0.7444 (t0) REVERT: A 739 LYS cc_start: 0.9096 (tppt) cc_final: 0.8632 (ttpp) REVERT: C 38 MET cc_start: 0.8348 (mmm) cc_final: 0.7912 (mmt) REVERT: C 59 ASP cc_start: 0.8082 (m-30) cc_final: 0.7577 (t70) REVERT: C 72 ARG cc_start: 0.8294 (mtm-85) cc_final: 0.7876 (mtm-85) REVERT: C 92 GLN cc_start: 0.7045 (tm-30) cc_final: 0.6535 (tm-30) REVERT: C 116 ASP cc_start: 0.7971 (m-30) cc_final: 0.7600 (t0) REVERT: D 42 ARG cc_start: 0.7573 (mtm180) cc_final: 0.7218 (mtp180) outliers start: 19 outliers final: 13 residues processed: 108 average time/residue: 0.1322 time to fit residues: 18.9874 Evaluate side-chains 108 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 0.321 ------------------------------------------------------------------------------- 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 257 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 A residue 993 ILE Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 100 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 21 optimal weight: 6.9990 chunk 87 optimal weight: 0.6980 chunk 79 optimal weight: 0.7980 chunk 63 optimal weight: 0.1980 chunk 17 optimal weight: 0.0670 chunk 48 optimal weight: 0.9990 chunk 96 optimal weight: 0.7980 chunk 75 optimal weight: 10.0000 chunk 35 optimal weight: 0.6980 chunk 58 optimal weight: 0.7980 chunk 118 optimal weight: 5.9990 overall best weight: 0.4918 ------------------------------------------------------------------------------- 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 = 0.3767 r_free = 0.3767 target = 0.134988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.085225 restraints weight = 13800.447| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 3.00 r_work: 0.2939 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9741 Z= 0.115 Angle : 0.489 7.524 13197 Z= 0.252 Chirality : 0.042 0.194 1471 Planarity : 0.004 0.070 1707 Dihedral : 5.790 78.561 1329 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.60 % Allowed : 8.67 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.25), residues: 1199 helix: 1.72 (0.24), residues: 499 sheet: 0.48 (0.36), residues: 207 loop : 0.31 (0.28), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 143 TYR 0.009 0.001 TYR C 134 PHE 0.010 0.001 PHE A 956 TRP 0.004 0.001 TRP C 93 HIS 0.002 0.000 HIS D 68 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 9738) covalent geometry : angle 0.48620 (13195) SS BOND : bond 0.00717 ( 1) SS BOND : angle 4.24288 ( 2) hydrogen bonds : bond 0.03654 ( 455) hydrogen bonds : angle 4.31060 ( 1275) Misc. bond : bond 0.00041 ( 2) *********************** 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: 17 poor density : 94 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 80 GLN cc_start: 0.8980 (OUTLIER) cc_final: 0.7498 (tm-30) REVERT: A 227 ARG cc_start: 0.6805 (mmm-85) cc_final: 0.6297 (mmt90) REVERT: A 333 GLN cc_start: 0.8553 (mp10) cc_final: 0.7324 (tm-30) REVERT: A 464 MET cc_start: 0.8746 (OUTLIER) cc_final: 0.7511 (pmt) REVERT: A 567 ASN cc_start: 0.8708 (p0) cc_final: 0.8422 (p0) REVERT: A 603 GLU cc_start: 0.8734 (mp0) cc_final: 0.8462 (mp0) REVERT: A 649 GLU cc_start: 0.8750 (mt-10) cc_final: 0.8411 (mm-30) REVERT: A 739 LYS cc_start: 0.9083 (tppt) cc_final: 0.8658 (ttpp) REVERT: C 38 MET cc_start: 0.8337 (mmm) cc_final: 0.7885 (mmm) REVERT: C 59 ASP cc_start: 0.7992 (m-30) cc_final: 0.7454 (t70) REVERT: C 72 ARG cc_start: 0.8309 (mtm-85) cc_final: 0.7913 (mtm-85) REVERT: C 92 GLN cc_start: 0.7046 (tm-30) cc_final: 0.6536 (tm-30) REVERT: C 116 ASP cc_start: 0.7955 (m-30) cc_final: 0.7628 (t0) REVERT: C 131 ARG cc_start: 0.7480 (tpt170) cc_final: 0.6967 (tpt90) REVERT: D 42 ARG cc_start: 0.7610 (mtm180) cc_final: 0.7245 (mtp180) REVERT: D 56 LEU cc_start: 0.8794 (mt) cc_final: 0.8551 (pp) outliers start: 17 outliers final: 9 residues processed: 106 average time/residue: 0.1427 time to fit residues: 19.7137 Evaluate side-chains 100 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 89 time to evaluate : 0.310 ------------------------------------------------------------------------------- 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 A residue 1003 VAL 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 43 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 116 optimal weight: 4.9990 chunk 95 optimal weight: 4.9990 chunk 82 optimal weight: 0.3980 chunk 10 optimal weight: 0.4980 chunk 67 optimal weight: 0.0770 chunk 7 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 105 optimal weight: 2.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- 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 = 0.3781 r_free = 0.3781 target = 0.136016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.084841 restraints weight = 13754.748| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 3.09 r_work: 0.2908 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9741 Z= 0.117 Angle : 0.488 7.576 13197 Z= 0.252 Chirality : 0.042 0.189 1471 Planarity : 0.004 0.064 1707 Dihedral : 5.732 77.677 1329 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.51 % Allowed : 9.33 % Favored : 89.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.25), residues: 1199 helix: 1.78 (0.24), residues: 498 sheet: 0.50 (0.35), residues: 209 loop : 0.32 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 841 TYR 0.009 0.001 TYR C 134 PHE 0.010 0.001 PHE D 4 TRP 0.004 0.001 TRP A 669 HIS 0.002 0.000 HIS D 68 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 9738) covalent geometry : angle 0.48547 (13195) SS BOND : bond 0.00185 ( 1) SS BOND : angle 4.08446 ( 2) hydrogen bonds : bond 0.03537 ( 455) hydrogen bonds : angle 4.27825 ( 1275) Misc. bond : bond 0.00082 ( 2) *********************** 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 105 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 89 time to evaluate : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 333 GLN cc_start: 0.8589 (mp10) cc_final: 0.7376 (tm-30) REVERT: A 464 MET cc_start: 0.8737 (OUTLIER) cc_final: 0.7574 (pmt) REVERT: A 567 ASN cc_start: 0.8702 (p0) cc_final: 0.8420 (p0) REVERT: A 603 GLU cc_start: 0.8702 (mp0) cc_final: 0.8413 (mp0) REVERT: A 649 GLU cc_start: 0.8758 (mt-10) cc_final: 0.8429 (mm-30) REVERT: A 739 LYS cc_start: 0.9124 (tppt) cc_final: 0.8715 (ttpp) REVERT: C 38 MET cc_start: 0.8334 (mmm) cc_final: 0.7877 (mmm) REVERT: C 59 ASP cc_start: 0.7988 (m-30) cc_final: 0.7418 (t0) REVERT: C 72 ARG cc_start: 0.8334 (mtm-85) cc_final: 0.7979 (mtm-85) REVERT: C 92 GLN cc_start: 0.7073 (tm-30) cc_final: 0.6562 (tm-30) REVERT: C 116 ASP cc_start: 0.7959 (m-30) cc_final: 0.7636 (t0) REVERT: C 131 ARG cc_start: 0.7404 (tpt170) cc_final: 0.6846 (tpt90) REVERT: D 42 ARG cc_start: 0.7630 (mtm180) cc_final: 0.7301 (mtm180) REVERT: D 56 LEU cc_start: 0.8799 (mt) cc_final: 0.8552 (pp) outliers start: 16 outliers final: 10 residues processed: 100 average time/residue: 0.1459 time to fit residues: 19.1090 Evaluate side-chains 100 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 89 time to evaluate : 0.463 ------------------------------------------------------------------------------- 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 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 39 optimal weight: 0.9990 chunk 21 optimal weight: 8.9990 chunk 94 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 79 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 49 optimal weight: 0.0060 chunk 114 optimal weight: 10.0000 overall best weight: 0.5996 ------------------------------------------------------------------------------- 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 = 0.3774 r_free = 0.3774 target = 0.135896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.085445 restraints weight = 13785.328| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 3.05 r_work: 0.2917 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9741 Z= 0.124 Angle : 0.500 9.366 13197 Z= 0.253 Chirality : 0.042 0.180 1471 Planarity : 0.004 0.058 1707 Dihedral : 5.679 76.437 1329 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.13 % Allowed : 9.90 % Favored : 88.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.25), residues: 1199 helix: 1.78 (0.24), residues: 499 sheet: 0.51 (0.36), residues: 209 loop : 0.31 (0.28), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 143 TYR 0.009 0.001 TYR C 134 PHE 0.009 0.001 PHE D 4 TRP 0.004 0.001 TRP A 669 HIS 0.002 0.000 HIS D 68 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 9738) covalent geometry : angle 0.49722 (13195) SS BOND : bond 0.00479 ( 1) SS BOND : angle 4.06346 ( 2) hydrogen bonds : bond 0.03504 ( 455) hydrogen bonds : angle 4.24175 ( 1275) Misc. bond : bond 0.00024 ( 2) *********************** 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: 12 poor density : 92 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 333 GLN cc_start: 0.8623 (mp10) cc_final: 0.7418 (tm-30) REVERT: A 464 MET cc_start: 0.8687 (OUTLIER) cc_final: 0.7450 (pmt) REVERT: A 567 ASN cc_start: 0.8656 (p0) cc_final: 0.8376 (p0) REVERT: A 603 GLU cc_start: 0.8710 (mp0) cc_final: 0.8384 (mp0) REVERT: A 649 GLU cc_start: 0.8756 (mt-10) cc_final: 0.8436 (mm-30) REVERT: A 739 LYS cc_start: 0.9152 (tppt) cc_final: 0.8726 (ttpp) REVERT: C 38 MET cc_start: 0.8305 (mmm) cc_final: 0.7828 (mmm) REVERT: C 59 ASP cc_start: 0.8009 (m-30) cc_final: 0.7404 (t0) REVERT: C 72 ARG cc_start: 0.8362 (mtm-85) cc_final: 0.8015 (mtm-85) REVERT: C 92 GLN cc_start: 0.6942 (tm-30) cc_final: 0.6463 (tm-30) REVERT: C 116 ASP cc_start: 0.7879 (m-30) cc_final: 0.7572 (t0) REVERT: C 131 ARG cc_start: 0.7359 (tpt170) cc_final: 0.6896 (tpt90) REVERT: C 144 LYS cc_start: 0.8607 (ttpp) cc_final: 0.8026 (mtmm) REVERT: D 42 ARG cc_start: 0.7525 (mtm180) cc_final: 0.7198 (mtm180) REVERT: D 56 LEU cc_start: 0.8822 (mt) cc_final: 0.8585 (pp) outliers start: 12 outliers final: 10 residues processed: 101 average time/residue: 0.1396 time to fit residues: 18.5354 Evaluate side-chains 98 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 87 time to evaluate : 0.385 ------------------------------------------------------------------------------- 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 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 63 optimal weight: 4.9990 chunk 4 optimal weight: 0.0270 chunk 68 optimal weight: 0.4980 chunk 39 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 78 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 29 optimal weight: 0.4980 overall best weight: 0.5638 ------------------------------------------------------------------------------- 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 = 0.3782 r_free = 0.3782 target = 0.136290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.085941 restraints weight = 13646.484| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 3.04 r_work: 0.2922 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9741 Z= 0.119 Angle : 0.482 7.662 13197 Z= 0.247 Chirality : 0.042 0.213 1471 Planarity : 0.004 0.055 1707 Dihedral : 5.656 74.935 1329 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.41 % Allowed : 9.43 % Favored : 89.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.25), residues: 1199 helix: 1.77 (0.24), residues: 498 sheet: 0.53 (0.35), residues: 209 loop : 0.34 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 841 TYR 0.009 0.001 TYR C 134 PHE 0.009 0.001 PHE D 4 TRP 0.004 0.001 TRP A 669 HIS 0.003 0.001 HIS D 68 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 9738) covalent geometry : angle 0.47976 (13195) SS BOND : bond 0.00928 ( 1) SS BOND : angle 3.84269 ( 2) hydrogen bonds : bond 0.03418 ( 455) hydrogen bonds : angle 4.22251 ( 1275) Misc. bond : bond 0.00052 ( 2) *********************** 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 105 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 90 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 333 GLN cc_start: 0.8625 (mp10) cc_final: 0.7451 (tm-30) REVERT: A 464 MET cc_start: 0.8684 (OUTLIER) cc_final: 0.7445 (pmt) REVERT: A 567 ASN cc_start: 0.8653 (p0) cc_final: 0.8378 (p0) REVERT: A 603 GLU cc_start: 0.8713 (mp0) cc_final: 0.8386 (mp0) REVERT: A 739 LYS cc_start: 0.9148 (tppt) cc_final: 0.8733 (ttpp) REVERT: C 38 MET cc_start: 0.8318 (mmm) cc_final: 0.7841 (mmm) REVERT: C 59 ASP cc_start: 0.8002 (m-30) cc_final: 0.7402 (t0) REVERT: C 72 ARG cc_start: 0.8492 (mtm-85) cc_final: 0.8141 (mtm-85) REVERT: C 92 GLN cc_start: 0.7123 (tm-30) cc_final: 0.6674 (tm-30) REVERT: C 116 ASP cc_start: 0.7848 (m-30) cc_final: 0.7561 (t0) REVERT: C 131 ARG cc_start: 0.7386 (tpt170) cc_final: 0.6896 (tpt90) REVERT: D 42 ARG cc_start: 0.7562 (mtm180) cc_final: 0.7090 (mtm180) REVERT: D 56 LEU cc_start: 0.8824 (mt) cc_final: 0.8583 (pp) outliers start: 15 outliers final: 12 residues processed: 102 average time/residue: 0.1418 time to fit residues: 19.0429 Evaluate side-chains 97 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 84 time to evaluate : 0.332 ------------------------------------------------------------------------------- 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 257 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 95 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 21 optimal weight: 0.0670 chunk 9 optimal weight: 0.0970 chunk 62 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 76 optimal weight: 0.0870 chunk 26 optimal weight: 1.9990 chunk 97 optimal weight: 0.0670 chunk 118 optimal weight: 7.9990 chunk 52 optimal weight: 0.9980 overall best weight: 0.2632 ------------------------------------------------------------------------------- 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 = 0.3805 r_free = 0.3805 target = 0.138335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.086588 restraints weight = 13656.875| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 3.15 r_work: 0.2932 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9741 Z= 0.093 Angle : 0.486 8.477 13197 Z= 0.244 Chirality : 0.041 0.155 1471 Planarity : 0.004 0.051 1707 Dihedral : 5.538 76.422 1329 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.04 % Allowed : 10.08 % Favored : 88.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.25), residues: 1199 helix: 1.86 (0.24), residues: 499 sheet: 0.64 (0.36), residues: 209 loop : 0.40 (0.29), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 143 TYR 0.009 0.001 TYR C 134 PHE 0.010 0.001 PHE D 4 TRP 0.005 0.000 TRP A 669 HIS 0.002 0.000 HIS D 68 Details of bonding type rmsd covalent geometry : bond 0.00214 ( 9738) covalent geometry : angle 0.48389 (13195) SS BOND : bond 0.00157 ( 1) SS BOND : angle 3.64692 ( 2) hydrogen bonds : bond 0.03117 ( 455) hydrogen bonds : angle 4.12182 ( 1275) Misc. bond : bond 0.00009 ( 2) *********************** 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 101 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 90 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 GLU cc_start: 0.8714 (tp30) cc_final: 0.8424 (tp30) REVERT: A 205 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7304 (pt0) REVERT: A 333 GLN cc_start: 0.8606 (mp10) cc_final: 0.7423 (tm-30) REVERT: A 464 MET cc_start: 0.8693 (OUTLIER) cc_final: 0.7495 (pmt) REVERT: A 546 ASP cc_start: 0.8685 (t70) cc_final: 0.8434 (t0) REVERT: A 567 ASN cc_start: 0.8631 (p0) cc_final: 0.8395 (p0) REVERT: A 603 GLU cc_start: 0.8687 (mp0) cc_final: 0.8392 (mp0) REVERT: A 649 GLU cc_start: 0.8621 (mt-10) cc_final: 0.8306 (mm-30) REVERT: A 739 LYS cc_start: 0.9156 (tppt) cc_final: 0.8742 (ttpp) REVERT: C 38 MET cc_start: 0.8237 (mmm) cc_final: 0.7776 (mmm) REVERT: C 59 ASP cc_start: 0.7982 (m-30) cc_final: 0.7391 (t0) REVERT: C 92 GLN cc_start: 0.7135 (tm-30) cc_final: 0.6671 (tm-30) REVERT: C 116 ASP cc_start: 0.7832 (m-30) cc_final: 0.7590 (t0) REVERT: C 144 LYS cc_start: 0.8690 (ttpp) cc_final: 0.8162 (mtmm) REVERT: D 6 LYS cc_start: 0.6065 (mmmm) cc_final: 0.5770 (mmmt) REVERT: D 42 ARG cc_start: 0.7406 (mtm180) cc_final: 0.7010 (mtp180) REVERT: D 56 LEU cc_start: 0.8817 (mt) cc_final: 0.8579 (pp) outliers start: 11 outliers final: 10 residues processed: 97 average time/residue: 0.1384 time to fit residues: 17.6642 Evaluate side-chains 97 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 86 time to evaluate : 0.335 ------------------------------------------------------------------------------- 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 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 1 optimal weight: 0.0870 chunk 102 optimal weight: 0.0770 chunk 18 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 72 optimal weight: 0.0970 chunk 65 optimal weight: 0.9990 chunk 82 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 overall best weight: 0.4314 ------------------------------------------------------------------------------- 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 = 0.3794 r_free = 0.3794 target = 0.137257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.088532 restraints weight = 13667.198| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 3.21 r_work: 0.2932 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.2812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9741 Z= 0.106 Angle : 0.511 12.686 13197 Z= 0.252 Chirality : 0.041 0.154 1471 Planarity : 0.004 0.051 1707 Dihedral : 5.509 74.582 1329 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.13 % Allowed : 9.99 % Favored : 88.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.50 (0.25), residues: 1199 helix: 1.85 (0.24), residues: 499 sheet: 0.59 (0.35), residues: 209 loop : 0.42 (0.29), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 8 TYR 0.008 0.001 TYR A 81 PHE 0.009 0.001 PHE D 4 TRP 0.004 0.001 TRP A 669 HIS 0.002 0.000 HIS D 68 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 9738) covalent geometry : angle 0.50946 (13195) SS BOND : bond 0.00411 ( 1) SS BOND : angle 3.57543 ( 2) hydrogen bonds : bond 0.03172 ( 455) hydrogen bonds : angle 4.11667 ( 1275) Misc. bond : bond 0.00054 ( 2) ********************** 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 101 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 89 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 GLU cc_start: 0.8689 (tp30) cc_final: 0.8384 (tp30) REVERT: A 205 GLU cc_start: 0.7934 (mt-10) cc_final: 0.7288 (pt0) REVERT: A 333 GLN cc_start: 0.8612 (mp10) cc_final: 0.7566 (tm-30) REVERT: A 464 MET cc_start: 0.8684 (OUTLIER) cc_final: 0.7496 (pmt) REVERT: A 567 ASN cc_start: 0.8628 (p0) cc_final: 0.8392 (p0) REVERT: A 603 GLU cc_start: 0.8717 (mp0) cc_final: 0.8410 (mp0) REVERT: A 649 GLU cc_start: 0.8601 (mt-10) cc_final: 0.8282 (mm-30) REVERT: A 739 LYS cc_start: 0.9154 (tppt) cc_final: 0.8743 (ttpp) REVERT: C 38 MET cc_start: 0.8232 (mmm) cc_final: 0.7771 (mmm) REVERT: C 59 ASP cc_start: 0.7984 (m-30) cc_final: 0.7384 (t0) REVERT: C 92 GLN cc_start: 0.7140 (tm-30) cc_final: 0.6671 (tm-30) REVERT: C 116 ASP cc_start: 0.7849 (m-30) cc_final: 0.7596 (t0) REVERT: C 144 LYS cc_start: 0.8427 (ttpp) cc_final: 0.8078 (mtmm) REVERT: D 6 LYS cc_start: 0.5844 (mmmm) cc_final: 0.5616 (mmtm) REVERT: D 42 ARG cc_start: 0.7385 (mtm180) cc_final: 0.7004 (mtp180) REVERT: D 56 LEU cc_start: 0.8819 (mt) cc_final: 0.8585 (pp) outliers start: 12 outliers final: 10 residues processed: 97 average time/residue: 0.1305 time to fit residues: 16.9469 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 : 0.355 ------------------------------------------------------------------------------- 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 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 66 optimal weight: 0.8980 chunk 55 optimal weight: 0.5980 chunk 79 optimal weight: 0.8980 chunk 116 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 chunk 64 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 102 optimal weight: 0.5980 chunk 108 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.135685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.085449 restraints weight = 13697.504| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 3.02 r_work: 0.2915 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9741 Z= 0.137 Angle : 0.520 12.653 13197 Z= 0.259 Chirality : 0.042 0.175 1471 Planarity : 0.004 0.052 1707 Dihedral : 5.591 72.392 1329 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.32 % Allowed : 9.99 % Favored : 88.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.42 (0.25), residues: 1199 helix: 1.79 (0.24), residues: 499 sheet: 0.61 (0.37), residues: 198 loop : 0.34 (0.28), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 841 TYR 0.012 0.001 TYR C 145 PHE 0.009 0.001 PHE A 431 TRP 0.004 0.001 TRP A 669 HIS 0.002 0.000 HIS A 305 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 9738) covalent geometry : angle 0.51834 (13195) SS BOND : bond 0.00530 ( 1) SS BOND : angle 3.84510 ( 2) hydrogen bonds : bond 0.03498 ( 455) hydrogen bonds : angle 4.16940 ( 1275) Misc. bond : bond 0.00059 ( 2) Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 2561.77 seconds wall clock time: 44 minutes 18.42 seconds (2658.42 seconds total)