Starting phenix.real_space_refine on Fri Nov 15 20:18:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b5o_44219/11_2024/9b5o_44219.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b5o_44219/11_2024/9b5o_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b5o_44219/11_2024/9b5o_44219.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b5o_44219/11_2024/9b5o_44219.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b5o_44219/11_2024/9b5o_44219.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b5o_44219/11_2024/9b5o_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-5513/modules/chem_data/mon_lib" Total number of atoms: 9527 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 985, 7734 Classifications: {'peptide': 985} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 55, 'TRANS': 928} Chain breaks: 1 Chain: "C" Number of atoms: 1158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1158 Classifications: {'peptide': 147} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 131} Chain: "D" Number of atoms: 596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 596 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 6 Unusual residues: {'A1AIV': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.57, per 1000 atoms: 0.69 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: 2.53 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: 1.48 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: 3.67 Time building geometry restraints manager: 2.89 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: 2.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 26.440 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.520 ------------------------------------------------------------------------------- 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 : 1.171 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: 0.3215 time to fit residues: 74.1081 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 : 1.178 ------------------------------------------------------------------------------- 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: 0.9990 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: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.1788 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= 0.276 Angle : 0.545 6.929 13195 Z= 0.278 Chirality : 0.044 0.265 1471 Planarity : 0.004 0.046 1707 Dihedral : 6.327 87.002 1333 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.25), residues: 1199 helix: 1.79 (0.24), residues: 503 sheet: 0.47 (0.36), residues: 201 loop : 0.39 (0.29), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 669 HIS 0.009 0.001 HIS D 68 PHE 0.018 0.001 PHE A 956 TYR 0.011 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 122 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 105 time to evaluate : 1.137 Fit side-chains REVERT: A 80 GLN cc_start: 0.8970 (OUTLIER) cc_final: 0.7819 (tm-30) REVERT: A 197 LEU cc_start: 0.6809 (mp) cc_final: 0.6255 (mt) REVERT: A 464 MET cc_start: 0.8916 (OUTLIER) cc_final: 0.7664 (pmt) REVERT: A 562 LEU cc_start: 0.8931 (tp) cc_final: 0.8720 (tp) REVERT: A 567 ASN cc_start: 0.8885 (p0) cc_final: 0.8641 (p0) REVERT: A 649 GLU cc_start: 0.8525 (mt-10) cc_final: 0.8267 (mm-30) REVERT: A 739 LYS cc_start: 0.8745 (tppt) cc_final: 0.8515 (ttpp) REVERT: C 7 ASN cc_start: 0.8694 (t0) cc_final: 0.8460 (p0) REVERT: C 59 ASP cc_start: 0.8035 (m-30) cc_final: 0.7700 (t0) REVERT: C 116 ASP cc_start: 0.7913 (m-30) cc_final: 0.7634 (t0) outliers start: 17 outliers final: 8 residues processed: 118 average time/residue: 0.2939 time to fit residues: 45.9099 Evaluate side-chains 96 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 86 time to evaluate : 1.168 ------------------------------------------------------------------------------- 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 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 60 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 89 optimal weight: 3.9990 chunk 73 optimal weight: 0.3980 chunk 29 optimal weight: 2.9990 chunk 108 optimal weight: 0.2980 chunk 116 optimal weight: 7.9990 chunk 96 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 36 optimal weight: 0.0870 chunk 86 optimal weight: 0.5980 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9738 Z= 0.169 Angle : 0.496 8.665 13195 Z= 0.255 Chirality : 0.042 0.152 1471 Planarity : 0.004 0.044 1707 Dihedral : 5.747 76.506 1329 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 0.85 % Allowed : 8.01 % Favored : 91.14 % 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: 1.84 (0.24), residues: 498 sheet: 0.63 (0.35), residues: 209 loop : 0.37 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 917 HIS 0.004 0.001 HIS D 68 PHE 0.014 0.001 PHE A 956 TYR 0.010 0.001 TYR C 134 ARG 0.008 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 104 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 95 time to evaluate : 1.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 ASP cc_start: 0.7533 (m-30) cc_final: 0.7295 (m-30) REVERT: A 218 MET cc_start: 0.4640 (mmt) cc_final: 0.4370 (mmt) REVERT: A 227 ARG cc_start: 0.7649 (mmm-85) cc_final: 0.7077 (mmt90) REVERT: A 464 MET cc_start: 0.8879 (OUTLIER) cc_final: 0.7693 (pmt) REVERT: A 562 LEU cc_start: 0.8873 (tp) cc_final: 0.8646 (tp) REVERT: A 649 GLU cc_start: 0.8539 (mt-10) cc_final: 0.8229 (mm-30) REVERT: C 38 MET cc_start: 0.8470 (mmm) cc_final: 0.8083 (mmm) REVERT: C 59 ASP cc_start: 0.7926 (m-30) cc_final: 0.7510 (t70) REVERT: C 92 GLN cc_start: 0.6723 (tm-30) cc_final: 0.6325 (tm-30) REVERT: C 116 ASP cc_start: 0.7825 (m-30) cc_final: 0.7566 (t0) outliers start: 9 outliers final: 6 residues processed: 101 average time/residue: 0.2933 time to fit residues: 39.5093 Evaluate side-chains 92 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 85 time to evaluate : 1.154 ------------------------------------------------------------------------------- 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 898 SER Chi-restraints excluded: chain A residue 993 ILE 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 106 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 72 optimal weight: 0.0770 chunk 108 optimal weight: 0.7980 chunk 115 optimal weight: 0.9990 chunk 102 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 overall best weight: 0.9744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9738 Z= 0.288 Angle : 0.525 7.177 13195 Z= 0.273 Chirality : 0.044 0.246 1471 Planarity : 0.004 0.055 1707 Dihedral : 5.823 73.709 1329 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % 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: 1.33 (0.25), residues: 1199 helix: 1.72 (0.24), residues: 497 sheet: 0.48 (0.35), residues: 212 loop : 0.33 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 93 HIS 0.003 0.001 HIS D 68 PHE 0.012 0.001 PHE D 4 TYR 0.011 0.001 TYR A 81 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 102 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 1.099 Fit side-chains revert: symmetry clash REVERT: A 80 GLN cc_start: 0.9012 (OUTLIER) cc_final: 0.7907 (tm-30) REVERT: A 218 MET cc_start: 0.4782 (mmt) cc_final: 0.4166 (mmt) REVERT: A 333 GLN cc_start: 0.8350 (mp10) cc_final: 0.7453 (tm-30) REVERT: A 464 MET cc_start: 0.8881 (OUTLIER) cc_final: 0.7611 (pmt) REVERT: A 649 GLU cc_start: 0.8483 (mt-10) cc_final: 0.8225 (mm-30) REVERT: C 38 MET cc_start: 0.8471 (mmm) cc_final: 0.8039 (mmt) REVERT: C 59 ASP cc_start: 0.8002 (m-30) cc_final: 0.7692 (t0) REVERT: C 92 GLN cc_start: 0.6936 (tm-30) cc_final: 0.6470 (tm-30) REVERT: C 116 ASP cc_start: 0.7836 (m-30) cc_final: 0.7620 (t0) REVERT: C 131 ARG cc_start: 0.7723 (tpt170) cc_final: 0.7124 (tpt90) outliers start: 14 outliers final: 9 residues processed: 99 average time/residue: 0.2888 time to fit residues: 38.3917 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 : 1.143 ------------------------------------------------------------------------------- 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 993 ILE 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 65 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 85 optimal weight: 0.0980 chunk 47 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 chunk 79 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 103 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2520 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= 0.206 Angle : 0.508 8.428 13195 Z= 0.259 Chirality : 0.042 0.180 1471 Planarity : 0.004 0.057 1707 Dihedral : 5.757 77.321 1329 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.41 % Allowed : 8.58 % Favored : 90.01 % 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: 1.35 (0.25), residues: 1199 helix: 1.73 (0.24), residues: 499 sheet: 0.51 (0.35), residues: 210 loop : 0.32 (0.28), residues: 490 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 0.010 0.001 PHE A 956 TYR 0.009 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 104 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 89 time to evaluate : 1.172 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 80 GLN cc_start: 0.8984 (OUTLIER) cc_final: 0.7858 (tm-30) REVERT: A 333 GLN cc_start: 0.8332 (mp10) cc_final: 0.7352 (tm-30) REVERT: A 464 MET cc_start: 0.8891 (OUTLIER) cc_final: 0.7728 (pmt) REVERT: A 649 GLU cc_start: 0.8526 (mt-10) cc_final: 0.8216 (mm-30) REVERT: C 38 MET cc_start: 0.8441 (mmm) cc_final: 0.8008 (mmm) REVERT: C 59 ASP cc_start: 0.7941 (m-30) cc_final: 0.7539 (t70) REVERT: C 92 GLN cc_start: 0.7001 (tm-30) cc_final: 0.6503 (tm-30) REVERT: C 131 ARG cc_start: 0.7636 (tpt170) cc_final: 0.6968 (tpt90) outliers start: 15 outliers final: 8 residues processed: 101 average time/residue: 0.3440 time to fit residues: 45.6018 Evaluate side-chains 93 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 83 time to evaluate : 1.181 ------------------------------------------------------------------------------- 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 710 THR Chi-restraints excluded: chain A residue 879 LYS Chi-restraints excluded: chain A residue 993 ILE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 103 optimal weight: 3.9990 chunk 22 optimal weight: 7.9990 chunk 67 optimal weight: 0.0980 chunk 28 optimal weight: 0.6980 chunk 115 optimal weight: 8.9990 chunk 95 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 chunk 60 optimal weight: 0.8980 chunk 111 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9738 Z= 0.217 Angle : 0.507 7.327 13195 Z= 0.261 Chirality : 0.042 0.173 1471 Planarity : 0.004 0.057 1707 Dihedral : 5.752 75.753 1329 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.32 % Allowed : 9.14 % 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: 1.35 (0.25), residues: 1199 helix: 1.70 (0.24), residues: 498 sheet: 0.55 (0.35), residues: 209 loop : 0.34 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 93 HIS 0.002 0.000 HIS A 305 PHE 0.010 0.001 PHE D 4 TYR 0.009 0.001 TYR C 134 ARG 0.009 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 100 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 86 time to evaluate : 1.029 Fit side-chains revert: symmetry clash REVERT: A 80 GLN cc_start: 0.8998 (OUTLIER) cc_final: 0.7871 (tm-30) REVERT: A 218 MET cc_start: 0.4608 (mmt) cc_final: 0.4324 (mmt) REVERT: A 333 GLN cc_start: 0.8411 (mp10) cc_final: 0.7444 (tm-30) REVERT: A 464 MET cc_start: 0.8889 (OUTLIER) cc_final: 0.7651 (pmt) REVERT: A 649 GLU cc_start: 0.8479 (mt-10) cc_final: 0.8207 (mm-30) REVERT: C 38 MET cc_start: 0.8342 (mmm) cc_final: 0.7900 (mmm) REVERT: C 59 ASP cc_start: 0.7933 (m-30) cc_final: 0.7513 (t0) REVERT: C 92 GLN cc_start: 0.6839 (tm-30) cc_final: 0.6399 (tm-30) REVERT: C 131 ARG cc_start: 0.7656 (tpt170) cc_final: 0.7148 (tpt90) outliers start: 14 outliers final: 11 residues processed: 98 average time/residue: 0.3208 time to fit residues: 41.6433 Evaluate side-chains 95 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 1.200 ------------------------------------------------------------------------------- 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 710 THR 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 C residue 13 LEU Chi-restraints excluded: chain C residue 43 SER 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 12 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 114 optimal weight: 3.9990 chunk 71 optimal weight: 0.1980 chunk 69 optimal weight: 0.5980 chunk 52 optimal weight: 0.9990 chunk 70 optimal weight: 0.0970 chunk 45 optimal weight: 3.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9738 Z= 0.187 Angle : 0.519 12.325 13195 Z= 0.259 Chirality : 0.042 0.149 1471 Planarity : 0.004 0.055 1707 Dihedral : 5.639 72.851 1329 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.32 % Allowed : 9.52 % 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 (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: 1.43 (0.25), residues: 1199 helix: 1.77 (0.24), residues: 499 sheet: 0.63 (0.36), residues: 209 loop : 0.37 (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 305 PHE 0.009 0.001 PHE D 4 TYR 0.009 0.001 TYR C 134 ARG 0.011 0.001 ARG D 42 *********************** 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 103 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 1.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 MET cc_start: 0.4552 (mmt) cc_final: 0.4174 (mmt) REVERT: A 333 GLN cc_start: 0.8404 (mp10) cc_final: 0.7447 (tm-30) REVERT: A 464 MET cc_start: 0.8876 (OUTLIER) cc_final: 0.7630 (pmt) REVERT: A 649 GLU cc_start: 0.8460 (mt-10) cc_final: 0.8177 (mm-30) REVERT: A 944 MET cc_start: 0.6833 (tmt) cc_final: 0.6512 (tmm) REVERT: C 38 MET cc_start: 0.8343 (mmm) cc_final: 0.7893 (mmm) REVERT: C 59 ASP cc_start: 0.7916 (m-30) cc_final: 0.7484 (t0) REVERT: C 92 GLN cc_start: 0.7006 (tm-30) cc_final: 0.6635 (tm-30) REVERT: C 131 ARG cc_start: 0.7638 (tpt170) cc_final: 0.7141 (tpt90) REVERT: C 144 LYS cc_start: 0.8657 (ttpp) cc_final: 0.8171 (mtmm) outliers start: 14 outliers final: 12 residues processed: 101 average time/residue: 0.3096 time to fit residues: 41.1121 Evaluate side-chains 96 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 1.138 ------------------------------------------------------------------------------- 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 335 ASP Chi-restraints excluded: chain A residue 461 VAL 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 993 ILE Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 43 SER 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 68 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 chunk 56 optimal weight: 0.2980 chunk 10 optimal weight: 0.7980 chunk 90 optimal weight: 2.9990 chunk 104 optimal weight: 0.0050 chunk 109 optimal weight: 0.0770 chunk 100 optimal weight: 0.0980 overall best weight: 0.2552 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9738 Z= 0.137 Angle : 0.502 12.556 13195 Z= 0.251 Chirality : 0.041 0.185 1471 Planarity : 0.004 0.054 1707 Dihedral : 5.436 68.601 1329 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.32 % Allowed : 9.71 % Favored : 88.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.25), residues: 1199 helix: 1.88 (0.24), residues: 498 sheet: 0.77 (0.36), residues: 209 loop : 0.42 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP A 669 HIS 0.002 0.000 HIS D 68 PHE 0.015 0.001 PHE D 45 TYR 0.009 0.001 TYR C 134 ARG 0.008 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 103 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 1.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 ASP cc_start: 0.7633 (m-30) cc_final: 0.7416 (m-30) REVERT: A 205 GLU cc_start: 0.7963 (mt-10) cc_final: 0.7481 (pt0) REVERT: A 333 GLN cc_start: 0.8388 (mp10) cc_final: 0.7589 (tm-30) REVERT: A 464 MET cc_start: 0.8879 (OUTLIER) cc_final: 0.7765 (pmt) REVERT: A 649 GLU cc_start: 0.8376 (mt-10) cc_final: 0.8052 (mm-30) REVERT: C 38 MET cc_start: 0.8342 (mmm) cc_final: 0.7901 (mmm) REVERT: C 59 ASP cc_start: 0.7903 (m-30) cc_final: 0.7450 (t0) REVERT: C 92 GLN cc_start: 0.7051 (tm-30) cc_final: 0.6600 (tm-30) REVERT: C 144 LYS cc_start: 0.8359 (ttpp) cc_final: 0.8022 (mtmm) outliers start: 14 outliers final: 13 residues processed: 100 average time/residue: 0.3223 time to fit residues: 42.7162 Evaluate side-chains 95 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 81 time to evaluate : 1.152 ------------------------------------------------------------------------------- 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 335 ASP Chi-restraints excluded: chain A residue 461 VAL 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 993 ILE Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain D residue 69 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 106 optimal weight: 0.1980 chunk 109 optimal weight: 0.6980 chunk 64 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 32 optimal weight: 0.3980 chunk 96 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 113 optimal weight: 6.9990 chunk 68 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.2958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9738 Z= 0.190 Angle : 0.530 12.964 13195 Z= 0.264 Chirality : 0.041 0.202 1471 Planarity : 0.004 0.054 1707 Dihedral : 5.423 66.616 1329 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.32 % Allowed : 9.90 % Favored : 88.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.25), residues: 1199 helix: 1.86 (0.24), residues: 498 sheet: 0.73 (0.36), residues: 209 loop : 0.42 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 669 HIS 0.002 0.000 HIS A 305 PHE 0.014 0.001 PHE D 45 TYR 0.008 0.001 TYR C 134 ARG 0.006 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: 14 poor density : 85 time to evaluate : 1.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 ASP cc_start: 0.7589 (m-30) cc_final: 0.7374 (m-30) REVERT: A 205 GLU cc_start: 0.7962 (mt-10) cc_final: 0.7486 (pt0) REVERT: A 218 MET cc_start: 0.4453 (mmt) cc_final: 0.4180 (mmt) REVERT: A 333 GLN cc_start: 0.8393 (mp10) cc_final: 0.7589 (tm-30) REVERT: A 464 MET cc_start: 0.8878 (OUTLIER) cc_final: 0.7762 (pmt) REVERT: A 649 GLU cc_start: 0.8389 (mt-10) cc_final: 0.8058 (mm-30) REVERT: C 38 MET cc_start: 0.8340 (mmm) cc_final: 0.7891 (mmm) REVERT: C 59 ASP cc_start: 0.7905 (m-30) cc_final: 0.7448 (t0) REVERT: C 92 GLN cc_start: 0.7080 (tm-30) cc_final: 0.6621 (tm-30) REVERT: C 144 LYS cc_start: 0.8367 (ttpp) cc_final: 0.8131 (mtmm) REVERT: D 6 LYS cc_start: 0.4921 (mmmm) cc_final: 0.4578 (mmtm) outliers start: 14 outliers final: 12 residues processed: 96 average time/residue: 0.3304 time to fit residues: 41.6829 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 : 1.146 ------------------------------------------------------------------------------- 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 879 LYS Chi-restraints excluded: chain A residue 898 SER Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain D residue 69 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 53 optimal weight: 0.9980 chunk 78 optimal weight: 0.3980 chunk 118 optimal weight: 3.9990 chunk 109 optimal weight: 0.0270 chunk 94 optimal weight: 0.6980 chunk 9 optimal weight: 0.0980 chunk 72 optimal weight: 0.7980 chunk 57 optimal weight: 0.7980 chunk 74 optimal weight: 0.0040 chunk 100 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 overall best weight: 0.2450 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9738 Z= 0.143 Angle : 0.521 13.727 13195 Z= 0.259 Chirality : 0.041 0.201 1471 Planarity : 0.004 0.052 1707 Dihedral : 5.362 63.318 1329 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.13 % Allowed : 10.18 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.25), residues: 1199 helix: 1.89 (0.24), residues: 498 sheet: 0.54 (0.36), residues: 217 loop : 0.54 (0.29), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 669 HIS 0.002 0.000 HIS D 68 PHE 0.012 0.001 PHE D 45 TYR 0.011 0.001 TYR A 579 ARG 0.007 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 : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 MET cc_start: 0.8965 (mtp) cc_final: 0.8550 (mtp) REVERT: A 154 ASP cc_start: 0.7638 (m-30) cc_final: 0.7418 (m-30) REVERT: A 218 MET cc_start: 0.4390 (mmt) cc_final: 0.4132 (mmt) REVERT: A 333 GLN cc_start: 0.8363 (mp10) cc_final: 0.7606 (tm-30) REVERT: A 464 MET cc_start: 0.8877 (OUTLIER) cc_final: 0.7750 (pmt) REVERT: A 649 GLU cc_start: 0.8395 (mt-10) cc_final: 0.8022 (mm-30) REVERT: C 38 MET cc_start: 0.8326 (mmm) cc_final: 0.7890 (mmm) REVERT: C 59 ASP cc_start: 0.7935 (m-30) cc_final: 0.7425 (t0) REVERT: C 92 GLN cc_start: 0.7074 (tm-30) cc_final: 0.6624 (tm-30) REVERT: C 144 LYS cc_start: 0.8428 (ttpp) cc_final: 0.8154 (mtmm) REVERT: D 6 LYS cc_start: 0.4896 (mmmm) cc_final: 0.4605 (mmtm) outliers start: 12 outliers final: 11 residues processed: 96 average time/residue: 0.3271 time to fit residues: 41.0974 Evaluate side-chains 95 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 83 time to evaluate : 1.105 ------------------------------------------------------------------------------- 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 879 LYS Chi-restraints excluded: chain A residue 898 SER Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 43 SER 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 87 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 11 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 83 optimal weight: 0.1980 chunk 5 optimal weight: 3.9990 chunk 68 optimal weight: 0.0050 overall best weight: 0.5194 ------------------------------------------------------------------------------- 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 = 0.3797 r_free = 0.3797 target = 0.137754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.086912 restraints weight = 13710.891| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 3.12 r_work: 0.2929 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9738 Z= 0.188 Angle : 0.533 13.225 13195 Z= 0.264 Chirality : 0.041 0.197 1471 Planarity : 0.004 0.051 1707 Dihedral : 5.340 57.767 1329 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.32 % Allowed : 9.90 % Favored : 88.78 % 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: 1.61 (0.25), residues: 1199 helix: 1.86 (0.24), residues: 498 sheet: 0.84 (0.36), residues: 209 loop : 0.47 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 669 HIS 0.002 0.000 HIS D 68 PHE 0.011 0.001 PHE D 45 TYR 0.009 0.001 TYR A 579 ARG 0.006 0.000 ARG A 841 Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 2391.12 seconds wall clock time: 44 minutes 2.32 seconds (2642.32 seconds total)