Starting phenix.real_space_refine on Fri Feb 14 00:38:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b5c_44207/02_2025/9b5c_44207.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b5c_44207/02_2025/9b5c_44207.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b5c_44207/02_2025/9b5c_44207.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b5c_44207/02_2025/9b5c_44207.map" model { file = "/net/cci-nas-00/data/ceres_data/9b5c_44207/02_2025/9b5c_44207.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b5c_44207/02_2025/9b5c_44207.cif" } resolution = 2.5 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= 0.070 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 6078 2.51 5 N 1575 2.21 5 O 1836 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 9536 Number of models: 1 Model: "" Number of chains: 6 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: "B" Number of atoms: 601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 601 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 73} 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: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Classifications: {'peptide': 1} 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: 6.88, per 1000 atoms: 0.72 Number of scatterers: 9536 At special positions: 0 Unit cell: (86.184, 98.952, 119.168, 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 1836 8.00 N 1575 7.00 C 6078 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=2.90 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: 2.62 Conformation dependent library (CDL) restraints added in 1.2 seconds 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 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 47.3% alpha, 15.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.25 Creating SS restraints... Processing helix chain 'A' and resid 20 through 25 removed outlier: 3.670A 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: 3.697A pdb=" N SER A 79 " --> pdb=" O ASP A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 88 removed outlier: 3.994A pdb=" N ILE A 88 " --> pdb=" O GLU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 101 removed outlier: 4.388A pdb=" N SER A 98 " --> pdb=" O LYS A 94 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N LYS A 99 " --> pdb=" O VAL A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 123 removed outlier: 3.514A pdb=" N LYS A 121 " --> pdb=" O GLU A 118 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASN A 122 " --> pdb=" O TYR A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 146 removed outlier: 3.660A pdb=" N PHE A 142 " --> pdb=" O GLU A 138 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LYS A 145 " --> pdb=" O ASP A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 223 removed outlier: 3.523A pdb=" N ASN A 222 " --> pdb=" O PRO A 219 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ASP A 223 " --> pdb=" O GLY A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 274 removed outlier: 4.350A pdb=" N LYS A 273 " --> pdb=" O ARG A 269 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASP A 274 " --> pdb=" O GLU A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 304 removed outlier: 3.608A pdb=" N ILE A 293 " --> pdb=" O PRO A 289 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLN A 296 " --> pdb=" O HIS A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 332 Processing helix chain 'A' and resid 339 through 349 Processing helix chain 'A' and resid 354 through 375 Processing helix chain 'A' and resid 389 through 392 Processing helix chain 'A' and resid 410 through 418 removed outlier: 4.388A pdb=" N VAL A 416 " --> pdb=" O GLY A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 427 removed outlier: 3.574A pdb=" N SER A 427 " --> pdb=" O GLU A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 450 Processing helix chain 'A' and resid 468 through 474 removed outlier: 3.582A pdb=" N ASN A 473 " --> pdb=" O SER A 470 " (cutoff:3.500A) removed outlier: 3.519A 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: 3.851A pdb=" N GLU A 518 " --> pdb=" O PRO A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 528 removed outlier: 3.839A pdb=" N LYS A 528 " --> pdb=" O GLU A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 553 removed outlier: 3.565A pdb=" N ARG A 542 " --> pdb=" O ASN A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 582 removed outlier: 3.501A pdb=" N SER A 581 " --> pdb=" O SER A 578 " (cutoff:3.500A) removed outlier: 3.845A 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 628 Processing helix chain 'A' and resid 632 through 641 removed outlier: 3.759A 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: 3.580A pdb=" N CYS A 666 " --> pdb=" O SER A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 689 Processing helix chain 'A' and resid 718 through 737 Processing helix chain 'A' and resid 743 through 753 removed outlier: 3.945A pdb=" N TYR A 747 " --> pdb=" O ASP A 743 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLY A 753 " --> pdb=" O ARG A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 781 through 794 removed outlier: 3.933A 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: 3.522A pdb=" N THR A 859 " --> pdb=" O MET A 855 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL A 871 " --> pdb=" O CYS A 867 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LYS A 872 " --> pdb=" O LEU A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 883 removed outlier: 3.681A pdb=" N GLU A 882 " --> pdb=" O LYS A 879 " (cutoff:3.500A) removed outlier: 3.648A 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 'B' and resid 22 through 35 Processing helix chain 'B' and resid 37 through 41 Processing helix chain 'B' and resid 55 through 60 Processing helix chain 'C' and resid 3 through 16 Processing helix chain 'C' and resid 86 through 90 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 sheet with id=AA1, first strand: chain 'A' and resid 109 through 111 removed outlier: 6.753A pdb=" N VAL A 64 " --> pdb=" O SER A 110 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ASN A 39 " --> pdb=" O CYS A 125 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N VAL A 127 " --> pdb=" O ASN A 39 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N LEU A 41 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N VAL A 126 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N ALA A 153 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N VAL A 128 " --> pdb=" O ALA A 153 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N SER A 155 " --> pdb=" O VAL A 128 " (cutoff:3.500A) removed outlier: 4.358A 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: 4.152A pdb=" N PHE A 209 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N THR A 195 " --> pdb=" O ALA A 186 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ILE A 188 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 6.228A 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: 4.152A 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: 6.471A pdb=" N ILE A 459 " --> pdb=" O THR A 507 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N TYR A 509 " --> pdb=" O ILE A 459 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VAL A 461 " --> pdb=" O TYR A 509 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N SER A 429 " --> pdb=" O LEU A 531 " (cutoff:3.500A) removed outlier: 8.326A pdb=" N THR A 533 " --> pdb=" O SER A 429 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N PHE A 431 " --> pdb=" O THR A 533 " (cutoff:3.500A) removed outlier: 4.265A 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: 6.351A pdb=" N TYR A 920 " --> pdb=" O CYS A1009 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N LYS A1011 " --> pdb=" O TYR A 920 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N LEU A 922 " --> pdb=" O LYS A1011 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N VAL A 990 " --> pdb=" O SER A 947 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N SER A 947 " --> pdb=" O VAL A 990 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N GLU A 992 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N LEU A 945 " --> pdb=" O GLU A 992 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N CYS A 994 " --> pdb=" O THR A 943 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N SER A 947 " --> pdb=" O LEU A 951 " (cutoff:3.500A) removed outlier: 5.368A 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: 6.351A pdb=" N TYR A 920 " --> pdb=" O CYS A1009 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N LYS A1011 " --> pdb=" O TYR A 920 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N LEU A 922 " --> pdb=" O LYS A1011 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N CYS A 995 " --> pdb=" O VAL A1003 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 12 through 16 removed outlier: 3.883A pdb=" N ARG B 42 " --> pdb=" O VAL B 70 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 21 through 26 removed outlier: 3.658A pdb=" N GLY C 24 " --> pdb=" O GLN C 34 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N HIS C 32 " --> pdb=" O VAL C 26 " (cutoff:3.500A) 459 hydrogen bonds defined for protein. 1248 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: 3.80 Time building geometry restraints manager: 2.96 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: 1619 1.27 - 1.40: 2292 1.40 - 1.54: 5651 1.54 - 1.67: 120 1.67 - 1.81: 64 Bond restraints: 9746 Sorted by residual: bond pdb=" C04 A1AIV D 201 " pdb=" C05 A1AIV D 201 " ideal model delta sigma weight residual 1.453 1.525 -0.072 2.00e-02 2.50e+03 1.29e+01 bond pdb=" N MET B 1 " pdb=" CA MET B 1 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.90e-02 2.77e+03 2.52e+00 bond pdb=" C1' ATP A1103 " pdb=" C2' ATP A1103 " ideal model delta sigma weight residual 1.531 1.518 0.013 1.20e-02 6.94e+03 1.12e+00 bond pdb=" CA VAL A1005 " pdb=" CB VAL A1005 " ideal model delta sigma weight residual 1.547 1.536 0.011 1.10e-02 8.26e+03 1.04e+00 bond pdb=" C05 A1AIV D 201 " pdb=" N06 A1AIV D 201 " ideal model delta sigma weight residual 1.151 1.132 0.019 2.00e-02 2.50e+03 9.16e-01 ... (remaining 9741 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.42: 13009 1.42 - 2.84: 120 2.84 - 4.26: 66 4.26 - 5.67: 5 5.67 - 7.09: 4 Bond angle restraints: 13204 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 121.70 128.79 -7.09 1.80e+00 3.09e-01 1.55e+01 angle pdb=" C2' ATP A1103 " pdb=" C1' ATP A1103 " pdb=" O4' ATP A1103 " ideal model delta sigma weight residual 106.53 103.21 3.32 1.18e+00 7.24e-01 7.97e+00 angle pdb=" C3' ATP A1103 " pdb=" C4' ATP A1103 " pdb=" C5' ATP A1103 " ideal model delta sigma weight residual 115.19 110.69 4.50 1.76e+00 3.23e-01 6.53e+00 angle pdb=" C2' ATP A1103 " pdb=" C3' ATP A1103 " pdb=" O3' ATP A1103 " ideal model delta sigma weight residual 111.83 105.17 6.66 2.67e+00 1.40e-01 6.23e+00 angle pdb=" C1' ATP A1103 " pdb=" C2' ATP A1103 " pdb=" O2' ATP A1103 " ideal model delta sigma weight residual 110.58 103.94 6.64 2.79e+00 1.28e-01 5.65e+00 ... (remaining 13199 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.59: 5657 17.59 - 35.19: 218 35.19 - 52.78: 47 52.78 - 70.38: 5 70.38 - 87.97: 4 Dihedral angle restraints: 5931 sinusoidal: 2425 harmonic: 3506 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 -141.90 55.90 1 1.00e+01 1.00e-02 4.22e+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 180.00 162.60 17.40 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" CA TYR A 277 " pdb=" C TYR A 277 " pdb=" N VAL A 278 " pdb=" CA VAL A 278 " ideal model delta harmonic sigma weight residual 180.00 163.27 16.73 0 5.00e+00 4.00e-02 1.12e+01 ... (remaining 5928 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1284 0.058 - 0.116: 158 0.116 - 0.174: 26 0.174 - 0.232: 1 0.232 - 0.290: 2 Chirality restraints: 1471 Sorted by residual: chirality pdb=" C2' ATP A1103 " pdb=" C1' ATP A1103 " pdb=" C3' ATP A1103 " pdb=" O2' ATP A1103 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" C3' ATP A1103 " pdb=" C2' ATP A1103 " pdb=" C4' ATP A1103 " pdb=" O3' ATP A1103 " both_signs ideal model delta sigma weight residual False -2.63 -2.91 0.28 2.00e-01 2.50e+01 1.94e+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 1.32e+00 ... (remaining 1468 not shown) Planarity restraints: 1709 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER C 94 " 0.025 5.00e-02 4.00e+02 3.78e-02 2.29e+00 pdb=" N PRO C 95 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO C 95 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 95 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 120 " -0.025 5.00e-02 4.00e+02 3.78e-02 2.28e+00 pdb=" N PRO C 121 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO C 121 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 121 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS C 75 " -0.022 5.00e-02 4.00e+02 3.39e-02 1.84e+00 pdb=" N PRO C 76 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO C 76 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 76 " -0.019 5.00e-02 4.00e+02 ... (remaining 1706 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 64 2.61 - 3.18: 8115 3.18 - 3.75: 14053 3.75 - 4.33: 21319 4.33 - 4.90: 35237 Nonbonded interactions: 78788 Sorted by model distance: nonbonded pdb="MG MG A1101 " pdb=" O2B ATP A1103 " model vdw 2.036 2.170 nonbonded pdb=" OD2 ASP A 537 " pdb="MG MG A1101 " model vdw 2.039 2.170 nonbonded pdb="MG MG A1101 " pdb=" O3G ATP A1103 " model vdw 2.221 2.170 nonbonded pdb=" OD2 ASP A 465 " pdb="MG MG A1102 " model vdw 2.254 2.170 nonbonded pdb=" N GLU A 489 " pdb=" OE1 GLU A 489 " model vdw 2.260 3.120 ... (remaining 78783 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: 3.120 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: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 26.470 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 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 9746 Z= 0.219 Angle : 0.483 7.092 13204 Z= 0.251 Chirality : 0.043 0.290 1471 Planarity : 0.004 0.038 1709 Dihedral : 10.211 87.973 3664 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 1.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.66 % Allowed : 2.73 % Favored : 96.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.25), residues: 1200 helix: 1.60 (0.25), residues: 489 sheet: 1.00 (0.36), residues: 184 loop : 0.27 (0.28), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 608 HIS 0.003 0.001 HIS C 75 PHE 0.011 0.001 PHE A 551 TYR 0.009 0.001 TYR A 544 ARG 0.003 0.000 ARG B 72 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 141 time to evaluate : 1.040 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 ARG cc_start: 0.7406 (mtp85) cc_final: 0.6632 (mmt-90) REVERT: A 135 LYS cc_start: 0.8064 (mmmt) cc_final: 0.7820 (mmmm) REVERT: A 196 MET cc_start: 0.8592 (mmp) cc_final: 0.8211 (mmm) REVERT: A 524 GLU cc_start: 0.7822 (mp0) cc_final: 0.7479 (mp0) REVERT: A 540 GLU cc_start: 0.7558 (tt0) cc_final: 0.7144 (mp0) REVERT: A 668 MET cc_start: 0.7230 (mmm) cc_final: 0.7009 (mmm) REVERT: A 841 ARG cc_start: 0.7444 (mtp180) cc_final: 0.7220 (mtp180) REVERT: A 879 LYS cc_start: 0.8464 (mmmm) cc_final: 0.7799 (mmtt) REVERT: A 1004 GLU cc_start: 0.7985 (mt-10) cc_final: 0.7746 (mt-10) REVERT: A 1011 LYS cc_start: 0.8494 (ttmm) cc_final: 0.8289 (ttmm) REVERT: C 12 ASP cc_start: 0.7747 (t70) cc_final: 0.7504 (t0) REVERT: C 31 PHE cc_start: 0.8630 (m-80) cc_final: 0.8360 (m-10) outliers start: 7 outliers final: 2 residues processed: 146 average time/residue: 1.5404 time to fit residues: 238.6078 Evaluate side-chains 123 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 121 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1003 VAL 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: 0.9990 chunk 90 optimal weight: 1.9990 chunk 50 optimal weight: 0.0270 chunk 30 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 chunk 93 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 69 optimal weight: 0.0000 chunk 108 optimal weight: 1.9990 overall best weight: 0.5044 ------------------------------------------------------------------------------- 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 = 0.3580 r_free = 0.3580 target = 0.127602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.087181 restraints weight = 11396.333| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 2.27 r_work: 0.3004 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.0794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9746 Z= 0.212 Angle : 0.486 5.436 13204 Z= 0.258 Chirality : 0.043 0.149 1471 Planarity : 0.004 0.042 1709 Dihedral : 6.060 79.268 1329 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.51 % Allowed : 8.11 % 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 (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: 1.45 (0.24), residues: 1200 helix: 1.71 (0.24), residues: 490 sheet: 1.10 (0.37), residues: 180 loop : 0.31 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 669 HIS 0.001 0.000 HIS A 717 PHE 0.011 0.001 PHE A 237 TYR 0.016 0.001 TYR A 654 ARG 0.005 0.000 ARG C 72 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 132 time to evaluate : 1.125 Fit side-chains REVERT: A 73 ARG cc_start: 0.7493 (mtp85) cc_final: 0.6761 (mtm-85) REVERT: A 196 MET cc_start: 0.8702 (mmp) cc_final: 0.8416 (mmm) REVERT: A 524 GLU cc_start: 0.8182 (mp0) cc_final: 0.7809 (mp0) REVERT: A 540 GLU cc_start: 0.7974 (tt0) cc_final: 0.7423 (mp0) REVERT: A 626 MET cc_start: 0.7251 (ttt) cc_final: 0.6947 (tmt) REVERT: A 668 MET cc_start: 0.7572 (mmm) cc_final: 0.7361 (mmm) REVERT: A 879 LYS cc_start: 0.8508 (mmmm) cc_final: 0.8292 (mmpt) REVERT: A 1004 GLU cc_start: 0.8282 (mt-10) cc_final: 0.8047 (mt-10) REVERT: C 12 ASP cc_start: 0.7851 (t70) cc_final: 0.7509 (t0) REVERT: C 31 PHE cc_start: 0.8472 (m-80) cc_final: 0.8099 (m-10) REVERT: C 143 ARG cc_start: 0.7577 (mtm110) cc_final: 0.7138 (ttm-80) outliers start: 16 outliers final: 6 residues processed: 138 average time/residue: 1.4297 time to fit residues: 210.1015 Evaluate side-chains 128 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 122 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain C residue 85 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 5 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 85 optimal weight: 0.0020 chunk 18 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 80 optimal weight: 0.9990 chunk 51 optimal weight: 0.5980 chunk 118 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 72 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 overall best weight: 0.5590 ------------------------------------------------------------------------------- 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 = 0.3580 r_free = 0.3580 target = 0.127609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.087261 restraints weight = 11609.585| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 2.29 r_work: 0.3009 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.0927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9746 Z= 0.220 Angle : 0.474 5.489 13204 Z= 0.250 Chirality : 0.043 0.149 1471 Planarity : 0.004 0.044 1709 Dihedral : 5.943 74.712 1329 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.51 % Allowed : 8.95 % 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: 1.46 (0.24), residues: 1200 helix: 1.75 (0.24), residues: 489 sheet: 1.12 (0.36), residues: 180 loop : 0.29 (0.27), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 669 HIS 0.001 0.001 HIS C 32 PHE 0.011 0.001 PHE C 62 TYR 0.009 0.001 TYR A 544 ARG 0.004 0.000 ARG C 8 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 125 time to evaluate : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 ARG cc_start: 0.7470 (mtp85) cc_final: 0.6750 (mtm-85) REVERT: A 196 MET cc_start: 0.8709 (mmp) cc_final: 0.8396 (mmm) REVERT: A 286 MET cc_start: 0.8639 (OUTLIER) cc_final: 0.8385 (mmm) REVERT: A 524 GLU cc_start: 0.8173 (mp0) cc_final: 0.7850 (mp0) REVERT: A 540 GLU cc_start: 0.8020 (tt0) cc_final: 0.7437 (mp0) REVERT: A 668 MET cc_start: 0.7529 (mmm) cc_final: 0.7300 (mmm) REVERT: A 879 LYS cc_start: 0.8550 (mmmm) cc_final: 0.8320 (mmmm) REVERT: A 987 LYS cc_start: 0.8455 (mtpt) cc_final: 0.8107 (mttm) REVERT: A 1004 GLU cc_start: 0.8309 (mt-10) cc_final: 0.8086 (mt-10) REVERT: B 71 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8779 (pp) REVERT: C 12 ASP cc_start: 0.7882 (t70) cc_final: 0.7420 (t0) REVERT: C 31 PHE cc_start: 0.8504 (m-80) cc_final: 0.8122 (m-10) REVERT: C 92 GLN cc_start: 0.8065 (mm110) cc_final: 0.7048 (tm-30) REVERT: C 143 ARG cc_start: 0.7579 (mtm110) cc_final: 0.7149 (ttm-80) outliers start: 16 outliers final: 10 residues processed: 132 average time/residue: 1.5031 time to fit residues: 210.4768 Evaluate side-chains 134 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 122 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 179 GLU Chi-restraints excluded: chain A residue 273 LYS Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 387 ASP Chi-restraints excluded: chain A residue 390 GLU Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 71 LEU 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 25 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 59 optimal weight: 0.5980 chunk 108 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 54 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 118 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.129805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.089665 restraints weight = 11605.296| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 2.24 r_work: 0.3079 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.0986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9746 Z= 0.239 Angle : 0.474 5.495 13204 Z= 0.250 Chirality : 0.043 0.144 1471 Planarity : 0.004 0.046 1709 Dihedral : 5.955 75.582 1329 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.51 % Allowed : 9.61 % 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 (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 (0.24), residues: 1200 helix: 1.73 (0.24), residues: 489 sheet: 1.04 (0.36), residues: 181 loop : 0.28 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 608 HIS 0.002 0.001 HIS A 818 PHE 0.011 0.001 PHE A 237 TYR 0.009 0.001 TYR A 544 ARG 0.006 0.000 ARG C 72 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 124 time to evaluate : 1.202 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 ARG cc_start: 0.7590 (mtp85) cc_final: 0.6908 (mtm-85) REVERT: A 196 MET cc_start: 0.8735 (mmp) cc_final: 0.8438 (mmm) REVERT: A 524 GLU cc_start: 0.8184 (mp0) cc_final: 0.7826 (mp0) REVERT: A 540 GLU cc_start: 0.8111 (tt0) cc_final: 0.7535 (mp0) REVERT: A 879 LYS cc_start: 0.8678 (mmmm) cc_final: 0.8456 (mmmm) REVERT: A 1004 GLU cc_start: 0.8264 (mt-10) cc_final: 0.8060 (mt-10) REVERT: B 71 LEU cc_start: 0.9223 (OUTLIER) cc_final: 0.8804 (pp) REVERT: C 31 PHE cc_start: 0.8555 (m-80) cc_final: 0.8201 (m-10) REVERT: C 92 GLN cc_start: 0.8197 (mm110) cc_final: 0.7082 (tm-30) REVERT: C 143 ARG cc_start: 0.7586 (mtm110) cc_final: 0.7142 (ttm-80) outliers start: 16 outliers final: 10 residues processed: 133 average time/residue: 1.5803 time to fit residues: 224.6412 Evaluate side-chains 130 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 119 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 GLU Chi-restraints excluded: chain A residue 218 MET Chi-restraints excluded: chain A residue 273 LYS Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 387 ASP Chi-restraints excluded: chain A residue 390 GLU Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain C residue 36 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 86 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 26 optimal weight: 0.0980 chunk 92 optimal weight: 0.5980 chunk 110 optimal weight: 0.4980 chunk 96 optimal weight: 1.9990 chunk 81 optimal weight: 0.0980 chunk 27 optimal weight: 0.0010 chunk 61 optimal weight: 0.5980 chunk 66 optimal weight: 0.9980 overall best weight: 0.2586 ------------------------------------------------------------------------------- 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 = 0.3653 r_free = 0.3653 target = 0.131569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.091744 restraints weight = 11678.406| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.24 r_work: 0.3114 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.1125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9746 Z= 0.142 Angle : 0.435 5.493 13204 Z= 0.229 Chirality : 0.041 0.139 1471 Planarity : 0.004 0.045 1709 Dihedral : 5.807 81.092 1329 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.70 % Allowed : 9.99 % Favored : 88.31 % 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: 1.60 (0.24), residues: 1200 helix: 1.86 (0.24), residues: 490 sheet: 1.13 (0.36), residues: 181 loop : 0.38 (0.27), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 669 HIS 0.002 0.000 HIS C 32 PHE 0.009 0.001 PHE A 360 TYR 0.014 0.001 TYR C 145 ARG 0.007 0.000 ARG C 5 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 124 time to evaluate : 1.248 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 ARG cc_start: 0.7519 (mtp85) cc_final: 0.6837 (mtm-85) REVERT: A 333 GLN cc_start: 0.8372 (OUTLIER) cc_final: 0.7988 (mp10) REVERT: A 524 GLU cc_start: 0.8162 (mp0) cc_final: 0.7795 (mp0) REVERT: A 540 GLU cc_start: 0.8035 (tt0) cc_final: 0.7490 (mp0) REVERT: A 879 LYS cc_start: 0.8605 (mmmm) cc_final: 0.8400 (mmmm) REVERT: B 16 GLU cc_start: 0.8682 (OUTLIER) cc_final: 0.7495 (tm-30) REVERT: B 22 THR cc_start: 0.7699 (OUTLIER) cc_final: 0.7367 (p) REVERT: B 39 ASP cc_start: 0.8340 (m-30) cc_final: 0.7991 (m-30) REVERT: B 71 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8763 (pp) REVERT: C 31 PHE cc_start: 0.8529 (m-80) cc_final: 0.8174 (m-10) REVERT: C 92 GLN cc_start: 0.8116 (mm110) cc_final: 0.7036 (tm-30) REVERT: C 143 ARG cc_start: 0.7583 (mtm110) cc_final: 0.7125 (ttm-80) outliers start: 18 outliers final: 9 residues processed: 135 average time/residue: 1.4740 time to fit residues: 211.7309 Evaluate side-chains 127 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 114 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 GLU Chi-restraints excluded: chain A residue 273 LYS Chi-restraints excluded: chain A residue 333 GLN Chi-restraints excluded: chain A residue 387 ASP Chi-restraints excluded: chain A residue 390 GLU Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 16 GLU Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain C residue 36 THR 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 77 optimal weight: 1.9990 chunk 33 optimal weight: 0.0670 chunk 108 optimal weight: 1.9990 chunk 78 optimal weight: 0.6980 chunk 63 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 106 optimal weight: 0.8980 chunk 112 optimal weight: 0.6980 chunk 49 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 overall best weight: 0.6718 ------------------------------------------------------------------------------- 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 = 0.3632 r_free = 0.3632 target = 0.129834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.089738 restraints weight = 11758.265| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 2.25 r_work: 0.3089 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.1104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9746 Z= 0.245 Angle : 0.472 5.478 13204 Z= 0.248 Chirality : 0.043 0.144 1471 Planarity : 0.004 0.046 1709 Dihedral : 5.966 82.542 1329 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.51 % Allowed : 10.84 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.24), residues: 1200 helix: 1.80 (0.24), residues: 490 sheet: 1.08 (0.36), residues: 181 loop : 0.34 (0.27), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 608 HIS 0.002 0.001 HIS C 32 PHE 0.012 0.001 PHE A 237 TYR 0.009 0.001 TYR A 544 ARG 0.009 0.000 ARG C 5 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 120 time to evaluate : 1.097 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 ARG cc_start: 0.7625 (mtp85) cc_final: 0.6975 (mtm-85) REVERT: A 524 GLU cc_start: 0.8182 (mp0) cc_final: 0.7821 (mp0) REVERT: A 540 GLU cc_start: 0.8104 (tt0) cc_final: 0.7506 (mp0) REVERT: A 879 LYS cc_start: 0.8665 (mmmm) cc_final: 0.8455 (mmmm) REVERT: B 16 GLU cc_start: 0.8686 (OUTLIER) cc_final: 0.7552 (tm-30) REVERT: B 39 ASP cc_start: 0.8362 (m-30) cc_final: 0.8019 (m-30) REVERT: B 71 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.8809 (pp) REVERT: C 31 PHE cc_start: 0.8543 (m-80) cc_final: 0.8155 (m-10) REVERT: C 92 GLN cc_start: 0.8145 (mm110) cc_final: 0.6999 (tm-30) REVERT: C 143 ARG cc_start: 0.7600 (mtm110) cc_final: 0.7132 (ttm-80) outliers start: 16 outliers final: 12 residues processed: 130 average time/residue: 1.5113 time to fit residues: 208.7442 Evaluate side-chains 129 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 115 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 GLU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 273 LYS Chi-restraints excluded: chain A residue 387 ASP Chi-restraints excluded: chain A residue 390 GLU Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain A residue 1004 GLU Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 16 GLU Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 85 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 64 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 53 optimal weight: 0.0870 chunk 21 optimal weight: 0.0670 chunk 81 optimal weight: 0.9990 chunk 73 optimal weight: 0.6980 chunk 45 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 overall best weight: 0.4696 ------------------------------------------------------------------------------- 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 = 0.3639 r_free = 0.3639 target = 0.130359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.090265 restraints weight = 11773.921| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 2.25 r_work: 0.3081 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.1142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9746 Z= 0.194 Angle : 0.456 5.538 13204 Z= 0.239 Chirality : 0.042 0.141 1471 Planarity : 0.004 0.046 1709 Dihedral : 5.934 83.982 1329 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.79 % Allowed : 10.74 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.24), residues: 1200 helix: 1.83 (0.24), residues: 490 sheet: 1.11 (0.36), residues: 181 loop : 0.36 (0.27), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 669 HIS 0.002 0.001 HIS C 32 PHE 0.011 0.001 PHE A 237 TYR 0.008 0.001 TYR A 736 ARG 0.009 0.000 ARG C 5 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 117 time to evaluate : 1.159 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 ARG cc_start: 0.7480 (mtp85) cc_final: 0.6812 (mtm-85) REVERT: A 333 GLN cc_start: 0.8362 (OUTLIER) cc_final: 0.7966 (mp10) REVERT: A 524 GLU cc_start: 0.8119 (mp0) cc_final: 0.7747 (mp0) REVERT: A 540 GLU cc_start: 0.8119 (tt0) cc_final: 0.7465 (mp0) REVERT: A 879 LYS cc_start: 0.8609 (mmmm) cc_final: 0.8394 (mmmm) REVERT: B 16 GLU cc_start: 0.8664 (OUTLIER) cc_final: 0.7529 (tm-30) REVERT: B 22 THR cc_start: 0.7702 (OUTLIER) cc_final: 0.7364 (p) REVERT: B 39 ASP cc_start: 0.8337 (m-30) cc_final: 0.7993 (m-30) REVERT: B 71 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8781 (pp) REVERT: C 31 PHE cc_start: 0.8509 (m-80) cc_final: 0.8128 (m-10) REVERT: C 143 ARG cc_start: 0.7553 (mtm110) cc_final: 0.7099 (ttm-80) outliers start: 19 outliers final: 12 residues processed: 131 average time/residue: 1.4788 time to fit residues: 205.9649 Evaluate side-chains 132 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 116 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 GLU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 273 LYS Chi-restraints excluded: chain A residue 333 GLN Chi-restraints excluded: chain A residue 387 ASP Chi-restraints excluded: chain A residue 390 GLU Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain A residue 1004 GLU Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 16 GLU Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 85 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 33 optimal weight: 0.9980 chunk 67 optimal weight: 0.8980 chunk 104 optimal weight: 0.3980 chunk 0 optimal weight: 2.9990 chunk 17 optimal weight: 0.3980 chunk 24 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 103 optimal weight: 0.8980 chunk 95 optimal weight: 1.9990 chunk 70 optimal weight: 0.3980 chunk 46 optimal weight: 0.3980 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 = 0.3641 r_free = 0.3641 target = 0.130583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.090453 restraints weight = 11755.792| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 2.25 r_work: 0.3101 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.1168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9746 Z= 0.189 Angle : 0.460 6.523 13204 Z= 0.241 Chirality : 0.042 0.140 1471 Planarity : 0.004 0.046 1709 Dihedral : 5.932 85.216 1329 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.79 % Allowed : 10.93 % Favored : 87.28 % 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 (0.24), residues: 1200 helix: 1.84 (0.24), residues: 489 sheet: 1.12 (0.36), residues: 181 loop : 0.38 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 669 HIS 0.002 0.001 HIS C 32 PHE 0.010 0.001 PHE A 237 TYR 0.011 0.001 TYR C 145 ARG 0.009 0.000 ARG C 5 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 118 time to evaluate : 1.194 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 ARG cc_start: 0.7540 (mtp85) cc_final: 0.6869 (mtm-85) REVERT: A 333 GLN cc_start: 0.8370 (OUTLIER) cc_final: 0.7970 (mp10) REVERT: A 524 GLU cc_start: 0.8163 (mp0) cc_final: 0.7796 (mp0) REVERT: A 540 GLU cc_start: 0.8165 (tt0) cc_final: 0.7514 (mp0) REVERT: A 879 LYS cc_start: 0.8651 (mmmm) cc_final: 0.8437 (mmmm) REVERT: B 16 GLU cc_start: 0.8702 (OUTLIER) cc_final: 0.7580 (tm-30) REVERT: B 22 THR cc_start: 0.7731 (OUTLIER) cc_final: 0.7394 (p) REVERT: B 39 ASP cc_start: 0.8364 (m-30) cc_final: 0.8027 (m-30) REVERT: B 71 LEU cc_start: 0.9211 (OUTLIER) cc_final: 0.8803 (pp) REVERT: C 31 PHE cc_start: 0.8489 (m-80) cc_final: 0.8119 (m-10) REVERT: C 72 ARG cc_start: 0.8200 (mmm-85) cc_final: 0.7985 (mmm-85) REVERT: C 143 ARG cc_start: 0.7520 (mtm110) cc_final: 0.7082 (ttm-80) outliers start: 19 outliers final: 13 residues processed: 131 average time/residue: 1.4861 time to fit residues: 207.5720 Evaluate side-chains 132 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 115 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 GLU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 273 LYS Chi-restraints excluded: chain A residue 333 GLN Chi-restraints excluded: chain A residue 387 ASP Chi-restraints excluded: chain A residue 390 GLU Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain A residue 1004 GLU Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 16 GLU Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 85 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 79 optimal weight: 0.7980 chunk 52 optimal weight: 0.7980 chunk 88 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 chunk 35 optimal weight: 0.3980 chunk 66 optimal weight: 0.9980 chunk 13 optimal weight: 0.5980 chunk 19 optimal weight: 0.0980 chunk 15 optimal weight: 0.8980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.130429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.090510 restraints weight = 11673.473| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 2.25 r_work: 0.3093 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.1178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9746 Z= 0.199 Angle : 0.463 6.794 13204 Z= 0.242 Chirality : 0.042 0.140 1471 Planarity : 0.004 0.046 1709 Dihedral : 5.948 86.052 1329 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 1.89 % Allowed : 10.74 % Favored : 87.37 % 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 (0.24), residues: 1200 helix: 1.83 (0.24), residues: 489 sheet: 1.11 (0.36), residues: 181 loop : 0.38 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 669 HIS 0.002 0.001 HIS C 32 PHE 0.019 0.001 PHE C 62 TYR 0.010 0.001 TYR C 145 ARG 0.007 0.000 ARG C 72 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 115 time to evaluate : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 ARG cc_start: 0.7537 (mtp85) cc_final: 0.6884 (mtm-85) REVERT: A 333 GLN cc_start: 0.8379 (OUTLIER) cc_final: 0.7979 (mp10) REVERT: A 524 GLU cc_start: 0.8159 (mp0) cc_final: 0.7792 (mp0) REVERT: A 540 GLU cc_start: 0.8166 (tt0) cc_final: 0.7536 (mp0) REVERT: A 879 LYS cc_start: 0.8653 (mmmm) cc_final: 0.8438 (mmmm) REVERT: B 16 GLU cc_start: 0.8693 (OUTLIER) cc_final: 0.7567 (tm-30) REVERT: B 39 ASP cc_start: 0.8362 (m-30) cc_final: 0.8025 (m-30) REVERT: B 71 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8798 (pp) REVERT: C 31 PHE cc_start: 0.8488 (m-80) cc_final: 0.8125 (m-10) REVERT: C 72 ARG cc_start: 0.8241 (mmm-85) cc_final: 0.8025 (mmm-85) REVERT: C 143 ARG cc_start: 0.7560 (mtm110) cc_final: 0.7119 (ttm-80) outliers start: 20 outliers final: 15 residues processed: 129 average time/residue: 1.4730 time to fit residues: 201.8650 Evaluate side-chains 132 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 114 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 GLU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 273 LYS Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 333 GLN Chi-restraints excluded: chain A residue 387 ASP Chi-restraints excluded: chain A residue 390 GLU Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain A residue 1004 GLU Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 16 GLU Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 85 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 14 optimal weight: 0.5980 chunk 116 optimal weight: 0.7980 chunk 85 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 89 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 27 optimal weight: 0.1980 chunk 17 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3631 r_free = 0.3631 target = 0.129819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.089622 restraints weight = 11864.290| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 2.26 r_work: 0.3081 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.1173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9746 Z= 0.246 Angle : 0.487 7.808 13204 Z= 0.255 Chirality : 0.043 0.144 1471 Planarity : 0.004 0.051 1709 Dihedral : 6.024 86.057 1329 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.70 % Allowed : 11.40 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.24), residues: 1200 helix: 1.78 (0.24), residues: 489 sheet: 1.08 (0.36), residues: 181 loop : 0.36 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 608 HIS 0.002 0.001 HIS C 32 PHE 0.018 0.001 PHE C 62 TYR 0.010 0.001 TYR C 145 ARG 0.009 0.000 ARG C 8 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 116 time to evaluate : 1.078 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 ARG cc_start: 0.7583 (mtp85) cc_final: 0.6883 (mtm-85) REVERT: A 333 GLN cc_start: 0.8359 (OUTLIER) cc_final: 0.7963 (mp10) REVERT: A 524 GLU cc_start: 0.8116 (mp0) cc_final: 0.7742 (mp0) REVERT: A 540 GLU cc_start: 0.8129 (tt0) cc_final: 0.7461 (mp0) REVERT: A 879 LYS cc_start: 0.8604 (mmmm) cc_final: 0.8383 (mmmm) REVERT: B 16 GLU cc_start: 0.8673 (OUTLIER) cc_final: 0.7553 (tm-30) REVERT: B 39 ASP cc_start: 0.8342 (m-30) cc_final: 0.8002 (m-30) REVERT: B 71 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8774 (pp) REVERT: C 31 PHE cc_start: 0.8462 (m-80) cc_final: 0.8021 (m-10) REVERT: C 143 ARG cc_start: 0.7534 (mtm110) cc_final: 0.7088 (ttm-80) outliers start: 18 outliers final: 15 residues processed: 127 average time/residue: 1.4939 time to fit residues: 201.4985 Evaluate side-chains 135 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 117 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 GLU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 273 LYS Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 333 GLN Chi-restraints excluded: chain A residue 387 ASP Chi-restraints excluded: chain A residue 390 GLU Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain A residue 1004 GLU Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 16 GLU Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 85 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 117 optimal weight: 0.4980 chunk 47 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 chunk 29 optimal weight: 0.0370 chunk 24 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 96 optimal weight: 0.8980 chunk 105 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 79 optimal weight: 0.8980 overall best weight: 0.5058 ------------------------------------------------------------------------------- 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 = 0.3638 r_free = 0.3638 target = 0.130195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.090169 restraints weight = 11724.645| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 2.27 r_work: 0.3083 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.1186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9746 Z= 0.205 Angle : 0.474 9.074 13204 Z= 0.247 Chirality : 0.042 0.142 1471 Planarity : 0.004 0.046 1709 Dihedral : 5.993 86.040 1329 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.89 % Allowed : 11.22 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.24), residues: 1200 helix: 1.79 (0.24), residues: 489 sheet: 1.09 (0.36), residues: 181 loop : 0.39 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 669 HIS 0.002 0.001 HIS C 32 PHE 0.018 0.001 PHE C 62 TYR 0.009 0.001 TYR C 145 ARG 0.008 0.000 ARG C 72 Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 8206.20 seconds wall clock time: 144 minutes 50.71 seconds (8690.71 seconds total)