Starting phenix.real_space_refine on Sun Aug 4 03:47:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b5c_44207/08_2024/9b5c_44207.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b5c_44207/08_2024/9b5c_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b5c_44207/08_2024/9b5c_44207.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b5c_44207/08_2024/9b5c_44207.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b5c_44207/08_2024/9b5c_44207.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b5c_44207/08_2024/9b5c_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 Residue "A PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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: 6.53, per 1000 atoms: 0.68 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 - 3.50 Amino acid : False - 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: 3.95 Conformation dependent library (CDL) restraints added in 1.7 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: 1.19 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: 3.69 Time building geometry restraints manager: 4.34 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: 99.61 - 115.53: 6298 115.53 - 131.45: 6893 131.45 - 147.36: 12 147.36 - 163.28: 0 163.28 - 179.20: 1 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: 3.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 30.990 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.180 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 7 poor density : 141 time to evaluate : 1.137 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: 1.4099 time to fit residues: 218.8388 Evaluate side-chains 123 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 121 time to evaluate : 1.073 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 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 fitting. rotamer outliers: 16 poor density : 132 time to evaluate : 1.054 Fit side-chains REVERT: A 73 ARG cc_start: 0.7263 (mtp85) cc_final: 0.6606 (mtm-85) REVERT: A 196 MET cc_start: 0.8617 (mmp) cc_final: 0.8349 (mmm) REVERT: A 524 GLU cc_start: 0.7933 (mp0) cc_final: 0.7545 (mp0) REVERT: A 540 GLU cc_start: 0.7559 (tt0) cc_final: 0.7154 (mp0) REVERT: A 626 MET cc_start: 0.7062 (ttt) cc_final: 0.6841 (tmt) REVERT: A 668 MET cc_start: 0.7250 (mmm) cc_final: 0.7010 (mmm) REVERT: A 879 LYS cc_start: 0.8457 (mmmm) cc_final: 0.8226 (mmpt) REVERT: A 1004 GLU cc_start: 0.8041 (mt-10) cc_final: 0.7828 (mt-10) REVERT: C 12 ASP cc_start: 0.7841 (t70) cc_final: 0.7504 (t0) REVERT: C 31 PHE cc_start: 0.8640 (m-80) cc_final: 0.8321 (m-10) REVERT: C 143 ARG cc_start: 0.7703 (mtm110) cc_final: 0.7277 (ttm-80) outliers start: 16 outliers final: 6 residues processed: 138 average time/residue: 1.3367 time to fit residues: 196.7553 Evaluate side-chains 128 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 122 time to evaluate : 1.077 ------------------------------------------------------------------------------- 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 60 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 89 optimal weight: 0.0070 chunk 73 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 108 optimal weight: 0.6980 chunk 116 optimal weight: 0.8980 chunk 96 optimal weight: 0.5980 chunk 107 optimal weight: 2.9990 chunk 36 optimal weight: 0.2980 chunk 86 optimal weight: 0.9980 overall best weight: 0.4598 ------------------------------------------------------------------------------- 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: 0.7726 moved from start: 0.0930 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= 0.193 Angle : 0.467 5.630 13204 Z= 0.246 Chirality : 0.042 0.158 1471 Planarity : 0.004 0.044 1709 Dihedral : 5.964 78.068 1329 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.41 % Allowed : 8.95 % Favored : 89.63 % 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: 1.49 (0.24), residues: 1200 helix: 1.76 (0.24), residues: 489 sheet: 1.10 (0.37), residues: 181 loop : 0.31 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 669 HIS 0.002 0.000 HIS C 75 PHE 0.011 0.001 PHE C 62 TYR 0.009 0.001 TYR A 736 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 142 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 127 time to evaluate : 1.168 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 ARG cc_start: 0.7244 (mtp85) cc_final: 0.6615 (mtm-85) REVERT: A 196 MET cc_start: 0.8636 (mmp) cc_final: 0.8333 (mmm) REVERT: A 286 MET cc_start: 0.8315 (OUTLIER) cc_final: 0.8051 (mmm) REVERT: A 524 GLU cc_start: 0.7923 (mp0) cc_final: 0.7582 (mp0) REVERT: A 540 GLU cc_start: 0.7599 (tt0) cc_final: 0.7179 (mp0) REVERT: A 668 MET cc_start: 0.7204 (mmm) cc_final: 0.6956 (mmm) REVERT: A 879 LYS cc_start: 0.8493 (mmmm) cc_final: 0.8245 (mmmm) REVERT: A 987 LYS cc_start: 0.8394 (mtpt) cc_final: 0.8060 (mttm) REVERT: A 1004 GLU cc_start: 0.8056 (mt-10) cc_final: 0.7855 (mt-10) REVERT: B 71 LEU cc_start: 0.9341 (OUTLIER) cc_final: 0.8952 (pp) REVERT: C 12 ASP cc_start: 0.7875 (t70) cc_final: 0.7420 (t0) REVERT: C 31 PHE cc_start: 0.8653 (m-80) cc_final: 0.8311 (m-10) REVERT: C 92 GLN cc_start: 0.8192 (mm110) cc_final: 0.7281 (tm-30) REVERT: C 143 ARG cc_start: 0.7705 (mtm110) cc_final: 0.7283 (ttm-80) outliers start: 15 outliers final: 9 residues processed: 134 average time/residue: 1.4036 time to fit residues: 200.2111 Evaluate side-chains 133 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 122 time to evaluate : 1.080 ------------------------------------------------------------------------------- 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 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 106 optimal weight: 0.1980 chunk 81 optimal weight: 0.4980 chunk 56 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 51 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 108 optimal weight: 0.6980 chunk 115 optimal weight: 0.5980 chunk 102 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 95 optimal weight: 0.8980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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: 0.7729 moved from start: 0.0992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9746 Z= 0.211 Angle : 0.464 5.492 13204 Z= 0.244 Chirality : 0.042 0.144 1471 Planarity : 0.004 0.046 1709 Dihedral : 5.915 76.114 1329 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.70 % Allowed : 9.14 % 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: 1.48 (0.24), residues: 1200 helix: 1.77 (0.24), residues: 489 sheet: 1.10 (0.36), residues: 181 loop : 0.29 (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 75 PHE 0.011 0.001 PHE C 62 TYR 0.009 0.001 TYR A 544 ARG 0.005 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 fitting. rotamer outliers: 18 poor density : 122 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 ARG cc_start: 0.7244 (mtp85) cc_final: 0.6612 (mtm-85) REVERT: A 196 MET cc_start: 0.8629 (mmp) cc_final: 0.8320 (mmm) REVERT: A 286 MET cc_start: 0.8312 (OUTLIER) cc_final: 0.8044 (mmm) REVERT: A 333 GLN cc_start: 0.8447 (OUTLIER) cc_final: 0.8062 (mp10) REVERT: A 524 GLU cc_start: 0.7884 (mp0) cc_final: 0.7507 (mp0) REVERT: A 540 GLU cc_start: 0.7600 (tt0) cc_final: 0.7177 (mp0) REVERT: A 668 MET cc_start: 0.7197 (mmm) cc_final: 0.6985 (mmm) REVERT: A 879 LYS cc_start: 0.8517 (mmmm) cc_final: 0.8275 (mmmm) REVERT: A 1004 GLU cc_start: 0.8075 (mt-10) cc_final: 0.7860 (mt-10) REVERT: B 71 LEU cc_start: 0.9343 (OUTLIER) cc_final: 0.8967 (pp) REVERT: C 31 PHE cc_start: 0.8657 (m-80) cc_final: 0.8332 (m-10) REVERT: C 92 GLN cc_start: 0.8246 (mm110) cc_final: 0.7298 (tm-30) REVERT: C 143 ARG cc_start: 0.7709 (mtm110) cc_final: 0.7260 (ttm-80) outliers start: 18 outliers final: 10 residues processed: 132 average time/residue: 1.5682 time to fit residues: 221.3808 Evaluate side-chains 131 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 118 time to evaluate : 1.102 ------------------------------------------------------------------------------- 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 286 MET 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 1003 VAL Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 22 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 65 optimal weight: 1.9990 chunk 1 optimal weight: 0.0570 chunk 85 optimal weight: 0.0060 chunk 47 optimal weight: 0.5980 chunk 98 optimal weight: 0.0040 chunk 79 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 103 optimal weight: 0.4980 chunk 29 optimal weight: 0.9980 chunk 38 optimal weight: 0.0470 overall best weight: 0.1224 ------------------------------------------------------------------------------- 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: 0.7694 moved from start: 0.1210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9746 Z= 0.117 Angle : 0.424 5.573 13204 Z= 0.222 Chirality : 0.040 0.138 1471 Planarity : 0.004 0.044 1709 Dihedral : 5.754 84.631 1329 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % 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: 1.67 (0.24), residues: 1200 helix: 1.91 (0.24), residues: 490 sheet: 1.21 (0.36), residues: 181 loop : 0.40 (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 0.008 0.001 PHE A 842 TYR 0.007 0.001 TYR A 736 ARG 0.008 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 fitting. rotamer outliers: 18 poor density : 124 time to evaluate : 1.155 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 ARG cc_start: 0.7188 (mtp85) cc_final: 0.6297 (mmt-90) REVERT: A 196 MET cc_start: 0.8619 (mmp) cc_final: 0.8293 (mmm) REVERT: A 524 GLU cc_start: 0.7924 (mp0) cc_final: 0.7542 (mp0) REVERT: A 540 GLU cc_start: 0.7573 (tt0) cc_final: 0.7160 (mp0) REVERT: A 668 MET cc_start: 0.7151 (mmm) cc_final: 0.6933 (mmm) REVERT: A 879 LYS cc_start: 0.8500 (mmmm) cc_final: 0.8262 (mmmm) REVERT: B 22 THR cc_start: 0.8292 (OUTLIER) cc_final: 0.7990 (p) REVERT: C 31 PHE cc_start: 0.8626 (m-80) cc_final: 0.8324 (m-10) REVERT: C 92 GLN cc_start: 0.8184 (mm110) cc_final: 0.7236 (tm-30) REVERT: C 143 ARG cc_start: 0.7678 (mtm110) cc_final: 0.7238 (ttm-80) outliers start: 18 outliers final: 8 residues processed: 135 average time/residue: 1.4160 time to fit residues: 203.7359 Evaluate side-chains 126 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 117 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 GLU Chi-restraints excluded: chain A residue 316 ILE 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 22 THR Chi-restraints excluded: chain B residue 28 SER 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 103 optimal weight: 1.9990 chunk 22 optimal weight: 0.0870 chunk 67 optimal weight: 0.2980 chunk 28 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 chunk 111 optimal weight: 0.6980 overall best weight: 0.5758 ------------------------------------------------------------------------------- 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: 0.7724 moved from start: 0.1144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9746 Z= 0.219 Angle : 0.459 5.468 13204 Z= 0.241 Chirality : 0.042 0.139 1471 Planarity : 0.004 0.046 1709 Dihedral : 5.827 81.517 1329 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.32 % Allowed : 11.12 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.24), residues: 1200 helix: 1.86 (0.24), residues: 490 sheet: 1.18 (0.36), residues: 181 loop : 0.39 (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 75 PHE 0.011 0.001 PHE A 237 TYR 0.008 0.001 TYR A 544 ARG 0.006 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 131 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 117 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 ARG cc_start: 0.7219 (mtp85) cc_final: 0.6577 (mtm-85) REVERT: A 524 GLU cc_start: 0.7862 (mp0) cc_final: 0.7473 (mp0) REVERT: A 540 GLU cc_start: 0.7634 (tt0) cc_final: 0.7151 (mp0) REVERT: A 668 MET cc_start: 0.7196 (mmm) cc_final: 0.6985 (mmm) REVERT: A 879 LYS cc_start: 0.8500 (mmmm) cc_final: 0.8274 (mmmm) REVERT: C 31 PHE cc_start: 0.8602 (m-80) cc_final: 0.8298 (m-10) REVERT: C 72 ARG cc_start: 0.8166 (mmm-85) cc_final: 0.7954 (mmm-85) REVERT: C 92 GLN cc_start: 0.8209 (mm110) cc_final: 0.7199 (tm-30) REVERT: C 143 ARG cc_start: 0.7701 (mtm110) cc_final: 0.7249 (ttm-80) outliers start: 14 outliers final: 10 residues processed: 126 average time/residue: 1.3807 time to fit residues: 185.2852 Evaluate side-chains 125 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 115 time to evaluate : 1.062 ------------------------------------------------------------------------------- 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 390 GLU Chi-restraints excluded: chain A residue 461 VAL 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 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 12 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 84 optimal weight: 0.0010 chunk 96 optimal weight: 0.6980 chunk 64 optimal weight: 0.0060 chunk 114 optimal weight: 0.0970 chunk 71 optimal weight: 0.6980 chunk 69 optimal weight: 0.0980 chunk 52 optimal weight: 0.4980 chunk 70 optimal weight: 0.9990 chunk 45 optimal weight: 0.3980 overall best weight: 0.1200 ------------------------------------------------------------------------------- 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: 0.7686 moved from start: 0.1344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9746 Z= 0.113 Angle : 0.415 5.550 13204 Z= 0.217 Chirality : 0.040 0.132 1471 Planarity : 0.004 0.044 1709 Dihedral : 5.666 85.894 1329 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.32 % Allowed : 10.93 % Favored : 87.75 % 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: 1.81 (0.24), residues: 1200 helix: 2.01 (0.24), residues: 490 sheet: 1.29 (0.37), residues: 181 loop : 0.50 (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 C 62 TYR 0.007 0.001 TYR A 736 ARG 0.006 0.000 ARG C 72 *********************** 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 132 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 118 time to evaluate : 1.134 Fit side-chains revert: symmetry clash REVERT: A 73 ARG cc_start: 0.7162 (mtp85) cc_final: 0.6245 (mmt-90) REVERT: A 524 GLU cc_start: 0.7862 (mp0) cc_final: 0.7467 (mp0) REVERT: A 540 GLU cc_start: 0.7586 (tt0) cc_final: 0.7144 (mp0) REVERT: A 668 MET cc_start: 0.7133 (mmm) cc_final: 0.6918 (mmm) REVERT: A 879 LYS cc_start: 0.8455 (mmmm) cc_final: 0.8223 (mmmm) REVERT: C 31 PHE cc_start: 0.8572 (m-80) cc_final: 0.8273 (m-10) REVERT: C 92 GLN cc_start: 0.8199 (mm110) cc_final: 0.7185 (tm-30) REVERT: C 143 ARG cc_start: 0.7644 (mtm110) cc_final: 0.7226 (ttm-80) outliers start: 14 outliers final: 8 residues processed: 126 average time/residue: 1.3713 time to fit residues: 184.4244 Evaluate side-chains 123 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 115 time to evaluate : 1.115 ------------------------------------------------------------------------------- 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 390 GLU Chi-restraints excluded: chain A residue 461 VAL 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 C residue 59 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 68 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 72 optimal weight: 0.0370 chunk 78 optimal weight: 2.9990 chunk 56 optimal weight: 0.5980 chunk 10 optimal weight: 0.0040 chunk 90 optimal weight: 1.9990 chunk 104 optimal weight: 0.5980 chunk 109 optimal weight: 0.7980 chunk 100 optimal weight: 0.5980 overall best weight: 0.3670 ------------------------------------------------------------------------------- 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: 0.7705 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9746 Z= 0.162 Angle : 0.458 11.849 13204 Z= 0.237 Chirality : 0.041 0.175 1471 Planarity : 0.004 0.046 1709 Dihedral : 5.590 87.163 1328 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.32 % Allowed : 11.22 % 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: 1.83 (0.24), residues: 1200 helix: 2.00 (0.24), residues: 490 sheet: 1.34 (0.36), residues: 186 loop : 0.51 (0.28), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 608 HIS 0.002 0.000 HIS C 32 PHE 0.014 0.001 PHE C 62 TYR 0.009 0.001 TYR C 145 ARG 0.008 0.000 ARG C 72 *********************** 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 130 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 116 time to evaluate : 1.046 Fit side-chains revert: symmetry clash REVERT: A 73 ARG cc_start: 0.7210 (mtp85) cc_final: 0.6239 (mmt-90) REVERT: A 524 GLU cc_start: 0.7864 (mp0) cc_final: 0.7465 (mp0) REVERT: A 540 GLU cc_start: 0.7618 (tt0) cc_final: 0.7181 (mp0) REVERT: A 668 MET cc_start: 0.7160 (mmm) cc_final: 0.6935 (mmm) REVERT: A 879 LYS cc_start: 0.8474 (mmmm) cc_final: 0.8239 (mmmm) REVERT: B 16 GLU cc_start: 0.8667 (OUTLIER) cc_final: 0.7530 (tm-30) REVERT: B 22 THR cc_start: 0.8270 (OUTLIER) cc_final: 0.7968 (p) REVERT: B 71 LEU cc_start: 0.9287 (OUTLIER) cc_final: 0.8926 (pp) REVERT: C 31 PHE cc_start: 0.8572 (m-80) cc_final: 0.8305 (m-10) REVERT: C 92 GLN cc_start: 0.8203 (mm110) cc_final: 0.7163 (tm-30) REVERT: C 143 ARG cc_start: 0.7664 (mtm110) cc_final: 0.7235 (ttm-80) outliers start: 14 outliers final: 8 residues processed: 126 average time/residue: 1.4347 time to fit residues: 192.9108 Evaluate side-chains 125 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 114 time to evaluate : 1.024 ------------------------------------------------------------------------------- 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 390 GLU Chi-restraints excluded: chain A residue 461 VAL 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 106 optimal weight: 10.0000 chunk 109 optimal weight: 0.8980 chunk 64 optimal weight: 0.9990 chunk 46 optimal weight: 0.2980 chunk 83 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 96 optimal weight: 0.6980 chunk 101 optimal weight: 0.0870 chunk 70 optimal weight: 0.8980 chunk 113 optimal weight: 0.0870 chunk 68 optimal weight: 1.9990 overall best weight: 0.4136 ------------------------------------------------------------------------------- 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: 0.7711 moved from start: 0.1314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9746 Z= 0.173 Angle : 0.456 10.873 13204 Z= 0.237 Chirality : 0.041 0.175 1471 Planarity : 0.004 0.045 1709 Dihedral : 5.659 88.776 1328 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.41 % Allowed : 11.03 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.24), residues: 1200 helix: 1.90 (0.24), residues: 496 sheet: 1.28 (0.36), residues: 186 loop : 0.53 (0.28), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 608 HIS 0.002 0.000 HIS C 32 PHE 0.015 0.001 PHE C 62 TYR 0.008 0.001 TYR C 145 ARG 0.005 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 131 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 116 time to evaluate : 1.139 Fit side-chains revert: symmetry clash REVERT: A 73 ARG cc_start: 0.7213 (mtp85) cc_final: 0.6263 (mmt-90) REVERT: A 524 GLU cc_start: 0.7862 (mp0) cc_final: 0.7466 (mp0) REVERT: A 540 GLU cc_start: 0.7622 (tt0) cc_final: 0.7182 (mp0) REVERT: A 668 MET cc_start: 0.7171 (mmm) cc_final: 0.6942 (mmm) REVERT: A 879 LYS cc_start: 0.8477 (mmmm) cc_final: 0.8238 (mmmm) REVERT: B 16 GLU cc_start: 0.8668 (OUTLIER) cc_final: 0.7535 (tm-30) REVERT: B 22 THR cc_start: 0.8297 (OUTLIER) cc_final: 0.7996 (p) REVERT: B 71 LEU cc_start: 0.9307 (OUTLIER) cc_final: 0.8938 (pp) REVERT: C 31 PHE cc_start: 0.8552 (m-80) cc_final: 0.8279 (m-10) REVERT: C 143 ARG cc_start: 0.7663 (mtm110) cc_final: 0.7273 (ttp80) outliers start: 15 outliers final: 11 residues processed: 126 average time/residue: 1.3793 time to fit residues: 185.3238 Evaluate side-chains 128 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 114 time to evaluate : 1.160 ------------------------------------------------------------------------------- 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 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 21 ASP 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 53 optimal weight: 0.0980 chunk 78 optimal weight: 1.9990 chunk 118 optimal weight: 0.7980 chunk 109 optimal weight: 0.1980 chunk 94 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 72 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 100 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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: 0.7719 moved from start: 0.1290 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= 0.204 Angle : 0.478 10.822 13204 Z= 0.248 Chirality : 0.042 0.171 1471 Planarity : 0.004 0.046 1709 Dihedral : 5.721 87.969 1328 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.60 % Allowed : 11.12 % 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: 1.69 (0.24), residues: 1200 helix: 1.85 (0.24), residues: 496 sheet: 1.22 (0.37), residues: 181 loop : 0.50 (0.28), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 608 HIS 0.002 0.001 HIS C 32 PHE 0.017 0.001 PHE C 62 TYR 0.008 0.001 TYR A 544 ARG 0.006 0.000 ARG C 72 ********************** 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 131 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 114 time to evaluate : 1.093 Fit side-chains revert: symmetry clash REVERT: A 73 ARG cc_start: 0.7299 (mtp85) cc_final: 0.6348 (mmt-90) REVERT: A 333 GLN cc_start: 0.8315 (OUTLIER) cc_final: 0.7948 (mp10) REVERT: A 524 GLU cc_start: 0.7858 (mp0) cc_final: 0.7464 (mp0) REVERT: A 540 GLU cc_start: 0.7636 (tt0) cc_final: 0.7172 (mp0) REVERT: A 668 MET cc_start: 0.7148 (mmm) cc_final: 0.6946 (mmm) REVERT: A 879 LYS cc_start: 0.8502 (mmmm) cc_final: 0.8264 (mmmm) REVERT: B 16 GLU cc_start: 0.8670 (OUTLIER) cc_final: 0.7543 (tm-30) REVERT: B 22 THR cc_start: 0.8324 (OUTLIER) cc_final: 0.8026 (p) REVERT: B 71 LEU cc_start: 0.9324 (OUTLIER) cc_final: 0.8951 (pp) REVERT: C 31 PHE cc_start: 0.8549 (m-80) cc_final: 0.8210 (m-10) REVERT: C 143 ARG cc_start: 0.7682 (mtm110) cc_final: 0.7291 (ttp80) outliers start: 17 outliers final: 11 residues processed: 125 average time/residue: 1.3666 time to fit residues: 182.5051 Evaluate side-chains 129 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 114 time to evaluate : 1.059 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 87 optimal weight: 1.9990 chunk 13 optimal weight: 0.4980 chunk 26 optimal weight: 0.9980 chunk 94 optimal weight: 0.5980 chunk 39 optimal weight: 0.1980 chunk 97 optimal weight: 0.0170 chunk 11 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 chunk 68 optimal weight: 0.9980 overall best weight: 0.3818 ------------------------------------------------------------------------------- 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 = 0.3656 r_free = 0.3656 target = 0.131505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.091752 restraints weight = 11675.913| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 2.24 r_work: 0.3119 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9746 Z= 0.167 Angle : 0.461 10.258 13204 Z= 0.238 Chirality : 0.042 0.202 1471 Planarity : 0.004 0.045 1709 Dihedral : 5.684 86.769 1328 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 1.32 % Allowed : 11.22 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.24), residues: 1200 helix: 1.85 (0.24), residues: 496 sheet: 1.22 (0.37), residues: 181 loop : 0.51 (0.28), residues: 523 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 0.015 0.001 PHE C 62 TYR 0.007 0.001 TYR A 736 ARG 0.005 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: 3988.79 seconds wall clock time: 70 minutes 10.04 seconds (4210.04 seconds total)