Starting phenix.real_space_refine on Sun Aug 4 04:37:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b5u_44225/08_2024/9b5u_44225.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b5u_44225/08_2024/9b5u_44225.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b5u_44225/08_2024/9b5u_44225.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b5u_44225/08_2024/9b5u_44225.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b5u_44225/08_2024/9b5u_44225.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b5u_44225/08_2024/9b5u_44225.cif" } resolution = 3.67 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= 0.046 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 3 5.49 5 Mg 2 5.21 5 S 42 5.16 5 C 6074 2.51 5 N 1573 2.21 5 O 1833 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 546": "OD1" <-> "OD2" Residue "C TYR 134": "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: 9527 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 985, 7734 Classifications: {'peptide': 985} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 55, 'TRANS': 928} Chain breaks: 1 Chain: "C" Number of atoms: 1158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1158 Classifications: {'peptide': 147} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 131} Chain: "D" Number of atoms: 596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 596 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 6 Unusual residues: {'A1AIV': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.43, per 1000 atoms: 0.67 Number of scatterers: 9527 At special positions: 0 Unit cell: (100.016, 100.016, 121.296, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 42 16.00 P 3 15.00 Mg 2 11.99 O 1833 8.00 N 1573 7.00 C 6074 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 593 " - pdb=" SG CYS C 85 " distance=2.92 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: 3.85 Conformation dependent library (CDL) restraints added in 1.8 seconds 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2264 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 11 sheets defined 46.6% alpha, 16.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.28 Creating SS restraints... Processing helix chain 'A' and resid 20 through 25 removed outlier: 3.968A 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: 3.842A pdb=" N SER A 79 " --> pdb=" O ASP A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 88 removed outlier: 3.911A pdb=" N ILE A 88 " --> pdb=" O GLU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 101 removed outlier: 3.552A pdb=" N VAL A 95 " --> pdb=" O PRO A 91 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N SER A 98 " --> pdb=" O LYS A 94 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N LYS A 99 " --> pdb=" O VAL A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 123 Processing helix chain 'A' and resid 132 through 144 removed outlier: 3.751A pdb=" N PHE A 142 " --> pdb=" O GLU A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 224 removed outlier: 3.844A pdb=" N GLY A 224 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 274 removed outlier: 4.412A pdb=" N LYS A 273 " --> pdb=" O ARG A 269 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASP A 274 " --> pdb=" O GLU A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 305 removed outlier: 3.671A pdb=" N ILE A 293 " --> pdb=" O PRO A 289 " (cutoff:3.500A) removed outlier: 3.679A 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: 4.619A pdb=" N VAL A 416 " --> pdb=" O GLY A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 427 Processing helix chain 'A' and resid 436 through 450 Processing helix chain 'A' and resid 468 through 474 removed outlier: 3.786A pdb=" N ASN A 473 " --> pdb=" O SER A 470 " (cutoff:3.500A) removed outlier: 3.574A 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 removed outlier: 3.537A pdb=" N CYS A 490 " --> pdb=" O LEU A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 503 Processing helix chain 'A' and resid 514 through 518 removed outlier: 3.662A pdb=" N GLU A 518 " --> pdb=" O PRO A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 527 Processing helix chain 'A' and resid 538 through 553 Processing helix chain 'A' and resid 579 through 583 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: 3.578A pdb=" N THR A 636 " --> pdb=" O ASN A 632 " (cutoff:3.500A) removed outlier: 3.544A 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 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: 4.045A pdb=" N TYR A 747 " --> pdb=" O ASP A 743 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLY A 753 " --> pdb=" O ARG A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 781 through 794 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: 3.546A pdb=" N VAL A 871 " --> pdb=" O CYS A 867 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LYS A 872 " --> pdb=" O LEU A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 883 removed outlier: 3.705A pdb=" N TYR A 883 " --> pdb=" O ILE A 880 " (cutoff:3.500A) Processing helix chain 'A' and resid 926 through 937 Processing helix chain 'A' and resid 958 through 966 Processing helix chain 'A' and resid 969 through 979 Processing helix chain 'C' and resid 3 through 16 Processing helix chain 'C' and resid 98 through 112 Processing helix chain 'C' and resid 120 through 130 Processing helix chain 'C' and resid 130 through 145 Processing helix chain 'D' and resid 22 through 35 Processing helix chain 'D' and resid 37 through 39 No H-bonds generated for 'chain 'D' and resid 37 through 39' Processing helix chain 'D' and resid 56 through 60 Processing sheet with id=AA1, first strand: chain 'A' and resid 109 through 111 removed outlier: 6.774A pdb=" N VAL A 64 " --> pdb=" O SER A 110 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ASN A 39 " --> pdb=" O CYS A 125 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N VAL A 127 " --> pdb=" O ASN A 39 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N LEU A 41 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N THR A 129 " --> pdb=" O LEU A 41 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N ILE A 43 " --> pdb=" O THR A 129 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N VAL A 126 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N ALA A 153 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N VAL A 128 " --> pdb=" O ALA A 153 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N SER A 155 " --> pdb=" O VAL A 128 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N VAL A 278 " --> pdb=" O TYR A 385 " (cutoff:3.500A) removed outlier: 8.977A pdb=" N ASP A 387 " --> 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: 3.525A pdb=" N VAL A 210 " --> pdb=" O ARG A 227 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N PHE A 209 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N THR A 195 " --> pdb=" O ALA A 186 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N ILE A 188 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 6.635A 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: 3.525A pdb=" N VAL A 210 " --> pdb=" O ARG A 227 " (cutoff:3.500A) removed outlier: 3.942A 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: 6.544A pdb=" N ILE A 459 " --> pdb=" O THR A 507 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N TYR A 509 " --> pdb=" O ILE A 459 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N VAL A 461 " --> pdb=" O TYR A 509 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LEU A 531 " --> pdb=" O SER A 429 " (cutoff:3.500A) removed outlier: 4.155A 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: 6.407A pdb=" N TYR A 920 " --> pdb=" O CYS A1009 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N VAL A 990 " --> pdb=" O SER A 947 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N SER A 947 " --> pdb=" O VAL A 990 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N GLU A 992 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N LEU A 945 " --> pdb=" O GLU A 992 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N CYS A 994 " --> pdb=" O THR A 943 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N SER A 947 " --> pdb=" O LEU A 951 " (cutoff:3.500A) removed outlier: 6.090A 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: 6.407A pdb=" N TYR A 920 " --> pdb=" O CYS A1009 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N CYS A 995 " --> pdb=" O VAL A1003 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 21 through 22 removed outlier: 6.153A pdb=" N HIS C 32 " --> pdb=" O VAL C 26 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 21 through 22 Processing sheet with id=AB2, first strand: chain 'D' and resid 12 through 16 464 hydrogen bonds defined for protein. 1254 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: 4.43 Time building geometry restraints manager: 4.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 1616 1.27 - 1.40: 2291 1.40 - 1.54: 5657 1.54 - 1.67: 110 1.67 - 1.81: 64 Bond restraints: 9738 Sorted by residual: bond pdb=" C04 A1AIV D 101 " pdb=" C05 A1AIV D 101 " ideal model delta sigma weight residual 1.453 1.528 -0.075 2.00e-02 2.50e+03 1.41e+01 bond pdb=" N MET D 1 " pdb=" CA MET D 1 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.65e+00 bond pdb=" C1' ATP A1103 " pdb=" C2' ATP A1103 " ideal model delta sigma weight residual 1.531 1.519 0.012 1.20e-02 6.94e+03 9.25e-01 bond pdb=" C1' ATP A1103 " pdb=" O4' ATP A1103 " ideal model delta sigma weight residual 1.416 1.404 0.012 1.30e-02 5.92e+03 8.07e-01 bond pdb=" C05 A1AIV D 101 " pdb=" N06 A1AIV D 101 " ideal model delta sigma weight residual 1.151 1.133 0.018 2.00e-02 2.50e+03 7.82e-01 ... (remaining 9733 not shown) Histogram of bond angle deviations from ideal: 100.20 - 116.07: 6492 116.07 - 131.95: 6691 131.95 - 147.82: 11 147.82 - 163.69: 0 163.69 - 179.56: 1 Bond angle restraints: 13195 Sorted by residual: angle pdb=" C LYS A 381 " pdb=" N GLN A 382 " pdb=" CA GLN A 382 " ideal model delta sigma weight residual 121.70 128.31 -6.61 1.80e+00 3.09e-01 1.35e+01 angle pdb=" C2' ATP A1103 " pdb=" C1' ATP A1103 " pdb=" O4' ATP A1103 " ideal model delta sigma weight residual 106.53 103.26 3.27 1.18e+00 7.24e-01 7.76e+00 angle pdb=" C3' ATP A1103 " pdb=" C4' ATP A1103 " pdb=" C5' ATP A1103 " ideal model delta sigma weight residual 115.19 110.64 4.55 1.76e+00 3.23e-01 6.68e+00 angle pdb=" C1' ATP A1103 " pdb=" C2' ATP A1103 " pdb=" O2' ATP A1103 " ideal model delta sigma weight residual 110.58 104.17 6.41 2.79e+00 1.28e-01 5.26e+00 angle pdb=" C2' ATP A1103 " pdb=" C3' ATP A1103 " pdb=" O3' ATP A1103 " ideal model delta sigma weight residual 111.83 106.44 5.39 2.67e+00 1.40e-01 4.08e+00 ... (remaining 13190 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.86: 5580 13.86 - 27.72: 266 27.72 - 41.57: 60 41.57 - 55.43: 17 55.43 - 69.29: 6 Dihedral angle restraints: 5929 sinusoidal: 2424 harmonic: 3505 Sorted by residual: dihedral pdb=" CB CYS A 593 " pdb=" SG CYS A 593 " pdb=" SG CYS C 85 " pdb=" CB CYS C 85 " ideal model delta sinusoidal sigma weight residual -86.00 -148.51 62.51 1 1.00e+01 1.00e-02 5.17e+01 dihedral pdb=" N GLU A 587 " pdb=" CA GLU A 587 " pdb=" CB GLU A 587 " pdb=" CG GLU A 587 " ideal model delta sinusoidal sigma weight residual -60.00 -119.20 59.20 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA ARG D 74 " pdb=" CB ARG D 74 " pdb=" CG ARG D 74 " pdb=" CD ARG D 74 " ideal model delta sinusoidal sigma weight residual -60.00 -116.13 56.13 3 1.50e+01 4.44e-03 9.38e+00 ... (remaining 5926 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1277 0.055 - 0.110: 166 0.110 - 0.165: 25 0.165 - 0.220: 0 0.220 - 0.275: 3 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 -2.96 0.28 2.00e-01 2.50e+01 1.89e+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 -2.88 0.24 2.00e-01 2.50e+01 1.46e+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 -2.71 0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 1468 not shown) Planarity restraints: 1707 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY C 39 " -0.024 5.00e-02 4.00e+02 3.68e-02 2.17e+00 pdb=" N PRO C 40 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO C 40 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 40 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG D 42 " -0.005 2.00e-02 2.50e+03 1.06e-02 1.13e+00 pdb=" C ARG D 42 " 0.018 2.00e-02 2.50e+03 pdb=" O ARG D 42 " -0.007 2.00e-02 2.50e+03 pdb=" N LEU D 43 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 922 " 0.017 5.00e-02 4.00e+02 2.54e-02 1.04e+00 pdb=" N PRO A 923 " -0.044 5.00e-02 4.00e+02 pdb=" CA PRO A 923 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 923 " 0.014 5.00e-02 4.00e+02 ... (remaining 1704 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 86 2.57 - 3.15: 7939 3.15 - 3.74: 14087 3.74 - 4.32: 19920 4.32 - 4.90: 34050 Nonbonded interactions: 76082 Sorted by model distance: nonbonded pdb=" O SER A 589 " pdb=" NH2 ARG C 90 " model vdw 1.989 3.120 nonbonded pdb="MG MG A1102 " pdb=" O1B ATP A1103 " model vdw 2.001 2.170 nonbonded pdb="MG MG A1101 " pdb=" O2A ATP A1103 " model vdw 2.006 2.170 nonbonded pdb=" OD2 ASP A 463 " pdb=" O3' ATP A1103 " model vdw 2.075 3.040 nonbonded pdb="MG MG A1101 " pdb=" O3G ATP A1103 " model vdw 2.095 2.170 ... (remaining 76077 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 group one per residue 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: 5.250 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: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 31.730 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 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 : 0.004 0.075 9738 Z= 0.224 Angle : 0.472 6.611 13195 Z= 0.242 Chirality : 0.041 0.275 1471 Planarity : 0.003 0.037 1707 Dihedral : 9.224 69.288 3662 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.70 % Allowed : 2.83 % Favored : 95.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.25), residues: 1199 helix: 1.82 (0.25), residues: 492 sheet: 0.50 (0.37), residues: 203 loop : 0.37 (0.29), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 93 HIS 0.002 0.001 HIS C 75 PHE 0.008 0.001 PHE A 842 TYR 0.010 0.001 TYR A 732 ARG 0.002 0.000 ARG C 131 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 184 time to evaluate : 1.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 MET cc_start: 0.9041 (mtp) cc_final: 0.8702 (mmm) REVERT: A 442 MET cc_start: 0.9481 (tpp) cc_final: 0.9080 (mmm) REVERT: A 510 GLN cc_start: 0.8583 (pt0) cc_final: 0.8306 (pp30) REVERT: A 650 ASN cc_start: 0.9079 (m-40) cc_final: 0.8652 (t0) REVERT: A 669 TRP cc_start: 0.9314 (t60) cc_final: 0.9039 (t60) REVERT: A 675 ASP cc_start: 0.9263 (OUTLIER) cc_final: 0.8967 (m-30) REVERT: A 676 LYS cc_start: 0.9187 (ttpp) cc_final: 0.8690 (tppt) REVERT: A 811 GLU cc_start: 0.8348 (tp30) cc_final: 0.8059 (tp30) REVERT: A 936 LYS cc_start: 0.9439 (OUTLIER) cc_final: 0.8784 (ptpp) REVERT: A 937 GLU cc_start: 0.9077 (OUTLIER) cc_final: 0.8847 (mm-30) REVERT: A 992 GLU cc_start: 0.8781 (mm-30) cc_final: 0.8505 (mm-30) REVERT: D 24 ASP cc_start: 0.7949 (m-30) cc_final: 0.7499 (t0) outliers start: 18 outliers final: 7 residues processed: 198 average time/residue: 0.2947 time to fit residues: 75.4589 Evaluate side-chains 100 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 90 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 317 ASP Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 675 ASP Chi-restraints excluded: chain A residue 919 ARG Chi-restraints excluded: chain A residue 936 LYS Chi-restraints excluded: chain A residue 937 GLU Chi-restraints excluded: chain D residue 74 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 100 optimal weight: 10.0000 chunk 90 optimal weight: 0.8980 chunk 50 optimal weight: 0.3980 chunk 30 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 48 optimal weight: 0.8980 chunk 93 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 108 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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: 0.8162 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9738 Z= 0.203 Angle : 0.606 10.014 13195 Z= 0.307 Chirality : 0.043 0.274 1471 Planarity : 0.004 0.044 1707 Dihedral : 6.101 64.960 1349 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.70 % Allowed : 8.58 % Favored : 89.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.25), residues: 1199 helix: 1.80 (0.24), residues: 501 sheet: 1.08 (0.39), residues: 193 loop : 0.46 (0.30), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 141 HIS 0.004 0.001 HIS C 32 PHE 0.017 0.001 PHE A 633 TYR 0.010 0.001 TYR C 145 ARG 0.005 0.001 ARG D 54 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 103 time to evaluate : 1.063 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 MET cc_start: 0.9147 (mtp) cc_final: 0.8912 (mmm) REVERT: A 154 ASP cc_start: 0.7435 (t0) cc_final: 0.6735 (m-30) REVERT: A 196 MET cc_start: 0.8609 (mmm) cc_final: 0.8299 (mmm) REVERT: A 286 MET cc_start: 0.6721 (tmm) cc_final: 0.6445 (tmm) REVERT: A 442 MET cc_start: 0.9502 (tpp) cc_final: 0.8940 (mmm) REVERT: A 669 TRP cc_start: 0.9359 (t60) cc_final: 0.9014 (t60) REVERT: A 675 ASP cc_start: 0.9139 (OUTLIER) cc_final: 0.8632 (t0) REVERT: A 676 LYS cc_start: 0.9127 (ttpp) cc_final: 0.8758 (tppt) REVERT: A 811 GLU cc_start: 0.8395 (tp30) cc_final: 0.8056 (tp30) REVERT: A 937 GLU cc_start: 0.9044 (OUTLIER) cc_final: 0.8786 (mm-30) REVERT: C 38 MET cc_start: 0.8408 (mpp) cc_final: 0.7304 (mpp) REVERT: C 122 GLU cc_start: 0.8564 (tm-30) cc_final: 0.8237 (tm-30) REVERT: C 130 ASP cc_start: 0.8658 (t0) cc_final: 0.8191 (t0) REVERT: D 1 MET cc_start: 0.3740 (ppp) cc_final: 0.2343 (pmm) REVERT: D 43 LEU cc_start: 0.8006 (mm) cc_final: 0.7556 (mm) REVERT: D 71 LEU cc_start: 0.7715 (mp) cc_final: 0.7179 (tp) outliers start: 18 outliers final: 11 residues processed: 116 average time/residue: 0.2543 time to fit residues: 40.4242 Evaluate side-chains 92 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 79 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 ARG Chi-restraints excluded: chain A residue 250 TYR Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 526 PHE Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 675 ASP Chi-restraints excluded: chain A residue 937 GLU Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 107 SER Chi-restraints excluded: chain D residue 48 LYS Chi-restraints excluded: chain D residue 74 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 60 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 73 optimal weight: 0.9980 chunk 29 optimal weight: 6.9990 chunk 108 optimal weight: 0.7980 chunk 116 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 86 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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: 0.8176 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9738 Z= 0.188 Angle : 0.544 8.662 13195 Z= 0.274 Chirality : 0.042 0.258 1471 Planarity : 0.004 0.044 1707 Dihedral : 5.842 61.256 1337 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.51 % Allowed : 9.99 % Favored : 88.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.25), residues: 1199 helix: 1.80 (0.24), residues: 502 sheet: 0.92 (0.37), residues: 210 loop : 0.44 (0.30), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 93 HIS 0.002 0.001 HIS D 68 PHE 0.013 0.001 PHE A 633 TYR 0.018 0.001 TYR C 134 ARG 0.012 0.000 ARG A 919 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 87 time to evaluate : 1.116 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 MET cc_start: 0.9128 (mtp) cc_final: 0.8920 (mmm) REVERT: A 154 ASP cc_start: 0.7496 (t0) cc_final: 0.6640 (m-30) REVERT: A 196 MET cc_start: 0.8647 (mmm) cc_final: 0.8272 (mmm) REVERT: A 442 MET cc_start: 0.9477 (tpp) cc_final: 0.9012 (mmm) REVERT: A 669 TRP cc_start: 0.9371 (t60) cc_final: 0.9075 (t60) REVERT: A 675 ASP cc_start: 0.9141 (OUTLIER) cc_final: 0.8870 (m-30) REVERT: A 676 LYS cc_start: 0.9122 (ttpp) cc_final: 0.8655 (tppt) REVERT: A 811 GLU cc_start: 0.8386 (tp30) cc_final: 0.8085 (tp30) REVERT: A 937 GLU cc_start: 0.9028 (OUTLIER) cc_final: 0.8792 (mp0) REVERT: A 944 MET cc_start: 0.7746 (tmm) cc_final: 0.7492 (tmm) REVERT: C 38 MET cc_start: 0.8419 (mpp) cc_final: 0.7330 (mpp) REVERT: C 122 GLU cc_start: 0.8722 (tm-30) cc_final: 0.8398 (tm-30) REVERT: D 1 MET cc_start: 0.3980 (ppp) cc_final: 0.3061 (pmm) REVERT: D 71 LEU cc_start: 0.7875 (mp) cc_final: 0.7356 (tp) outliers start: 16 outliers final: 9 residues processed: 99 average time/residue: 0.2243 time to fit residues: 31.5352 Evaluate side-chains 87 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 76 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 TYR Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 675 ASP Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 937 GLU Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 74 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 106 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 chunk 56 optimal weight: 0.0970 chunk 11 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 108 optimal weight: 0.6980 chunk 115 optimal weight: 7.9990 chunk 102 optimal weight: 7.9990 chunk 30 optimal weight: 0.9980 chunk 95 optimal weight: 3.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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: 0.8190 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9738 Z= 0.185 Angle : 0.526 10.472 13195 Z= 0.264 Chirality : 0.041 0.221 1471 Planarity : 0.003 0.045 1707 Dihedral : 5.734 59.815 1337 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.51 % Allowed : 10.27 % Favored : 88.22 % 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: 1.63 (0.25), residues: 1199 helix: 1.81 (0.24), residues: 503 sheet: 0.97 (0.37), residues: 208 loop : 0.49 (0.30), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 93 HIS 0.002 0.001 HIS A 305 PHE 0.015 0.001 PHE A 633 TYR 0.023 0.001 TYR C 134 ARG 0.008 0.000 ARG A 919 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 83 time to evaluate : 1.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 ASP cc_start: 0.7571 (t0) cc_final: 0.6757 (m-30) REVERT: A 442 MET cc_start: 0.9456 (tpp) cc_final: 0.9014 (mmm) REVERT: A 669 TRP cc_start: 0.9371 (t60) cc_final: 0.9100 (t60) REVERT: A 675 ASP cc_start: 0.9129 (OUTLIER) cc_final: 0.8833 (m-30) REVERT: A 676 LYS cc_start: 0.9142 (ttpp) cc_final: 0.8620 (tppt) REVERT: A 811 GLU cc_start: 0.8404 (tp30) cc_final: 0.8090 (tp30) REVERT: A 937 GLU cc_start: 0.9041 (OUTLIER) cc_final: 0.8751 (mp0) REVERT: A 944 MET cc_start: 0.8012 (tmm) cc_final: 0.7765 (tmm) REVERT: C 38 MET cc_start: 0.8435 (mpp) cc_final: 0.7354 (mpp) REVERT: C 122 GLU cc_start: 0.8772 (tm-30) cc_final: 0.8478 (tm-30) REVERT: D 1 MET cc_start: 0.4141 (ppp) cc_final: 0.2727 (pmm) outliers start: 16 outliers final: 10 residues processed: 94 average time/residue: 0.2486 time to fit residues: 32.7012 Evaluate side-chains 85 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 73 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 TYR Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 675 ASP Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 937 GLU Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 74 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 65 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 85 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 58 optimal weight: 0.5980 chunk 103 optimal weight: 5.9990 chunk 29 optimal weight: 0.4980 chunk 38 optimal weight: 7.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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: 0.8197 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9738 Z= 0.183 Angle : 0.524 12.206 13195 Z= 0.260 Chirality : 0.041 0.212 1471 Planarity : 0.003 0.044 1707 Dihedral : 5.690 59.203 1337 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.70 % Allowed : 10.93 % 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: 1.64 (0.25), residues: 1199 helix: 1.84 (0.24), residues: 504 sheet: 0.90 (0.38), residues: 212 loop : 0.51 (0.30), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 93 HIS 0.002 0.001 HIS A 305 PHE 0.017 0.001 PHE A 633 TYR 0.024 0.001 TYR C 134 ARG 0.005 0.000 ARG A 919 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 78 time to evaluate : 1.175 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 196 MET cc_start: 0.8516 (mmm) cc_final: 0.8221 (mmm) REVERT: A 218 MET cc_start: 0.7771 (mmm) cc_final: 0.7556 (mmt) REVERT: A 442 MET cc_start: 0.9436 (tpp) cc_final: 0.8998 (mmm) REVERT: A 668 MET cc_start: 0.8493 (tmm) cc_final: 0.8206 (tmm) REVERT: A 669 TRP cc_start: 0.9394 (t60) cc_final: 0.9095 (t60) REVERT: A 675 ASP cc_start: 0.9123 (OUTLIER) cc_final: 0.8798 (m-30) REVERT: A 676 LYS cc_start: 0.9129 (ttpp) cc_final: 0.8606 (tppt) REVERT: A 811 GLU cc_start: 0.8415 (tp30) cc_final: 0.8121 (tp30) REVERT: A 937 GLU cc_start: 0.9056 (OUTLIER) cc_final: 0.8758 (mp0) REVERT: A 944 MET cc_start: 0.7897 (tmm) cc_final: 0.7638 (tmm) REVERT: C 38 MET cc_start: 0.8454 (mpp) cc_final: 0.7377 (mpp) REVERT: C 122 GLU cc_start: 0.8757 (tm-30) cc_final: 0.8462 (tm-30) REVERT: D 1 MET cc_start: 0.4177 (ppp) cc_final: 0.3599 (pmm) REVERT: D 39 ASP cc_start: 0.7204 (p0) cc_final: 0.6800 (p0) outliers start: 18 outliers final: 9 residues processed: 90 average time/residue: 0.2354 time to fit residues: 29.9761 Evaluate side-chains 80 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 69 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 TYR Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 675 ASP Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 937 GLU Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 74 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 103 optimal weight: 5.9990 chunk 22 optimal weight: 0.5980 chunk 67 optimal weight: 0.1980 chunk 28 optimal weight: 3.9990 chunk 115 optimal weight: 0.0010 chunk 95 optimal weight: 8.9990 chunk 53 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 38 optimal weight: 6.9990 chunk 60 optimal weight: 0.9990 chunk 111 optimal weight: 0.9980 overall best weight: 0.5586 ------------------------------------------------------------------------------- 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: 0.8185 moved from start: 0.2799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9738 Z= 0.147 Angle : 0.507 12.303 13195 Z= 0.252 Chirality : 0.041 0.205 1471 Planarity : 0.003 0.041 1707 Dihedral : 5.551 58.818 1337 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.23 % Allowed : 11.50 % 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: 1.70 (0.25), residues: 1199 helix: 1.89 (0.24), residues: 505 sheet: 0.93 (0.38), residues: 212 loop : 0.53 (0.30), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 93 HIS 0.001 0.000 HIS A 305 PHE 0.018 0.001 PHE A 633 TYR 0.023 0.001 TYR C 134 ARG 0.005 0.000 ARG A 919 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 76 time to evaluate : 1.185 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 80 GLN cc_start: 0.8720 (OUTLIER) cc_final: 0.7964 (tm-30) REVERT: A 196 MET cc_start: 0.8558 (mmm) cc_final: 0.8267 (mmm) REVERT: A 218 MET cc_start: 0.7608 (mmm) cc_final: 0.7374 (mmt) REVERT: A 442 MET cc_start: 0.9412 (tpp) cc_final: 0.8992 (mmm) REVERT: A 668 MET cc_start: 0.8481 (tmm) cc_final: 0.8193 (tmm) REVERT: A 669 TRP cc_start: 0.9389 (t60) cc_final: 0.9092 (t60) REVERT: A 811 GLU cc_start: 0.8455 (tp30) cc_final: 0.8145 (tp30) REVERT: A 937 GLU cc_start: 0.9044 (OUTLIER) cc_final: 0.8735 (mp0) REVERT: A 944 MET cc_start: 0.7817 (tmm) cc_final: 0.7445 (tmm) REVERT: C 38 MET cc_start: 0.8464 (mpp) cc_final: 0.7458 (mpp) REVERT: C 122 GLU cc_start: 0.8773 (tm-30) cc_final: 0.8486 (tm-30) outliers start: 13 outliers final: 10 residues processed: 85 average time/residue: 0.2582 time to fit residues: 31.0654 Evaluate side-chains 82 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 70 time to evaluate : 1.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 250 TYR Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 526 PHE Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 937 GLU Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 74 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 12 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 96 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 114 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 69 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 70 optimal weight: 0.9980 chunk 45 optimal weight: 0.0870 overall best weight: 0.7558 ------------------------------------------------------------------------------- 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: 0.8192 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9738 Z= 0.163 Angle : 0.502 11.718 13195 Z= 0.251 Chirality : 0.041 0.200 1471 Planarity : 0.003 0.047 1707 Dihedral : 5.348 59.120 1335 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.32 % Allowed : 11.78 % 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: 1.74 (0.25), residues: 1199 helix: 1.94 (0.24), residues: 504 sheet: 0.95 (0.38), residues: 212 loop : 0.54 (0.30), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 93 HIS 0.002 0.000 HIS A 305 PHE 0.019 0.001 PHE A 633 TYR 0.027 0.001 TYR C 134 ARG 0.004 0.000 ARG A 919 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 73 time to evaluate : 1.172 Fit side-chains revert: symmetry clash REVERT: A 80 GLN cc_start: 0.8724 (OUTLIER) cc_final: 0.8082 (tm-30) REVERT: A 218 MET cc_start: 0.7519 (mmm) cc_final: 0.7260 (mmt) REVERT: A 442 MET cc_start: 0.9406 (tpp) cc_final: 0.8981 (mmm) REVERT: A 668 MET cc_start: 0.8563 (tmm) cc_final: 0.8270 (tmm) REVERT: A 669 TRP cc_start: 0.9392 (t60) cc_final: 0.9088 (t60) REVERT: A 811 GLU cc_start: 0.8464 (tp30) cc_final: 0.8166 (tp30) REVERT: A 937 GLU cc_start: 0.9062 (OUTLIER) cc_final: 0.8833 (mp0) REVERT: A 944 MET cc_start: 0.7858 (tmm) cc_final: 0.7542 (tmm) REVERT: C 38 MET cc_start: 0.8495 (mpp) cc_final: 0.7578 (mpp) REVERT: C 122 GLU cc_start: 0.8800 (tm-30) cc_final: 0.8495 (tm-30) REVERT: D 1 MET cc_start: 0.4038 (pmm) cc_final: 0.2314 (ppp) outliers start: 14 outliers final: 10 residues processed: 84 average time/residue: 0.2340 time to fit residues: 28.0908 Evaluate side-chains 81 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 69 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 250 TYR Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 937 GLU Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 74 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 68 optimal weight: 0.3980 chunk 34 optimal weight: 0.6980 chunk 22 optimal weight: 9.9990 chunk 72 optimal weight: 0.6980 chunk 78 optimal weight: 5.9990 chunk 56 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 104 optimal weight: 0.8980 chunk 109 optimal weight: 0.8980 chunk 100 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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: 0.8191 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9738 Z= 0.162 Angle : 0.521 11.978 13195 Z= 0.258 Chirality : 0.041 0.194 1471 Planarity : 0.003 0.046 1707 Dihedral : 5.310 58.961 1335 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.41 % Allowed : 12.16 % Favored : 86.43 % 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: 1.73 (0.25), residues: 1199 helix: 1.93 (0.24), residues: 505 sheet: 0.98 (0.38), residues: 212 loop : 0.51 (0.30), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 93 HIS 0.002 0.000 HIS A 305 PHE 0.019 0.001 PHE A 633 TYR 0.027 0.001 TYR C 134 ARG 0.008 0.000 ARG D 54 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 72 time to evaluate : 1.087 Fit side-chains revert: symmetry clash REVERT: A 80 GLN cc_start: 0.8730 (OUTLIER) cc_final: 0.8083 (tm-30) REVERT: A 218 MET cc_start: 0.7521 (mmm) cc_final: 0.7295 (mmt) REVERT: A 285 MET cc_start: 0.7482 (mpp) cc_final: 0.7152 (mpp) REVERT: A 442 MET cc_start: 0.9402 (tpp) cc_final: 0.8996 (mmm) REVERT: A 510 GLN cc_start: 0.8476 (pt0) cc_final: 0.8128 (pp30) REVERT: A 668 MET cc_start: 0.8584 (tmm) cc_final: 0.8290 (tmm) REVERT: A 669 TRP cc_start: 0.9390 (t60) cc_final: 0.9094 (t60) REVERT: A 811 GLU cc_start: 0.8464 (tp30) cc_final: 0.8173 (tp30) REVERT: A 937 GLU cc_start: 0.9057 (OUTLIER) cc_final: 0.8818 (mp0) REVERT: C 38 MET cc_start: 0.8509 (mpp) cc_final: 0.7592 (mpp) REVERT: C 122 GLU cc_start: 0.8809 (tm-30) cc_final: 0.8500 (tm-30) REVERT: C 135 GLU cc_start: 0.8960 (mm-30) cc_final: 0.8697 (mm-30) REVERT: D 1 MET cc_start: 0.4133 (pmm) cc_final: 0.2290 (ppp) outliers start: 15 outliers final: 12 residues processed: 84 average time/residue: 0.2255 time to fit residues: 27.2281 Evaluate side-chains 83 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 69 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 250 TYR Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 526 PHE Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 937 GLU Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 74 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 106 optimal weight: 0.9980 chunk 109 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 chunk 83 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 113 optimal weight: 6.9990 chunk 68 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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: 0.8195 moved from start: 0.3011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9738 Z= 0.177 Angle : 0.535 11.111 13195 Z= 0.262 Chirality : 0.041 0.194 1471 Planarity : 0.004 0.045 1707 Dihedral : 5.285 58.723 1335 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.41 % Allowed : 12.44 % Favored : 86.15 % 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: 1.76 (0.25), residues: 1199 helix: 1.95 (0.24), residues: 504 sheet: 0.98 (0.38), residues: 212 loop : 0.54 (0.30), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 93 HIS 0.002 0.001 HIS A 305 PHE 0.019 0.001 PHE A 633 TYR 0.028 0.001 TYR C 134 ARG 0.007 0.000 ARG D 54 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 72 time to evaluate : 1.126 Fit side-chains revert: symmetry clash REVERT: A 80 GLN cc_start: 0.8734 (OUTLIER) cc_final: 0.8082 (tm-30) REVERT: A 218 MET cc_start: 0.7478 (mmm) cc_final: 0.7258 (mmt) REVERT: A 285 MET cc_start: 0.7443 (mpp) cc_final: 0.7110 (mpp) REVERT: A 442 MET cc_start: 0.9399 (tpp) cc_final: 0.8978 (mmm) REVERT: A 510 GLN cc_start: 0.8516 (pt0) cc_final: 0.8162 (pp30) REVERT: A 668 MET cc_start: 0.8594 (tmm) cc_final: 0.8297 (tmm) REVERT: A 669 TRP cc_start: 0.9393 (t60) cc_final: 0.9094 (t60) REVERT: A 811 GLU cc_start: 0.8508 (tp30) cc_final: 0.8229 (tp30) REVERT: A 937 GLU cc_start: 0.9062 (OUTLIER) cc_final: 0.8818 (mp0) REVERT: C 38 MET cc_start: 0.8522 (mpp) cc_final: 0.7609 (mpp) REVERT: C 122 GLU cc_start: 0.8807 (tm-30) cc_final: 0.8500 (tm-30) REVERT: C 135 GLU cc_start: 0.8977 (mm-30) cc_final: 0.8566 (mm-30) REVERT: D 1 MET cc_start: 0.4056 (pmm) cc_final: 0.2415 (ppp) REVERT: D 52 ASP cc_start: 0.7354 (t70) cc_final: 0.7152 (t70) outliers start: 15 outliers final: 12 residues processed: 83 average time/residue: 0.2295 time to fit residues: 27.3808 Evaluate side-chains 85 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 71 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 250 TYR Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 937 GLU Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 74 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 53 optimal weight: 0.9980 chunk 78 optimal weight: 0.0970 chunk 118 optimal weight: 5.9990 chunk 109 optimal weight: 0.9980 chunk 94 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 72 optimal weight: 0.0570 chunk 57 optimal weight: 0.2980 chunk 74 optimal weight: 0.1980 chunk 100 optimal weight: 8.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.3296 ------------------------------------------------------------------------------- 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: 0.8173 moved from start: 0.3091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9738 Z= 0.138 Angle : 0.530 11.103 13195 Z= 0.259 Chirality : 0.041 0.189 1471 Planarity : 0.003 0.044 1707 Dihedral : 5.206 59.391 1335 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.13 % Allowed : 12.63 % Favored : 86.24 % 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: 1.76 (0.25), residues: 1199 helix: 1.97 (0.24), residues: 502 sheet: 1.00 (0.38), residues: 212 loop : 0.50 (0.30), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 608 HIS 0.002 0.000 HIS A 721 PHE 0.017 0.001 PHE A 633 TYR 0.029 0.001 TYR C 134 ARG 0.008 0.000 ARG D 54 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 72 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 80 GLN cc_start: 0.8668 (OUTLIER) cc_final: 0.8023 (tm-30) REVERT: A 218 MET cc_start: 0.7506 (mmm) cc_final: 0.7301 (mmt) REVERT: A 285 MET cc_start: 0.7420 (mpp) cc_final: 0.7069 (mpp) REVERT: A 442 MET cc_start: 0.9380 (tpp) cc_final: 0.9008 (mmm) REVERT: A 510 GLN cc_start: 0.8438 (pt0) cc_final: 0.8049 (pp30) REVERT: A 669 TRP cc_start: 0.9368 (t60) cc_final: 0.9148 (t60) REVERT: A 811 GLU cc_start: 0.8459 (tp30) cc_final: 0.8175 (tp30) REVERT: A 937 GLU cc_start: 0.9073 (OUTLIER) cc_final: 0.8819 (mp0) REVERT: C 38 MET cc_start: 0.8485 (mpp) cc_final: 0.7575 (mpp) REVERT: C 122 GLU cc_start: 0.8828 (tm-30) cc_final: 0.8605 (tm-30) REVERT: C 135 GLU cc_start: 0.8977 (mm-30) cc_final: 0.8561 (mm-30) outliers start: 12 outliers final: 8 residues processed: 81 average time/residue: 0.2162 time to fit residues: 25.2144 Evaluate side-chains 80 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 70 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 526 PHE Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 937 GLU Chi-restraints excluded: chain D residue 74 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 87 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 17 optimal weight: 10.0000 chunk 83 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 68 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3469 r_free = 0.3469 target = 0.070593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.052958 restraints weight = 37666.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.054882 restraints weight = 19628.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.056151 restraints weight = 12891.133| |-----------------------------------------------------------------------------| r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9738 Z= 0.183 Angle : 0.544 10.610 13195 Z= 0.267 Chirality : 0.041 0.183 1471 Planarity : 0.004 0.049 1707 Dihedral : 5.188 58.959 1335 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.94 % Allowed : 12.91 % Favored : 86.15 % 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 (0.25), residues: 1199 helix: 2.00 (0.24), residues: 502 sheet: 0.99 (0.38), residues: 212 loop : 0.56 (0.30), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 93 HIS 0.002 0.001 HIS A 458 PHE 0.016 0.001 PHE A 633 TYR 0.026 0.001 TYR C 134 ARG 0.005 0.000 ARG D 54 Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 1932.82 seconds wall clock time: 35 minutes 8.55 seconds (2108.55 seconds total)