Starting phenix.real_space_refine on Fri Mar 14 04:44:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b5g_44211/03_2025/9b5g_44211.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b5g_44211/03_2025/9b5g_44211.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b5g_44211/03_2025/9b5g_44211.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b5g_44211/03_2025/9b5g_44211.map" model { file = "/net/cci-nas-00/data/ceres_data/9b5g_44211/03_2025/9b5g_44211.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b5g_44211/03_2025/9b5g_44211.cif" } resolution = 2.67 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= 0.075 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 3 5.49 5 Mg 2 5.21 5 S 42 5.16 5 C 6078 2.51 5 N 1575 2.21 5 O 1836 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 6.83, per 1000 atoms: 0.72 Number of scatterers: 9536 At special positions: 0 Unit cell: (86.184, 98.952, 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 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=2.91 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.20 Conformation dependent library (CDL) restraints added in 1.1 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: 51 helices and 10 sheets defined 46.8% alpha, 15.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.27 Creating SS restraints... Processing helix chain 'A' and resid 20 through 25 removed outlier: 3.732A 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 74 through 79 removed outlier: 3.677A pdb=" N SER A 79 " --> pdb=" O ASP A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 88 removed outlier: 4.034A pdb=" N ILE A 88 " --> pdb=" O GLU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 101 removed outlier: 4.351A pdb=" N SER A 98 " --> pdb=" O LYS A 94 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N LYS A 99 " --> pdb=" O VAL A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 123 removed outlier: 3.518A pdb=" N LYS A 121 " --> pdb=" O GLU A 118 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN A 122 " --> pdb=" O TYR A 119 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE A 123 " --> pdb=" O LEU A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 146 removed outlier: 3.663A pdb=" N PHE A 142 " --> pdb=" O GLU A 138 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LYS A 145 " --> pdb=" O ASP A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 223 Processing helix chain 'A' and resid 267 through 274 removed outlier: 4.269A pdb=" N LYS A 273 " --> pdb=" O ARG A 269 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASP A 274 " --> pdb=" O GLU A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 305 removed outlier: 3.617A pdb=" N ILE A 293 " --> pdb=" O PRO A 289 " (cutoff:3.500A) removed outlier: 3.614A 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: 4.433A pdb=" N VAL A 416 " --> pdb=" O GLY A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 427 removed outlier: 3.512A 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: 3.697A pdb=" N ASN A 473 " --> pdb=" O SER A 470 " (cutoff:3.500A) removed outlier: 3.521A 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: 3.863A pdb=" N LYS A 528 " --> pdb=" O GLU A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 553 removed outlier: 3.562A pdb=" N ARG A 542 " --> pdb=" O ASN A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 582 removed outlier: 3.885A pdb=" N SER A 582 " --> pdb=" O TYR A 579 " (cutoff:3.500A) 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: 3.542A pdb=" N THR A 636 " --> pdb=" O ASN A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 643 through 656 removed outlier: 3.558A pdb=" N VAL A 647 " --> pdb=" O ASN A 643 " (cutoff:3.500A) 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: 3.880A pdb=" N TYR A 747 " --> pdb=" O ASP A 743 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLY A 753 " --> pdb=" O ARG A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 through 794 Processing helix chain 'A' and resid 796 through 800 Processing helix chain 'A' and resid 818 through 835 Processing helix chain 'A' and resid 840 through 849 Processing helix chain 'A' and resid 855 through 876 removed outlier: 3.661A pdb=" N THR A 859 " --> pdb=" O MET A 855 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL A 871 " --> pdb=" O CYS A 867 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LYS A 872 " --> pdb=" O LEU A 868 " (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 '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: 6.728A pdb=" N VAL A 64 " --> pdb=" O SER A 110 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ASN A 39 " --> pdb=" O CYS A 125 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N VAL A 127 " --> pdb=" O ASN A 39 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N LEU A 41 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N VAL A 126 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N ALA A 153 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N VAL A 128 " --> pdb=" O ALA A 153 " (cutoff:3.500A) removed outlier: 8.281A pdb=" N SER A 155 " --> pdb=" O VAL A 128 " (cutoff:3.500A) removed outlier: 4.293A 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: 4.151A pdb=" N PHE A 209 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N THR A 195 " --> pdb=" O ALA A 186 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ILE A 188 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 6.275A 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: 4.151A 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: 6.567A pdb=" N ILE A 459 " --> pdb=" O THR A 507 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N TYR A 509 " --> pdb=" O ILE A 459 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N VAL A 461 " --> pdb=" O TYR A 509 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU A 531 " --> pdb=" O SER A 429 " (cutoff:3.500A) removed outlier: 4.215A 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: 6.377A pdb=" N TYR A 920 " --> pdb=" O CYS A1009 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N LYS A1011 " --> pdb=" O TYR A 920 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N LEU A 922 " --> pdb=" O LYS A1011 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N VAL A 990 " --> pdb=" O SER A 947 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N SER A 947 " --> pdb=" O VAL A 990 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N GLU A 992 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LEU A 945 " --> pdb=" O GLU A 992 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N CYS A 994 " --> pdb=" O THR A 943 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N SER A 947 " --> pdb=" O LEU A 951 " (cutoff:3.500A) removed outlier: 5.387A 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: 6.377A pdb=" N TYR A 920 " --> pdb=" O CYS A1009 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N LYS A1011 " --> pdb=" O TYR A 920 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N LEU A 922 " --> pdb=" O LYS A1011 " (cutoff:3.500A) removed outlier: 4.448A 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: 8.900A pdb=" N LEU B 67 " --> pdb=" O GLN B 2 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N PHE B 4 " --> pdb=" O LEU B 67 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N LEU B 69 " --> pdb=" O PHE B 4 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LYS B 6 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ARG B 42 " --> pdb=" O VAL B 70 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 24 through 26 removed outlier: 6.187A pdb=" N HIS C 32 " --> pdb=" O VAL C 26 " (cutoff:3.500A) 460 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: 3.74 Time building geometry restraints manager: 2.67 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: 5640 1.54 - 1.67: 131 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 1.28e+01 bond pdb=" N MET B 1 " pdb=" CA MET B 1 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.71e+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 1.06e+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 9.40e-01 bond pdb=" C SER C 94 " pdb=" N PRO C 95 " ideal model delta sigma weight residual 1.334 1.354 -0.020 2.34e-02 1.83e+03 7.48e-01 ... (remaining 9741 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.37: 13021 1.37 - 2.74: 104 2.74 - 4.11: 70 4.11 - 5.48: 5 5.48 - 6.85: 4 Bond angle restraints: 13204 Sorted by residual: angle pdb=" C LYS A 381 " pdb=" N GLN A 382 " pdb=" CA GLN A 382 " ideal model delta sigma weight residual 121.70 128.55 -6.85 1.80e+00 3.09e-01 1.45e+01 angle pdb=" C2' ATP A1103 " pdb=" C1' ATP A1103 " pdb=" O4' ATP A1103 " ideal model delta sigma weight residual 106.53 103.29 3.24 1.18e+00 7.24e-01 7.58e+00 angle pdb=" C3' ATP A1103 " pdb=" C4' ATP A1103 " pdb=" C5' ATP A1103 " ideal model delta sigma weight residual 115.19 110.58 4.61 1.76e+00 3.23e-01 6.86e+00 angle pdb=" C2' ATP A1103 " pdb=" C3' ATP A1103 " pdb=" O3' ATP A1103 " ideal model delta sigma weight residual 111.83 105.07 6.76 2.67e+00 1.40e-01 6.42e+00 angle pdb=" C1' ATP A1103 " pdb=" C2' ATP A1103 " pdb=" O2' ATP A1103 " ideal model delta sigma weight residual 110.58 104.12 6.46 2.79e+00 1.28e-01 5.34e+00 ... (remaining 13199 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.46: 5673 17.46 - 34.93: 204 34.93 - 52.39: 43 52.39 - 69.85: 6 69.85 - 87.32: 5 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 -139.70 53.70 1 1.00e+01 1.00e-02 3.92e+01 dihedral pdb=" CA LYS A 884 " pdb=" C LYS A 884 " pdb=" N ASN A 885 " pdb=" CA ASN A 885 " ideal model delta harmonic sigma weight residual 180.00 164.25 15.75 0 5.00e+00 4.00e-02 9.92e+00 dihedral pdb=" N GLN A 80 " pdb=" CA GLN A 80 " pdb=" CB GLN A 80 " pdb=" CG GLN A 80 " ideal model delta sinusoidal sigma weight residual -180.00 -120.49 -59.51 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 5928 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1291 0.058 - 0.116: 155 0.116 - 0.174: 22 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 -2.92 0.28 2.00e-01 2.50e+01 1.99e+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 -2.73 0.23 2.00e-01 2.50e+01 1.33e+00 ... (remaining 1468 not shown) Planarity restraints: 1709 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER C 94 " 0.022 5.00e-02 4.00e+02 3.31e-02 1.75e+00 pdb=" N PRO C 95 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO C 95 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 95 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS C 75 " -0.018 5.00e-02 4.00e+02 2.73e-02 1.19e+00 pdb=" N PRO C 76 " 0.047 5.00e-02 4.00e+02 pdb=" CA PRO C 76 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO C 76 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 120 " -0.017 5.00e-02 4.00e+02 2.61e-02 1.09e+00 pdb=" N PRO C 121 " 0.045 5.00e-02 4.00e+02 pdb=" CA PRO C 121 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO C 121 " -0.015 5.00e-02 4.00e+02 ... (remaining 1706 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 56 2.61 - 3.18: 8150 3.18 - 3.75: 14006 3.75 - 4.33: 21197 4.33 - 4.90: 35260 Nonbonded interactions: 78669 Sorted by model distance: nonbonded pdb="MG MG A1101 " pdb=" O2B ATP A1103 " model vdw 2.032 2.170 nonbonded pdb=" OD2 ASP A1002 " pdb=" NH1 ARG C 8 " model vdw 2.142 3.120 nonbonded pdb=" OD2 ASP A 537 " pdb="MG MG A1101 " model vdw 2.142 2.170 nonbonded pdb=" OD2 ASP A 465 " pdb="MG MG A1102 " model vdw 2.167 2.170 nonbonded pdb=" O PRO C 18 " pdb=" OG SER C 19 " model vdw 2.184 3.040 ... (remaining 78664 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: 3.220 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: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 26.350 Find NCS groups from input model: 0.090 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:13.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 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= 0.214 Angle : 0.467 6.846 13204 Z= 0.239 Chirality : 0.042 0.290 1471 Planarity : 0.004 0.033 1709 Dihedral : 10.029 87.315 3664 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 1.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.94 % Allowed : 2.07 % Favored : 96.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.24), residues: 1200 helix: 1.77 (0.25), residues: 488 sheet: 0.93 (0.36), residues: 177 loop : 0.36 (0.27), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 608 HIS 0.002 0.001 HIS C 75 PHE 0.011 0.001 PHE A 360 TYR 0.008 0.001 TYR A 736 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 155 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 145 time to evaluate : 0.861 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 ARG cc_start: 0.7368 (mmt-90) cc_final: 0.7123 (mmt180) REVERT: A 196 MET cc_start: 0.8690 (mmp) cc_final: 0.8395 (mmm) REVERT: A 235 TYR cc_start: 0.8427 (m-80) cc_final: 0.8132 (m-80) REVERT: A 583 GLN cc_start: 0.8018 (mt0) cc_final: 0.7283 (mm-40) REVERT: A 909 ASN cc_start: 0.7733 (t0) cc_final: 0.7288 (t0) REVERT: A 919 ARG cc_start: 0.8546 (OUTLIER) cc_final: 0.8338 (pmm-80) REVERT: A 936 LYS cc_start: 0.7933 (ttpp) cc_final: 0.7686 (ttpp) REVERT: A 937 GLU cc_start: 0.7569 (tp30) cc_final: 0.7286 (tp30) REVERT: C 91 ASP cc_start: 0.7471 (p0) cc_final: 0.7109 (p0) outliers start: 10 outliers final: 4 residues processed: 154 average time/residue: 1.3985 time to fit residues: 229.4592 Evaluate side-chains 124 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 119 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 919 ARG 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: 1.9990 chunk 90 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 56 optimal weight: 0.0470 chunk 69 optimal weight: 0.0870 chunk 108 optimal weight: 0.8980 overall best weight: 0.6058 ------------------------------------------------------------------------------- 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 = 0.3425 r_free = 0.3425 target = 0.122450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.085815 restraints weight = 10876.337| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 1.86 r_work: 0.2708 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2562 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.0883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9746 Z= 0.223 Angle : 0.490 5.709 13204 Z= 0.257 Chirality : 0.043 0.150 1471 Planarity : 0.004 0.038 1709 Dihedral : 6.188 84.338 1335 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.89 % Allowed : 7.07 % Favored : 91.05 % 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 (0.25), residues: 1200 helix: 1.67 (0.24), residues: 498 sheet: 1.10 (0.37), residues: 178 loop : 0.35 (0.28), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 608 HIS 0.002 0.001 HIS A 818 PHE 0.011 0.001 PHE A 360 TYR 0.011 0.001 TYR A 736 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 145 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 125 time to evaluate : 0.993 Fit side-chains revert: symmetry clash REVERT: A 33 LYS cc_start: 0.8271 (ttmm) cc_final: 0.8041 (ttmm) REVERT: A 179 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7850 (mp0) REVERT: A 196 MET cc_start: 0.9018 (mmp) cc_final: 0.8758 (mmm) REVERT: A 235 TYR cc_start: 0.8856 (m-80) cc_final: 0.8623 (m-80) REVERT: A 337 GLU cc_start: 0.7306 (OUTLIER) cc_final: 0.7105 (tt0) REVERT: A 583 GLN cc_start: 0.8583 (mt0) cc_final: 0.8045 (mm-40) REVERT: A 919 ARG cc_start: 0.9027 (OUTLIER) cc_final: 0.8818 (pmm-80) REVERT: C 91 ASP cc_start: 0.7601 (p0) cc_final: 0.7183 (p0) outliers start: 20 outliers final: 10 residues processed: 137 average time/residue: 1.3188 time to fit residues: 193.0775 Evaluate side-chains 134 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 121 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 179 GLU Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 337 GLU Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 919 ARG 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 39 ASP Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 110 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 5 optimal weight: 0.6980 chunk 92 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 80 optimal weight: 0.2980 chunk 51 optimal weight: 0.7980 chunk 118 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 72 optimal weight: 0.2980 chunk 93 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3426 r_free = 0.3426 target = 0.122553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.085789 restraints weight = 11013.177| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 1.87 r_work: 0.2716 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2566 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.1008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9746 Z= 0.224 Angle : 0.484 5.729 13204 Z= 0.252 Chirality : 0.042 0.149 1471 Planarity : 0.004 0.043 1709 Dihedral : 6.167 82.530 1334 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.98 % Allowed : 8.01 % Favored : 90.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.25), residues: 1200 helix: 1.66 (0.24), residues: 499 sheet: 1.13 (0.37), residues: 178 loop : 0.32 (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 125 PHE 0.010 0.001 PHE A 360 TYR 0.010 0.001 TYR C 145 ARG 0.008 0.000 ARG C 5 *********************** 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 146 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 125 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 LYS cc_start: 0.8263 (ttmm) cc_final: 0.8015 (ttmm) REVERT: A 85 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.8119 (mp0) REVERT: A 179 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7863 (mp0) REVERT: A 196 MET cc_start: 0.9020 (mmp) cc_final: 0.8756 (mmm) REVERT: A 235 TYR cc_start: 0.8843 (m-80) cc_final: 0.8612 (m-80) REVERT: A 337 GLU cc_start: 0.7236 (OUTLIER) cc_final: 0.7032 (tt0) REVERT: A 583 GLN cc_start: 0.8574 (mt0) cc_final: 0.7968 (mm-40) REVERT: A 869 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.8001 (mp0) REVERT: C 62 PHE cc_start: 0.7175 (m-80) cc_final: 0.6921 (m-80) REVERT: C 91 ASP cc_start: 0.7653 (p0) cc_final: 0.7304 (p0) outliers start: 21 outliers final: 13 residues processed: 136 average time/residue: 1.3696 time to fit residues: 199.4317 Evaluate side-chains 136 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 119 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 179 GLU Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 337 GLU Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain C residue 42 ASP Chi-restraints excluded: chain C residue 85 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 25 optimal weight: 0.6980 chunk 37 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 113 optimal weight: 0.0770 chunk 32 optimal weight: 0.0970 chunk 54 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 118 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 overall best weight: 0.4936 ------------------------------------------------------------------------------- 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 = 0.3432 r_free = 0.3432 target = 0.123073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.086415 restraints weight = 10816.949| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 1.86 r_work: 0.2724 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2576 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.1120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 9746 Z= 0.195 Angle : 0.469 6.036 13204 Z= 0.243 Chirality : 0.042 0.146 1471 Planarity : 0.004 0.045 1709 Dihedral : 5.846 72.624 1330 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.89 % Allowed : 8.86 % Favored : 89.26 % 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 (0.25), residues: 1200 helix: 1.70 (0.24), residues: 499 sheet: 1.18 (0.37), residues: 178 loop : 0.33 (0.28), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 608 HIS 0.001 0.000 HIS A 818 PHE 0.011 0.001 PHE A 360 TYR 0.009 0.001 TYR A 736 ARG 0.006 0.000 ARG C 5 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 120 time to evaluate : 1.132 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 LYS cc_start: 0.8266 (ttmm) cc_final: 0.8016 (ttmm) REVERT: A 85 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.8118 (mp0) REVERT: A 179 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7854 (mp0) REVERT: A 235 TYR cc_start: 0.8844 (m-80) cc_final: 0.8610 (m-80) REVERT: A 337 GLU cc_start: 0.7231 (OUTLIER) cc_final: 0.7028 (tt0) REVERT: A 583 GLN cc_start: 0.8587 (mt0) cc_final: 0.7990 (mm-40) REVERT: A 835 ASP cc_start: 0.8303 (m-30) cc_final: 0.8057 (t70) REVERT: A 869 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.8145 (mm-30) REVERT: B 31 GLN cc_start: 0.8279 (OUTLIER) cc_final: 0.7778 (tt0) REVERT: C 91 ASP cc_start: 0.7666 (p0) cc_final: 0.7320 (p0) outliers start: 20 outliers final: 12 residues processed: 131 average time/residue: 1.3075 time to fit residues: 183.7755 Evaluate side-chains 140 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 123 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 179 GLU Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 337 GLU Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 31 GLN Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 110 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 86 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 32 optimal weight: 0.2980 chunk 26 optimal weight: 0.8980 chunk 92 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 96 optimal weight: 0.6980 chunk 81 optimal weight: 0.9990 chunk 27 optimal weight: 0.4980 chunk 61 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3427 r_free = 0.3427 target = 0.122618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.085965 restraints weight = 10886.341| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 1.86 r_work: 0.2718 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2569 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.1188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9746 Z= 0.221 Angle : 0.473 5.770 13204 Z= 0.246 Chirality : 0.042 0.167 1471 Planarity : 0.004 0.046 1709 Dihedral : 5.867 72.169 1330 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.98 % Allowed : 9.43 % Favored : 88.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.25), residues: 1200 helix: 1.67 (0.24), residues: 499 sheet: 1.10 (0.37), residues: 180 loop : 0.36 (0.28), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 608 HIS 0.002 0.001 HIS C 125 PHE 0.010 0.001 PHE A 360 TYR 0.009 0.001 TYR A 736 ARG 0.006 0.000 ARG C 5 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 121 time to evaluate : 1.245 Fit side-chains revert: symmetry clash REVERT: A 33 LYS cc_start: 0.8270 (ttmm) cc_final: 0.8028 (ttmm) REVERT: A 85 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.8092 (mp0) REVERT: A 179 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7831 (mp0) REVERT: A 235 TYR cc_start: 0.8855 (m-80) cc_final: 0.8628 (m-80) REVERT: A 337 GLU cc_start: 0.7245 (OUTLIER) cc_final: 0.7042 (tt0) REVERT: A 583 GLN cc_start: 0.8518 (mt0) cc_final: 0.7950 (mm110) REVERT: A 835 ASP cc_start: 0.8296 (m-30) cc_final: 0.8058 (t70) REVERT: A 869 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.8151 (mm-30) REVERT: A 937 GLU cc_start: 0.8086 (tp30) cc_final: 0.7688 (mp0) REVERT: B 31 GLN cc_start: 0.8319 (OUTLIER) cc_final: 0.7807 (tt0) REVERT: C 91 ASP cc_start: 0.7602 (p0) cc_final: 0.7234 (p0) outliers start: 21 outliers final: 12 residues processed: 131 average time/residue: 1.6737 time to fit residues: 234.8432 Evaluate side-chains 135 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 118 time to evaluate : 1.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 179 GLU Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 337 GLU Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 31 GLN Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain C residue 85 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 77 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 108 optimal weight: 0.9980 chunk 78 optimal weight: 0.7980 chunk 63 optimal weight: 0.9980 chunk 73 optimal weight: 0.8980 chunk 106 optimal weight: 1.9990 chunk 112 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 86 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3419 r_free = 0.3419 target = 0.121994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.085183 restraints weight = 10961.162| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 1.88 r_work: 0.2700 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2550 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.1204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9746 Z= 0.272 Angle : 0.497 6.158 13204 Z= 0.258 Chirality : 0.043 0.162 1471 Planarity : 0.004 0.046 1709 Dihedral : 5.947 72.356 1330 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.26 % Allowed : 9.52 % 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: 1.39 (0.24), residues: 1200 helix: 1.58 (0.24), residues: 498 sheet: 1.10 (0.37), residues: 180 loop : 0.32 (0.28), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 608 HIS 0.002 0.001 HIS A 818 PHE 0.011 0.001 PHE A 551 TYR 0.009 0.001 TYR A 736 ARG 0.007 0.001 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 146 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 122 time to evaluate : 1.018 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 LYS cc_start: 0.8286 (ttmm) cc_final: 0.8044 (ttmm) REVERT: A 85 GLU cc_start: 0.8495 (OUTLIER) cc_final: 0.8147 (mp0) REVERT: A 179 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7819 (mp0) REVERT: A 235 TYR cc_start: 0.8849 (m-80) cc_final: 0.8612 (m-80) REVERT: A 337 GLU cc_start: 0.7246 (OUTLIER) cc_final: 0.7024 (tt0) REVERT: A 583 GLN cc_start: 0.8574 (mt0) cc_final: 0.8003 (mm110) REVERT: A 835 ASP cc_start: 0.8318 (m-30) cc_final: 0.8081 (t70) REVERT: A 869 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.8166 (mm-30) REVERT: B 31 GLN cc_start: 0.8305 (OUTLIER) cc_final: 0.7797 (tt0) REVERT: C 91 ASP cc_start: 0.7613 (p0) cc_final: 0.7221 (p0) outliers start: 24 outliers final: 15 residues processed: 136 average time/residue: 1.3172 time to fit residues: 191.8014 Evaluate side-chains 146 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 126 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 34 GLN Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 179 GLU Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 337 GLU Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 713 SER Chi-restraints excluded: chain A residue 869 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 31 GLN Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 144 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 64 optimal weight: 0.2980 chunk 49 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 chunk 53 optimal weight: 0.6980 chunk 21 optimal weight: 0.0270 chunk 81 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 chunk 37 optimal weight: 0.9980 overall best weight: 0.4838 ------------------------------------------------------------------------------- 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 = 0.3432 r_free = 0.3432 target = 0.123069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.086279 restraints weight = 10978.009| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 1.88 r_work: 0.2721 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2571 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.1270 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= 0.185 Angle : 0.466 5.429 13204 Z= 0.243 Chirality : 0.042 0.144 1471 Planarity : 0.004 0.046 1709 Dihedral : 5.886 72.977 1330 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.64 % Allowed : 9.33 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.25), residues: 1200 helix: 1.65 (0.24), residues: 499 sheet: 1.14 (0.37), residues: 180 loop : 0.37 (0.28), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 608 HIS 0.002 0.001 HIS C 125 PHE 0.011 0.001 PHE A 360 TYR 0.009 0.001 TYR A 736 ARG 0.007 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 155 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 127 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 LYS cc_start: 0.8197 (ttmm) cc_final: 0.7953 (ttmm) REVERT: A 85 GLU cc_start: 0.8493 (OUTLIER) cc_final: 0.8143 (mp0) REVERT: A 135 LYS cc_start: 0.8136 (OUTLIER) cc_final: 0.7837 (mmmm) REVERT: A 179 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7830 (mp0) REVERT: A 235 TYR cc_start: 0.8849 (m-80) cc_final: 0.8610 (m-80) REVERT: A 337 GLU cc_start: 0.7232 (OUTLIER) cc_final: 0.7010 (tt0) REVERT: A 583 GLN cc_start: 0.8558 (mt0) cc_final: 0.7993 (mm110) REVERT: A 835 ASP cc_start: 0.8286 (m-30) cc_final: 0.8050 (t70) REVERT: A 869 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.8171 (mm-30) REVERT: B 31 GLN cc_start: 0.8297 (OUTLIER) cc_final: 0.7784 (tt0) REVERT: C 91 ASP cc_start: 0.7615 (p0) cc_final: 0.7226 (p0) outliers start: 28 outliers final: 18 residues processed: 145 average time/residue: 1.3487 time to fit residues: 209.2090 Evaluate side-chains 145 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 121 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 34 GLN Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 135 LYS Chi-restraints excluded: chain A residue 179 GLU Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 337 GLU Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 713 SER Chi-restraints excluded: chain A residue 869 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 31 GLN Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 144 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 33 optimal weight: 0.9980 chunk 67 optimal weight: 0.6980 chunk 104 optimal weight: 0.0000 chunk 0 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 24 optimal weight: 0.9990 chunk 31 optimal weight: 0.0670 chunk 103 optimal weight: 0.8980 chunk 95 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 46 optimal weight: 0.4980 overall best weight: 0.4122 ------------------------------------------------------------------------------- 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 = 0.3440 r_free = 0.3440 target = 0.123678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.087015 restraints weight = 10917.275| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 1.85 r_work: 0.2732 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2584 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.1317 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= 0.173 Angle : 0.470 5.410 13204 Z= 0.245 Chirality : 0.042 0.164 1471 Planarity : 0.004 0.045 1709 Dihedral : 5.821 73.091 1330 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.36 % Allowed : 10.37 % 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: 1.49 (0.25), residues: 1200 helix: 1.66 (0.24), residues: 499 sheet: 1.16 (0.37), residues: 180 loop : 0.38 (0.28), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 608 HIS 0.001 0.000 HIS C 55 PHE 0.011 0.001 PHE A 360 TYR 0.008 0.001 TYR A 736 ARG 0.007 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 149 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 124 time to evaluate : 1.051 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 LYS cc_start: 0.8230 (ttmm) cc_final: 0.7981 (ttmm) REVERT: A 85 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.8082 (mp0) REVERT: A 135 LYS cc_start: 0.8131 (OUTLIER) cc_final: 0.7833 (mmmm) REVERT: A 179 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7813 (mp0) REVERT: A 235 TYR cc_start: 0.8850 (m-80) cc_final: 0.8609 (m-80) REVERT: A 337 GLU cc_start: 0.7203 (OUTLIER) cc_final: 0.7001 (tt0) REVERT: A 583 GLN cc_start: 0.8511 (mt0) cc_final: 0.7980 (mm110) REVERT: A 835 ASP cc_start: 0.8261 (m-30) cc_final: 0.8027 (t70) REVERT: A 869 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.8162 (mm-30) REVERT: B 31 GLN cc_start: 0.8315 (OUTLIER) cc_final: 0.7803 (tt0) REVERT: C 91 ASP cc_start: 0.7611 (p0) cc_final: 0.7176 (p0) outliers start: 25 outliers final: 16 residues processed: 141 average time/residue: 1.2177 time to fit residues: 184.1422 Evaluate side-chains 144 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 122 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 34 GLN Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 135 LYS Chi-restraints excluded: chain A residue 179 GLU Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 337 GLU Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 713 SER Chi-restraints excluded: chain A residue 869 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 31 GLN Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 110 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 79 optimal weight: 0.6980 chunk 52 optimal weight: 0.7980 chunk 88 optimal weight: 0.9990 chunk 11 optimal weight: 0.3980 chunk 106 optimal weight: 4.9990 chunk 36 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 66 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 19 optimal weight: 0.1980 chunk 15 optimal weight: 0.7980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3487 r_free = 0.3487 target = 0.124771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.088071 restraints weight = 10995.943| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 1.88 r_work: 0.2789 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2642 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.1348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9746 Z= 0.203 Angle : 0.484 6.674 13204 Z= 0.252 Chirality : 0.043 0.272 1471 Planarity : 0.004 0.051 1709 Dihedral : 5.823 72.355 1330 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.45 % Allowed : 10.27 % 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: 1.43 (0.24), residues: 1200 helix: 1.60 (0.24), residues: 498 sheet: 1.16 (0.37), residues: 180 loop : 0.37 (0.28), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 608 HIS 0.002 0.001 HIS C 125 PHE 0.011 0.001 PHE A 360 TYR 0.008 0.001 TYR A 736 ARG 0.007 0.000 ARG C 5 *********************** 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 148 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 122 time to evaluate : 1.027 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 LYS cc_start: 0.8210 (ttmm) cc_final: 0.7949 (ttmm) REVERT: A 85 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.8052 (mp0) REVERT: A 135 LYS cc_start: 0.8125 (OUTLIER) cc_final: 0.7829 (mmmm) REVERT: A 179 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7802 (mp0) REVERT: A 235 TYR cc_start: 0.8861 (m-80) cc_final: 0.8621 (m-80) REVERT: A 337 GLU cc_start: 0.7267 (OUTLIER) cc_final: 0.7066 (tt0) REVERT: A 583 GLN cc_start: 0.8530 (mt0) cc_final: 0.7986 (mm110) REVERT: A 835 ASP cc_start: 0.8203 (m-30) cc_final: 0.7992 (t70) REVERT: B 31 GLN cc_start: 0.8344 (OUTLIER) cc_final: 0.7835 (tt0) REVERT: C 91 ASP cc_start: 0.7622 (p0) cc_final: 0.7237 (p0) outliers start: 26 outliers final: 19 residues processed: 139 average time/residue: 1.2552 time to fit residues: 187.4332 Evaluate side-chains 150 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 126 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 34 GLN Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 135 LYS Chi-restraints excluded: chain A residue 179 GLU Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 337 GLU Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 713 SER Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 31 GLN Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 144 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 14 optimal weight: 0.8980 chunk 116 optimal weight: 0.7980 chunk 85 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 35 optimal weight: 0.3980 chunk 89 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 71 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 27 optimal weight: 0.1980 chunk 17 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3490 r_free = 0.3490 target = 0.124911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.088151 restraints weight = 11138.013| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 1.90 r_work: 0.2791 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2646 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9746 Z= 0.203 Angle : 0.493 7.960 13204 Z= 0.254 Chirality : 0.043 0.319 1471 Planarity : 0.004 0.054 1709 Dihedral : 5.823 71.230 1330 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.17 % Allowed : 10.65 % Favored : 87.18 % 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: 1.41 (0.24), residues: 1200 helix: 1.56 (0.24), residues: 498 sheet: 1.16 (0.37), residues: 180 loop : 0.36 (0.28), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 608 HIS 0.001 0.001 HIS A 29 PHE 0.011 0.001 PHE A 360 TYR 0.008 0.001 TYR A 736 ARG 0.007 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 147 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 124 time to evaluate : 1.192 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 LYS cc_start: 0.8221 (ttmm) cc_final: 0.7963 (ttmm) REVERT: A 85 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.8063 (mp0) REVERT: A 135 LYS cc_start: 0.8134 (OUTLIER) cc_final: 0.7837 (mmmm) REVERT: A 179 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7798 (mp0) REVERT: A 235 TYR cc_start: 0.8863 (m-80) cc_final: 0.8625 (m-80) REVERT: A 337 GLU cc_start: 0.7258 (OUTLIER) cc_final: 0.7055 (tt0) REVERT: A 583 GLN cc_start: 0.8528 (mt0) cc_final: 0.7992 (mm110) REVERT: A 835 ASP cc_start: 0.8202 (m-30) cc_final: 0.7996 (t70) REVERT: B 31 GLN cc_start: 0.8350 (OUTLIER) cc_final: 0.7836 (tt0) REVERT: C 91 ASP cc_start: 0.7623 (p0) cc_final: 0.7178 (p0) outliers start: 23 outliers final: 18 residues processed: 139 average time/residue: 1.4247 time to fit residues: 213.2024 Evaluate side-chains 147 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 124 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 34 GLN Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 135 LYS Chi-restraints excluded: chain A residue 179 GLU Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 337 GLU Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 713 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 31 GLN Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 144 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 117 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 29 optimal weight: 0.0870 chunk 24 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 chunk 4 optimal weight: 0.5980 chunk 96 optimal weight: 0.0980 chunk 105 optimal weight: 0.7980 chunk 33 optimal weight: 0.5980 chunk 79 optimal weight: 0.6980 overall best weight: 0.4158 ------------------------------------------------------------------------------- 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 = 0.3494 r_free = 0.3494 target = 0.125334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.088540 restraints weight = 11027.510| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 1.96 r_work: 0.2784 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2638 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9746 Z= 0.173 Angle : 0.483 8.918 13204 Z= 0.250 Chirality : 0.043 0.322 1471 Planarity : 0.004 0.055 1709 Dihedral : 5.778 70.754 1330 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.07 % Allowed : 10.65 % 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: 1.45 (0.24), residues: 1200 helix: 1.61 (0.24), residues: 498 sheet: 1.18 (0.37), residues: 180 loop : 0.38 (0.28), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 608 HIS 0.002 0.000 HIS C 125 PHE 0.011 0.001 PHE A 360 TYR 0.008 0.001 TYR A 736 ARG 0.007 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: 7403.58 seconds wall clock time: 129 minutes 3.78 seconds (7743.78 seconds total)