Starting phenix.real_space_refine on Sat Aug 23 04:02:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b5j_44214/08_2025/9b5j_44214.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b5j_44214/08_2025/9b5j_44214.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9b5j_44214/08_2025/9b5j_44214.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b5j_44214/08_2025/9b5j_44214.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9b5j_44214/08_2025/9b5j_44214.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b5j_44214/08_2025/9b5j_44214.map" } resolution = 2.86 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.074 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 42 5.16 5 C 6078 2.51 5 N 1575 2.21 5 O 1829 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9525 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: "B" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'AMP%rna2p': 1} Classifications: {'RNA_mixed': 1} Modifications used: {'rna2p': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 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: 2.14, per 1000 atoms: 0.22 Number of scatterers: 9525 At special positions: 0 Unit cell: (82.992, 97.888, 120.232, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 42 16.00 P 1 15.00 O 1829 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=2.93 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.73 Conformation dependent library (CDL) restraints added in 262.7 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 50 helices and 9 sheets defined 46.4% alpha, 14.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 20 through 25 removed outlier: 3.759A pdb=" N TYR A 25 " --> pdb=" O SER A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 36 removed outlier: 3.787A pdb=" N MET A 32 " --> pdb=" O GLY A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 60 Processing helix chain 'A' and resid 73 through 79 removed outlier: 3.596A pdb=" N SER A 79 " --> pdb=" O ASP A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 88 removed outlier: 3.892A pdb=" N ILE A 88 " --> pdb=" O GLU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 101 removed outlier: 4.369A pdb=" N SER A 98 " --> pdb=" O LYS A 94 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N LYS A 99 " --> pdb=" O VAL A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 123 removed outlier: 3.527A pdb=" N LYS A 121 " --> pdb=" O GLU A 118 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASN A 122 " --> pdb=" O TYR A 119 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE A 123 " --> pdb=" O LEU A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 146 removed outlier: 3.697A pdb=" N PHE A 142 " --> pdb=" O GLU A 138 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LYS A 145 " --> pdb=" O ASP A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 224 removed outlier: 4.032A pdb=" N GLY A 224 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 274 removed outlier: 4.286A pdb=" N LYS A 273 " --> pdb=" O ARG A 269 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ASP A 274 " --> pdb=" O GLU A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 305 removed outlier: 3.625A pdb=" N ILE A 293 " --> pdb=" O PRO A 289 " (cutoff:3.500A) removed outlier: 3.642A 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: 3.978A pdb=" N VAL A 416 " --> pdb=" O GLY A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 427 removed outlier: 3.577A 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 479 through 483 removed outlier: 3.678A pdb=" N VAL A 483 " --> pdb=" O PRO A 480 " (cutoff:3.500A) 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: 4.001A pdb=" N GLU A 518 " --> pdb=" O PRO A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 528 removed outlier: 3.888A pdb=" N LYS A 528 " --> pdb=" O GLU A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 553 removed outlier: 3.628A pdb=" N ARG A 542 " --> pdb=" O ASN A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 582 removed outlier: 3.518A pdb=" N SER A 581 " --> pdb=" O SER A 578 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N SER A 582 " --> pdb=" O TYR A 579 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 578 through 582' Processing helix chain 'A' and resid 591 through 597 Processing helix chain 'A' and resid 601 through 618 Processing helix chain 'A' and resid 618 through 628 Processing helix chain 'A' and resid 632 through 641 removed outlier: 3.556A pdb=" N THR A 636 " --> pdb=" O ASN A 632 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LYS A 639 " --> pdb=" O GLU A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 643 through 656 removed outlier: 3.817A pdb=" N VAL A 647 " --> pdb=" O ASN A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 679 Processing helix chain 'A' and resid 679 through 689 removed outlier: 3.557A pdb=" N GLN A 683 " --> pdb=" O ASN A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 737 Processing helix chain 'A' and resid 743 through 752 removed outlier: 3.846A pdb=" N TYR A 747 " --> pdb=" O ASP A 743 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 781 through 794 removed outlier: 3.622A pdb=" N LEU A 794 " --> pdb=" O ILE A 790 " (cutoff:3.500A) Processing helix chain 'A' and resid 796 through 800 Processing helix chain 'A' and resid 818 through 834 Processing helix chain 'A' and resid 840 through 850 Processing helix chain 'A' and resid 855 through 876 removed outlier: 3.678A pdb=" N VAL A 871 " --> pdb=" O CYS A 867 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LYS A 872 " --> pdb=" O LEU A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 883 removed outlier: 3.837A 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 '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 98 through 112 Processing helix chain 'C' and resid 120 through 130 Processing helix chain 'C' and resid 130 through 146 Processing sheet with id=AA1, first strand: chain 'A' and resid 109 through 111 removed outlier: 6.739A pdb=" N VAL A 64 " --> pdb=" O SER A 110 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ASN A 39 " --> pdb=" O CYS A 125 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N VAL A 127 " --> pdb=" O ASN A 39 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N LEU A 41 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N VAL A 126 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N ALA A 153 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N VAL A 128 " --> pdb=" O ALA A 153 " (cutoff:3.500A) removed outlier: 8.242A pdb=" N SER A 155 " --> pdb=" O VAL A 128 " (cutoff:3.500A) removed outlier: 4.334A 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: 4.290A pdb=" N PHE A 209 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N THR A 195 " --> pdb=" O ALA A 186 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ILE A 188 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N VAL A 193 " --> pdb=" O ILE A 188 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 506 through 509 removed outlier: 6.367A pdb=" N ILE A 459 " --> pdb=" O THR A 507 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N TYR A 509 " --> pdb=" O ILE A 459 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N VAL A 461 " --> pdb=" O TYR A 509 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU A 531 " --> pdb=" O SER A 429 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N SER A 559 " --> pdb=" O ASN A 534 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 905 through 908 Processing sheet with id=AA6, first strand: chain 'A' and resid 920 through 922 removed outlier: 6.402A pdb=" N TYR A 920 " --> pdb=" O CYS A1009 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N LYS A1011 " --> pdb=" O TYR A 920 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N LEU A 922 " --> pdb=" O LYS A1011 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ASP A 996 " --> pdb=" O VAL A 942 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N VAL A 942 " --> pdb=" O ASP A 996 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N SER A 947 " --> pdb=" O LEU A 951 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N LEU A 951 " --> pdb=" O SER A 947 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 920 through 922 removed outlier: 6.402A pdb=" N TYR A 920 " --> pdb=" O CYS A1009 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N LYS A1011 " --> pdb=" O TYR A 920 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N LEU A 922 " --> pdb=" O LYS A1011 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N CYS A 995 " --> pdb=" O VAL A1003 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 12 through 16 removed outlier: 3.839A pdb=" N ARG B 42 " --> pdb=" O VAL B 70 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 24 through 26 removed outlier: 3.635A pdb=" N GLY C 24 " --> pdb=" O GLN C 34 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N HIS C 32 " --> pdb=" O VAL C 26 " (cutoff:3.500A) 445 hydrogen bonds defined for protein. 1230 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: 1.10 Time building geometry restraints manager: 0.92 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: 2291 1.40 - 1.54: 5697 1.54 - 1.67: 66 1.67 - 1.81: 64 Bond restraints: 9737 Sorted by residual: bond pdb=" C04 A1AIV D 201 " pdb=" C05 A1AIV D 201 " ideal model delta sigma weight residual 1.453 1.526 -0.073 2.00e-02 2.50e+03 1.34e+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 2.61e+00 bond pdb=" C4 AMP B 101 " pdb=" C5 AMP B 101 " ideal model delta sigma weight residual 1.490 1.463 0.027 2.00e-02 2.50e+03 1.88e+00 bond pdb=" C4' AMP B 101 " pdb=" O4' AMP B 101 " ideal model delta sigma weight residual 1.426 1.451 -0.025 2.00e-02 2.50e+03 1.50e+00 bond pdb=" C2' AMP B 101 " pdb=" O2' AMP B 101 " ideal model delta sigma weight residual 1.432 1.408 0.024 2.00e-02 2.50e+03 1.42e+00 ... (remaining 9732 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 13072 1.84 - 3.67: 97 3.67 - 5.51: 14 5.51 - 7.34: 3 7.34 - 9.18: 1 Bond angle restraints: 13187 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 121.70 128.22 -6.52 1.80e+00 3.09e-01 1.31e+01 angle pdb=" C1' AMP B 101 " pdb=" C2' AMP B 101 " pdb=" C3' AMP B 101 " ideal model delta sigma weight residual 111.00 101.82 9.18 3.00e+00 1.11e-01 9.35e+00 angle pdb=" C2' AMP B 101 " pdb=" C3' AMP B 101 " pdb=" C4' AMP B 101 " ideal model delta sigma weight residual 111.00 103.71 7.29 3.00e+00 1.11e-01 5.90e+00 angle pdb=" O1P AMP B 101 " pdb=" P AMP B 101 " pdb=" O2P AMP B 101 " ideal model delta sigma weight residual 119.60 112.37 7.23 3.00e+00 1.11e-01 5.82e+00 angle pdb=" N ASP A 813 " pdb=" CA ASP A 813 " pdb=" CB ASP A 813 " ideal model delta sigma weight residual 113.65 111.05 2.60 1.47e+00 4.63e-01 3.13e+00 ... (remaining 13182 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 5671 17.81 - 35.63: 185 35.63 - 53.44: 38 53.44 - 71.26: 8 71.26 - 89.07: 3 Dihedral angle restraints: 5905 sinusoidal: 2399 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 -136.30 50.30 1 1.00e+01 1.00e-02 3.47e+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 180.00 161.58 18.42 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" N LEU A 115 " pdb=" CA LEU A 115 " pdb=" CB LEU A 115 " pdb=" CG LEU A 115 " ideal model delta sinusoidal sigma weight residual -60.00 -119.59 59.59 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 5902 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1058 0.038 - 0.075: 297 0.075 - 0.113: 86 0.113 - 0.150: 28 0.150 - 0.188: 2 Chirality restraints: 1471 Sorted by residual: chirality pdb=" C3' AMP B 101 " pdb=" C2' AMP B 101 " pdb=" C4' AMP B 101 " pdb=" O3' AMP B 101 " both_signs ideal model delta sigma weight residual False -2.51 -2.70 0.19 2.00e-01 2.50e+01 8.85e-01 chirality pdb=" CA ILE B 13 " pdb=" N ILE B 13 " pdb=" C ILE B 13 " pdb=" CB ILE B 13 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.71e-01 chirality pdb=" CA ILE B 36 " pdb=" N ILE B 36 " pdb=" C ILE B 36 " pdb=" CB ILE B 36 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.80e-01 ... (remaining 1468 not shown) Planarity restraints: 1709 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER C 94 " 0.023 5.00e-02 4.00e+02 3.43e-02 1.89e+00 pdb=" N PRO C 95 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO C 95 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 95 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 120 " 0.018 5.00e-02 4.00e+02 2.74e-02 1.20e+00 pdb=" N PRO C 121 " -0.047 5.00e-02 4.00e+02 pdb=" CA PRO C 121 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO C 121 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 90 " 0.017 5.00e-02 4.00e+02 2.56e-02 1.05e+00 pdb=" N PRO A 91 " -0.044 5.00e-02 4.00e+02 pdb=" CA PRO A 91 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 91 " 0.014 5.00e-02 4.00e+02 ... (remaining 1706 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 250 2.71 - 3.26: 9335 3.26 - 3.80: 14628 3.80 - 4.35: 19624 4.35 - 4.90: 33842 Nonbonded interactions: 77679 Sorted by model distance: nonbonded pdb=" O PRO C 18 " pdb=" OG SER C 19 " model vdw 2.161 3.040 nonbonded pdb=" ND2 ASN A 534 " pdb=" OE2 GLU A 558 " model vdw 2.235 3.120 nonbonded pdb=" OE1 GLU A 658 " pdb=" OH TYR A 732 " model vdw 2.264 3.040 nonbonded pdb=" OD1 ASP A 463 " pdb=" O2' AMP B 101 " model vdw 2.264 3.040 nonbonded pdb=" O GLU A 809 " pdb=" NE2 HIS A 819 " model vdw 2.269 3.120 ... (remaining 77674 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: 4.560 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: 0.020 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 8.740 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 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 : 0.010 0.900 9741 Z= 0.502 Angle : 0.664 51.470 13189 Z= 0.321 Chirality : 0.041 0.188 1471 Planarity : 0.003 0.034 1709 Dihedral : 9.888 89.073 3638 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 1.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.04 % Allowed : 2.83 % Favored : 96.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.00 (0.25), residues: 1200 helix: 1.59 (0.25), residues: 496 sheet: 0.29 (0.37), residues: 189 loop : -0.02 (0.28), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 409 TYR 0.009 0.001 TYR A 544 PHE 0.009 0.001 PHE A 237 TRP 0.006 0.001 TRP A 669 HIS 0.002 0.000 HIS C 75 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 9737) covalent geometry : angle 0.47885 (13187) SS BOND : bond 0.89966 ( 1) SS BOND : angle 37.38884 ( 2) hydrogen bonds : bond 0.13970 ( 441) hydrogen bonds : angle 5.89306 ( 1230) Misc. bond : bond 0.08441 ( 3) *********************** 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 142 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 131 time to evaluate : 0.284 Fit side-chains revert: symmetry clash REVERT: A 105 GLN cc_start: 0.8001 (pt0) cc_final: 0.7762 (mp10) REVERT: A 196 MET cc_start: 0.8737 (mmp) cc_final: 0.8453 (mmm) REVERT: A 540 GLU cc_start: 0.7472 (tt0) cc_final: 0.7266 (mp0) REVERT: A 583 GLN cc_start: 0.8129 (mt0) cc_final: 0.7261 (mm-40) REVERT: A 614 GLU cc_start: 0.7511 (tp30) cc_final: 0.6492 (tm-30) REVERT: A 619 GLN cc_start: 0.7466 (tp40) cc_final: 0.6890 (tm-30) REVERT: A 811 GLU cc_start: 0.5932 (OUTLIER) cc_final: 0.5524 (tp30) REVERT: A 840 ASP cc_start: 0.7768 (p0) cc_final: 0.7459 (p0) REVERT: A 879 LYS cc_start: 0.8373 (mttm) cc_final: 0.8092 (mttm) REVERT: B 51 GLU cc_start: 0.8411 (mt-10) cc_final: 0.8118 (mt-10) REVERT: C 32 HIS cc_start: 0.7849 (t-170) cc_final: 0.7533 (t70) REVERT: C 72 ARG cc_start: 0.8471 (mmm-85) cc_final: 0.8237 (mmm-85) REVERT: C 140 GLU cc_start: 0.7594 (tm-30) cc_final: 0.7303 (tm-30) outliers start: 11 outliers final: 2 residues processed: 142 average time/residue: 0.6350 time to fit residues: 95.0127 Evaluate side-chains 98 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 95 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 811 GLU Chi-restraints excluded: chain C residue 85 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 108 optimal weight: 0.4980 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 0.6980 chunk 113 optimal weight: 0.5980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.4980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 117 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3616 r_free = 0.3616 target = 0.134368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.094566 restraints weight = 11976.871| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 2.39 r_work: 0.2940 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2794 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.0952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 9741 Z= 0.139 Angle : 0.520 7.861 13189 Z= 0.266 Chirality : 0.042 0.157 1471 Planarity : 0.004 0.044 1709 Dihedral : 5.664 80.111 1308 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 2.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.51 % Allowed : 8.01 % Favored : 90.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.07 (0.25), residues: 1200 helix: 1.50 (0.24), residues: 503 sheet: 0.68 (0.37), residues: 186 loop : 0.01 (0.28), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 74 TYR 0.010 0.001 TYR A 736 PHE 0.013 0.001 PHE A 722 TRP 0.007 0.001 TRP A 669 HIS 0.008 0.001 HIS A 819 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 9737) covalent geometry : angle 0.51551 (13187) SS BOND : bond 0.01218 ( 1) SS BOND : angle 5.70143 ( 2) hydrogen bonds : bond 0.04251 ( 441) hydrogen bonds : angle 4.78117 ( 1230) Misc. bond : bond 0.00069 ( 3) *********************** 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 119 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 103 time to evaluate : 0.271 Fit side-chains revert: symmetry clash REVERT: A 105 GLN cc_start: 0.8214 (pt0) cc_final: 0.7890 (mp10) REVERT: A 469 LYS cc_start: 0.8334 (mppt) cc_final: 0.8125 (mmtm) REVERT: A 540 GLU cc_start: 0.7864 (tt0) cc_final: 0.7446 (mp0) REVERT: A 583 GLN cc_start: 0.8286 (mt0) cc_final: 0.7341 (mm-40) REVERT: A 614 GLU cc_start: 0.7227 (tp30) cc_final: 0.6446 (tm-30) REVERT: A 619 GLN cc_start: 0.7359 (tp40) cc_final: 0.6812 (tm-30) REVERT: A 840 ASP cc_start: 0.7484 (p0) cc_final: 0.7175 (p0) REVERT: B 51 GLU cc_start: 0.8353 (mt-10) cc_final: 0.7975 (mt-10) REVERT: B 60 ASN cc_start: 0.8537 (m-40) cc_final: 0.8196 (t0) REVERT: C 32 HIS cc_start: 0.7508 (t-170) cc_final: 0.7208 (t70) REVERT: C 72 ARG cc_start: 0.8443 (mmm-85) cc_final: 0.8105 (mmm-85) REVERT: C 140 GLU cc_start: 0.7517 (tm-30) cc_final: 0.7281 (tm-30) outliers start: 16 outliers final: 5 residues processed: 112 average time/residue: 0.6411 time to fit residues: 76.1095 Evaluate side-chains 100 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 95 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain C residue 85 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 56 optimal weight: 1.9990 chunk 106 optimal weight: 0.0050 chunk 58 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 89 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 84 optimal weight: 0.0030 overall best weight: 0.5808 ------------------------------------------------------------------------------- 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 = 0.3619 r_free = 0.3619 target = 0.134761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.094726 restraints weight = 12013.991| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 2.41 r_work: 0.2939 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2794 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.1160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9741 Z= 0.134 Angle : 0.490 6.875 13189 Z= 0.250 Chirality : 0.042 0.149 1471 Planarity : 0.004 0.047 1709 Dihedral : 5.168 75.187 1305 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.60 % Allowed : 8.86 % Favored : 89.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.08 (0.25), residues: 1200 helix: 1.49 (0.24), residues: 503 sheet: 0.78 (0.38), residues: 186 loop : 0.01 (0.28), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 841 TYR 0.015 0.001 TYR A 250 PHE 0.011 0.001 PHE A 237 TRP 0.008 0.001 TRP A 669 HIS 0.005 0.001 HIS A 819 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 9737) covalent geometry : angle 0.48619 (13187) SS BOND : bond 0.02264 ( 1) SS BOND : angle 4.76627 ( 2) hydrogen bonds : bond 0.03841 ( 441) hydrogen bonds : angle 4.60397 ( 1230) Misc. bond : bond 0.00132 ( 3) *********************** 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 122 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 105 time to evaluate : 0.356 Fit side-chains revert: symmetry clash REVERT: A 105 GLN cc_start: 0.8226 (pt0) cc_final: 0.7888 (mp-120) REVERT: A 216 LYS cc_start: 0.7235 (pttm) cc_final: 0.6782 (pptt) REVERT: A 540 GLU cc_start: 0.7879 (tt0) cc_final: 0.7457 (mp0) REVERT: A 583 GLN cc_start: 0.8321 (mt0) cc_final: 0.7370 (mm-40) REVERT: A 614 GLU cc_start: 0.7302 (tp30) cc_final: 0.6484 (tm-30) REVERT: A 619 GLN cc_start: 0.7348 (tp40) cc_final: 0.6730 (tm-30) REVERT: A 840 ASP cc_start: 0.7487 (p0) cc_final: 0.7184 (p0) REVERT: A 842 PHE cc_start: 0.7078 (t80) cc_final: 0.6870 (t80) REVERT: A 869 GLU cc_start: 0.7979 (tp30) cc_final: 0.7734 (tp30) REVERT: B 51 GLU cc_start: 0.8295 (mt-10) cc_final: 0.7945 (mt-10) REVERT: B 60 ASN cc_start: 0.8520 (m-40) cc_final: 0.8201 (t0) REVERT: C 32 HIS cc_start: 0.7561 (t-170) cc_final: 0.7239 (t70) REVERT: C 72 ARG cc_start: 0.8500 (mmm-85) cc_final: 0.8176 (mmm-85) REVERT: C 101 LYS cc_start: 0.8406 (mptp) cc_final: 0.8136 (mmtp) REVERT: C 140 GLU cc_start: 0.7557 (tm-30) cc_final: 0.7286 (tm-30) outliers start: 17 outliers final: 7 residues processed: 115 average time/residue: 0.6586 time to fit residues: 80.6839 Evaluate side-chains 105 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 98 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain C residue 85 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 49 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 108 optimal weight: 0.8980 chunk 67 optimal weight: 0.8980 chunk 113 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 47 optimal weight: 0.0980 chunk 44 optimal weight: 0.6980 chunk 41 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.134458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.094627 restraints weight = 12107.173| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 2.41 r_work: 0.2937 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2792 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.1265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9741 Z= 0.139 Angle : 0.488 6.624 13189 Z= 0.249 Chirality : 0.042 0.146 1471 Planarity : 0.004 0.049 1709 Dihedral : 5.096 69.343 1305 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.07 % Allowed : 9.80 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.14 (0.25), residues: 1200 helix: 1.57 (0.24), residues: 497 sheet: 0.83 (0.38), residues: 185 loop : 0.02 (0.27), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 841 TYR 0.014 0.001 TYR A 250 PHE 0.011 0.001 PHE A 237 TRP 0.008 0.001 TRP A 669 HIS 0.004 0.001 HIS A 819 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 9737) covalent geometry : angle 0.48510 (13187) SS BOND : bond 0.01128 ( 1) SS BOND : angle 4.44268 ( 2) hydrogen bonds : bond 0.03741 ( 441) hydrogen bonds : angle 4.52759 ( 1230) Misc. bond : bond 0.00074 ( 3) *********************** 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 118 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 96 time to evaluate : 0.330 Fit side-chains REVERT: A 105 GLN cc_start: 0.8226 (pt0) cc_final: 0.7876 (mp-120) REVERT: A 540 GLU cc_start: 0.7853 (tt0) cc_final: 0.7428 (mp0) REVERT: A 583 GLN cc_start: 0.8320 (mt0) cc_final: 0.7356 (mm-40) REVERT: A 614 GLU cc_start: 0.7325 (tp30) cc_final: 0.6495 (tm-30) REVERT: A 619 GLN cc_start: 0.7287 (tp40) cc_final: 0.6653 (tm-30) REVERT: A 840 ASP cc_start: 0.7487 (p0) cc_final: 0.7199 (p0) REVERT: A 869 GLU cc_start: 0.8023 (tp30) cc_final: 0.7772 (tp30) REVERT: B 51 GLU cc_start: 0.8305 (mt-10) cc_final: 0.7955 (mt-10) REVERT: B 60 ASN cc_start: 0.8463 (m-40) cc_final: 0.8156 (t0) REVERT: C 32 HIS cc_start: 0.7575 (t-170) cc_final: 0.7256 (t70) REVERT: C 72 ARG cc_start: 0.8502 (mmm-85) cc_final: 0.8184 (mmm-85) REVERT: C 101 LYS cc_start: 0.8423 (mptp) cc_final: 0.8150 (mmtp) REVERT: C 140 GLU cc_start: 0.7565 (tm-30) cc_final: 0.7284 (tm-30) outliers start: 22 outliers final: 7 residues processed: 111 average time/residue: 0.6791 time to fit residues: 80.3611 Evaluate side-chains 102 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 95 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 71 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 63 optimal weight: 0.8980 chunk 106 optimal weight: 6.9990 chunk 116 optimal weight: 0.9990 chunk 73 optimal weight: 0.8980 chunk 100 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 58 optimal weight: 0.1980 chunk 60 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.134044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.094020 restraints weight = 12088.433| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 2.42 r_work: 0.2933 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9741 Z= 0.147 Angle : 0.517 12.948 13189 Z= 0.260 Chirality : 0.043 0.214 1471 Planarity : 0.004 0.049 1709 Dihedral : 5.030 77.866 1304 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.23 % Allowed : 11.12 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.13 (0.25), residues: 1200 helix: 1.56 (0.24), residues: 497 sheet: 0.78 (0.38), residues: 187 loop : 0.04 (0.27), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 841 TYR 0.008 0.001 TYR C 74 PHE 0.011 0.001 PHE A 237 TRP 0.008 0.001 TRP A 669 HIS 0.003 0.001 HIS A 819 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 9737) covalent geometry : angle 0.51614 (13187) SS BOND : bond 0.02920 ( 1) SS BOND : angle 2.11613 ( 2) hydrogen bonds : bond 0.03790 ( 441) hydrogen bonds : angle 4.49014 ( 1230) Misc. bond : bond 0.00043 ( 3) *********************** 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 110 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 0.485 Fit side-chains REVERT: A 105 GLN cc_start: 0.8200 (pt0) cc_final: 0.7858 (mp-120) REVERT: A 221 LEU cc_start: 0.8040 (OUTLIER) cc_final: 0.7791 (tp) REVERT: A 540 GLU cc_start: 0.7828 (tt0) cc_final: 0.7396 (mp0) REVERT: A 583 GLN cc_start: 0.8327 (mt0) cc_final: 0.7361 (mm-40) REVERT: A 614 GLU cc_start: 0.7320 (tp30) cc_final: 0.6512 (tm-30) REVERT: A 619 GLN cc_start: 0.7248 (tp40) cc_final: 0.6612 (tm-30) REVERT: A 840 ASP cc_start: 0.7453 (p0) cc_final: 0.7168 (p0) REVERT: A 869 GLU cc_start: 0.7968 (tp30) cc_final: 0.7713 (tp30) REVERT: B 51 GLU cc_start: 0.8305 (mt-10) cc_final: 0.7961 (mt-10) REVERT: B 60 ASN cc_start: 0.8456 (m-40) cc_final: 0.8152 (t0) REVERT: C 32 HIS cc_start: 0.7558 (t-170) cc_final: 0.7238 (t70) REVERT: C 72 ARG cc_start: 0.8500 (mmm-85) cc_final: 0.8181 (mmm-85) REVERT: C 140 GLU cc_start: 0.7564 (tm-30) cc_final: 0.7272 (tm-30) outliers start: 13 outliers final: 9 residues processed: 108 average time/residue: 0.6805 time to fit residues: 78.6681 Evaluate side-chains 106 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 96 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 136 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 91 optimal weight: 3.9990 chunk 84 optimal weight: 0.6980 chunk 76 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 20 optimal weight: 0.0670 chunk 118 optimal weight: 0.7980 chunk 86 optimal weight: 0.9980 chunk 100 optimal weight: 0.4980 chunk 52 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 overall best weight: 0.5718 ------------------------------------------------------------------------------- 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 = 0.3606 r_free = 0.3606 target = 0.133778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.093209 restraints weight = 12077.063| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 2.46 r_work: 0.2936 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9741 Z= 0.131 Angle : 0.503 11.281 13189 Z= 0.254 Chirality : 0.042 0.224 1471 Planarity : 0.004 0.048 1709 Dihedral : 4.958 74.341 1304 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.32 % Allowed : 11.31 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.16 (0.25), residues: 1200 helix: 1.58 (0.24), residues: 498 sheet: 0.81 (0.38), residues: 187 loop : 0.06 (0.28), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 841 TYR 0.009 0.001 TYR C 74 PHE 0.011 0.001 PHE A 237 TRP 0.008 0.001 TRP A 669 HIS 0.004 0.001 HIS A 819 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 9737) covalent geometry : angle 0.50300 (13187) SS BOND : bond 0.02990 ( 1) SS BOND : angle 1.08283 ( 2) hydrogen bonds : bond 0.03642 ( 441) hydrogen bonds : angle 4.43447 ( 1230) Misc. bond : bond 0.00036 ( 3) *********************** 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 112 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 98 time to evaluate : 0.430 Fit side-chains REVERT: A 105 GLN cc_start: 0.8195 (pt0) cc_final: 0.7848 (mp-120) REVERT: A 221 LEU cc_start: 0.8036 (OUTLIER) cc_final: 0.7800 (tp) REVERT: A 540 GLU cc_start: 0.7816 (tt0) cc_final: 0.7376 (mp0) REVERT: A 583 GLN cc_start: 0.8322 (mt0) cc_final: 0.7347 (mm-40) REVERT: A 614 GLU cc_start: 0.7283 (tp30) cc_final: 0.6518 (tm-30) REVERT: A 619 GLN cc_start: 0.7220 (tp40) cc_final: 0.6593 (tm-30) REVERT: A 840 ASP cc_start: 0.7405 (p0) cc_final: 0.7119 (p0) REVERT: B 51 GLU cc_start: 0.8287 (mt-10) cc_final: 0.7942 (mt-10) REVERT: B 60 ASN cc_start: 0.8407 (m-40) cc_final: 0.8107 (t0) REVERT: C 32 HIS cc_start: 0.7509 (t-170) cc_final: 0.7199 (t70) REVERT: C 72 ARG cc_start: 0.8489 (mmm-85) cc_final: 0.8175 (mmm-85) REVERT: C 140 GLU cc_start: 0.7549 (tm-30) cc_final: 0.7258 (tm-30) outliers start: 14 outliers final: 11 residues processed: 109 average time/residue: 0.6485 time to fit residues: 75.5584 Evaluate side-chains 107 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 95 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 913 ILE Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 136 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 93 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 110 optimal weight: 0.8980 chunk 99 optimal weight: 2.9990 chunk 40 optimal weight: 0.3980 chunk 48 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.3598 r_free = 0.3598 target = 0.133147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.092363 restraints weight = 12133.263| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 2.47 r_work: 0.2925 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2780 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9741 Z= 0.159 Angle : 0.513 11.135 13189 Z= 0.259 Chirality : 0.043 0.203 1471 Planarity : 0.004 0.049 1709 Dihedral : 4.945 69.187 1304 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.41 % Allowed : 11.59 % Favored : 86.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.13 (0.25), residues: 1200 helix: 1.56 (0.24), residues: 498 sheet: 0.81 (0.38), residues: 187 loop : 0.02 (0.27), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 841 TYR 0.020 0.001 TYR C 127 PHE 0.011 0.001 PHE A 237 TRP 0.007 0.001 TRP A 669 HIS 0.003 0.001 HIS A 819 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 9737) covalent geometry : angle 0.51270 (13187) SS BOND : bond 0.02692 ( 1) SS BOND : angle 0.69100 ( 2) hydrogen bonds : bond 0.03847 ( 441) hydrogen bonds : angle 4.47072 ( 1230) Misc. bond : bond 0.00037 ( 3) *********************** 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 114 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 99 time to evaluate : 0.391 Fit side-chains REVERT: A 105 GLN cc_start: 0.8211 (pt0) cc_final: 0.7861 (mp-120) REVERT: A 221 LEU cc_start: 0.8062 (OUTLIER) cc_final: 0.7834 (tp) REVERT: A 540 GLU cc_start: 0.7845 (tt0) cc_final: 0.7406 (mp0) REVERT: A 583 GLN cc_start: 0.8332 (mt0) cc_final: 0.7357 (mm-40) REVERT: A 614 GLU cc_start: 0.7307 (tp30) cc_final: 0.6550 (tm-30) REVERT: A 619 GLN cc_start: 0.7328 (tp40) cc_final: 0.6659 (tm-30) REVERT: A 811 GLU cc_start: 0.6140 (OUTLIER) cc_final: 0.5786 (tp30) REVERT: A 840 ASP cc_start: 0.7419 (p0) cc_final: 0.7137 (p0) REVERT: A 869 GLU cc_start: 0.8008 (tp30) cc_final: 0.7730 (tp30) REVERT: B 51 GLU cc_start: 0.8309 (mt-10) cc_final: 0.7962 (mt-10) REVERT: B 60 ASN cc_start: 0.8426 (m-40) cc_final: 0.8135 (t0) REVERT: C 32 HIS cc_start: 0.7541 (t-170) cc_final: 0.7234 (t70) REVERT: C 72 ARG cc_start: 0.8507 (mmm-85) cc_final: 0.8190 (mmm-85) REVERT: C 140 GLU cc_start: 0.7564 (tm-30) cc_final: 0.7273 (tm-30) outliers start: 15 outliers final: 10 residues processed: 112 average time/residue: 0.6862 time to fit residues: 82.1910 Evaluate side-chains 106 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 94 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 811 GLU Chi-restraints excluded: chain A residue 913 ILE Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 136 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 34 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 118 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 43 optimal weight: 0.9990 chunk 115 optimal weight: 0.6980 chunk 103 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 52 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3598 r_free = 0.3598 target = 0.133216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.092470 restraints weight = 12170.493| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 2.48 r_work: 0.2932 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9741 Z= 0.155 Angle : 0.513 10.839 13189 Z= 0.258 Chirality : 0.043 0.207 1471 Planarity : 0.004 0.049 1709 Dihedral : 4.931 67.115 1304 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.23 % Allowed : 12.25 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.12 (0.25), residues: 1200 helix: 1.55 (0.24), residues: 498 sheet: 0.86 (0.38), residues: 185 loop : -0.01 (0.27), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 841 TYR 0.021 0.001 TYR C 127 PHE 0.011 0.001 PHE A 237 TRP 0.008 0.001 TRP A 669 HIS 0.003 0.001 HIS A 819 Details of bonding type rmsd covalent geometry : bond 0.00383 ( 9737) covalent geometry : angle 0.51252 (13187) SS BOND : bond 0.02432 ( 1) SS BOND : angle 0.76343 ( 2) hydrogen bonds : bond 0.03791 ( 441) hydrogen bonds : angle 4.44652 ( 1230) Misc. bond : bond 0.00028 ( 3) *********************** 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 108 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 95 time to evaluate : 0.485 Fit side-chains REVERT: A 105 GLN cc_start: 0.8192 (pt0) cc_final: 0.7844 (mp-120) REVERT: A 221 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7911 (tp) REVERT: A 540 GLU cc_start: 0.7858 (tt0) cc_final: 0.7410 (mp0) REVERT: A 583 GLN cc_start: 0.8311 (mt0) cc_final: 0.7329 (mm-40) REVERT: A 614 GLU cc_start: 0.7275 (tp30) cc_final: 0.6507 (tm-30) REVERT: A 619 GLN cc_start: 0.7471 (tp40) cc_final: 0.6789 (tm-30) REVERT: A 811 GLU cc_start: 0.6166 (OUTLIER) cc_final: 0.5803 (tp30) REVERT: A 840 ASP cc_start: 0.7394 (p0) cc_final: 0.7112 (p0) REVERT: A 869 GLU cc_start: 0.7934 (tp30) cc_final: 0.7661 (tp30) REVERT: B 51 GLU cc_start: 0.8249 (mt-10) cc_final: 0.7899 (mt-10) REVERT: B 60 ASN cc_start: 0.8415 (m-40) cc_final: 0.8131 (t0) REVERT: C 32 HIS cc_start: 0.7511 (t-170) cc_final: 0.7196 (t70) REVERT: C 72 ARG cc_start: 0.8509 (mmm-85) cc_final: 0.8183 (mmm-85) REVERT: C 140 GLU cc_start: 0.7503 (tm-30) cc_final: 0.7213 (tm-30) outliers start: 13 outliers final: 9 residues processed: 108 average time/residue: 0.6291 time to fit residues: 72.6900 Evaluate side-chains 104 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 93 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 811 GLU Chi-restraints excluded: chain A residue 913 ILE Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain C residue 85 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 93 optimal weight: 0.0970 chunk 113 optimal weight: 0.1980 chunk 56 optimal weight: 0.5980 chunk 74 optimal weight: 0.0170 chunk 81 optimal weight: 1.9990 chunk 50 optimal weight: 0.3980 chunk 92 optimal weight: 0.7980 chunk 66 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 61 optimal weight: 5.9990 chunk 106 optimal weight: 2.9990 overall best weight: 0.2616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.136284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.095639 restraints weight = 12137.070| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 2.50 r_work: 0.2960 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9741 Z= 0.093 Angle : 0.482 9.689 13189 Z= 0.243 Chirality : 0.041 0.172 1471 Planarity : 0.004 0.047 1709 Dihedral : 4.634 56.775 1304 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.66 % Allowed : 13.20 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.27 (0.25), residues: 1200 helix: 1.70 (0.24), residues: 497 sheet: 0.86 (0.38), residues: 188 loop : 0.07 (0.28), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 841 TYR 0.022 0.001 TYR C 127 PHE 0.009 0.001 PHE A 842 TRP 0.009 0.001 TRP A 669 HIS 0.003 0.001 HIS A 819 Details of bonding type rmsd covalent geometry : bond 0.00207 ( 9737) covalent geometry : angle 0.48162 (13187) SS BOND : bond 0.01555 ( 1) SS BOND : angle 0.82880 ( 2) hydrogen bonds : bond 0.03131 ( 441) hydrogen bonds : angle 4.26826 ( 1230) Misc. bond : bond 0.00032 ( 3) *********************** 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 101 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 94 time to evaluate : 0.414 Fit side-chains REVERT: A 105 GLN cc_start: 0.8215 (pt0) cc_final: 0.7853 (mp-120) REVERT: A 221 LEU cc_start: 0.8112 (OUTLIER) cc_final: 0.7884 (tp) REVERT: A 540 GLU cc_start: 0.7805 (tt0) cc_final: 0.7393 (mp0) REVERT: A 543 MET cc_start: 0.8020 (mmt) cc_final: 0.7752 (mmt) REVERT: A 583 GLN cc_start: 0.8322 (mt0) cc_final: 0.7338 (mm-40) REVERT: A 614 GLU cc_start: 0.7289 (tp30) cc_final: 0.6510 (tm-30) REVERT: A 619 GLN cc_start: 0.7223 (tp40) cc_final: 0.6599 (tm-30) REVERT: A 840 ASP cc_start: 0.7361 (p0) cc_final: 0.7086 (p0) REVERT: A 869 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.7621 (tp30) REVERT: B 51 GLU cc_start: 0.8238 (mt-10) cc_final: 0.7886 (mt-10) REVERT: B 60 ASN cc_start: 0.8386 (m-40) cc_final: 0.8111 (t0) REVERT: C 32 HIS cc_start: 0.7527 (t-170) cc_final: 0.7212 (t70) REVERT: C 72 ARG cc_start: 0.8528 (mmm-85) cc_final: 0.8211 (mmm-85) REVERT: C 140 GLU cc_start: 0.7567 (tm-30) cc_final: 0.7280 (tm-30) outliers start: 7 outliers final: 4 residues processed: 100 average time/residue: 0.6979 time to fit residues: 74.4850 Evaluate side-chains 98 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 92 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 71 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 112 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 57 optimal weight: 0.0670 chunk 42 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 overall best weight: 0.7120 ------------------------------------------------------------------------------- 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 = 0.3607 r_free = 0.3607 target = 0.133786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.093033 restraints weight = 12063.199| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 2.47 r_work: 0.2941 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9741 Z= 0.152 Angle : 0.508 10.157 13189 Z= 0.256 Chirality : 0.043 0.190 1471 Planarity : 0.004 0.048 1709 Dihedral : 4.745 58.514 1304 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.57 % Allowed : 13.38 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.22 (0.25), residues: 1200 helix: 1.65 (0.24), residues: 498 sheet: 0.89 (0.38), residues: 187 loop : 0.03 (0.28), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 841 TYR 0.022 0.001 TYR C 127 PHE 0.012 0.001 PHE A 237 TRP 0.007 0.001 TRP A 669 HIS 0.003 0.001 HIS A 819 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 9737) covalent geometry : angle 0.50809 (13187) SS BOND : bond 0.02201 ( 1) SS BOND : angle 0.71888 ( 2) hydrogen bonds : bond 0.03656 ( 441) hydrogen bonds : angle 4.34957 ( 1230) Misc. bond : bond 0.00023 ( 3) ********************** 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 100 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 94 time to evaluate : 0.413 Fit side-chains REVERT: A 105 GLN cc_start: 0.8174 (pt0) cc_final: 0.7817 (mp-120) REVERT: A 221 LEU cc_start: 0.8090 (OUTLIER) cc_final: 0.7882 (tp) REVERT: A 442 MET cc_start: 0.7791 (mpp) cc_final: 0.7412 (mmm) REVERT: A 540 GLU cc_start: 0.7784 (tt0) cc_final: 0.7347 (mp0) REVERT: A 583 GLN cc_start: 0.8311 (mt0) cc_final: 0.7306 (mm-40) REVERT: A 614 GLU cc_start: 0.7203 (tp30) cc_final: 0.6451 (tm-30) REVERT: A 619 GLN cc_start: 0.7444 (tp40) cc_final: 0.6706 (tm-30) REVERT: A 840 ASP cc_start: 0.7311 (p0) cc_final: 0.7050 (p0) REVERT: A 869 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7644 (tp30) REVERT: B 51 GLU cc_start: 0.8192 (mt-10) cc_final: 0.7835 (mt-10) REVERT: B 60 ASN cc_start: 0.8364 (m-40) cc_final: 0.8088 (t0) REVERT: C 32 HIS cc_start: 0.7495 (t-170) cc_final: 0.7146 (t-90) REVERT: C 72 ARG cc_start: 0.8516 (mmm-85) cc_final: 0.8177 (mmm-85) REVERT: C 140 GLU cc_start: 0.7458 (tm-30) cc_final: 0.7180 (tm-30) outliers start: 6 outliers final: 4 residues processed: 99 average time/residue: 0.7088 time to fit residues: 74.7503 Evaluate side-chains 99 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 93 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 71 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 0 optimal weight: 5.9990 chunk 14 optimal weight: 0.3980 chunk 45 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 62 optimal weight: 10.0000 chunk 97 optimal weight: 0.6980 chunk 61 optimal weight: 0.8980 chunk 71 optimal weight: 3.9990 chunk 40 optimal weight: 0.5980 chunk 81 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.134700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.094863 restraints weight = 12009.635| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 2.40 r_work: 0.2950 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9741 Z= 0.142 Angle : 0.505 10.072 13189 Z= 0.254 Chirality : 0.042 0.190 1471 Planarity : 0.004 0.048 1709 Dihedral : 4.762 58.654 1304 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.66 % Allowed : 13.38 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.20 (0.25), residues: 1200 helix: 1.63 (0.24), residues: 498 sheet: 0.89 (0.38), residues: 187 loop : 0.03 (0.28), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 841 TYR 0.022 0.001 TYR C 127 PHE 0.011 0.001 PHE A 842 TRP 0.007 0.001 TRP A 669 HIS 0.003 0.001 HIS A 819 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 9737) covalent geometry : angle 0.50497 (13187) SS BOND : bond 0.02095 ( 1) SS BOND : angle 0.75202 ( 2) hydrogen bonds : bond 0.03609 ( 441) hydrogen bonds : angle 4.34376 ( 1230) Misc. bond : bond 0.00020 ( 3) Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 3358.62 seconds wall clock time: 57 minutes 48.09 seconds (3468.09 seconds total)