Starting phenix.real_space_refine on Fri Sep 11 13:31:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b5j_44214/09_2026/9b5j_44214.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b5j_44214/09_2026/9b5j_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_44214/09_2026/9b5j_44214.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b5j_44214/09_2026/9b5j_44214.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9b5j_44214/09_2026/9b5j_44214.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b5j_44214/09_2026/9b5j_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): 0.16s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/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: 2.18, per 1000 atoms: 0.23 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: 0.68 Conformation dependent library (CDL) restraints added in 384.1 milliseconds 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: 0.29 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: 1.45 Time building geometry restraints manager: 0.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 1619 1.27 - 1.40: 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=" C VAL A 949 " pdb=" O VAL A 949 " ideal model delta sigma weight residual 1.236 1.223 0.013 1.19e-02 7.06e+03 1.24e+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 9.32e-01 ... (remaining 9732 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.51: 13037 1.51 - 3.01: 83 3.01 - 4.52: 62 4.52 - 6.03: 3 6.03 - 7.53: 2 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=" C5' AMP B 101 " pdb=" O5' AMP B 101 " pdb=" P AMP B 101 " ideal model delta sigma weight residual 120.90 116.66 4.24 1.50e+00 4.44e-01 7.98e+00 angle pdb=" O1P AMP B 101 " pdb=" P AMP B 101 " pdb=" O2P AMP B 101 " ideal model delta sigma weight residual 119.90 112.37 7.53 3.00e+00 1.11e-01 6.31e+00 angle pdb=" C4' AMP B 101 " pdb=" C5' AMP B 101 " pdb=" O5' AMP B 101 " ideal model delta sigma weight residual 111.70 108.35 3.35 1.50e+00 4.44e-01 4.99e+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 - 0.030: 908 0.030 - 0.060: 410 0.060 - 0.091: 66 0.091 - 0.121: 72 0.121 - 0.151: 15 Chirality restraints: 1471 Sorted by residual: 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 chirality pdb=" CA VAL A 852 " pdb=" N VAL A 852 " pdb=" C VAL A 852 " pdb=" CB VAL A 852 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.44e-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: 5.580 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: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.760 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:8.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 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 : 0.652 51.470 13189 Z= 0.319 Chirality : 0.040 0.151 1471 Planarity : 0.003 0.034 1709 Dihedral : 9.887 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 are 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/Z covalent geometry : bond 0.00358 / 0.15 ( 9737) covalent geometry : angle 0.46164 / 0.23 (13187) SS BOND : bond 0.89966 / 47.35 ( 1) SS BOND : angle 37.38884 / 21.76 ( 2) hydrogen bonds : bond 0.13970 / 9.54 ( 441) hydrogen bonds : angle 5.89306 / 4.10 ( 1230) Misc. bond : bond 0.08441 / 3.71 ( 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 : 0.378 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: 0.7868 time to fit residues: 117.7751 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 : 0.391 ------------------------------------------------------------------------------- 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... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.134445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.094609 restraints weight = 11979.549| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 2.40 r_work: 0.2941 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.0966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9741 Z= 0.138 Angle : 0.510 7.518 13189 Z= 0.263 Chirality : 0.042 0.154 1471 Planarity : 0.004 0.042 1709 Dihedral : 5.725 79.426 1308 Min Nonbonded Distance : 2.481 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 are not related in a simple way. whole: 1.07 (0.25), residues: 1200 helix: 1.51 (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 0.012 0.001 PHE A 722 TRP 0.007 0.001 TRP A 669 HIS 0.007 0.001 HIS A 819 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 ( 9737) covalent geometry : angle 0.50572 / 0.26 (13187) SS BOND : bond 0.01515 / 0.80 ( 1) SS BOND : angle 5.43313 / 3.17 ( 2) hydrogen bonds : bond 0.04261 / 2.86 ( 441) hydrogen bonds : angle 4.76786 / 3.27 ( 1230) Misc. bond : bond 0.00092 / 0.04 ( 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 121 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 105 time to evaluate : 0.375 Fit side-chains revert: symmetry clash REVERT: A 105 GLN cc_start: 0.8212 (pt0) cc_final: 0.7890 (mp10) REVERT: A 469 LYS cc_start: 0.8317 (mppt) cc_final: 0.8109 (mmtm) REVERT: A 540 GLU cc_start: 0.7856 (tt0) cc_final: 0.7437 (mp0) REVERT: A 583 GLN cc_start: 0.8286 (mt0) cc_final: 0.7342 (mm-40) REVERT: A 614 GLU cc_start: 0.7387 (tp30) cc_final: 0.6606 (tm-30) REVERT: A 619 GLN cc_start: 0.7377 (tp40) cc_final: 0.6828 (tm-30) REVERT: A 840 ASP cc_start: 0.7499 (p0) cc_final: 0.7191 (p0) REVERT: B 21 ASP cc_start: 0.8236 (OUTLIER) cc_final: 0.8035 (m-30) REVERT: B 51 GLU cc_start: 0.8356 (mt-10) cc_final: 0.7978 (mt-10) REVERT: B 60 ASN cc_start: 0.8537 (m-40) cc_final: 0.8201 (t0) REVERT: C 32 HIS cc_start: 0.7518 (t-170) cc_final: 0.7217 (t70) REVERT: C 72 ARG cc_start: 0.8505 (mmm-85) cc_final: 0.8178 (mmm-85) REVERT: C 140 GLU cc_start: 0.7527 (tm-30) cc_final: 0.7306 (tm-30) outliers start: 16 outliers final: 5 residues processed: 114 average time/residue: 0.7236 time to fit residues: 87.5092 Evaluate side-chains 101 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 95 time to evaluate : 0.345 ------------------------------------------------------------------------------- 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 21 ASP 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: 0.0370 chunk 58 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 104 optimal weight: 0.7980 chunk 23 optimal weight: 4.9990 chunk 89 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 84 optimal weight: 0.5980 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.134543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.094510 restraints weight = 12017.481| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 2.41 r_work: 0.2936 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.1169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 9741 Z= 0.140 Angle : 0.485 7.122 13189 Z= 0.250 Chirality : 0.042 0.145 1471 Planarity : 0.004 0.047 1709 Dihedral : 5.276 71.756 1305 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.79 % Allowed : 8.86 % Favored : 89.35 % 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 are not related in a simple way. whole: 1.06 (0.25), residues: 1200 helix: 1.49 (0.24), residues: 503 sheet: 0.75 (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 A 841 TYR 0.019 0.001 TYR C 127 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/Z covalent geometry : bond 0.00344 / 0.14 ( 9737) covalent geometry : angle 0.48096 / 0.25 (13187) SS BOND : bond 0.01174 / 0.62 ( 1) SS BOND : angle 5.05919 / 2.97 ( 2) hydrogen bonds : bond 0.03909 / 2.62 ( 441) hydrogen bonds : angle 4.62084 / 3.17 ( 1230) Misc. bond : bond 0.00074 / 0.03 ( 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 123 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 104 time to evaluate : 0.401 Fit side-chains revert: symmetry clash REVERT: A 105 GLN cc_start: 0.8214 (pt0) cc_final: 0.7874 (mp-120) REVERT: A 216 LYS cc_start: 0.7195 (pttm) cc_final: 0.6753 (pptt) REVERT: A 540 GLU cc_start: 0.7860 (tt0) cc_final: 0.7435 (mp0) REVERT: A 583 GLN cc_start: 0.8300 (mt0) cc_final: 0.7347 (mm-40) REVERT: A 614 GLU cc_start: 0.7273 (tp30) cc_final: 0.6458 (tm-30) REVERT: A 619 GLN cc_start: 0.7332 (tp40) cc_final: 0.6715 (tm-30) REVERT: A 840 ASP cc_start: 0.7457 (p0) cc_final: 0.7159 (p0) REVERT: A 842 PHE cc_start: 0.7047 (t80) cc_final: 0.6842 (t80) REVERT: A 869 GLU cc_start: 0.7956 (tp30) cc_final: 0.7690 (tp30) REVERT: B 51 GLU cc_start: 0.8286 (mt-10) cc_final: 0.7937 (mt-10) REVERT: B 60 ASN cc_start: 0.8505 (m-40) cc_final: 0.8197 (t0) REVERT: C 32 HIS cc_start: 0.7547 (t-170) cc_final: 0.7223 (t70) REVERT: C 72 ARG cc_start: 0.8489 (mmm-85) cc_final: 0.8160 (mmm-85) REVERT: C 101 LYS cc_start: 0.8391 (mptp) cc_final: 0.8118 (mmtp) REVERT: C 140 GLU cc_start: 0.7542 (tm-30) cc_final: 0.7286 (tm-30) outliers start: 19 outliers final: 7 residues processed: 115 average time/residue: 0.6899 time to fit residues: 84.5093 Evaluate side-chains 107 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 100 time to evaluate : 0.347 ------------------------------------------------------------------------------- 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: 0.9980 chunk 67 optimal weight: 0.4980 chunk 113 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 47 optimal weight: 0.0270 chunk 44 optimal weight: 0.8980 chunk 41 optimal weight: 0.6980 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.134902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.094913 restraints weight = 12097.151| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 2.42 r_work: 0.2943 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2798 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.1280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9741 Z= 0.127 Angle : 0.474 6.550 13189 Z= 0.244 Chirality : 0.042 0.144 1471 Planarity : 0.004 0.047 1709 Dihedral : 5.207 68.871 1305 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.60 % Allowed : 10.08 % Favored : 88.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.25), residues: 1200 helix: 1.53 (0.24), residues: 503 sheet: 0.80 (0.38), residues: 185 loop : 0.02 (0.28), residues: 512 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/Z covalent geometry : bond 0.00313 / 0.13 ( 9737) covalent geometry : angle 0.47110 / 0.24 (13187) SS BOND : bond 0.00935 / 0.49 ( 1) SS BOND : angle 4.25409 / 2.46 ( 2) hydrogen bonds : bond 0.03616 / 2.42 ( 441) hydrogen bonds : angle 4.49162 / 3.07 ( 1230) Misc. bond : bond 0.00054 / 0.02 ( 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 115 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 0.393 Fit side-chains REVERT: A 105 GLN cc_start: 0.8227 (pt0) cc_final: 0.7878 (mp-120) REVERT: A 540 GLU cc_start: 0.7846 (tt0) cc_final: 0.7427 (mp0) REVERT: A 583 GLN cc_start: 0.8323 (mt0) cc_final: 0.7365 (mm-40) REVERT: A 614 GLU cc_start: 0.7334 (tp30) cc_final: 0.6505 (tm-30) REVERT: A 619 GLN cc_start: 0.7285 (tp40) cc_final: 0.6652 (tm-30) REVERT: A 840 ASP cc_start: 0.7480 (p0) cc_final: 0.7165 (p0) REVERT: A 869 GLU cc_start: 0.7965 (tp30) cc_final: 0.7710 (tp30) REVERT: B 51 GLU cc_start: 0.8301 (mt-10) cc_final: 0.7951 (mt-10) REVERT: B 60 ASN cc_start: 0.8461 (m-40) cc_final: 0.8157 (t0) REVERT: C 32 HIS cc_start: 0.7576 (t-170) cc_final: 0.7254 (t70) REVERT: C 72 ARG cc_start: 0.8497 (mmm-85) cc_final: 0.8179 (mmm-85) REVERT: C 101 LYS cc_start: 0.8431 (mptp) cc_final: 0.8159 (mmtp) REVERT: C 140 GLU cc_start: 0.7565 (tm-30) cc_final: 0.7278 (tm-30) outliers start: 17 outliers final: 7 residues processed: 109 average time/residue: 0.6331 time to fit residues: 73.4858 Evaluate side-chains 104 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 97 time to evaluate : 0.364 ------------------------------------------------------------------------------- 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: 0.0770 chunk 106 optimal weight: 0.0770 chunk 116 optimal weight: 0.9990 chunk 73 optimal weight: 0.7980 chunk 100 optimal weight: 1.9990 chunk 56 optimal weight: 0.3980 chunk 35 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 chunk 60 optimal weight: 0.4980 chunk 11 optimal weight: 0.6980 overall best weight: 0.3296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.136792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.097053 restraints weight = 12064.904| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 2.41 r_work: 0.2961 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9741 Z= 0.101 Angle : 0.477 11.761 13189 Z= 0.241 Chirality : 0.041 0.203 1471 Planarity : 0.004 0.047 1709 Dihedral : 4.969 68.870 1304 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % 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 are not related in a simple way. whole: 1.25 (0.25), residues: 1200 helix: 1.68 (0.24), residues: 498 sheet: 0.79 (0.38), residues: 188 loop : 0.09 (0.28), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 841 TYR 0.008 0.001 TYR C 74 PHE 0.009 0.001 PHE A 237 TRP 0.007 0.001 TRP A 669 HIS 0.003 0.000 HIS A 819 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.10 ( 9737) covalent geometry : angle 0.47709 / 0.24 (13187) SS BOND : bond 0.01967 / 1.04 ( 1) SS BOND : angle 1.28649 / 0.63 ( 2) hydrogen bonds : bond 0.03295 / 2.21 ( 441) hydrogen bonds : angle 4.35191 / 2.98 ( 1230) Misc. bond : bond 0.00044 / 0.02 ( 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 112 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 99 time to evaluate : 0.323 Fit side-chains REVERT: A 105 GLN cc_start: 0.8166 (pt0) cc_final: 0.7811 (mp-120) REVERT: A 221 LEU cc_start: 0.7936 (OUTLIER) cc_final: 0.7704 (tp) REVERT: A 540 GLU cc_start: 0.7733 (tt0) cc_final: 0.7300 (mp0) REVERT: A 583 GLN cc_start: 0.8295 (mt0) cc_final: 0.7322 (mm-40) REVERT: A 614 GLU cc_start: 0.7210 (tp30) cc_final: 0.6424 (tm-30) REVERT: A 619 GLN cc_start: 0.7189 (tp40) cc_final: 0.6636 (tm-30) REVERT: A 840 ASP cc_start: 0.7323 (p0) cc_final: 0.7045 (p0) REVERT: A 869 GLU cc_start: 0.7828 (tp30) cc_final: 0.7567 (tp30) REVERT: B 51 GLU cc_start: 0.8230 (mt-10) cc_final: 0.7881 (mt-10) REVERT: B 60 ASN cc_start: 0.8358 (m-40) cc_final: 0.8049 (t0) REVERT: C 32 HIS cc_start: 0.7461 (t-170) cc_final: 0.7143 (t70) REVERT: C 72 ARG cc_start: 0.8451 (mmm-85) cc_final: 0.8114 (mmm-85) REVERT: C 140 GLU cc_start: 0.7519 (tm-30) cc_final: 0.7218 (tm-30) outliers start: 13 outliers final: 7 residues processed: 110 average time/residue: 0.6134 time to fit residues: 72.3467 Evaluate side-chains 104 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 96 time to evaluate : 0.395 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 91 optimal weight: 0.7980 chunk 84 optimal weight: 0.7980 chunk 76 optimal weight: 0.0170 chunk 17 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 118 optimal weight: 0.6980 chunk 86 optimal weight: 0.7980 chunk 100 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 chunk 37 optimal weight: 0.9980 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.134973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.095005 restraints weight = 12034.282| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 2.42 r_work: 0.2955 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.1447 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= 0.130 Angle : 0.480 10.645 13189 Z= 0.244 Chirality : 0.042 0.204 1471 Planarity : 0.004 0.048 1709 Dihedral : 5.046 72.614 1304 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.32 % Allowed : 11.78 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.25), residues: 1200 helix: 1.68 (0.24), residues: 498 sheet: 0.82 (0.38), residues: 188 loop : 0.08 (0.28), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 841 TYR 0.018 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/Z covalent geometry : bond 0.00319 / 0.13 ( 9737) covalent geometry : angle 0.48001 / 0.24 (13187) SS BOND : bond 0.01640 / 0.86 ( 1) SS BOND : angle 1.73022 / 0.85 ( 2) hydrogen bonds : bond 0.03499 / 2.35 ( 441) hydrogen bonds : angle 4.35618 / 2.99 ( 1230) Misc. bond : bond 0.00037 / 0.02 ( 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 111 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 97 time to evaluate : 0.452 Fit side-chains REVERT: A 105 GLN cc_start: 0.8188 (pt0) cc_final: 0.7840 (mp-120) REVERT: A 221 LEU cc_start: 0.8005 (OUTLIER) cc_final: 0.7757 (tp) REVERT: A 540 GLU cc_start: 0.7828 (tt0) cc_final: 0.7388 (mp0) REVERT: A 583 GLN cc_start: 0.8326 (mt0) cc_final: 0.7351 (mm-40) REVERT: A 614 GLU cc_start: 0.7281 (tp30) cc_final: 0.6492 (tm-30) REVERT: A 619 GLN cc_start: 0.7222 (tp40) cc_final: 0.6595 (tm-30) REVERT: A 840 ASP cc_start: 0.7405 (p0) cc_final: 0.7119 (p0) REVERT: B 51 GLU cc_start: 0.8295 (mt-10) cc_final: 0.7954 (mt-10) REVERT: B 60 ASN cc_start: 0.8413 (m-40) cc_final: 0.8125 (t0) REVERT: C 32 HIS cc_start: 0.7525 (t-170) cc_final: 0.7212 (t70) REVERT: C 72 ARG cc_start: 0.8491 (mmm-85) cc_final: 0.8157 (mmm-85) REVERT: C 140 GLU cc_start: 0.7547 (tm-30) cc_final: 0.7239 (tm-30) outliers start: 14 outliers final: 10 residues processed: 108 average time/residue: 0.6330 time to fit residues: 72.9687 Evaluate side-chains 108 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 97 time to evaluate : 0.343 ------------------------------------------------------------------------------- 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 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: 0.0270 chunk 71 optimal weight: 3.9990 chunk 110 optimal weight: 0.9990 chunk 99 optimal weight: 0.9980 chunk 40 optimal weight: 0.5980 chunk 48 optimal weight: 0.8980 chunk 61 optimal weight: 5.9990 chunk 53 optimal weight: 0.1980 chunk 70 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 chunk 39 optimal weight: 0.5980 overall best weight: 0.4638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.134785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.094113 restraints weight = 12110.997| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 2.47 r_work: 0.2952 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9741 Z= 0.114 Angle : 0.475 9.716 13189 Z= 0.242 Chirality : 0.042 0.189 1471 Planarity : 0.004 0.048 1709 Dihedral : 5.011 71.924 1304 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.23 % Allowed : 11.78 % 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 are not related in a simple way. whole: 1.26 (0.25), residues: 1200 helix: 1.69 (0.24), residues: 498 sheet: 0.85 (0.38), residues: 188 loop : 0.07 (0.28), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 841 TYR 0.021 0.001 TYR C 127 PHE 0.010 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/Z covalent geometry : bond 0.00272 / 0.11 ( 9737) covalent geometry : angle 0.47499 / 0.24 (13187) SS BOND : bond 0.02506 / 1.32 ( 1) SS BOND : angle 0.85257 / 0.50 ( 2) hydrogen bonds : bond 0.03385 / 2.28 ( 441) hydrogen bonds : angle 4.31411 / 2.95 ( 1230) Misc. bond : bond 0.00035 / 0.02 ( 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 112 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 99 time to evaluate : 0.386 Fit side-chains REVERT: A 105 GLN cc_start: 0.8201 (pt0) cc_final: 0.7844 (mp-120) REVERT: A 221 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7841 (tp) REVERT: A 540 GLU cc_start: 0.7790 (tt0) cc_final: 0.7365 (mp0) REVERT: A 583 GLN cc_start: 0.8344 (mt0) cc_final: 0.7357 (mm-40) REVERT: A 614 GLU cc_start: 0.7283 (tp30) cc_final: 0.6496 (tm-30) REVERT: A 619 GLN cc_start: 0.7217 (tp40) cc_final: 0.6583 (tm-30) REVERT: A 840 ASP cc_start: 0.7370 (p0) cc_final: 0.7091 (p0) REVERT: B 51 GLU cc_start: 0.8285 (mt-10) cc_final: 0.7940 (mt-10) REVERT: B 60 ASN cc_start: 0.8395 (m-40) cc_final: 0.8110 (t0) REVERT: C 32 HIS cc_start: 0.7526 (t-170) cc_final: 0.7217 (t70) REVERT: C 72 ARG cc_start: 0.8521 (mmm-85) cc_final: 0.8189 (mmm-85) REVERT: C 140 GLU cc_start: 0.7549 (tm-30) cc_final: 0.7240 (tm-30) outliers start: 13 outliers final: 10 residues processed: 109 average time/residue: 0.6475 time to fit residues: 75.3365 Evaluate side-chains 106 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 95 time to evaluate : 0.413 ------------------------------------------------------------------------------- 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 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: 0.0370 chunk 118 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 26 optimal weight: 0.5980 chunk 43 optimal weight: 0.9980 chunk 115 optimal weight: 0.6980 chunk 103 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 52 optimal weight: 0.4980 chunk 63 optimal weight: 0.9980 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.134405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.093872 restraints weight = 12126.858| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 2.42 r_work: 0.2962 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9741 Z= 0.129 Angle : 0.485 9.987 13189 Z= 0.247 Chirality : 0.042 0.195 1471 Planarity : 0.004 0.048 1709 Dihedral : 5.001 68.258 1304 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.32 % Allowed : 12.16 % 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 are not related in a simple way. whole: 1.26 (0.25), residues: 1200 helix: 1.70 (0.24), residues: 497 sheet: 0.85 (0.38), residues: 188 loop : 0.06 (0.28), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 841 TYR 0.021 0.001 TYR C 127 PHE 0.010 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/Z covalent geometry : bond 0.00313 / 0.13 ( 9737) covalent geometry : angle 0.48471 / 0.25 (13187) SS BOND : bond 0.02164 / 1.14 ( 1) SS BOND : angle 0.66352 / 0.38 ( 2) hydrogen bonds : bond 0.03475 / 2.34 ( 441) hydrogen bonds : angle 4.32640 / 2.96 ( 1230) Misc. bond : bond 0.00067 / 0.03 ( 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 109 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 95 time to evaluate : 0.399 Fit side-chains REVERT: A 105 GLN cc_start: 0.8205 (pt0) cc_final: 0.7855 (mp-120) REVERT: A 221 LEU cc_start: 0.8128 (OUTLIER) cc_final: 0.7884 (tp) REVERT: A 540 GLU cc_start: 0.7854 (tt0) cc_final: 0.7425 (mp0) REVERT: A 583 GLN cc_start: 0.8355 (mt0) cc_final: 0.7366 (mm-40) REVERT: A 614 GLU cc_start: 0.7310 (tp30) cc_final: 0.6557 (tm-30) REVERT: A 619 GLN cc_start: 0.7241 (tp40) cc_final: 0.6612 (tm-30) REVERT: A 840 ASP cc_start: 0.7409 (p0) cc_final: 0.7125 (p0) REVERT: A 869 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7715 (tp30) REVERT: B 51 GLU cc_start: 0.8316 (mt-10) cc_final: 0.7975 (mt-10) REVERT: B 60 ASN cc_start: 0.8426 (m-40) cc_final: 0.8140 (t0) REVERT: C 32 HIS cc_start: 0.7550 (t-170) cc_final: 0.7237 (t70) REVERT: C 72 ARG cc_start: 0.8531 (mmm-85) cc_final: 0.8207 (mmm-85) REVERT: C 140 GLU cc_start: 0.7554 (tm-30) cc_final: 0.7251 (tm-30) outliers start: 14 outliers final: 10 residues processed: 107 average time/residue: 0.6232 time to fit residues: 71.3225 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 : 0.366 ------------------------------------------------------------------------------- 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 869 GLU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 93 optimal weight: 0.9990 chunk 113 optimal weight: 0.6980 chunk 56 optimal weight: 0.0970 chunk 74 optimal weight: 0.9990 chunk 81 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 92 optimal weight: 0.6980 chunk 66 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 61 optimal weight: 5.9990 chunk 106 optimal weight: 0.0170 overall best weight: 0.4616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.134810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.094080 restraints weight = 12110.427| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 2.47 r_work: 0.2954 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9741 Z= 0.116 Angle : 0.477 9.802 13189 Z= 0.243 Chirality : 0.041 0.184 1471 Planarity : 0.004 0.048 1709 Dihedral : 4.943 63.481 1304 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.13 % Allowed : 12.35 % 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 are not related in a simple way. whole: 1.28 (0.25), residues: 1200 helix: 1.73 (0.24), residues: 497 sheet: 0.87 (0.38), residues: 188 loop : 0.06 (0.28), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 841 TYR 0.021 0.001 TYR C 127 PHE 0.010 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/Z covalent geometry : bond 0.00280 / 0.12 ( 9737) covalent geometry : angle 0.47741 / 0.24 (13187) SS BOND : bond 0.02120 / 1.12 ( 1) SS BOND : angle 0.40577 / 0.21 ( 2) hydrogen bonds : bond 0.03378 / 2.28 ( 441) hydrogen bonds : angle 4.30095 / 2.94 ( 1230) Misc. bond : bond 0.00021 / 0.01 ( 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 106 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 94 time to evaluate : 0.446 Fit side-chains REVERT: A 105 GLN cc_start: 0.8173 (pt0) cc_final: 0.7827 (mp-120) REVERT: A 221 LEU cc_start: 0.8081 (OUTLIER) cc_final: 0.7844 (tp) REVERT: A 540 GLU cc_start: 0.7794 (tt0) cc_final: 0.7359 (mp0) REVERT: A 583 GLN cc_start: 0.8333 (mt0) cc_final: 0.7337 (mm-40) REVERT: A 614 GLU cc_start: 0.7263 (tp30) cc_final: 0.6498 (tm-30) REVERT: A 619 GLN cc_start: 0.7211 (tp40) cc_final: 0.6580 (tm-30) REVERT: A 840 ASP cc_start: 0.7321 (p0) cc_final: 0.7057 (p0) REVERT: A 869 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7575 (tp30) REVERT: B 51 GLU cc_start: 0.8260 (mt-10) cc_final: 0.7914 (mt-10) REVERT: B 60 ASN cc_start: 0.8376 (m-40) cc_final: 0.8092 (t0) REVERT: C 32 HIS cc_start: 0.7510 (t-170) cc_final: 0.7207 (t70) REVERT: C 72 ARG cc_start: 0.8505 (mmm-85) cc_final: 0.8175 (mmm-85) REVERT: C 140 GLU cc_start: 0.7539 (tm-30) cc_final: 0.7241 (tm-30) outliers start: 12 outliers final: 10 residues processed: 104 average time/residue: 0.6475 time to fit residues: 71.9946 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 : 0.351 ------------------------------------------------------------------------------- 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 869 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 112 optimal weight: 0.5980 chunk 63 optimal weight: 0.9990 chunk 21 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 106 optimal weight: 5.9990 chunk 50 optimal weight: 0.0970 chunk 57 optimal weight: 0.0060 chunk 42 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 85 optimal weight: 0.4980 chunk 22 optimal weight: 1.9990 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.134924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.094191 restraints weight = 12019.377| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 2.46 r_work: 0.2959 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9741 Z= 0.111 Angle : 0.478 9.680 13189 Z= 0.242 Chirality : 0.042 0.181 1471 Planarity : 0.004 0.048 1709 Dihedral : 4.879 60.429 1304 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.13 % Allowed : 12.35 % 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 are not related in a simple way. whole: 1.31 (0.25), residues: 1200 helix: 1.75 (0.24), residues: 497 sheet: 0.89 (0.38), residues: 188 loop : 0.07 (0.28), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 143 TYR 0.021 0.001 TYR C 127 PHE 0.010 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/Z covalent geometry : bond 0.00265 / 0.11 ( 9737) covalent geometry : angle 0.47763 / 0.24 (13187) SS BOND : bond 0.01994 / 1.05 ( 1) SS BOND : angle 0.14338 / 0.07 ( 2) hydrogen bonds : bond 0.03330 / 2.24 ( 441) hydrogen bonds : angle 4.28365 / 2.93 ( 1230) Misc. bond : bond 0.00023 / 0.01 ( 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 107 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 95 time to evaluate : 0.403 Fit side-chains REVERT: A 105 GLN cc_start: 0.8191 (pt0) cc_final: 0.7843 (mp-120) REVERT: A 221 LEU cc_start: 0.8104 (OUTLIER) cc_final: 0.7872 (tp) REVERT: A 540 GLU cc_start: 0.7822 (tt0) cc_final: 0.7392 (mp0) REVERT: A 583 GLN cc_start: 0.8349 (mt0) cc_final: 0.7356 (mm-40) REVERT: A 614 GLU cc_start: 0.7275 (tp30) cc_final: 0.6509 (tm-30) REVERT: A 619 GLN cc_start: 0.7221 (tp40) cc_final: 0.6590 (tm-30) REVERT: A 840 ASP cc_start: 0.7284 (p0) cc_final: 0.7030 (p0) REVERT: A 869 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7596 (tp30) REVERT: B 51 GLU cc_start: 0.8275 (mt-10) cc_final: 0.7928 (mt-10) REVERT: B 60 ASN cc_start: 0.8388 (m-40) cc_final: 0.8110 (t0) REVERT: C 32 HIS cc_start: 0.7539 (t-170) cc_final: 0.7181 (t-90) REVERT: C 72 ARG cc_start: 0.8509 (mmm-85) cc_final: 0.8178 (mmm-85) REVERT: C 140 GLU cc_start: 0.7558 (tm-30) cc_final: 0.7255 (tm-30) outliers start: 12 outliers final: 10 residues processed: 105 average time/residue: 0.5992 time to fit residues: 67.4804 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 : 0.367 ------------------------------------------------------------------------------- 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 869 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 0 optimal weight: 5.9990 chunk 14 optimal weight: 0.8980 chunk 45 optimal weight: 0.6980 chunk 99 optimal weight: 1.9990 chunk 68 optimal weight: 0.0070 chunk 62 optimal weight: 9.9990 chunk 97 optimal weight: 0.0770 chunk 61 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 81 optimal weight: 0.6980 overall best weight: 0.4556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.134978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.094288 restraints weight = 12025.111| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 2.46 r_work: 0.2961 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9741 Z= 0.114 Angle : 0.474 9.548 13189 Z= 0.241 Chirality : 0.041 0.174 1471 Planarity : 0.004 0.047 1709 Dihedral : 4.800 57.676 1304 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.04 % Allowed : 12.35 % Favored : 86.62 % 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 are not related in a simple way. whole: 1.31 (0.25), residues: 1200 helix: 1.73 (0.24), residues: 498 sheet: 0.91 (0.38), residues: 188 loop : 0.08 (0.28), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 841 TYR 0.023 0.001 TYR C 127 PHE 0.010 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/Z covalent geometry : bond 0.00273 / 0.11 ( 9737) covalent geometry : angle 0.47446 / 0.24 (13187) SS BOND : bond 0.01850 / 0.97 ( 1) SS BOND : angle 0.22073 / 0.10 ( 2) hydrogen bonds : bond 0.03316 / 2.23 ( 441) hydrogen bonds : angle 4.26441 / 2.91 ( 1230) Misc. bond : bond 0.00048 / 0.02 ( 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: 3612.80 seconds wall clock time: 62 minutes 4.02 seconds (3724.02 seconds total)