Starting phenix.real_space_refine on Sun Jun 8 12:50:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b5j_44214/06_2025/9b5j_44214.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b5j_44214/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9b5j_44214/06_2025/9b5j_44214.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b5j_44214/06_2025/9b5j_44214.map" model { file = "/net/cci-nas-00/data/ceres_data/9b5j_44214/06_2025/9b5j_44214.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b5j_44214/06_2025/9b5j_44214.cif" } resolution = 2.86 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.074 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 6.82, per 1000 atoms: 0.72 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: 2.36 Conformation dependent library (CDL) restraints added in 1.2 seconds 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2264 Finding SS restraints... Secondary structure from input PDB file: 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: 1.49 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: 3.39 Time building geometry restraints manager: 2.81 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: 3.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 27.230 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.570 ------------------------------------------------------------------------------- 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 : 1.53 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (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 TRP 0.006 0.001 TRP A 669 HIS 0.002 0.000 HIS C 75 PHE 0.009 0.001 PHE A 237 TYR 0.009 0.001 TYR A 544 ARG 0.002 0.000 ARG A 409 Details of bonding type rmsd hydrogen bonds : bond 0.13970 ( 441) hydrogen bonds : angle 5.89306 ( 1230) SS BOND : bond 0.89966 ( 1) SS BOND : angle 37.38884 ( 2) covalent geometry : bond 0.00362 ( 9737) covalent geometry : angle 0.47885 (13187) 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 : 1.084 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: 1.8515 time to fit residues: 279.2996 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 : 1.333 ------------------------------------------------------------------------------- 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 100 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 69 optimal weight: 0.9980 chunk 108 optimal weight: 0.4980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3608 r_free = 0.3608 target = 0.133663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.093809 restraints weight = 11966.837| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 2.38 r_work: 0.2925 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 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 : 0.004 0.064 9741 Z= 0.170 Angle : 0.539 7.502 13189 Z= 0.276 Chirality : 0.044 0.159 1471 Planarity : 0.004 0.043 1709 Dihedral : 5.704 79.153 1308 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 2.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.70 % Allowed : 8.11 % Favored : 90.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.25), residues: 1200 helix: 1.43 (0.24), residues: 503 sheet: 0.65 (0.37), residues: 186 loop : -0.02 (0.28), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 669 HIS 0.007 0.001 HIS A 819 PHE 0.014 0.001 PHE A 722 TYR 0.010 0.001 TYR A 834 ARG 0.005 0.001 ARG B 74 Details of bonding type rmsd hydrogen bonds : bond 0.04424 ( 441) hydrogen bonds : angle 4.81655 ( 1230) SS BOND : bond 0.01482 ( 1) SS BOND : angle 5.37451 ( 2) covalent geometry : bond 0.00423 ( 9737) covalent geometry : angle 0.53525 (13187) Misc. bond : bond 0.00139 ( 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 123 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 105 time to evaluate : 1.111 Fit side-chains revert: symmetry clash REVERT: A 105 GLN cc_start: 0.8197 (pt0) cc_final: 0.7870 (mp10) REVERT: A 196 MET cc_start: 0.8773 (mmp) cc_final: 0.8519 (mmm) REVERT: A 469 LYS cc_start: 0.8311 (mppt) cc_final: 0.8086 (mmtm) REVERT: A 540 GLU cc_start: 0.7841 (tt0) cc_final: 0.7396 (mp0) REVERT: A 583 GLN cc_start: 0.8265 (mt0) cc_final: 0.7312 (mm-40) REVERT: A 614 GLU cc_start: 0.7263 (tp30) cc_final: 0.6442 (tm-30) REVERT: A 619 GLN cc_start: 0.7341 (tp40) cc_final: 0.6749 (tm-30) REVERT: A 840 ASP cc_start: 0.7515 (p0) cc_final: 0.7238 (p0) REVERT: A 913 ILE cc_start: 0.7496 (OUTLIER) cc_final: 0.7047 (mp) REVERT: B 51 GLU cc_start: 0.8336 (mt-10) cc_final: 0.7955 (mt-10) REVERT: B 60 ASN cc_start: 0.8515 (m-40) cc_final: 0.8178 (t0) REVERT: C 32 HIS cc_start: 0.7482 (t-170) cc_final: 0.7181 (t70) REVERT: C 72 ARG cc_start: 0.8490 (mmm-85) cc_final: 0.8158 (mmm-85) REVERT: C 140 GLU cc_start: 0.7509 (tm-30) cc_final: 0.7275 (tm-30) outliers start: 18 outliers final: 7 residues processed: 115 average time/residue: 1.9252 time to fit residues: 236.7681 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 : 1.457 ------------------------------------------------------------------------------- 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 316 ILE Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 913 ILE 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 3 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 70 optimal weight: 0.3980 chunk 60 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 85 optimal weight: 0.0870 chunk 55 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 67 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- 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 = 0.3621 r_free = 0.3621 target = 0.134844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.094826 restraints weight = 12091.105| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 2.42 r_work: 0.2942 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.1180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9741 Z= 0.124 Angle : 0.484 6.835 13189 Z= 0.247 Chirality : 0.042 0.144 1471 Planarity : 0.004 0.046 1709 Dihedral : 5.151 74.273 1305 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.70 % Allowed : 8.86 % Favored : 89.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.25), residues: 1200 helix: 1.46 (0.24), residues: 503 sheet: 0.82 (0.38), residues: 184 loop : -0.03 (0.28), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 669 HIS 0.005 0.001 HIS A 819 PHE 0.011 0.001 PHE A 237 TYR 0.009 0.001 TYR A 736 ARG 0.005 0.000 ARG A 841 Details of bonding type rmsd hydrogen bonds : bond 0.03751 ( 441) hydrogen bonds : angle 4.59932 ( 1230) SS BOND : bond 0.01523 ( 1) SS BOND : angle 4.66437 ( 2) covalent geometry : bond 0.00298 ( 9737) covalent geometry : angle 0.48072 (13187) Misc. bond : bond 0.00150 ( 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 120 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 102 time to evaluate : 1.216 Fit side-chains revert: symmetry clash REVERT: A 105 GLN cc_start: 0.8190 (pt0) cc_final: 0.7852 (mp-120) REVERT: A 216 LYS cc_start: 0.7158 (pttm) cc_final: 0.6719 (pptt) REVERT: A 540 GLU cc_start: 0.7828 (tt0) cc_final: 0.7398 (mp0) REVERT: A 583 GLN cc_start: 0.8287 (mt0) cc_final: 0.7330 (mm-40) REVERT: A 614 GLU cc_start: 0.7255 (tp30) cc_final: 0.6443 (tm-30) REVERT: A 619 GLN cc_start: 0.7310 (tp40) cc_final: 0.6750 (tm-30) REVERT: A 840 ASP cc_start: 0.7436 (p0) cc_final: 0.7145 (p0) REVERT: A 869 GLU cc_start: 0.7912 (tp30) cc_final: 0.7644 (tp30) REVERT: A 913 ILE cc_start: 0.7552 (OUTLIER) cc_final: 0.7044 (mp) REVERT: B 51 GLU cc_start: 0.8263 (mt-10) cc_final: 0.7906 (mt-10) REVERT: B 60 ASN cc_start: 0.8430 (m-40) cc_final: 0.8106 (t0) REVERT: C 32 HIS cc_start: 0.7507 (t-170) cc_final: 0.7185 (t70) REVERT: C 72 ARG cc_start: 0.8476 (mmm-85) cc_final: 0.8144 (mmm-85) REVERT: C 101 LYS cc_start: 0.8373 (mptp) cc_final: 0.8106 (mmtp) REVERT: C 140 GLU cc_start: 0.7532 (tm-30) cc_final: 0.7261 (tm-30) outliers start: 18 outliers final: 7 residues processed: 113 average time/residue: 1.3677 time to fit residues: 165.4255 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 : 1.112 ------------------------------------------------------------------------------- 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 568 THR Chi-restraints excluded: chain A residue 913 ILE 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 61 optimal weight: 6.9990 chunk 41 optimal weight: 0.9980 chunk 116 optimal weight: 1.9990 chunk 112 optimal weight: 0.7980 chunk 3 optimal weight: 0.0980 chunk 53 optimal weight: 0.1980 chunk 25 optimal weight: 0.9980 chunk 84 optimal weight: 0.5980 chunk 16 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.135023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.095168 restraints weight = 11921.340| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 2.40 r_work: 0.2943 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2798 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.1283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9741 Z= 0.126 Angle : 0.482 6.722 13189 Z= 0.245 Chirality : 0.042 0.143 1471 Planarity : 0.004 0.047 1709 Dihedral : 5.095 72.012 1305 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.51 % Allowed : 9.99 % Favored : 88.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.25), residues: 1200 helix: 1.52 (0.24), residues: 503 sheet: 0.80 (0.38), residues: 185 loop : -0.00 (0.28), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 669 HIS 0.004 0.001 HIS A 819 PHE 0.011 0.001 PHE A 237 TYR 0.017 0.001 TYR C 127 ARG 0.005 0.000 ARG A 841 Details of bonding type rmsd hydrogen bonds : bond 0.03620 ( 441) hydrogen bonds : angle 4.50564 ( 1230) SS BOND : bond 0.00875 ( 1) SS BOND : angle 4.28668 ( 2) covalent geometry : bond 0.00305 ( 9737) covalent geometry : angle 0.47899 (13187) Misc. bond : bond 0.00054 ( 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 114 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 98 time to evaluate : 1.151 Fit side-chains REVERT: A 105 GLN cc_start: 0.8223 (pt0) cc_final: 0.7879 (mp-120) REVERT: A 216 LYS cc_start: 0.7274 (pttm) cc_final: 0.6959 (pptt) REVERT: A 540 GLU cc_start: 0.7852 (tt0) cc_final: 0.7434 (mp0) REVERT: A 583 GLN cc_start: 0.8327 (mt0) cc_final: 0.7369 (mm-40) REVERT: A 614 GLU cc_start: 0.7332 (tp30) cc_final: 0.6500 (tm-30) REVERT: A 619 GLN cc_start: 0.7286 (tp40) cc_final: 0.6655 (tm-30) REVERT: A 840 ASP cc_start: 0.7480 (p0) cc_final: 0.7156 (p0) REVERT: A 842 PHE cc_start: 0.7158 (t80) cc_final: 0.6949 (t80) REVERT: A 869 GLU cc_start: 0.7965 (tp30) cc_final: 0.7707 (tp30) REVERT: A 913 ILE cc_start: 0.7610 (OUTLIER) cc_final: 0.7122 (mp) REVERT: B 51 GLU cc_start: 0.8295 (mt-10) cc_final: 0.7944 (mt-10) REVERT: B 60 ASN cc_start: 0.8462 (m-40) cc_final: 0.8160 (t0) REVERT: C 32 HIS cc_start: 0.7577 (t-170) cc_final: 0.7257 (t70) REVERT: C 72 ARG cc_start: 0.8508 (mmm-85) cc_final: 0.8191 (mmm-85) REVERT: C 101 LYS cc_start: 0.8421 (mptp) cc_final: 0.8154 (mmtp) REVERT: C 140 GLU cc_start: 0.7570 (tm-30) cc_final: 0.7287 (tm-30) outliers start: 16 outliers final: 5 residues processed: 109 average time/residue: 1.3123 time to fit residues: 153.1754 Evaluate side-chains 102 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 96 time to evaluate : 1.050 ------------------------------------------------------------------------------- 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 913 ILE 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 20 optimal weight: 0.0970 chunk 11 optimal weight: 0.9980 chunk 6 optimal weight: 0.5980 chunk 71 optimal weight: 0.9980 chunk 23 optimal weight: 0.1980 chunk 27 optimal weight: 0.8980 chunk 75 optimal weight: 0.7980 chunk 85 optimal weight: 0.0370 chunk 33 optimal weight: 0.8980 chunk 43 optimal weight: 0.0980 chunk 76 optimal weight: 8.9990 overall best weight: 0.2056 ------------------------------------------------------------------------------- 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 = 0.3645 r_free = 0.3645 target = 0.137283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.097616 restraints weight = 11964.517| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 2.41 r_work: 0.2963 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9741 Z= 0.090 Angle : 0.484 11.742 13189 Z= 0.242 Chirality : 0.041 0.189 1471 Planarity : 0.004 0.047 1709 Dihedral : 4.864 76.035 1304 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.94 % Allowed : 11.40 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.25), residues: 1200 helix: 1.63 (0.24), residues: 504 sheet: 0.93 (0.38), residues: 184 loop : 0.05 (0.28), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 669 HIS 0.003 0.000 HIS A 819 PHE 0.009 0.001 PHE A 237 TYR 0.019 0.001 TYR C 127 ARG 0.005 0.000 ARG A 841 Details of bonding type rmsd hydrogen bonds : bond 0.03192 ( 441) hydrogen bonds : angle 4.33982 ( 1230) SS BOND : bond 0.00303 ( 1) SS BOND : angle 0.78112 ( 2) covalent geometry : bond 0.00199 ( 9737) covalent geometry : angle 0.48414 (13187) Misc. bond : bond 0.00113 ( 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: 10 poor density : 100 time to evaluate : 1.156 Fit side-chains REVERT: A 105 GLN cc_start: 0.8182 (pt0) cc_final: 0.7830 (mp-120) REVERT: A 221 LEU cc_start: 0.7965 (OUTLIER) cc_final: 0.7723 (tp) REVERT: A 540 GLU cc_start: 0.7750 (tt0) cc_final: 0.7328 (mp0) REVERT: A 543 MET cc_start: 0.7861 (mmt) cc_final: 0.7654 (mmt) REVERT: A 583 GLN cc_start: 0.8300 (mt0) cc_final: 0.7332 (mm-40) REVERT: A 614 GLU cc_start: 0.7192 (tp30) cc_final: 0.6385 (tm-30) REVERT: A 619 GLN cc_start: 0.7216 (tp40) cc_final: 0.6661 (tm-30) REVERT: A 840 ASP cc_start: 0.7356 (p0) cc_final: 0.7075 (p0) REVERT: A 869 GLU cc_start: 0.7834 (tp30) cc_final: 0.7570 (tp30) REVERT: B 51 GLU cc_start: 0.8237 (mt-10) cc_final: 0.7888 (mt-10) REVERT: B 60 ASN cc_start: 0.8364 (m-40) cc_final: 0.8058 (t0) REVERT: C 32 HIS cc_start: 0.7470 (t-170) cc_final: 0.7161 (t70) REVERT: C 72 ARG cc_start: 0.8459 (mmm-85) cc_final: 0.8133 (mmm-85) REVERT: C 140 GLU cc_start: 0.7529 (tm-30) cc_final: 0.7236 (tm-30) outliers start: 10 outliers final: 5 residues processed: 108 average time/residue: 1.3219 time to fit residues: 152.9958 Evaluate side-chains 102 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 96 time to evaluate : 1.187 ------------------------------------------------------------------------------- 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 286 MET Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 71 LEU 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 24 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 chunk 54 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 chunk 56 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 65 optimal weight: 0.1980 chunk 12 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 7 optimal weight: 0.4980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.134456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.093935 restraints weight = 12066.764| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 2.45 r_work: 0.2954 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.1477 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= 0.128 Angle : 0.486 10.494 13189 Z= 0.245 Chirality : 0.042 0.192 1471 Planarity : 0.004 0.048 1709 Dihedral : 4.897 77.769 1304 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.32 % Allowed : 11.78 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.25), residues: 1200 helix: 1.69 (0.24), residues: 498 sheet: 0.84 (0.38), residues: 188 loop : 0.07 (0.28), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 669 HIS 0.003 0.001 HIS A 819 PHE 0.011 0.001 PHE A 237 TYR 0.020 0.001 TYR C 127 ARG 0.005 0.000 ARG A 841 Details of bonding type rmsd hydrogen bonds : bond 0.03450 ( 441) hydrogen bonds : angle 4.34793 ( 1230) SS BOND : bond 0.02211 ( 1) SS BOND : angle 1.71652 ( 2) covalent geometry : bond 0.00311 ( 9737) covalent geometry : angle 0.48569 (13187) Misc. bond : bond 0.00030 ( 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 110 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 96 time to evaluate : 1.159 Fit side-chains REVERT: A 105 GLN cc_start: 0.8205 (pt0) cc_final: 0.7858 (mp-120) REVERT: A 154 ASP cc_start: 0.8363 (m-30) cc_final: 0.8082 (m-30) REVERT: A 216 LYS cc_start: 0.7280 (pttm) cc_final: 0.6872 (pptt) REVERT: A 221 LEU cc_start: 0.8040 (OUTLIER) cc_final: 0.7794 (tp) REVERT: A 540 GLU cc_start: 0.7855 (tt0) cc_final: 0.7415 (mp0) REVERT: A 583 GLN cc_start: 0.8349 (mt0) cc_final: 0.7365 (mm-40) REVERT: A 614 GLU cc_start: 0.7302 (tp30) cc_final: 0.6497 (tm-30) REVERT: A 619 GLN cc_start: 0.7233 (tp40) cc_final: 0.6611 (tm-30) REVERT: A 840 ASP cc_start: 0.7431 (p0) cc_final: 0.7152 (p0) REVERT: B 51 GLU cc_start: 0.8319 (mt-10) cc_final: 0.7979 (mt-10) REVERT: B 60 ASN cc_start: 0.8435 (m-40) cc_final: 0.8141 (t0) REVERT: C 32 HIS cc_start: 0.7529 (t-170) cc_final: 0.7218 (t70) REVERT: C 72 ARG cc_start: 0.8506 (mmm-85) cc_final: 0.8179 (mmm-85) REVERT: C 140 GLU cc_start: 0.7565 (tm-30) cc_final: 0.7274 (tm-30) outliers start: 14 outliers final: 7 residues processed: 107 average time/residue: 1.3466 time to fit residues: 154.4201 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 : 1.068 ------------------------------------------------------------------------------- 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 1 optimal weight: 0.8980 chunk 105 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 chunk 67 optimal weight: 0.0570 chunk 41 optimal weight: 0.9990 chunk 95 optimal weight: 0.8980 chunk 85 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 chunk 101 optimal weight: 0.4980 chunk 45 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 overall best weight: 0.6298 ------------------------------------------------------------------------------- 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 = 0.3612 r_free = 0.3612 target = 0.134198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.093556 restraints weight = 12040.915| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 2.45 r_work: 0.2951 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.1506 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= 0.139 Angle : 0.496 9.955 13189 Z= 0.250 Chirality : 0.042 0.197 1471 Planarity : 0.004 0.048 1709 Dihedral : 4.974 81.572 1304 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.13 % Allowed : 11.78 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.25), residues: 1200 helix: 1.67 (0.24), residues: 498 sheet: 0.83 (0.38), residues: 188 loop : 0.06 (0.28), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 669 HIS 0.003 0.001 HIS A 819 PHE 0.011 0.001 PHE A 237 TYR 0.020 0.001 TYR C 127 ARG 0.005 0.000 ARG A 841 Details of bonding type rmsd hydrogen bonds : bond 0.03573 ( 441) hydrogen bonds : angle 4.36228 ( 1230) SS BOND : bond 0.03197 ( 1) SS BOND : angle 1.13859 ( 2) covalent geometry : bond 0.00341 ( 9737) covalent geometry : angle 0.49551 (13187) Misc. bond : bond 0.00055 ( 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 109 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 97 time to evaluate : 1.122 Fit side-chains REVERT: A 105 GLN cc_start: 0.8173 (pt0) cc_final: 0.7828 (mp-120) REVERT: A 154 ASP cc_start: 0.8331 (m-30) cc_final: 0.8039 (m-30) REVERT: A 216 LYS cc_start: 0.7233 (pttm) cc_final: 0.6848 (pptt) REVERT: A 221 LEU cc_start: 0.8004 (OUTLIER) cc_final: 0.7762 (tp) REVERT: A 540 GLU cc_start: 0.7814 (tt0) cc_final: 0.7368 (mp0) REVERT: A 583 GLN cc_start: 0.8320 (mt0) cc_final: 0.7324 (mm-40) REVERT: A 614 GLU cc_start: 0.7249 (tp30) cc_final: 0.6453 (tm-30) REVERT: A 619 GLN cc_start: 0.7202 (tp40) cc_final: 0.6584 (tm-30) REVERT: A 840 ASP cc_start: 0.7370 (p0) cc_final: 0.7091 (p0) REVERT: B 51 GLU cc_start: 0.8279 (mt-10) cc_final: 0.7935 (mt-10) REVERT: B 60 ASN cc_start: 0.8399 (m-40) cc_final: 0.8109 (t0) REVERT: C 32 HIS cc_start: 0.7478 (t-170) cc_final: 0.7169 (t70) REVERT: C 72 ARG cc_start: 0.8487 (mmm-85) cc_final: 0.8149 (mmm-85) REVERT: C 140 GLU cc_start: 0.7542 (tm-30) cc_final: 0.7243 (tm-30) outliers start: 12 outliers final: 10 residues processed: 107 average time/residue: 1.3131 time to fit residues: 150.5962 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 : 1.041 ------------------------------------------------------------------------------- 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 104 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 4 optimal weight: 0.3980 chunk 56 optimal weight: 0.0980 chunk 24 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 chunk 67 optimal weight: 0.3980 chunk 51 optimal weight: 0.9980 chunk 92 optimal weight: 0.8980 chunk 82 optimal weight: 0.8980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.3617 r_free = 0.3617 target = 0.134626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.093925 restraints weight = 12239.482| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 2.48 r_work: 0.2952 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.1553 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= 0.122 Angle : 0.487 10.160 13189 Z= 0.245 Chirality : 0.042 0.188 1471 Planarity : 0.004 0.047 1709 Dihedral : 4.843 72.499 1304 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.13 % Allowed : 12.16 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.25), residues: 1200 helix: 1.69 (0.24), residues: 498 sheet: 0.89 (0.38), residues: 187 loop : 0.06 (0.28), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 669 HIS 0.003 0.001 HIS A 819 PHE 0.010 0.001 PHE A 237 TYR 0.021 0.001 TYR C 127 ARG 0.004 0.000 ARG A 841 Details of bonding type rmsd hydrogen bonds : bond 0.03443 ( 441) hydrogen bonds : angle 4.32716 ( 1230) SS BOND : bond 0.02302 ( 1) SS BOND : angle 0.76754 ( 2) covalent geometry : bond 0.00296 ( 9737) covalent geometry : angle 0.48724 (13187) Misc. bond : bond 0.00068 ( 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: 12 poor density : 97 time to evaluate : 1.070 Fit side-chains REVERT: A 105 GLN cc_start: 0.8208 (pt0) cc_final: 0.7850 (mp-120) REVERT: A 154 ASP cc_start: 0.8345 (m-30) cc_final: 0.8050 (m-30) REVERT: A 216 LYS cc_start: 0.7142 (pttm) cc_final: 0.6791 (pptt) REVERT: A 221 LEU cc_start: 0.8015 (OUTLIER) cc_final: 0.7779 (tp) REVERT: A 540 GLU cc_start: 0.7838 (tt0) cc_final: 0.7400 (mp0) REVERT: A 583 GLN cc_start: 0.8351 (mt0) cc_final: 0.7360 (mm-40) REVERT: A 614 GLU cc_start: 0.7294 (tp30) cc_final: 0.6527 (tm-30) REVERT: A 619 GLN cc_start: 0.7231 (tp40) cc_final: 0.6597 (tm-30) REVERT: A 840 ASP cc_start: 0.7381 (p0) cc_final: 0.7099 (p0) REVERT: B 51 GLU cc_start: 0.8290 (mt-10) cc_final: 0.7945 (mt-10) REVERT: B 60 ASN cc_start: 0.8398 (m-40) cc_final: 0.8113 (t0) REVERT: C 32 HIS cc_start: 0.7527 (t-170) cc_final: 0.7220 (t70) REVERT: C 72 ARG cc_start: 0.8525 (mmm-85) cc_final: 0.8199 (mmm-85) REVERT: C 140 GLU cc_start: 0.7497 (tm-30) cc_final: 0.7224 (tm-30) outliers start: 12 outliers final: 9 residues processed: 107 average time/residue: 1.2863 time to fit residues: 147.6009 Evaluate side-chains 104 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 94 time to evaluate : 1.058 ------------------------------------------------------------------------------- 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 8 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 chunk 70 optimal weight: 0.7980 chunk 101 optimal weight: 0.0970 chunk 111 optimal weight: 0.0870 chunk 18 optimal weight: 1.9990 chunk 3 optimal weight: 0.1980 chunk 114 optimal weight: 0.8980 chunk 10 optimal weight: 0.2980 chunk 45 optimal weight: 2.9990 chunk 80 optimal weight: 0.7980 overall best weight: 0.2956 ------------------------------------------------------------------------------- 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 = 0.3638 r_free = 0.3638 target = 0.136593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.095921 restraints weight = 12074.750| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 2.49 r_work: 0.2966 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9741 Z= 0.097 Angle : 0.475 9.467 13189 Z= 0.239 Chirality : 0.041 0.170 1471 Planarity : 0.004 0.047 1709 Dihedral : 4.623 59.648 1304 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.25), residues: 1200 helix: 1.77 (0.24), residues: 497 sheet: 0.92 (0.38), residues: 188 loop : 0.09 (0.28), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 669 HIS 0.003 0.000 HIS A 819 PHE 0.009 0.001 PHE A 237 TYR 0.020 0.001 TYR C 127 ARG 0.004 0.000 ARG A 841 Details of bonding type rmsd hydrogen bonds : bond 0.03120 ( 441) hydrogen bonds : angle 4.23341 ( 1230) SS BOND : bond 0.01497 ( 1) SS BOND : angle 0.27966 ( 2) covalent geometry : bond 0.00221 ( 9737) covalent geometry : angle 0.47508 (13187) Misc. bond : bond 0.00060 ( 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 107 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 95 time to evaluate : 1.052 Fit side-chains REVERT: A 105 GLN cc_start: 0.8132 (pt0) cc_final: 0.7793 (mp-120) REVERT: A 154 ASP cc_start: 0.8328 (m-30) cc_final: 0.8020 (m-30) REVERT: A 216 LYS cc_start: 0.7128 (pttm) cc_final: 0.6784 (pptt) REVERT: A 221 LEU cc_start: 0.8082 (OUTLIER) cc_final: 0.7858 (tp) REVERT: A 540 GLU cc_start: 0.7778 (tt0) cc_final: 0.7503 (pt0) REVERT: A 583 GLN cc_start: 0.8338 (mt0) cc_final: 0.7347 (mm-40) REVERT: A 614 GLU cc_start: 0.7255 (tp30) cc_final: 0.6459 (tm-30) REVERT: A 619 GLN cc_start: 0.7204 (tp40) cc_final: 0.6592 (tm-30) REVERT: A 840 ASP cc_start: 0.7253 (p0) cc_final: 0.6951 (p0) REVERT: A 869 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7569 (tp30) REVERT: B 51 GLU cc_start: 0.8257 (mt-10) cc_final: 0.7908 (mt-10) REVERT: B 60 ASN cc_start: 0.8370 (m-40) cc_final: 0.8090 (t0) REVERT: C 32 HIS cc_start: 0.7502 (t-170) cc_final: 0.7147 (t-90) REVERT: C 72 ARG cc_start: 0.8519 (mmm-85) cc_final: 0.8184 (mmm-85) REVERT: C 140 GLU cc_start: 0.7453 (tm-30) cc_final: 0.7189 (tm-30) outliers start: 12 outliers final: 9 residues processed: 105 average time/residue: 1.3054 time to fit residues: 146.7196 Evaluate side-chains 105 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 1.048 ------------------------------------------------------------------------------- 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 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 100 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 3 optimal weight: 0.0770 chunk 70 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 chunk 6 optimal weight: 0.5980 chunk 67 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 118 optimal weight: 1.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- 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 = 0.3620 r_free = 0.3620 target = 0.134783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.094349 restraints weight = 12189.832| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 2.42 r_work: 0.2965 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.1633 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= 0.132 Angle : 0.495 9.711 13189 Z= 0.248 Chirality : 0.042 0.180 1471 Planarity : 0.004 0.048 1709 Dihedral : 4.671 58.711 1304 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.04 % Allowed : 12.63 % Favored : 86.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.25), residues: 1200 helix: 1.72 (0.24), residues: 498 sheet: 0.93 (0.38), residues: 188 loop : 0.08 (0.28), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 669 HIS 0.003 0.001 HIS A 819 PHE 0.011 0.001 PHE A 237 TYR 0.021 0.001 TYR C 127 ARG 0.004 0.000 ARG A 841 Details of bonding type rmsd hydrogen bonds : bond 0.03454 ( 441) hydrogen bonds : angle 4.28884 ( 1230) SS BOND : bond 0.02037 ( 1) SS BOND : angle 0.21227 ( 2) covalent geometry : bond 0.00325 ( 9737) covalent geometry : angle 0.49477 (13187) Misc. bond : bond 0.00038 ( 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: 11 poor density : 96 time to evaluate : 1.041 Fit side-chains REVERT: A 105 GLN cc_start: 0.8192 (pt0) cc_final: 0.7844 (mp-120) REVERT: A 154 ASP cc_start: 0.8361 (m-30) cc_final: 0.8057 (m-30) REVERT: A 216 LYS cc_start: 0.7223 (pttm) cc_final: 0.6945 (pptt) REVERT: A 221 LEU cc_start: 0.8125 (OUTLIER) cc_final: 0.7901 (tp) REVERT: A 442 MET cc_start: 0.7854 (mpp) cc_final: 0.7499 (mmm) REVERT: A 540 GLU cc_start: 0.7805 (tt0) cc_final: 0.7375 (mp0) REVERT: A 583 GLN cc_start: 0.8360 (mt0) cc_final: 0.7363 (mm-40) REVERT: A 614 GLU cc_start: 0.7257 (tp30) cc_final: 0.6508 (tm-30) REVERT: A 619 GLN cc_start: 0.7322 (tp40) cc_final: 0.6670 (tm-30) REVERT: A 840 ASP cc_start: 0.7283 (p0) cc_final: 0.6977 (p0) REVERT: A 869 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7669 (tp30) REVERT: B 51 GLU cc_start: 0.8292 (mt-10) cc_final: 0.7945 (mt-10) REVERT: B 60 ASN cc_start: 0.8386 (m-40) cc_final: 0.8111 (t0) REVERT: C 32 HIS cc_start: 0.7544 (t-170) cc_final: 0.7181 (t-90) REVERT: C 72 ARG cc_start: 0.8524 (mmm-85) cc_final: 0.8193 (mmm-85) REVERT: C 140 GLU cc_start: 0.7472 (tm-30) cc_final: 0.7217 (tm-30) outliers start: 11 outliers final: 8 residues processed: 105 average time/residue: 1.3172 time to fit residues: 148.1616 Evaluate side-chains 105 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 95 time to evaluate : 1.123 ------------------------------------------------------------------------------- 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 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 90 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 82 optimal weight: 0.0870 chunk 87 optimal weight: 0.5980 chunk 48 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 chunk 97 optimal weight: 0.9990 chunk 69 optimal weight: 0.0070 chunk 9 optimal weight: 1.9990 chunk 1 optimal weight: 0.2980 chunk 76 optimal weight: 0.0670 overall best weight: 0.2114 ------------------------------------------------------------------------------- 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 = 0.3643 r_free = 0.3643 target = 0.137036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.096380 restraints weight = 12124.581| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 2.50 r_work: 0.2980 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2835 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9741 Z= 0.089 Angle : 0.473 9.093 13189 Z= 0.237 Chirality : 0.041 0.160 1471 Planarity : 0.004 0.047 1709 Dihedral : 4.500 57.658 1304 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 0.75 % Allowed : 12.91 % Favored : 86.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.25), residues: 1200 helix: 1.81 (0.24), residues: 498 sheet: 0.98 (0.38), residues: 188 loop : 0.11 (0.28), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 669 HIS 0.003 0.000 HIS A 819 PHE 0.008 0.001 PHE A 360 TYR 0.020 0.001 TYR C 127 ARG 0.004 0.000 ARG A 841 Details of bonding type rmsd hydrogen bonds : bond 0.03032 ( 441) hydrogen bonds : angle 4.18677 ( 1230) SS BOND : bond 0.01505 ( 1) SS BOND : angle 0.29338 ( 2) covalent geometry : bond 0.00198 ( 9737) covalent geometry : angle 0.47306 (13187) Misc. bond : bond 0.00019 ( 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: 7191.51 seconds wall clock time: 125 minutes 39.49 seconds (7539.49 seconds total)