Starting phenix.real_space_refine on Sat Aug 23 03:59:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b5h_44212/08_2025/9b5h_44212.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b5h_44212/08_2025/9b5h_44212.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b5h_44212/08_2025/9b5h_44212.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b5h_44212/08_2025/9b5h_44212.map" model { file = "/net/cci-nas-00/data/ceres_data/9b5h_44212/08_2025/9b5h_44212.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b5h_44212/08_2025/9b5h_44212.cif" } resolution = 2.69 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= 0.071 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 3 5.49 5 Mg 2 5.21 5 S 42 5.16 5 C 6078 2.51 5 N 1575 2.21 5 O 1836 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9536 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 7734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 985, 7734 Classifications: {'peptide': 985} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 55, 'TRANS': 928} Chain breaks: 1 Chain: "B" Number of atoms: 601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 601 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 73} Chain: "C" Number of atoms: 1158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1158 Classifications: {'peptide': 147} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 131} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Classifications: {'peptide': 1} Chain: "A" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 11 Unusual residues: {' MG': 2, 'POP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: 1.91, per 1000 atoms: 0.20 Number of scatterers: 9536 At special positions: 0 Unit cell: (86.184, 98.952, 120.232, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 42 16.00 P 3 15.00 Mg 2 11.99 O 1836 8.00 N 1575 7.00 C 6078 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 593 " - pdb=" SG CYS C 85 " distance=2.91 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.90 Conformation dependent library (CDL) restraints added in 332.5 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2264 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 10 sheets defined 47.4% alpha, 15.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 20 through 25 removed outlier: 3.717A pdb=" N TYR A 25 " --> pdb=" O SER A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 36 Processing helix chain 'A' and resid 46 through 60 Processing helix chain 'A' and resid 74 through 79 removed outlier: 3.692A pdb=" N SER A 79 " --> pdb=" O ASP A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 88 removed outlier: 4.021A pdb=" N ILE A 88 " --> pdb=" O GLU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 101 removed outlier: 4.293A pdb=" N SER A 98 " --> pdb=" O LYS A 94 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N LYS A 99 " --> pdb=" O VAL A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 123 removed outlier: 3.520A pdb=" N LYS A 121 " --> pdb=" O GLU A 118 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASN A 122 " --> pdb=" O TYR A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 146 removed outlier: 3.643A pdb=" N PHE A 142 " --> pdb=" O GLU A 138 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LYS A 145 " --> pdb=" O ASP A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 224 removed outlier: 4.146A pdb=" N GLY A 224 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 274 removed outlier: 4.319A pdb=" N LYS A 273 " --> pdb=" O ARG A 269 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ASP A 274 " --> pdb=" O GLU A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 305 removed outlier: 3.599A pdb=" N ILE A 293 " --> pdb=" O PRO A 289 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLN A 296 " --> pdb=" O HIS A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 332 Processing helix chain 'A' and resid 339 through 349 Processing helix chain 'A' and resid 354 through 375 Processing helix chain 'A' and resid 389 through 392 Processing helix chain 'A' and resid 410 through 418 removed outlier: 4.378A pdb=" N VAL A 416 " --> pdb=" O GLY A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 427 removed outlier: 3.536A pdb=" N SER A 427 " --> pdb=" O GLU A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 450 Processing helix chain 'A' and resid 468 through 474 removed outlier: 3.654A pdb=" N ASN A 473 " --> pdb=" O SER A 470 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG A 474 " --> pdb=" O ASN A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 483 Processing helix chain 'A' and resid 486 through 499 Processing helix chain 'A' and resid 500 through 503 Processing helix chain 'A' and resid 514 through 518 removed outlier: 3.934A pdb=" N GLU A 518 " --> pdb=" O PRO A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 528 removed outlier: 3.850A pdb=" N LYS A 528 " --> pdb=" O GLU A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 553 removed outlier: 3.601A pdb=" N ARG A 542 " --> pdb=" O ASN A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 582 removed outlier: 3.531A pdb=" N SER A 581 " --> pdb=" O SER A 578 " (cutoff:3.500A) removed outlier: 3.910A 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 630 Processing helix chain 'A' and resid 632 through 640 removed outlier: 3.992A pdb=" N LYS A 639 " --> pdb=" O GLU A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 643 through 656 Processing helix chain 'A' and resid 662 through 679 removed outlier: 3.595A pdb=" N CYS A 666 " --> pdb=" O SER A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 689 Processing helix chain 'A' and resid 718 through 737 Processing helix chain 'A' and resid 743 through 753 removed outlier: 3.979A pdb=" N TYR A 747 " --> pdb=" O ASP A 743 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N GLY A 753 " --> pdb=" O ARG A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 through 794 Processing helix chain 'A' and resid 796 through 800 Processing helix chain 'A' and resid 818 through 835 Processing helix chain 'A' and resid 840 through 849 Processing helix chain 'A' and resid 855 through 876 removed outlier: 3.511A pdb=" N THR A 859 " --> pdb=" O MET A 855 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL A 871 " --> pdb=" O CYS A 867 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LYS A 872 " --> pdb=" O LEU A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 883 removed outlier: 3.645A pdb=" N GLU A 882 " --> pdb=" O LYS A 879 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N TYR A 883 " --> pdb=" O ILE A 880 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 879 through 883' Processing helix chain 'A' and resid 926 through 937 Processing helix chain 'A' and resid 958 through 966 Processing helix chain 'A' and resid 969 through 979 Processing helix chain 'B' and resid 22 through 35 Processing helix chain 'B' and resid 37 through 41 Processing helix chain 'B' and resid 55 through 60 Processing helix chain 'C' and resid 3 through 16 Processing helix chain 'C' and resid 86 through 90 Processing helix chain 'C' and resid 98 through 112 Processing helix chain 'C' and resid 120 through 130 Processing helix chain 'C' and resid 130 through 145 Processing sheet with id=AA1, first strand: chain 'A' and resid 109 through 111 removed outlier: 6.791A pdb=" N VAL A 64 " --> pdb=" O SER A 110 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ASN A 39 " --> pdb=" O CYS A 125 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N VAL A 127 " --> pdb=" O ASN A 39 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N LEU A 41 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N VAL A 126 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N ALA A 153 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N VAL A 128 " --> pdb=" O ALA A 153 " (cutoff:3.500A) removed outlier: 8.270A pdb=" N SER A 155 " --> pdb=" O VAL A 128 " (cutoff:3.500A) removed outlier: 4.290A 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: 4.158A pdb=" N PHE A 209 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N THR A 195 " --> pdb=" O ALA A 186 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ILE A 188 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N VAL A 193 " --> pdb=" O ILE A 188 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 227 through 228 removed outlier: 4.158A pdb=" N PHE A 209 " --> pdb=" O VAL A 257 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 506 through 509 removed outlier: 6.553A pdb=" N ILE A 459 " --> pdb=" O THR A 507 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N TYR A 509 " --> pdb=" O ILE A 459 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL A 461 " --> pdb=" O TYR A 509 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU A 531 " --> pdb=" O SER A 429 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N SER A 559 " --> pdb=" O ASN A 534 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 905 through 908 Processing sheet with id=AA7, first strand: chain 'A' and resid 920 through 923 removed outlier: 6.419A pdb=" N TYR A 920 " --> pdb=" O CYS A1009 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N LYS A1011 " --> pdb=" O TYR A 920 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N LEU A 922 " --> pdb=" O LYS A1011 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N VAL A 990 " --> pdb=" O SER A 947 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N SER A 947 " --> pdb=" O VAL A 990 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N GLU A 992 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LEU A 945 " --> pdb=" O GLU A 992 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N CYS A 994 " --> pdb=" O THR A 943 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N SER A 947 " --> pdb=" O LEU A 951 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N LEU A 951 " --> pdb=" O SER A 947 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 920 through 923 removed outlier: 6.419A pdb=" N TYR A 920 " --> pdb=" O CYS A1009 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N LYS A1011 " --> pdb=" O TYR A 920 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N LEU A 922 " --> pdb=" O LYS A1011 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N CYS A 995 " --> pdb=" O VAL A1003 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 12 through 16 removed outlier: 3.889A pdb=" N ARG B 42 " --> pdb=" O VAL B 70 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 21 through 26 removed outlier: 6.241A pdb=" N HIS C 32 " --> pdb=" O VAL C 26 " (cutoff:3.500A) 466 hydrogen bonds defined for protein. 1269 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: 1.77 Time building geometry restraints manager: 1.21 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: 5639 1.54 - 1.67: 132 1.67 - 1.81: 64 Bond restraints: 9745 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 1.33e+01 bond pdb=" O POP A1103 " pdb=" P1 POP A1103 " ideal model delta sigma weight residual 1.660 1.610 0.050 2.00e-02 2.50e+03 6.26e+00 bond pdb=" O POP A1103 " pdb=" P2 POP A1103 " ideal model delta sigma weight residual 1.661 1.611 0.050 2.00e-02 2.50e+03 6.16e+00 bond pdb=" N MET B 1 " pdb=" CA MET B 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.88e+00 bond pdb=" C4 AMP B 101 " pdb=" C5 AMP B 101 " ideal model delta sigma weight residual 1.490 1.465 0.025 2.00e-02 2.50e+03 1.57e+00 ... (remaining 9740 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.26: 13141 3.26 - 6.52: 53 6.52 - 9.78: 5 9.78 - 13.03: 0 13.03 - 16.29: 1 Bond angle restraints: 13200 Sorted by residual: angle pdb=" P1 POP A1103 " pdb=" O POP A1103 " pdb=" P2 POP A1103 " ideal model delta sigma weight residual 139.66 123.37 16.29 3.00e+00 1.11e-01 2.95e+01 angle pdb=" C LYS A 381 " pdb=" N GLN A 382 " pdb=" CA GLN A 382 " ideal model delta sigma weight residual 121.70 128.78 -7.08 1.80e+00 3.09e-01 1.55e+01 angle pdb=" C1' AMP B 101 " pdb=" C2' AMP B 101 " pdb=" C3' AMP B 101 " ideal model delta sigma weight residual 111.00 102.16 8.84 3.00e+00 1.11e-01 8.68e+00 angle pdb=" O POP A1103 " pdb=" P1 POP A1103 " pdb=" O2 POP A1103 " ideal model delta sigma weight residual 102.11 110.62 -8.51 3.00e+00 1.11e-01 8.05e+00 angle pdb=" C2' AMP B 101 " pdb=" C3' AMP B 101 " pdb=" C4' AMP B 101 " ideal model delta sigma weight residual 111.00 103.85 7.15 3.00e+00 1.11e-01 5.69e+00 ... (remaining 13195 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.22: 5640 17.22 - 34.44: 218 34.44 - 51.65: 44 51.65 - 68.87: 5 68.87 - 86.09: 4 Dihedral angle restraints: 5911 sinusoidal: 2405 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 -142.16 56.16 1 1.00e+01 1.00e-02 4.25e+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 180.00 161.95 18.05 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CA TYR A 277 " pdb=" C TYR A 277 " pdb=" N VAL A 278 " pdb=" CA VAL A 278 " ideal model delta harmonic sigma weight residual 180.00 164.26 15.74 0 5.00e+00 4.00e-02 9.91e+00 ... (remaining 5908 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1134 0.040 - 0.081: 230 0.081 - 0.121: 91 0.121 - 0.162: 15 0.162 - 0.202: 1 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 -2.71 0.20 2.00e-01 2.50e+01 1.02e+00 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 5.60e-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 2.58 -0.14 2.00e-01 2.50e+01 4.59e-01 ... (remaining 1468 not shown) Planarity restraints: 1709 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER C 94 " 0.028 5.00e-02 4.00e+02 4.20e-02 2.82e+00 pdb=" N PRO C 95 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO C 95 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 95 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 120 " -0.024 5.00e-02 4.00e+02 3.63e-02 2.10e+00 pdb=" N PRO C 121 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO C 121 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO C 121 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS C 75 " -0.020 5.00e-02 4.00e+02 3.08e-02 1.52e+00 pdb=" N PRO C 76 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO C 76 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 76 " -0.017 5.00e-02 4.00e+02 ... (remaining 1706 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 40 2.56 - 3.14: 7429 3.14 - 3.73: 14057 3.73 - 4.31: 21271 4.31 - 4.90: 35822 Nonbonded interactions: 78619 Sorted by model distance: nonbonded pdb="MG MG A1101 " pdb=" O6 POP A1103 " model vdw 1.969 2.170 nonbonded pdb="MG MG A1101 " pdb=" O2 POP A1103 " model vdw 2.035 2.170 nonbonded pdb="MG MG A1102 " pdb=" O4 POP A1103 " model vdw 2.049 2.170 nonbonded pdb=" OD2 ASP A 465 " pdb="MG MG A1102 " model vdw 2.064 2.170 nonbonded pdb=" O PRO C 18 " pdb=" OG SER C 19 " model vdw 2.230 3.040 ... (remaining 78614 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: 3.500 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: 0.090 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.140 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:7.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 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 : 0.009 0.879 9749 Z= 0.486 Angle : 0.665 46.056 13202 Z= 0.315 Chirality : 0.041 0.202 1471 Planarity : 0.004 0.042 1709 Dihedral : 10.005 86.090 3644 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 1.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.85 % Allowed : 3.58 % Favored : 95.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.11 (0.24), residues: 1200 helix: 1.42 (0.24), residues: 492 sheet: 0.81 (0.37), residues: 183 loop : 0.16 (0.27), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 830 TYR 0.008 0.001 TYR C 74 PHE 0.010 0.001 PHE A 360 TRP 0.006 0.001 TRP A 608 HIS 0.003 0.001 HIS A 721 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 9745) covalent geometry : angle 0.51612 (13200) SS BOND : bond 0.87878 ( 1) SS BOND : angle 34.12442 ( 2) hydrogen bonds : bond 0.14690 ( 453) hydrogen bonds : angle 5.89315 ( 1269) Misc. bond : bond 0.08488 ( 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 140 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 131 time to evaluate : 0.240 Fit side-chains revert: symmetry clash REVERT: A 73 ARG cc_start: 0.7214 (mmp80) cc_final: 0.6891 (mmp80) REVERT: A 196 MET cc_start: 0.8666 (mmp) cc_final: 0.8310 (mmp) REVERT: A 216 LYS cc_start: 0.6970 (mtmm) cc_final: 0.6563 (mttm) REVERT: A 250 TYR cc_start: 0.7423 (m-80) cc_final: 0.6826 (m-80) REVERT: A 262 LYS cc_start: 0.8732 (ttpp) cc_final: 0.8461 (tmtp) REVERT: A 274 ASP cc_start: 0.7724 (t0) cc_final: 0.7201 (p0) REVERT: A 333 GLN cc_start: 0.8598 (mm-40) cc_final: 0.8378 (mp10) REVERT: A 406 ARG cc_start: 0.7869 (mtm180) cc_final: 0.6723 (mtp85) REVERT: A 516 GLU cc_start: 0.8211 (mp0) cc_final: 0.7967 (pm20) REVERT: A 540 GLU cc_start: 0.7291 (tt0) cc_final: 0.7039 (mp0) REVERT: A 583 GLN cc_start: 0.7969 (mt0) cc_final: 0.7243 (mm110) REVERT: A 611 ASP cc_start: 0.7460 (m-30) cc_final: 0.7203 (m-30) REVERT: A 626 MET cc_start: 0.7243 (ttt) cc_final: 0.6844 (mpt) REVERT: A 668 MET cc_start: 0.7090 (mmm) cc_final: 0.6846 (mmm) REVERT: A 699 GLN cc_start: 0.7780 (mm110) cc_final: 0.7543 (mp10) REVERT: A 738 LEU cc_start: 0.7659 (mt) cc_final: 0.7438 (mt) REVERT: A 879 LYS cc_start: 0.8440 (mmtt) cc_final: 0.8148 (mmtt) REVERT: A 909 ASN cc_start: 0.7480 (t0) cc_final: 0.7260 (t0) REVERT: A 1004 GLU cc_start: 0.7949 (mt-10) cc_final: 0.7641 (mt-10) REVERT: B 29 LYS cc_start: 0.8291 (mttp) cc_final: 0.8024 (mttm) REVERT: C 72 ARG cc_start: 0.8343 (mmm-85) cc_final: 0.8070 (mmm-85) REVERT: C 111 THR cc_start: 0.8950 (t) cc_final: 0.8677 (m) REVERT: C 139 ARG cc_start: 0.7756 (ttm-80) cc_final: 0.7547 (ttm-80) REVERT: C 143 ARG cc_start: 0.7858 (ttp-170) cc_final: 0.7507 (ttp-110) outliers start: 9 outliers final: 2 residues processed: 138 average time/residue: 0.5774 time to fit residues: 84.3648 Evaluate side-chains 111 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 109 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 869 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: 2.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.0000 chunk 113 optimal weight: 0.0060 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 0.5980 chunk 117 optimal weight: 0.9990 overall best weight: 0.3600 ------------------------------------------------------------------------------- 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 = 0.3541 r_free = 0.3541 target = 0.126615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.088425 restraints weight = 11652.215| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 2.24 r_work: 0.2985 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.0801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9749 Z= 0.113 Angle : 0.486 8.023 13202 Z= 0.250 Chirality : 0.042 0.149 1471 Planarity : 0.004 0.044 1709 Dihedral : 5.522 80.904 1311 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.51 % Allowed : 7.16 % Favored : 91.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.33 (0.25), residues: 1200 helix: 1.60 (0.25), residues: 496 sheet: 1.10 (0.37), residues: 178 loop : 0.22 (0.27), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 8 TYR 0.014 0.001 TYR C 145 PHE 0.011 0.001 PHE A 237 TRP 0.005 0.001 TRP A 669 HIS 0.002 0.001 HIS A 29 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 9745) covalent geometry : angle 0.47998 (13200) SS BOND : bond 0.01423 ( 1) SS BOND : angle 6.00260 ( 2) hydrogen bonds : bond 0.04252 ( 453) hydrogen bonds : angle 4.67460 ( 1269) Misc. bond : bond 0.00165 ( 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 134 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 118 time to evaluate : 0.281 Fit side-chains revert: symmetry clash REVERT: A 196 MET cc_start: 0.8731 (mmp) cc_final: 0.8313 (mmp) REVERT: A 216 LYS cc_start: 0.7366 (mtmm) cc_final: 0.7020 (mttp) REVERT: A 250 TYR cc_start: 0.7568 (m-80) cc_final: 0.7079 (m-80) REVERT: A 262 LYS cc_start: 0.8885 (ttpp) cc_final: 0.8605 (tmtp) REVERT: A 274 ASP cc_start: 0.7775 (t0) cc_final: 0.7192 (p0) REVERT: A 333 GLN cc_start: 0.8611 (mm-40) cc_final: 0.8395 (mp10) REVERT: A 406 ARG cc_start: 0.8012 (mtm180) cc_final: 0.6809 (mtp85) REVERT: A 516 GLU cc_start: 0.8369 (mp0) cc_final: 0.8006 (pm20) REVERT: A 540 GLU cc_start: 0.7694 (tt0) cc_final: 0.7248 (mp0) REVERT: A 583 GLN cc_start: 0.8113 (mt0) cc_final: 0.7318 (mm110) REVERT: A 611 ASP cc_start: 0.7773 (m-30) cc_final: 0.7553 (m-30) REVERT: A 626 MET cc_start: 0.7295 (ttt) cc_final: 0.6871 (mpt) REVERT: A 668 MET cc_start: 0.7477 (mmm) cc_final: 0.7258 (mmm) REVERT: A 699 GLN cc_start: 0.7893 (mm110) cc_final: 0.7632 (mp10) REVERT: A 879 LYS cc_start: 0.8497 (mmtt) cc_final: 0.8227 (mmtt) REVERT: A 909 ASN cc_start: 0.7415 (t0) cc_final: 0.7133 (t0) REVERT: A 1004 GLU cc_start: 0.8101 (mt-10) cc_final: 0.7841 (mt-10) REVERT: C 139 ARG cc_start: 0.7343 (ttm-80) cc_final: 0.7087 (ttm-80) REVERT: C 143 ARG cc_start: 0.7655 (ttp-170) cc_final: 0.7318 (ttp-110) outliers start: 16 outliers final: 6 residues processed: 127 average time/residue: 0.5342 time to fit residues: 71.9138 Evaluate side-chains 118 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 112 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 337 GLU Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 57 SER 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 10 optimal weight: 0.3980 chunk 34 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 60 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 83 optimal weight: 0.5980 chunk 1 optimal weight: 0.5980 chunk 18 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.125623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.089504 restraints weight = 11638.153| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 2.15 r_work: 0.3016 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.0904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 9749 Z= 0.159 Angle : 0.505 8.320 13202 Z= 0.259 Chirality : 0.043 0.152 1471 Planarity : 0.004 0.044 1709 Dihedral : 5.194 69.373 1311 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.60 % Allowed : 8.48 % Favored : 89.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.34 (0.25), residues: 1200 helix: 1.61 (0.24), residues: 489 sheet: 1.02 (0.37), residues: 178 loop : 0.26 (0.27), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 8 TYR 0.009 0.001 TYR A 150 PHE 0.012 0.001 PHE A 237 TRP 0.007 0.001 TRP A 608 HIS 0.002 0.001 HIS A 29 Details of bonding type rmsd covalent geometry : bond 0.00393 ( 9745) covalent geometry : angle 0.49957 (13200) SS BOND : bond 0.02047 ( 1) SS BOND : angle 5.96453 ( 2) hydrogen bonds : bond 0.04410 ( 453) hydrogen bonds : angle 4.58076 ( 1269) Misc. bond : bond 0.00062 ( 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 126 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 109 time to evaluate : 0.279 Fit side-chains revert: symmetry clash REVERT: A 196 MET cc_start: 0.8760 (mmp) cc_final: 0.8431 (mmp) REVERT: A 216 LYS cc_start: 0.7431 (mtmm) cc_final: 0.7067 (mttp) REVERT: A 250 TYR cc_start: 0.7626 (m-80) cc_final: 0.7171 (m-80) REVERT: A 262 LYS cc_start: 0.8921 (ttpp) cc_final: 0.8667 (tmtp) REVERT: A 274 ASP cc_start: 0.7784 (t0) cc_final: 0.7201 (p0) REVERT: A 333 GLN cc_start: 0.8619 (mm-40) cc_final: 0.8399 (mp10) REVERT: A 406 ARG cc_start: 0.8058 (mtm180) cc_final: 0.6878 (mtp85) REVERT: A 516 GLU cc_start: 0.8355 (mp0) cc_final: 0.8004 (pm20) REVERT: A 540 GLU cc_start: 0.7778 (tt0) cc_final: 0.7319 (mp0) REVERT: A 583 GLN cc_start: 0.8219 (mt0) cc_final: 0.7381 (mm110) REVERT: A 611 ASP cc_start: 0.7827 (m-30) cc_final: 0.7600 (m-30) REVERT: A 626 MET cc_start: 0.7322 (ttt) cc_final: 0.6927 (mpt) REVERT: A 668 MET cc_start: 0.7586 (mmm) cc_final: 0.7343 (mmm) REVERT: A 699 GLN cc_start: 0.7958 (mm110) cc_final: 0.7704 (mp10) REVERT: A 879 LYS cc_start: 0.8605 (mmtt) cc_final: 0.8385 (mmtt) REVERT: A 909 ASN cc_start: 0.7426 (t0) cc_final: 0.7164 (t0) REVERT: B 71 LEU cc_start: 0.9105 (OUTLIER) cc_final: 0.8662 (pp) REVERT: C 143 ARG cc_start: 0.7680 (ttp-170) cc_final: 0.7304 (ttp-170) outliers start: 17 outliers final: 9 residues processed: 120 average time/residue: 0.4933 time to fit residues: 63.1411 Evaluate side-chains 114 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 104 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 337 GLU Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 28 SER 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 97 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 42 optimal weight: 0.5980 chunk 111 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 104 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 108 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 = 0.3507 r_free = 0.3507 target = 0.124041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.088294 restraints weight = 11870.595| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 2.17 r_work: 0.2991 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.0991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 9749 Z= 0.210 Angle : 0.540 7.556 13202 Z= 0.277 Chirality : 0.045 0.158 1471 Planarity : 0.005 0.045 1709 Dihedral : 5.272 64.776 1311 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.98 % Allowed : 9.14 % Favored : 88.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.18 (0.24), residues: 1200 helix: 1.45 (0.24), residues: 489 sheet: 0.93 (0.37), residues: 180 loop : 0.22 (0.27), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 8 TYR 0.011 0.002 TYR A 544 PHE 0.013 0.002 PHE A 237 TRP 0.008 0.001 TRP A 608 HIS 0.002 0.001 HIS C 125 Details of bonding type rmsd covalent geometry : bond 0.00529 ( 9745) covalent geometry : angle 0.53614 (13200) SS BOND : bond 0.01609 ( 1) SS BOND : angle 5.19981 ( 2) hydrogen bonds : bond 0.04890 ( 453) hydrogen bonds : angle 4.63802 ( 1269) Misc. bond : bond 0.00046 ( 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 125 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 104 time to evaluate : 0.249 Fit side-chains revert: symmetry clash REVERT: A 196 MET cc_start: 0.8763 (mmp) cc_final: 0.8525 (mmp) REVERT: A 216 LYS cc_start: 0.7416 (mtmm) cc_final: 0.7025 (mttp) REVERT: A 250 TYR cc_start: 0.7661 (m-80) cc_final: 0.7196 (m-80) REVERT: A 262 LYS cc_start: 0.8872 (ttpp) cc_final: 0.8616 (tmtp) REVERT: A 274 ASP cc_start: 0.7800 (t0) cc_final: 0.7218 (p0) REVERT: A 333 GLN cc_start: 0.8626 (mm-40) cc_final: 0.8400 (mp10) REVERT: A 406 ARG cc_start: 0.8093 (mtm180) cc_final: 0.6938 (mtp85) REVERT: A 465 ASP cc_start: 0.8649 (OUTLIER) cc_final: 0.7928 (t0) REVERT: A 516 GLU cc_start: 0.8381 (mp0) cc_final: 0.8038 (pm20) REVERT: A 540 GLU cc_start: 0.7841 (tt0) cc_final: 0.7329 (mp0) REVERT: A 543 MET cc_start: 0.8341 (mmt) cc_final: 0.8124 (mmt) REVERT: A 583 GLN cc_start: 0.8234 (mt0) cc_final: 0.7418 (mm110) REVERT: A 611 ASP cc_start: 0.7930 (m-30) cc_final: 0.7712 (m-30) REVERT: A 626 MET cc_start: 0.7380 (ttt) cc_final: 0.6986 (mpt) REVERT: A 668 MET cc_start: 0.7683 (mmm) cc_final: 0.7474 (mmm) REVERT: A 699 GLN cc_start: 0.7995 (mm110) cc_final: 0.7727 (mp10) REVERT: A 909 ASN cc_start: 0.7453 (t0) cc_final: 0.7173 (t0) REVERT: B 71 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8730 (pp) REVERT: C 143 ARG cc_start: 0.7760 (ttp-170) cc_final: 0.7369 (ttp-170) outliers start: 21 outliers final: 11 residues processed: 119 average time/residue: 0.5358 time to fit residues: 67.6962 Evaluate side-chains 116 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 103 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 337 GLU Chi-restraints excluded: chain A residue 465 ASP Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 815 ASP Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain C residue 85 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 77 optimal weight: 3.9990 chunk 58 optimal weight: 0.5980 chunk 30 optimal weight: 0.7980 chunk 79 optimal weight: 0.5980 chunk 72 optimal weight: 0.5980 chunk 42 optimal weight: 0.5980 chunk 34 optimal weight: 0.9980 chunk 56 optimal weight: 0.5980 chunk 75 optimal weight: 10.0000 chunk 49 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3522 r_free = 0.3522 target = 0.125195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.087033 restraints weight = 11686.224| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 2.22 r_work: 0.2959 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.1025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9749 Z= 0.145 Angle : 0.497 7.267 13202 Z= 0.255 Chirality : 0.043 0.151 1471 Planarity : 0.004 0.043 1709 Dihedral : 5.230 69.085 1311 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.70 % Allowed : 10.74 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.27 (0.24), residues: 1200 helix: 1.56 (0.24), residues: 489 sheet: 0.97 (0.37), residues: 180 loop : 0.24 (0.27), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 8 TYR 0.009 0.001 TYR A 736 PHE 0.011 0.001 PHE A 237 TRP 0.006 0.001 TRP A 608 HIS 0.002 0.001 HIS A 29 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 9745) covalent geometry : angle 0.49374 (13200) SS BOND : bond 0.01125 ( 1) SS BOND : angle 4.61567 ( 2) hydrogen bonds : bond 0.04287 ( 453) hydrogen bonds : angle 4.52115 ( 1269) Misc. bond : bond 0.00027 ( 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 124 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 106 time to evaluate : 0.229 Fit side-chains revert: symmetry clash REVERT: A 196 MET cc_start: 0.8684 (mmp) cc_final: 0.8423 (mmp) REVERT: A 216 LYS cc_start: 0.7305 (mtmm) cc_final: 0.6919 (mttp) REVERT: A 250 TYR cc_start: 0.7601 (m-80) cc_final: 0.7136 (m-80) REVERT: A 262 LYS cc_start: 0.8886 (ttpp) cc_final: 0.8645 (tmtp) REVERT: A 274 ASP cc_start: 0.7775 (t0) cc_final: 0.7162 (p0) REVERT: A 333 GLN cc_start: 0.8612 (mm-40) cc_final: 0.8380 (mp10) REVERT: A 406 ARG cc_start: 0.8028 (mtm180) cc_final: 0.6854 (mtp85) REVERT: A 516 GLU cc_start: 0.8375 (mp0) cc_final: 0.8003 (pm20) REVERT: A 540 GLU cc_start: 0.7738 (tt0) cc_final: 0.7267 (mp0) REVERT: A 583 GLN cc_start: 0.8214 (mt0) cc_final: 0.7342 (mm110) REVERT: A 611 ASP cc_start: 0.7861 (m-30) cc_final: 0.7650 (m-30) REVERT: A 626 MET cc_start: 0.7295 (ttt) cc_final: 0.6897 (mpt) REVERT: A 668 MET cc_start: 0.7508 (mmm) cc_final: 0.7278 (mmm) REVERT: A 699 GLN cc_start: 0.7942 (mm110) cc_final: 0.7661 (mp10) REVERT: A 909 ASN cc_start: 0.7396 (t0) cc_final: 0.7124 (t0) REVERT: B 31 GLN cc_start: 0.7535 (OUTLIER) cc_final: 0.7050 (tt0) REVERT: B 71 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8632 (pp) REVERT: C 143 ARG cc_start: 0.7719 (ttp-170) cc_final: 0.7337 (ttp-170) outliers start: 18 outliers final: 11 residues processed: 120 average time/residue: 0.5401 time to fit residues: 68.9522 Evaluate side-chains 117 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 104 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 337 GLU Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 31 GLN Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain C residue 85 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 18 optimal weight: 0.0970 chunk 32 optimal weight: 0.0050 chunk 0 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 95 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 39 optimal weight: 0.0020 chunk 10 optimal weight: 0.0970 chunk 65 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 overall best weight: 0.1998 ------------------------------------------------------------------------------- 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 = 0.3559 r_free = 0.3559 target = 0.128348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.092907 restraints weight = 11688.433| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 2.17 r_work: 0.3060 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.1227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9749 Z= 0.087 Angle : 0.445 6.650 13202 Z= 0.227 Chirality : 0.041 0.145 1471 Planarity : 0.004 0.043 1709 Dihedral : 5.000 76.407 1311 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.04 % Allowed : 11.69 % Favored : 87.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.50 (0.25), residues: 1200 helix: 1.75 (0.24), residues: 489 sheet: 1.03 (0.37), residues: 181 loop : 0.37 (0.28), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 8 TYR 0.007 0.001 TYR A 736 PHE 0.008 0.001 PHE A 842 TRP 0.005 0.001 TRP A 669 HIS 0.002 0.000 HIS A 819 Details of bonding type rmsd covalent geometry : bond 0.00191 ( 9745) covalent geometry : angle 0.44289 (13200) SS BOND : bond 0.00582 ( 1) SS BOND : angle 3.64610 ( 2) hydrogen bonds : bond 0.03178 ( 453) hydrogen bonds : angle 4.22416 ( 1269) Misc. bond : bond 0.00037 ( 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 114 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 103 time to evaluate : 0.240 Fit side-chains REVERT: A 196 MET cc_start: 0.8689 (mmp) cc_final: 0.8378 (mmp) REVERT: A 216 LYS cc_start: 0.7412 (mtmm) cc_final: 0.7021 (mttp) REVERT: A 250 TYR cc_start: 0.7632 (m-80) cc_final: 0.7234 (m-80) REVERT: A 262 LYS cc_start: 0.8927 (ttpp) cc_final: 0.8718 (tmtp) REVERT: A 274 ASP cc_start: 0.7741 (t0) cc_final: 0.7152 (p0) REVERT: A 286 MET cc_start: 0.8371 (OUTLIER) cc_final: 0.8164 (mmm) REVERT: A 333 GLN cc_start: 0.8626 (mm-40) cc_final: 0.8388 (mp10) REVERT: A 406 ARG cc_start: 0.8044 (mtm180) cc_final: 0.6857 (mtp85) REVERT: A 516 GLU cc_start: 0.8382 (mp0) cc_final: 0.8066 (pm20) REVERT: A 540 GLU cc_start: 0.7755 (tt0) cc_final: 0.7294 (mp0) REVERT: A 583 GLN cc_start: 0.8106 (mt0) cc_final: 0.7377 (mm110) REVERT: A 611 ASP cc_start: 0.7830 (m-30) cc_final: 0.7571 (m-30) REVERT: A 626 MET cc_start: 0.7311 (ttt) cc_final: 0.6916 (mpt) REVERT: A 668 MET cc_start: 0.7597 (mmm) cc_final: 0.7394 (mmm) REVERT: A 699 GLN cc_start: 0.7969 (mm110) cc_final: 0.7720 (mp10) REVERT: A 909 ASN cc_start: 0.7409 (t0) cc_final: 0.7149 (t0) REVERT: A 981 LYS cc_start: 0.8472 (mmtp) cc_final: 0.8116 (mtpp) REVERT: B 71 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8635 (pp) REVERT: C 143 ARG cc_start: 0.7708 (ttp-170) cc_final: 0.7421 (ttp-170) outliers start: 11 outliers final: 4 residues processed: 110 average time/residue: 0.5482 time to fit residues: 64.1958 Evaluate side-chains 108 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 102 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 71 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 65 optimal weight: 0.9980 chunk 82 optimal weight: 0.5980 chunk 60 optimal weight: 0.4980 chunk 114 optimal weight: 3.9990 chunk 117 optimal weight: 0.5980 chunk 109 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 110 optimal weight: 0.8980 chunk 85 optimal weight: 0.6980 chunk 103 optimal weight: 0.0030 chunk 36 optimal weight: 0.9990 overall best weight: 0.4790 ------------------------------------------------------------------------------- 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 = 0.3543 r_free = 0.3543 target = 0.127016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.089028 restraints weight = 11812.865| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 2.22 r_work: 0.2994 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.1206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9749 Z= 0.121 Angle : 0.482 12.768 13202 Z= 0.244 Chirality : 0.042 0.171 1471 Planarity : 0.004 0.043 1709 Dihedral : 4.930 80.278 1310 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.23 % Allowed : 11.88 % 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 aren not related in a simple way. whole: 1.51 (0.25), residues: 1200 helix: 1.76 (0.24), residues: 490 sheet: 1.07 (0.37), residues: 181 loop : 0.37 (0.28), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 8 TYR 0.015 0.001 TYR C 145 PHE 0.010 0.001 PHE A 237 TRP 0.005 0.001 TRP A 669 HIS 0.002 0.000 HIS A 29 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 9745) covalent geometry : angle 0.48131 (13200) SS BOND : bond 0.02677 ( 1) SS BOND : angle 2.73539 ( 2) hydrogen bonds : bond 0.03599 ( 453) hydrogen bonds : angle 4.27186 ( 1269) Misc. bond : bond 0.00040 ( 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 118 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 105 time to evaluate : 0.236 Fit side-chains REVERT: A 196 MET cc_start: 0.8693 (mmp) cc_final: 0.8384 (mmp) REVERT: A 216 LYS cc_start: 0.7402 (mtmm) cc_final: 0.7010 (mttp) REVERT: A 250 TYR cc_start: 0.7538 (m-80) cc_final: 0.7171 (m-80) REVERT: A 262 LYS cc_start: 0.8923 (ttpp) cc_final: 0.8696 (tmtp) REVERT: A 274 ASP cc_start: 0.7759 (t0) cc_final: 0.7164 (p0) REVERT: A 333 GLN cc_start: 0.8613 (mm-40) cc_final: 0.8375 (mp10) REVERT: A 516 GLU cc_start: 0.8380 (mp0) cc_final: 0.8078 (pm20) REVERT: A 540 GLU cc_start: 0.7756 (tt0) cc_final: 0.7300 (mp0) REVERT: A 583 GLN cc_start: 0.8148 (mt0) cc_final: 0.7392 (mm110) REVERT: A 611 ASP cc_start: 0.7827 (m-30) cc_final: 0.7588 (m-30) REVERT: A 626 MET cc_start: 0.7350 (ttt) cc_final: 0.6959 (mpt) REVERT: A 699 GLN cc_start: 0.7980 (mm110) cc_final: 0.7724 (mp10) REVERT: A 909 ASN cc_start: 0.7398 (t0) cc_final: 0.7131 (t0) REVERT: A 981 LYS cc_start: 0.8488 (mmtp) cc_final: 0.8135 (mtpp) REVERT: B 71 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8677 (pp) REVERT: C 143 ARG cc_start: 0.7766 (ttp-170) cc_final: 0.7485 (ttp-170) outliers start: 13 outliers final: 6 residues processed: 114 average time/residue: 0.5246 time to fit residues: 63.6665 Evaluate side-chains 110 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 103 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 71 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 66 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 107 optimal weight: 4.9990 chunk 68 optimal weight: 0.6980 chunk 78 optimal weight: 0.2980 chunk 18 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 40 optimal weight: 0.2980 chunk 96 optimal weight: 0.6980 chunk 113 optimal weight: 0.7980 chunk 110 optimal weight: 0.7980 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 = 0.3541 r_free = 0.3541 target = 0.126687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.088700 restraints weight = 11643.739| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 2.21 r_work: 0.2985 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.1196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9749 Z= 0.134 Angle : 0.490 11.600 13202 Z= 0.249 Chirality : 0.042 0.175 1471 Planarity : 0.004 0.045 1709 Dihedral : 4.987 81.671 1310 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.41 % Allowed : 12.16 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.49 (0.25), residues: 1200 helix: 1.74 (0.24), residues: 490 sheet: 1.05 (0.37), residues: 181 loop : 0.36 (0.28), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 8 TYR 0.018 0.001 TYR C 145 PHE 0.011 0.001 PHE A 237 TRP 0.006 0.001 TRP A 608 HIS 0.002 0.001 HIS A 29 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 9745) covalent geometry : angle 0.48962 (13200) SS BOND : bond 0.01834 ( 1) SS BOND : angle 1.96052 ( 2) hydrogen bonds : bond 0.03764 ( 453) hydrogen bonds : angle 4.29971 ( 1269) Misc. bond : bond 0.00059 ( 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 119 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 104 time to evaluate : 0.275 Fit side-chains REVERT: A 196 MET cc_start: 0.8667 (mmp) cc_final: 0.8355 (mmp) REVERT: A 216 LYS cc_start: 0.7318 (mtmm) cc_final: 0.6921 (mttp) REVERT: A 250 TYR cc_start: 0.7418 (m-80) cc_final: 0.7071 (m-80) REVERT: A 262 LYS cc_start: 0.8942 (ttpp) cc_final: 0.8692 (tmtp) REVERT: A 274 ASP cc_start: 0.7762 (t0) cc_final: 0.7136 (p0) REVERT: A 333 GLN cc_start: 0.8607 (mm-40) cc_final: 0.8375 (mp10) REVERT: A 516 GLU cc_start: 0.8372 (mp0) cc_final: 0.8045 (pm20) REVERT: A 540 GLU cc_start: 0.7745 (tt0) cc_final: 0.7253 (mp0) REVERT: A 583 GLN cc_start: 0.8127 (mt0) cc_final: 0.7340 (mm110) REVERT: A 611 ASP cc_start: 0.7828 (m-30) cc_final: 0.7602 (m-30) REVERT: A 626 MET cc_start: 0.7307 (ttt) cc_final: 0.6902 (mpt) REVERT: A 699 GLN cc_start: 0.7957 (mm110) cc_final: 0.7682 (mp10) REVERT: A 909 ASN cc_start: 0.7366 (t0) cc_final: 0.7102 (t0) REVERT: A 981 LYS cc_start: 0.8454 (mmtp) cc_final: 0.8088 (mtpp) REVERT: B 71 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8655 (pp) REVERT: C 143 ARG cc_start: 0.7710 (ttp-170) cc_final: 0.7462 (ttp-170) outliers start: 15 outliers final: 11 residues processed: 114 average time/residue: 0.5248 time to fit residues: 63.6058 Evaluate side-chains 114 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 102 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 337 GLU Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 815 ASP Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain C residue 110 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 30 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 101 optimal weight: 0.0040 chunk 61 optimal weight: 0.7980 chunk 111 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 46 optimal weight: 0.5980 chunk 60 optimal weight: 0.0980 chunk 52 optimal weight: 0.9990 overall best weight: 0.4392 ------------------------------------------------------------------------------- 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 = 0.3544 r_free = 0.3544 target = 0.126985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.091009 restraints weight = 11708.812| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 2.16 r_work: 0.3015 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.1237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9749 Z= 0.117 Angle : 0.480 10.679 13202 Z= 0.243 Chirality : 0.042 0.167 1471 Planarity : 0.004 0.044 1709 Dihedral : 4.934 79.915 1310 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.23 % Allowed : 12.35 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.51 (0.25), residues: 1200 helix: 1.70 (0.24), residues: 496 sheet: 1.05 (0.37), residues: 181 loop : 0.43 (0.28), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 8 TYR 0.016 0.001 TYR C 145 PHE 0.010 0.001 PHE A 237 TRP 0.005 0.001 TRP A 669 HIS 0.001 0.000 HIS A 29 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 9745) covalent geometry : angle 0.47983 (13200) SS BOND : bond 0.01603 ( 1) SS BOND : angle 1.89111 ( 2) hydrogen bonds : bond 0.03636 ( 453) hydrogen bonds : angle 4.26827 ( 1269) Misc. bond : bond 0.00048 ( 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 118 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 105 time to evaluate : 0.378 Fit side-chains REVERT: A 196 MET cc_start: 0.8621 (mmp) cc_final: 0.8306 (mmp) REVERT: A 216 LYS cc_start: 0.7286 (mtmm) cc_final: 0.6889 (mttp) REVERT: A 250 TYR cc_start: 0.7400 (m-80) cc_final: 0.7060 (m-80) REVERT: A 262 LYS cc_start: 0.8931 (ttpp) cc_final: 0.8673 (tmtp) REVERT: A 274 ASP cc_start: 0.7772 (t0) cc_final: 0.7104 (p0) REVERT: A 516 GLU cc_start: 0.8380 (mp0) cc_final: 0.7996 (pm20) REVERT: A 540 GLU cc_start: 0.7726 (tt0) cc_final: 0.7240 (mp0) REVERT: A 583 GLN cc_start: 0.8077 (mt0) cc_final: 0.7280 (mm110) REVERT: A 611 ASP cc_start: 0.7793 (m-30) cc_final: 0.7558 (m-30) REVERT: A 626 MET cc_start: 0.7262 (ttt) cc_final: 0.6864 (mpt) REVERT: A 699 GLN cc_start: 0.7932 (mm110) cc_final: 0.7651 (mp10) REVERT: A 909 ASN cc_start: 0.7349 (t0) cc_final: 0.7085 (t0) REVERT: A 981 LYS cc_start: 0.8440 (mmtp) cc_final: 0.8069 (mtpp) REVERT: B 71 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8609 (pp) REVERT: C 143 ARG cc_start: 0.7682 (ttp-170) cc_final: 0.7435 (ttp-170) outliers start: 13 outliers final: 10 residues processed: 114 average time/residue: 0.5744 time to fit residues: 69.9953 Evaluate side-chains 115 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 104 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 337 GLU Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain C residue 110 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 53 optimal weight: 0.0970 chunk 74 optimal weight: 0.9990 chunk 112 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 19 optimal weight: 0.5980 chunk 108 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 chunk 60 optimal weight: 0.0970 chunk 114 optimal weight: 0.0470 overall best weight: 0.2874 ------------------------------------------------------------------------------- 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 = 0.3554 r_free = 0.3554 target = 0.127836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.089904 restraints weight = 11644.378| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 2.22 r_work: 0.3005 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.1294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9749 Z= 0.098 Angle : 0.467 9.894 13202 Z= 0.236 Chirality : 0.041 0.162 1471 Planarity : 0.004 0.045 1709 Dihedral : 4.836 76.806 1310 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.13 % Allowed : 12.54 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.60 (0.25), residues: 1200 helix: 1.77 (0.24), residues: 496 sheet: 1.10 (0.36), residues: 187 loop : 0.48 (0.28), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 8 TYR 0.015 0.001 TYR C 145 PHE 0.010 0.001 PHE A 360 TRP 0.005 0.001 TRP A 669 HIS 0.001 0.000 HIS A 819 Details of bonding type rmsd covalent geometry : bond 0.00227 ( 9745) covalent geometry : angle 0.46646 (13200) SS BOND : bond 0.01550 ( 1) SS BOND : angle 1.77621 ( 2) hydrogen bonds : bond 0.03362 ( 453) hydrogen bonds : angle 4.19457 ( 1269) Misc. bond : bond 0.00042 ( 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 117 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 105 time to evaluate : 0.383 Fit side-chains REVERT: A 196 MET cc_start: 0.8644 (mmp) cc_final: 0.8320 (mmp) REVERT: A 216 LYS cc_start: 0.7308 (mtmm) cc_final: 0.6912 (mttp) REVERT: A 250 TYR cc_start: 0.7412 (m-80) cc_final: 0.7068 (m-80) REVERT: A 262 LYS cc_start: 0.8934 (ttpp) cc_final: 0.8692 (tmtp) REVERT: A 274 ASP cc_start: 0.7782 (t0) cc_final: 0.7137 (p0) REVERT: A 286 MET cc_start: 0.8390 (mmp) cc_final: 0.8176 (mmm) REVERT: A 516 GLU cc_start: 0.8366 (mp0) cc_final: 0.8038 (pm20) REVERT: A 540 GLU cc_start: 0.7797 (tt0) cc_final: 0.7316 (mp0) REVERT: A 583 GLN cc_start: 0.8115 (mt0) cc_final: 0.7357 (mm110) REVERT: A 611 ASP cc_start: 0.7802 (m-30) cc_final: 0.7559 (m-30) REVERT: A 626 MET cc_start: 0.7294 (ttt) cc_final: 0.6901 (mpt) REVERT: A 699 GLN cc_start: 0.7954 (mm110) cc_final: 0.7675 (mp10) REVERT: A 909 ASN cc_start: 0.7358 (t0) cc_final: 0.7096 (t0) REVERT: A 981 LYS cc_start: 0.8450 (mmtp) cc_final: 0.8080 (mtpp) REVERT: B 71 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8638 (pp) REVERT: C 143 ARG cc_start: 0.7694 (ttp-170) cc_final: 0.7449 (ttp-170) outliers start: 12 outliers final: 8 residues processed: 114 average time/residue: 0.5276 time to fit residues: 64.3515 Evaluate side-chains 113 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 104 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 110 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 8 optimal weight: 0.7980 chunk 56 optimal weight: 0.6980 chunk 76 optimal weight: 0.2980 chunk 116 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 99 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 101 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 45 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.126221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.088195 restraints weight = 11726.889| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 2.22 r_work: 0.2978 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2856 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.1248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9749 Z= 0.143 Angle : 0.498 10.356 13202 Z= 0.252 Chirality : 0.043 0.165 1471 Planarity : 0.004 0.044 1709 Dihedral : 4.903 73.231 1310 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.32 % Allowed : 12.63 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.49 (0.25), residues: 1200 helix: 1.67 (0.24), residues: 496 sheet: 1.07 (0.37), residues: 181 loop : 0.43 (0.28), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 8 TYR 0.017 0.001 TYR C 145 PHE 0.012 0.001 PHE A 237 TRP 0.007 0.001 TRP A 608 HIS 0.002 0.001 HIS C 75 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 9745) covalent geometry : angle 0.49728 (13200) SS BOND : bond 0.01818 ( 1) SS BOND : angle 1.54775 ( 2) hydrogen bonds : bond 0.03951 ( 453) hydrogen bonds : angle 4.32038 ( 1269) Misc. bond : bond 0.00028 ( 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: 2999.38 seconds wall clock time: 51 minutes 25.89 seconds (3085.89 seconds total)