Starting phenix.real_space_refine on Sat Sep 12 00:27:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7jl0_22368/09_2026/7jl0_22368.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jl0_22368/09_2026/7jl0_22368.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7jl0_22368/09_2026/7jl0_22368.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7jl0_22368/09_2026/7jl0_22368.cif" model { file = "/net/cci-nas-00/data/ceres_data/7jl0_22368/09_2026/7jl0_22368.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jl0_22368/09_2026/7jl0_22368.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7jl0_22368/09_2026/7jl0_22368.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jl0_22368/09_2026/7jl0_22368.map" } resolution = 4.3 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5893 atoms to isotropic. 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: 9 Type Number sf(0) Gaussians Zn 1 6.06 5 Al 1 5.89 5 P 30 5.49 5 Mg 1 5.21 5 S 42 5.16 5 C 4554 2.51 5 N 1283 2.21 5 O 1438 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7354 Number of models: 1 Model: "" Number of chains: 5 Chain: "X" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 300 Classifications: {'RNAv2': 14} Modifications used: {'rna3p_pur': 8, 'rna3p_pyr': 6} Link IDs: {'rna3p': 13} Chain: "Y" Number of atoms: 295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 295 Classifications: {'RNAv2': 14} Modifications used: {'rna3p_pur': 6, 'rna3p_pyr': 8} Link IDs: {'rna3p': 13} Chain: "A" Number of atoms: 5311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 662, 5311 Classifications: {'peptide': 662} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 21, 'TRANS': 640} Chain breaks: 8 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'GLU:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "B" Number of atoms: 1414 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 180, 1404 Classifications: {'peptide': 180} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 167} Chain breaks: 1 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 5, 'GLN:plan1': 3, 'ASP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 43 Conformer: "B" Number of residues, atoms: 180, 1404 Classifications: {'peptide': 180} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 167} Chain breaks: 1 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 5, 'GLN:plan1': 3, 'ASP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 43 bond proxies already assigned to first conformer: 1438 Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' MG': 1, ' ZN': 1, 'ADP': 1, 'ALF': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5098 SG CYS A 907 86.171 20.420 28.789 1.00 67.24 S ATOM 5121 SG CYS A 910 86.717 17.188 28.952 1.00 79.54 S ATOM 5454 SG CYS A 962 86.167 18.607 25.327 1.00 82.04 S ATOM 5469 SG CYS A 964 83.656 17.332 28.245 1.00 96.45 S Time building chain proxies: 1.68, per 1000 atoms: 0.23 Number of scatterers: 7354 At special positions: 0 Unit cell: (114.989, 102.558, 71.4799, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Zn 1 29.99 S 42 16.00 P 30 15.00 Al 1 13.00 Mg 1 11.99 F 4 9.00 O 1438 8.00 N 1283 7.00 C 4554 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=0, symmetry=0 Time building additional restraints: 0.80 Conformation dependent library (CDL) restraints added in 300.0 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1101 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 910 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 907 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 964 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 962 " Number of angles added : 6 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1602 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 7 sheets defined 43.0% alpha, 15.1% beta 10 base pairs and 18 stacking pairs defined. Time for finding SS restraints: 0.75 Creating SS restraints... Processing helix chain 'A' and resid 309 through 317 Processing helix chain 'A' and resid 318 through 321 removed outlier: 3.667A pdb=" N GLU A 321 " --> pdb=" O PRO A 318 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 318 through 321' Processing helix chain 'A' and resid 334 through 353 removed outlier: 3.672A pdb=" N ALA A 353 " --> pdb=" O LYS A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 375 removed outlier: 3.584A pdb=" N VAL A 369 " --> pdb=" O LYS A 365 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU A 370 " --> pdb=" O VAL A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 381 removed outlier: 3.718A pdb=" N PHE A 380 " --> pdb=" O GLU A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 407 Processing helix chain 'A' and resid 414 through 422 Processing helix chain 'A' and resid 445 through 448 Processing helix chain 'A' and resid 452 through 472 removed outlier: 3.668A pdb=" N ASN A 456 " --> pdb=" O ALA A 452 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ILE A 457 " --> pdb=" O VAL A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 514 Processing helix chain 'A' and resid 524 through 532 Processing helix chain 'A' and resid 548 through 566 removed outlier: 4.626A pdb=" N GLU A 552 " --> pdb=" O ASP A 548 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N CYS A 565 " --> pdb=" O ILE A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 593 removed outlier: 3.725A pdb=" N GLU A 579 " --> pdb=" O THR A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 617 Processing helix chain 'A' and resid 618 through 640 removed outlier: 3.812A pdb=" N ALA A 622 " --> pdb=" O ARG A 618 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLU A 632 " --> pdb=" O THR A 628 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA A 639 " --> pdb=" O ASP A 635 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N VAL A 640 " --> pdb=" O LYS A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 673 through 692 removed outlier: 4.114A pdb=" N MET A 677 " --> pdb=" O ASP A 673 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N LEU A 679 " --> pdb=" O PHE A 675 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N GLU A 682 " --> pdb=" O THR A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 716 removed outlier: 3.687A pdb=" N LYS A 703 " --> pdb=" O GLU A 699 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU A 716 " --> pdb=" O TYR A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 727 through 741 removed outlier: 4.069A pdb=" N ASN A 741 " --> pdb=" O TRP A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 747 removed outlier: 3.881A pdb=" N GLU A 746 " --> pdb=" O GLU A 742 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N VAL A 747 " --> pdb=" O LYS A 743 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 742 through 747' Processing helix chain 'A' and resid 767 through 781 removed outlier: 3.861A pdb=" N THR A 780 " --> pdb=" O SER A 776 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLY A 781 " --> pdb=" O LYS A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 790 through 793 Processing helix chain 'A' and resid 813 through 822 removed outlier: 4.360A pdb=" N ALA A 819 " --> pdb=" O ALA A 815 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG A 820 " --> pdb=" O MET A 816 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY A 821 " --> pdb=" O VAL A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 840 through 862 Processing helix chain 'A' and resid 865 through 895 removed outlier: 3.617A pdb=" N ILE A 881 " --> pdb=" O GLN A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 933 through 939 removed outlier: 4.151A pdb=" N TYR A 939 " --> pdb=" O PHE A 935 " (cutoff:3.500A) Processing helix chain 'A' and resid 983 through 985 No H-bonds generated for 'chain 'A' and resid 983 through 985' Processing helix chain 'B' and resid 322 through 327 Processing helix chain 'B' and resid 328 through 330 No H-bonds generated for 'chain 'B' and resid 328 through 330' Processing sheet with id=AA1, first strand: chain 'A' and resid 325 through 328 removed outlier: 7.083A pdb=" N ILE A 325 " --> pdb=" O GLY A 486 " (cutoff:3.500A) removed outlier: 8.720A pdb=" N THR A 488 " --> pdb=" O ILE A 325 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ILE A 327 " --> pdb=" O THR A 488 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N ILE A 440 " --> pdb=" O LEU A 485 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N LEU A 487 " --> pdb=" O ILE A 440 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ILE A 442 " --> pdb=" O LEU A 487 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 536 through 541 removed outlier: 3.656A pdb=" N ALA A 834 " --> pdb=" O ALA A 540 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N GLY A 721 " --> pdb=" O LEU A 786 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N ALA A 788 " --> pdb=" O GLY A 721 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N ILE A 723 " --> pdb=" O ALA A 788 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N HIS A 752 " --> pdb=" O LEU A 785 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 913 through 916 removed outlier: 6.903A pdb=" N LEU A 913 " --> pdb=" O CYS A 907 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N CYS A 907 " --> pdb=" O LEU A 913 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N CYS A 915 " --> pdb=" O PHE A 905 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 920 through 923 Processing sheet with id=AA5, first strand: chain 'A' and resid 940 through 942 removed outlier: 4.532A pdb=" N GLY A 969 " --> pdb=" O ILE A 960 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU A 979 " --> pdb=" O MET A 972 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 344 through 347 removed outlier: 3.934A pdb=" N TYR B 475 " --> pdb=" O PHE B 464 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N SER B 466 " --> pdb=" O PRO B 473 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 372 through 374 309 hydrogen bonds defined for protein. 886 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 25 hydrogen bonds 50 hydrogen bond angles 0 basepair planarities 10 basepair parallelities 18 stacking parallelities Total time for adding SS restraints: 1.43 Time building geometry restraints manager: 1.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1806 1.33 - 1.45: 1678 1.45 - 1.58: 3941 1.58 - 1.70: 58 1.70 - 1.82: 69 Bond restraints: 7552 Sorted by residual: bond pdb=" CA LYS A 782 " pdb=" C LYS A 782 " ideal model delta sigma weight residual 1.521 1.601 -0.079 1.29e-02 6.01e+03 3.79e+01 bond pdb=" F1 ALF A1103 " pdb="AL ALF A1103 " ideal model delta sigma weight residual 1.684 1.780 -0.096 2.00e-02 2.50e+03 2.30e+01 bond pdb=" F3 ALF A1103 " pdb="AL ALF A1103 " ideal model delta sigma weight residual 1.685 1.780 -0.095 2.00e-02 2.50e+03 2.24e+01 bond pdb=" F4 ALF A1103 " pdb="AL ALF A1103 " ideal model delta sigma weight residual 1.686 1.780 -0.094 2.00e-02 2.50e+03 2.21e+01 bond pdb=" F2 ALF A1103 " pdb="AL ALF A1103 " ideal model delta sigma weight residual 1.685 1.778 -0.093 2.00e-02 2.50e+03 2.17e+01 ... (remaining 7547 not shown) Histogram of bond angle deviations from ideal: 0.00 - 13.82: 10321 13.82 - 27.64: 5 27.64 - 41.46: 0 41.46 - 55.29: 0 55.29 - 69.11: 2 Bond angle restraints: 10328 Sorted by residual: angle pdb=" F3 ALF A1103 " pdb="AL ALF A1103 " pdb=" F4 ALF A1103 " ideal model delta sigma weight residual 109.63 178.74 -69.11 3.00e+00 1.11e-01 5.31e+02 angle pdb=" F1 ALF A1103 " pdb="AL ALF A1103 " pdb=" F2 ALF A1103 " ideal model delta sigma weight residual 108.68 177.20 -68.52 3.00e+00 1.11e-01 5.22e+02 angle pdb=" N ILE A 783 " pdb=" CA ILE A 783 " pdb=" CB ILE A 783 " ideal model delta sigma weight residual 111.41 123.55 -12.14 1.38e+00 5.25e-01 7.74e+01 angle pdb=" F2 ALF A1103 " pdb="AL ALF A1103 " pdb=" F3 ALF A1103 " ideal model delta sigma weight residual 109.59 88.39 21.20 3.00e+00 1.11e-01 4.99e+01 angle pdb=" F1 ALF A1103 " pdb="AL ALF A1103 " pdb=" F4 ALF A1103 " ideal model delta sigma weight residual 109.02 88.09 20.93 3.00e+00 1.11e-01 4.87e+01 ... (remaining 10323 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.18: 4407 33.18 - 66.37: 107 66.37 - 99.55: 10 99.55 - 132.73: 2 132.73 - 165.91: 1 Dihedral angle restraints: 4527 sinusoidal: 2064 harmonic: 2463 Sorted by residual: dihedral pdb=" O5' C X 7 " pdb=" C5' C X 7 " pdb=" C4' C X 7 " pdb=" C3' C X 7 " ideal model delta sinusoidal sigma weight residual 180.00 128.77 51.23 3 6.40e+00 2.44e-02 4.94e+01 dihedral pdb=" O5' U X 4 " pdb=" C5' U X 4 " pdb=" C4' U X 4 " pdb=" C3' U X 4 " ideal model delta sinusoidal sigma weight residual 180.00 129.59 50.41 3 6.40e+00 2.44e-02 4.89e+01 dihedral pdb=" C5' ADP A1102 " pdb=" O5' ADP A1102 " pdb=" PA ADP A1102 " pdb=" O2A ADP A1102 " ideal model delta sinusoidal sigma weight residual -60.00 105.92 -165.91 1 2.00e+01 2.50e-03 4.73e+01 ... (remaining 4524 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 874 0.056 - 0.113: 238 0.113 - 0.169: 33 0.169 - 0.225: 19 0.225 - 0.281: 13 Chirality restraints: 1177 Sorted by residual: chirality pdb=" CA LYS A 782 " pdb=" N LYS A 782 " pdb=" C LYS A 782 " pdb=" CB LYS A 782 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.98e+00 chirality pdb=" P U Y 1 " pdb=" OP1 U Y 1 " pdb=" OP2 U Y 1 " pdb=" O5' U Y 1 " both_signs ideal model delta sigma weight residual True 2.17 -2.44 -0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" CB ILE A 479 " pdb=" CA ILE A 479 " pdb=" CG1 ILE A 479 " pdb=" CG2 ILE A 479 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.75e+00 ... (remaining 1174 not shown) Planarity restraints: 1210 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN A 711 " 0.016 2.00e-02 2.50e+03 3.18e-02 1.01e+01 pdb=" CD GLN A 711 " -0.055 2.00e-02 2.50e+03 pdb=" OE1 GLN A 711 " 0.021 2.00e-02 2.50e+03 pdb=" NE2 GLN A 711 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 377 " 0.021 2.00e-02 2.50e+03 1.79e-02 5.61e+00 pdb=" CG PHE A 377 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 PHE A 377 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE A 377 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE A 377 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE A 377 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE A 377 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 763 " -0.003 2.00e-02 2.50e+03 1.67e-02 4.87e+00 pdb=" CG PHE A 763 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 PHE A 763 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 PHE A 763 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 PHE A 763 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE A 763 " -0.006 2.00e-02 2.50e+03 pdb=" CZ PHE A 763 " 0.006 2.00e-02 2.50e+03 ... (remaining 1207 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 39 2.47 - 3.08: 5085 3.08 - 3.68: 10739 3.68 - 4.29: 15233 4.29 - 4.90: 24550 Nonbonded interactions: 55646 Sorted by model distance: nonbonded pdb=" F4 ALF A1103 " pdb="MG MG A1104 " model vdw 1.860 2.120 nonbonded pdb=" O1B ADP A1102 " pdb=" F1 ALF A1103 " model vdw 2.119 2.990 nonbonded pdb=" F1 ALF A1103 " pdb="MG MG A1104 " model vdw 2.148 2.120 nonbonded pdb=" NH2 ARG A 822 " pdb=" F3 ALF A1103 " model vdw 2.155 3.070 nonbonded pdb=" O2B ADP A1102 " pdb=" F3 ALF A1103 " model vdw 2.166 2.990 ... (remaining 55641 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.690 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 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 : 0.008 0.096 7556 Z= 0.374 Angle : 1.461 69.108 10334 Z= 0.632 Chirality : 0.061 0.281 1177 Planarity : 0.005 0.053 1210 Dihedral : 14.719 165.915 2925 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 0.14 % Allowed : 0.55 % Favored : 99.32 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.52 (0.27), residues: 822 helix: -0.02 (0.27), residues: 307 sheet: -0.96 (0.37), residues: 164 loop : -1.88 (0.30), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 824 TYR 0.019 0.003 TYR A 311 PHE 0.042 0.003 PHE A 377 TRP 0.011 0.002 TRP B 423 HIS 0.011 0.002 HIS A 835 Details of bonding type rmsd/Z covalent geometry : bond 0.00809 / 0.37 ( 7552) covalent geometry : angle 1.41959 / 0.63 (10328) hydrogen bonds : bond 0.13591 / 7.01 ( 334) hydrogen bonds : angle 6.23491 / 2.39 ( 936) metal coordination : bond 0.01580 / 0.79 ( 4) metal coordination : angle 14.33987 / 4.78 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 182 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 333 SER cc_start: 0.8185 (p) cc_final: 0.7858 (t) REVERT: A 391 SER cc_start: 0.8429 (p) cc_final: 0.8175 (p) REVERT: A 529 LYS cc_start: 0.8656 (mmtp) cc_final: 0.8401 (tmtt) REVERT: A 783 ILE cc_start: 0.9457 (mt) cc_final: 0.9171 (mm) REVERT: A 853 MET cc_start: 0.8725 (ttm) cc_final: 0.8211 (ttm) REVERT: A 875 GLU cc_start: 0.7772 (mt-10) cc_final: 0.7199 (tp30) REVERT: A 942 ARG cc_start: 0.8417 (ttp-110) cc_final: 0.7977 (ptt90) REVERT: B 331 ARG cc_start: 0.4894 (mmt-90) cc_final: 0.4661 (mmt90) REVERT: B 387 GLU cc_start: 0.7754 (mm-30) cc_final: 0.7384 (mp0) outliers start: 1 outliers final: 0 residues processed: 183 average time/residue: 0.1076 time to fit residues: 25.0001 Evaluate side-chains 96 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.0000 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 505 HIS A 562 GLN A 784 ASN A 877 GLN B 343 HIS B 436 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.101783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.080296 restraints weight = 34261.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.083184 restraints weight = 19793.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.083959 restraints weight = 12259.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.084255 restraints weight = 9477.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.084387 restraints weight = 9031.686| |-----------------------------------------------------------------------------| r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3155 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3155 r_free = 0.3155 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3155 r_free = 0.3155 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3155 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.3174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7556 Z= 0.143 Angle : 0.986 30.250 10334 Z= 0.408 Chirality : 0.048 0.172 1177 Planarity : 0.004 0.050 1210 Dihedral : 10.776 154.467 1239 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 0.14 % Allowed : 4.10 % Favored : 95.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.28), residues: 822 helix: 1.07 (0.28), residues: 321 sheet: -0.62 (0.37), residues: 173 loop : -1.41 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 323 TYR 0.017 0.002 TYR A 732 PHE 0.016 0.002 PHE B 335 TRP 0.024 0.002 TRP B 386 HIS 0.010 0.001 HIS B 436 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.14 ( 7552) covalent geometry : angle 0.94882 / 0.40 (10328) hydrogen bonds : bond 0.04793 / 2.46 ( 334) hydrogen bonds : angle 4.57682 / 1.77 ( 936) metal coordination : bond 0.01539 / 0.77 ( 4) metal coordination : angle 11.15211 / 3.72 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 122 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 333 SER cc_start: 0.8077 (p) cc_final: 0.7679 (t) REVERT: A 391 SER cc_start: 0.8541 (p) cc_final: 0.8260 (p) REVERT: A 584 GLN cc_start: 0.8239 (OUTLIER) cc_final: 0.7899 (pm20) REVERT: A 686 MET cc_start: 0.7946 (tpp) cc_final: 0.7717 (tpp) REVERT: A 853 MET cc_start: 0.8659 (ttm) cc_final: 0.8057 (ttm) REVERT: A 854 MET cc_start: 0.8453 (tmm) cc_final: 0.8075 (tmm) REVERT: A 875 GLU cc_start: 0.7672 (mt-10) cc_final: 0.7145 (tp30) REVERT: A 926 MET cc_start: 0.8154 (mtp) cc_final: 0.7917 (mtp) REVERT: A 942 ARG cc_start: 0.8207 (ttp-110) cc_final: 0.7576 (tmm-80) REVERT: B 335 PHE cc_start: 0.7521 (m-10) cc_final: 0.7290 (m-10) REVERT: B 348 ARG cc_start: 0.8185 (tpp80) cc_final: 0.7138 (ttm110) REVERT: B 387 GLU cc_start: 0.7456 (mm-30) cc_final: 0.6831 (mm-30) REVERT: B 465 TYR cc_start: 0.7300 (m-10) cc_final: 0.6931 (m-10) outliers start: 1 outliers final: 0 residues processed: 123 average time/residue: 0.1035 time to fit residues: 16.5351 Evaluate side-chains 87 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 86 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 53 optimal weight: 3.9990 chunk 22 optimal weight: 0.0000 chunk 76 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 83 optimal weight: 6.9990 chunk 55 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 524 ASN A 818 GLN B 343 HIS ** B 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.097881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.076272 restraints weight = 30535.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.078570 restraints weight = 20184.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.079787 restraints weight = 11954.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.080012 restraints weight = 9091.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.080284 restraints weight = 8754.296| |-----------------------------------------------------------------------------| r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3086 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3086 r_free = 0.3086 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3086 r_free = 0.3086 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3086 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.4053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7556 Z= 0.150 Angle : 0.960 30.471 10334 Z= 0.397 Chirality : 0.047 0.170 1177 Planarity : 0.004 0.043 1210 Dihedral : 10.550 156.341 1239 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.29), residues: 822 helix: 1.38 (0.29), residues: 327 sheet: -0.25 (0.39), residues: 171 loop : -1.34 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 331 TYR 0.015 0.002 TYR A 732 PHE 0.014 0.002 PHE B 335 TRP 0.017 0.002 TRP B 327 HIS 0.004 0.001 HIS A 603 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 ( 7552) covalent geometry : angle 0.93602 / 0.39 (10328) hydrogen bonds : bond 0.04844 / 2.49 ( 334) hydrogen bonds : angle 4.54151 / 1.74 ( 936) metal coordination : bond 0.00769 / 0.38 ( 4) metal coordination : angle 8.81740 / 2.94 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 686 MET cc_start: 0.7835 (tpp) cc_final: 0.7547 (tpp) REVERT: A 853 MET cc_start: 0.8701 (ttm) cc_final: 0.7997 (ttm) REVERT: A 875 GLU cc_start: 0.7708 (mt-10) cc_final: 0.7350 (tp30) REVERT: A 879 GLN cc_start: 0.7159 (tt0) cc_final: 0.6066 (tp40) REVERT: A 942 ARG cc_start: 0.8270 (ttp-110) cc_final: 0.7808 (tmm-80) REVERT: B 335 PHE cc_start: 0.7368 (m-10) cc_final: 0.7119 (m-10) outliers start: 0 outliers final: 0 residues processed: 111 average time/residue: 0.0929 time to fit residues: 13.9237 Evaluate side-chains 84 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 8 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 71 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 18 optimal weight: 0.1980 chunk 60 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 711 GLN B 343 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.098357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.078511 restraints weight = 38148.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.080365 restraints weight = 24592.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.080889 restraints weight = 17978.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.081564 restraints weight = 11829.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.081818 restraints weight = 10709.572| |-----------------------------------------------------------------------------| r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3118 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3118 r_free = 0.3118 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3118 r_free = 0.3118 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3118 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.4556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7556 Z= 0.124 Angle : 0.922 29.930 10334 Z= 0.375 Chirality : 0.045 0.165 1177 Planarity : 0.004 0.041 1210 Dihedral : 10.248 145.618 1239 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.30), residues: 822 helix: 1.58 (0.29), residues: 326 sheet: 0.08 (0.40), residues: 172 loop : -1.20 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 348 TYR 0.014 0.001 TYR A 732 PHE 0.013 0.002 PHE B 489 TRP 0.015 0.001 TRP B 386 HIS 0.006 0.001 HIS B 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 ( 7552) covalent geometry : angle 0.90288 / 0.37 (10328) hydrogen bonds : bond 0.04307 / 2.21 ( 334) hydrogen bonds : angle 4.40985 / 1.70 ( 936) metal coordination : bond 0.00685 / 0.34 ( 4) metal coordination : angle 7.80409 / 2.60 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 686 MET cc_start: 0.7845 (tpp) cc_final: 0.7609 (tpp) REVERT: A 793 GLU cc_start: 0.8102 (pt0) cc_final: 0.7780 (pt0) REVERT: A 853 MET cc_start: 0.8634 (ttm) cc_final: 0.7959 (ttm) REVERT: A 875 GLU cc_start: 0.7772 (mt-10) cc_final: 0.7324 (tp30) REVERT: A 942 ARG cc_start: 0.8350 (ttp-110) cc_final: 0.7950 (tmm-80) REVERT: B 453 MET cc_start: 0.3768 (mmm) cc_final: 0.2827 (mmp) REVERT: B 470 GLN cc_start: 0.8229 (mm-40) cc_final: 0.7542 (pp30) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.0844 time to fit residues: 12.3093 Evaluate side-chains 83 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 1 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 50 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 84 optimal weight: 5.9990 chunk 70 optimal weight: 8.9990 chunk 27 optimal weight: 6.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 371 GLN ** A 928 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 470 GLN B 478 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.091217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.071790 restraints weight = 41395.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.074003 restraints weight = 29554.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.074202 restraints weight = 19909.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.075015 restraints weight = 13490.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.075193 restraints weight = 11450.151| |-----------------------------------------------------------------------------| r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2976 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2976 r_free = 0.2976 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2976 r_free = 0.2976 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2976 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.5242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 7556 Z= 0.294 Angle : 1.086 30.411 10334 Z= 0.467 Chirality : 0.053 0.251 1177 Planarity : 0.005 0.062 1210 Dihedral : 11.140 171.082 1239 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 0.14 % Allowed : 3.96 % Favored : 95.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.29), residues: 822 helix: 1.00 (0.29), residues: 319 sheet: -0.39 (0.43), residues: 146 loop : -1.21 (0.31), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 689 TYR 0.019 0.003 TYR A 732 PHE 0.022 0.002 PHE B 489 TRP 0.035 0.002 TRP B 386 HIS 0.008 0.002 HIS A 974 Details of bonding type rmsd/Z covalent geometry : bond 0.00664 / 0.29 ( 7552) covalent geometry : angle 1.05571 / 0.47 (10328) hydrogen bonds : bond 0.06579 / 3.39 ( 334) hydrogen bonds : angle 5.13773 / 1.94 ( 936) metal coordination : bond 0.01098 / 0.55 ( 4) metal coordination : angle 10.54418 / 3.51 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 98 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 354 SER cc_start: 0.8942 (m) cc_final: 0.8554 (p) REVERT: A 686 MET cc_start: 0.8157 (tpp) cc_final: 0.7939 (tpp) REVERT: A 853 MET cc_start: 0.8687 (ttm) cc_final: 0.8049 (ttm) REVERT: A 875 GLU cc_start: 0.7996 (mt-10) cc_final: 0.7698 (tp30) REVERT: A 942 ARG cc_start: 0.8204 (ttp-110) cc_final: 0.7897 (tmm-80) REVERT: A 986 ASN cc_start: 0.9165 (m110) cc_final: 0.8517 (m110) outliers start: 1 outliers final: 0 residues processed: 99 average time/residue: 0.0827 time to fit residues: 11.3343 Evaluate side-chains 80 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 14 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 31 optimal weight: 0.8980 chunk 76 optimal weight: 3.9990 chunk 10 optimal weight: 0.3980 chunk 28 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 68 optimal weight: 0.5980 chunk 32 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 371 GLN A 928 HIS A 999 GLN ** B 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 384 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.097439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.078234 restraints weight = 45367.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.080491 restraints weight = 38587.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.081668 restraints weight = 21555.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.082255 restraints weight = 14672.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.084222 restraints weight = 12195.282| |-----------------------------------------------------------------------------| r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3138 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3138 r_free = 0.3138 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3138 r_free = 0.3138 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3138 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.5635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7556 Z= 0.125 Angle : 0.941 30.272 10334 Z= 0.385 Chirality : 0.047 0.175 1177 Planarity : 0.004 0.043 1210 Dihedral : 10.334 147.676 1239 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.30), residues: 822 helix: 1.53 (0.29), residues: 326 sheet: -0.14 (0.39), residues: 171 loop : -1.10 (0.34), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 348 TYR 0.017 0.001 TYR B 475 PHE 0.018 0.001 PHE A 763 TRP 0.021 0.002 TRP B 386 HIS 0.005 0.001 HIS B 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.13 ( 7552) covalent geometry : angle 0.92227 / 0.38 (10328) hydrogen bonds : bond 0.04460 / 2.28 ( 334) hydrogen bonds : angle 4.47278 / 1.71 ( 936) metal coordination : bond 0.00609 / 0.30 ( 4) metal coordination : angle 7.82664 / 2.61 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 354 SER cc_start: 0.8804 (m) cc_final: 0.8367 (p) REVERT: A 391 SER cc_start: 0.8656 (p) cc_final: 0.8296 (t) REVERT: A 689 ARG cc_start: 0.8337 (mmm-85) cc_final: 0.8036 (ttp80) REVERT: A 853 MET cc_start: 0.8718 (ttm) cc_final: 0.8177 (ttm) REVERT: A 875 GLU cc_start: 0.7656 (mt-10) cc_final: 0.7211 (tp30) REVERT: A 878 MET cc_start: 0.8653 (mtt) cc_final: 0.8361 (mtt) REVERT: A 926 MET cc_start: 0.8625 (mtp) cc_final: 0.8239 (mtm) REVERT: A 942 ARG cc_start: 0.8238 (ttp-110) cc_final: 0.8019 (tmm-80) REVERT: A 986 ASN cc_start: 0.8898 (m110) cc_final: 0.8546 (m-40) REVERT: B 372 GLN cc_start: 0.8171 (mp10) cc_final: 0.7965 (mp10) REVERT: B 377 GLN cc_start: 0.4260 (mp10) cc_final: 0.3390 (mm-40) REVERT: B 470 GLN cc_start: 0.8276 (mm110) cc_final: 0.7652 (pp30) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.0864 time to fit residues: 13.6255 Evaluate side-chains 87 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 72 optimal weight: 0.1980 chunk 31 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 16 optimal weight: 0.5980 chunk 81 optimal weight: 7.9990 chunk 36 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 28 optimal weight: 0.0770 chunk 85 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 455 ASN A 771 GLN A 986 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.098708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.078023 restraints weight = 22720.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.079572 restraints weight = 14628.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.080665 restraints weight = 10705.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.081388 restraints weight = 8651.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.081914 restraints weight = 7468.315| |-----------------------------------------------------------------------------| r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3125 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3125 r_free = 0.3125 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3125 r_free = 0.3125 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3125 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.5904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 7556 Z= 0.112 Angle : 0.922 30.041 10334 Z= 0.373 Chirality : 0.045 0.171 1177 Planarity : 0.004 0.042 1210 Dihedral : 10.026 140.940 1239 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 0.14 % Allowed : 0.82 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.30), residues: 822 helix: 1.68 (0.29), residues: 332 sheet: -0.16 (0.40), residues: 163 loop : -1.10 (0.33), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 348 TYR 0.023 0.001 TYR B 475 PHE 0.011 0.001 PHE B 477 TRP 0.019 0.001 TRP B 386 HIS 0.006 0.001 HIS B 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 ( 7552) covalent geometry : angle 0.90175 / 0.37 (10328) hydrogen bonds : bond 0.04058 / 2.07 ( 334) hydrogen bonds : angle 4.44068 / 1.72 ( 936) metal coordination : bond 0.00641 / 0.32 ( 4) metal coordination : angle 7.97360 / 2.66 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 109 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 354 SER cc_start: 0.8621 (m) cc_final: 0.8180 (p) REVERT: A 455 ASN cc_start: 0.7574 (OUTLIER) cc_final: 0.6783 (t0) REVERT: A 689 ARG cc_start: 0.8280 (mmm-85) cc_final: 0.7471 (ptm160) REVERT: A 793 GLU cc_start: 0.8027 (pt0) cc_final: 0.7793 (pt0) REVERT: A 853 MET cc_start: 0.8797 (ttm) cc_final: 0.8286 (ttm) REVERT: A 854 MET cc_start: 0.8552 (tmm) cc_final: 0.8110 (tmm) REVERT: A 875 GLU cc_start: 0.7410 (mt-10) cc_final: 0.7105 (tp30) REVERT: A 942 ARG cc_start: 0.8215 (ttp-110) cc_final: 0.7938 (tmm-80) REVERT: B 377 GLN cc_start: 0.3992 (mp10) cc_final: 0.3313 (mm-40) REVERT: B 453 MET cc_start: 0.4777 (mmp) cc_final: 0.3678 (mmp) REVERT: B 470 GLN cc_start: 0.8189 (mm110) cc_final: 0.7467 (pp30) REVERT: B 493 GLU cc_start: 0.7251 (tm-30) cc_final: 0.6719 (tt0) REVERT: B 496 THR cc_start: 0.8936 (m) cc_final: 0.8456 (p) outliers start: 1 outliers final: 0 residues processed: 110 average time/residue: 0.0766 time to fit residues: 11.7815 Evaluate side-chains 87 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 86 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 55 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 82 optimal weight: 8.9990 chunk 34 optimal weight: 3.9990 chunk 32 optimal weight: 0.5980 chunk 62 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 455 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.095126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.075612 restraints weight = 43141.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.078264 restraints weight = 27520.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.078766 restraints weight = 16310.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.079598 restraints weight = 11341.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.079864 restraints weight = 9719.168| |-----------------------------------------------------------------------------| r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3068 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3068 r_free = 0.3068 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3068 r_free = 0.3068 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3068 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.5970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7556 Z= 0.150 Angle : 0.956 30.042 10334 Z= 0.390 Chirality : 0.046 0.187 1177 Planarity : 0.004 0.042 1210 Dihedral : 10.253 147.381 1239 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.29), residues: 822 helix: 1.48 (0.29), residues: 333 sheet: -0.07 (0.39), residues: 175 loop : -0.97 (0.35), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 331 TYR 0.015 0.001 TYR A 732 PHE 0.013 0.001 PHE B 489 TRP 0.025 0.002 TRP B 386 HIS 0.007 0.001 HIS B 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 ( 7552) covalent geometry : angle 0.93249 / 0.39 (10328) hydrogen bonds : bond 0.04618 / 2.36 ( 334) hydrogen bonds : angle 4.51205 / 1.74 ( 936) metal coordination : bond 0.00888 / 0.44 ( 4) metal coordination : angle 8.80455 / 2.93 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 354 SER cc_start: 0.8813 (m) cc_final: 0.8437 (p) REVERT: A 391 SER cc_start: 0.8764 (p) cc_final: 0.8444 (t) REVERT: A 689 ARG cc_start: 0.8222 (mmm-85) cc_final: 0.7368 (ptm160) REVERT: A 793 GLU cc_start: 0.8222 (pt0) cc_final: 0.7793 (pt0) REVERT: A 853 MET cc_start: 0.8604 (ttm) cc_final: 0.8107 (ttm) REVERT: A 875 GLU cc_start: 0.7888 (mt-10) cc_final: 0.7335 (tp30) REVERT: A 942 ARG cc_start: 0.8215 (ttp-110) cc_final: 0.7954 (tmm-80) REVERT: B 331 ARG cc_start: 0.7206 (mmt90) cc_final: 0.4629 (mmt-90) REVERT: B 335 PHE cc_start: 0.7164 (m-10) cc_final: 0.6949 (m-10) REVERT: B 377 GLN cc_start: 0.4179 (mp10) cc_final: 0.3454 (mm-40) REVERT: B 453 MET cc_start: 0.5375 (mmp) cc_final: 0.3361 (mmp) REVERT: B 470 GLN cc_start: 0.7943 (mm110) cc_final: 0.7463 (pp30) REVERT: B 496 THR cc_start: 0.8984 (m) cc_final: 0.8593 (p) outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.0846 time to fit residues: 11.9193 Evaluate side-chains 85 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 80 optimal weight: 0.7980 chunk 23 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 77 optimal weight: 10.0000 chunk 1 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 455 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.095144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.076265 restraints weight = 56936.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.078123 restraints weight = 45250.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.079568 restraints weight = 22072.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.080545 restraints weight = 14734.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.080961 restraints weight = 11736.445| |-----------------------------------------------------------------------------| r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3072 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3072 r_free = 0.3072 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3072 r_free = 0.3072 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3072 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.6099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7556 Z= 0.170 Angle : 0.975 30.214 10334 Z= 0.400 Chirality : 0.047 0.186 1177 Planarity : 0.004 0.044 1210 Dihedral : 10.421 153.444 1239 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.29), residues: 822 helix: 1.45 (0.29), residues: 331 sheet: -0.22 (0.40), residues: 161 loop : -1.05 (0.33), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 348 TYR 0.015 0.002 TYR A 732 PHE 0.029 0.002 PHE A 763 TRP 0.026 0.002 TRP B 386 HIS 0.004 0.001 HIS A 835 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.17 ( 7552) covalent geometry : angle 0.94876 / 0.40 (10328) hydrogen bonds : bond 0.04857 / 2.49 ( 334) hydrogen bonds : angle 4.59618 / 1.77 ( 936) metal coordination : bond 0.00871 / 0.44 ( 4) metal coordination : angle 9.28283 / 3.09 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 354 SER cc_start: 0.8869 (m) cc_final: 0.8484 (p) REVERT: A 689 ARG cc_start: 0.8260 (mmm-85) cc_final: 0.7429 (ptm160) REVERT: A 793 GLU cc_start: 0.8221 (pt0) cc_final: 0.7929 (pt0) REVERT: A 853 MET cc_start: 0.8609 (ttm) cc_final: 0.8076 (ttm) REVERT: A 854 MET cc_start: 0.8732 (tmm) cc_final: 0.8400 (tmm) REVERT: A 875 GLU cc_start: 0.7920 (mt-10) cc_final: 0.7685 (tp30) REVERT: A 942 ARG cc_start: 0.8213 (ttp-110) cc_final: 0.7986 (tmm-80) REVERT: B 331 ARG cc_start: 0.6870 (mmt90) cc_final: 0.4773 (mmt-90) REVERT: B 335 PHE cc_start: 0.7200 (m-10) cc_final: 0.6943 (m-10) REVERT: B 377 GLN cc_start: 0.3818 (mp10) cc_final: 0.3214 (mm-40) REVERT: B 453 MET cc_start: 0.5267 (mmp) cc_final: 0.3352 (mmp) REVERT: B 470 GLN cc_start: 0.7763 (mm110) cc_final: 0.7485 (pp30) REVERT: B 496 THR cc_start: 0.9019 (m) cc_final: 0.8547 (p) outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.0904 time to fit residues: 12.6415 Evaluate side-chains 85 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 5 optimal weight: 1.9990 chunk 53 optimal weight: 0.2980 chunk 60 optimal weight: 4.9990 chunk 36 optimal weight: 0.8980 chunk 72 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 2 optimal weight: 0.0060 chunk 75 optimal weight: 10.0000 chunk 37 optimal weight: 4.9990 chunk 8 optimal weight: 0.8980 chunk 50 optimal weight: 5.9990 overall best weight: 0.8198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 455 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.096774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.077510 restraints weight = 41039.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.079657 restraints weight = 29628.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.080366 restraints weight = 17733.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.080871 restraints weight = 12558.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.081153 restraints weight = 11611.739| |-----------------------------------------------------------------------------| r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3094 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3094 r_free = 0.3094 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3094 r_free = 0.3094 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3094 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.6234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7556 Z= 0.125 Angle : 0.939 30.105 10334 Z= 0.380 Chirality : 0.046 0.172 1177 Planarity : 0.004 0.046 1210 Dihedral : 10.157 143.494 1239 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.30), residues: 822 helix: 1.57 (0.29), residues: 333 sheet: 0.07 (0.40), residues: 169 loop : -1.04 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 418 TYR 0.013 0.001 TYR A 732 PHE 0.019 0.001 PHE B 477 TRP 0.024 0.002 TRP B 386 HIS 0.007 0.001 HIS B 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 ( 7552) covalent geometry : angle 0.91758 / 0.38 (10328) hydrogen bonds : bond 0.04306 / 2.20 ( 334) hydrogen bonds : angle 4.41628 / 1.71 ( 936) metal coordination : bond 0.00712 / 0.36 ( 4) metal coordination : angle 8.31867 / 2.77 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 354 SER cc_start: 0.8813 (m) cc_final: 0.8443 (p) REVERT: A 391 SER cc_start: 0.8755 (p) cc_final: 0.8411 (t) REVERT: A 689 ARG cc_start: 0.8184 (mmm-85) cc_final: 0.7384 (ptm160) REVERT: A 793 GLU cc_start: 0.8183 (pt0) cc_final: 0.7790 (pt0) REVERT: A 853 MET cc_start: 0.8609 (ttm) cc_final: 0.8084 (ttm) REVERT: A 854 MET cc_start: 0.8760 (tmm) cc_final: 0.8388 (tmm) REVERT: A 875 GLU cc_start: 0.7864 (mt-10) cc_final: 0.7657 (tp30) REVERT: A 942 ARG cc_start: 0.8178 (ttp-110) cc_final: 0.7920 (tmm-80) REVERT: B 331 ARG cc_start: 0.6799 (mmt90) cc_final: 0.4951 (mmt-90) REVERT: B 377 GLN cc_start: 0.3915 (mp10) cc_final: 0.3264 (mm-40) REVERT: B 453 MET cc_start: 0.5044 (mmp) cc_final: 0.3283 (mmp) REVERT: B 470 GLN cc_start: 0.7581 (mm110) cc_final: 0.7346 (pp30) REVERT: B 496 THR cc_start: 0.9024 (m) cc_final: 0.8555 (p) outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.0877 time to fit residues: 12.4864 Evaluate side-chains 86 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 80 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 chunk 85 optimal weight: 10.0000 chunk 30 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 38 optimal weight: 0.6980 chunk 68 optimal weight: 0.0170 chunk 43 optimal weight: 0.0870 chunk 35 optimal weight: 2.9990 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 455 ASN B 412 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.097389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.076808 restraints weight = 33633.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.079309 restraints weight = 22641.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.080020 restraints weight = 14298.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.080411 restraints weight = 10513.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.080695 restraints weight = 9510.206| |-----------------------------------------------------------------------------| r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3098 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3098 r_free = 0.3098 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3098 r_free = 0.3098 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3098 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.6379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7556 Z= 0.112 Angle : 0.923 30.082 10334 Z= 0.372 Chirality : 0.045 0.164 1177 Planarity : 0.004 0.045 1210 Dihedral : 9.925 135.684 1239 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.30), residues: 822 helix: 1.60 (0.29), residues: 333 sheet: 0.06 (0.39), residues: 175 loop : -0.93 (0.35), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 348 TYR 0.013 0.001 TYR A 732 PHE 0.016 0.001 PHE B 477 TRP 0.022 0.002 TRP B 386 HIS 0.010 0.001 HIS B 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 ( 7552) covalent geometry : angle 0.90291 / 0.37 (10328) hydrogen bonds : bond 0.04012 / 2.05 ( 334) hydrogen bonds : angle 4.38391 / 1.70 ( 936) metal coordination : bond 0.00629 / 0.31 ( 4) metal coordination : angle 7.98432 / 2.66 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1253.35 seconds wall clock time: 22 minutes 26.51 seconds (1346.51 seconds total)