Starting phenix.real_space_refine on Thu Feb 15 19:21:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jl0_22368/02_2024/7jl0_22368_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jl0_22368/02_2024/7jl0_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jl0_22368/02_2024/7jl0_22368.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jl0_22368/02_2024/7jl0_22368.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jl0_22368/02_2024/7jl0_22368_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jl0_22368/02_2024/7jl0_22368_updated.pdb" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 Residue "A GLU 321": "OE1" <-> "OE2" Residue "A TYR 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 370": "OE1" <-> "OE2" Residue "A PHE 437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 461": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 514": "OD1" <-> "OD2" Residue "A PHE 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 523": "OE1" <-> "OE2" Residue "A PHE 550": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 572": "OD1" <-> "OD2" Residue "A PHE 573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 630": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 712": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 794": "OE1" <-> "OE2" Residue "A TYR 807": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 824": "NH1" <-> "NH2" Residue "A TYR 869": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 875": "OE1" <-> "OE2" Residue "A GLU 883": "OE1" <-> "OE2" Residue "A PHE 905": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 939": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 987": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 991": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1005": "OE1" <-> "OE2" Residue "A PHE 1010": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1015": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 357": "NH1" <-> "NH2" Residue "B TYR 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 418": "NH1" <-> "NH2" Residue "B GLU 429": "OE1" <-> "OE2" Residue "B PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/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: {'RNA': 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: {'RNA': 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: {'TYR:plan': 1, 'GLU:plan': 2} 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: {'GLN:plan1': 3, 'ARG:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 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: {'GLN:plan1': 3, 'ARG:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 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: 5.31, per 1000 atoms: 0.72 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 - 3.50 Amino acid : False - 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: 3.14 Conformation dependent library (CDL) restraints added in 1.4 seconds 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... running ksdssp... Secondary structure from input PDB file: 28 helices and 8 sheets defined 38.5% alpha, 15.0% beta 10 base pairs and 18 stacking pairs defined. Time for finding SS restraints: 3.17 Creating SS restraints... Processing helix chain 'A' and resid 310 through 316 Processing helix chain 'A' and resid 318 through 320 No H-bonds generated for 'chain 'A' and resid 318 through 320' Processing helix chain 'A' and resid 335 through 352 Processing helix chain 'A' and resid 366 through 374 removed outlier: 3.658A pdb=" N GLU A 370 " --> pdb=" O VAL A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 380 No H-bonds generated for 'chain 'A' and resid 377 through 380' Processing helix chain 'A' and resid 400 through 406 Processing helix chain 'A' and resid 414 through 421 Processing helix chain 'A' and resid 445 through 447 No H-bonds generated for 'chain 'A' and resid 445 through 447' Processing helix chain 'A' and resid 453 through 471 removed outlier: 4.274A pdb=" N ILE A 457 " --> pdb=" O VAL A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 513 Processing helix chain 'A' and resid 525 through 531 Processing helix chain 'A' and resid 549 through 565 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 576 through 592 Processing helix chain 'A' and resid 598 through 616 Processing helix chain 'A' and resid 619 through 641 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) removed outlier: 4.050A pdb=" N ILE A 641 " --> pdb=" O LYS A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 673 through 691 removed outlier: 4.432A pdb=" N THR A 678 " --> pdb=" O PHE A 675 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N PHE A 681 " --> pdb=" O THR A 678 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA A 691 " --> pdb=" O LYS A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 700 through 715 Processing helix chain 'A' and resid 728 through 740 Processing helix chain 'A' and resid 743 through 747 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 743 through 747' Processing helix chain 'A' and resid 768 through 780 removed outlier: 3.861A pdb=" N THR A 780 " --> pdb=" O SER A 776 " (cutoff:3.500A) Processing helix chain 'A' and resid 790 through 792 No H-bonds generated for 'chain 'A' and resid 790 through 792' Processing helix chain 'A' and resid 814 through 821 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 841 through 863 removed outlier: 4.089A pdb=" N ASN A 863 " --> pdb=" O HIS A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 894 removed outlier: 3.617A pdb=" N ILE A 881 " --> pdb=" O GLN A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 919 No H-bonds generated for 'chain 'A' and resid 917 through 919' Processing helix chain 'A' and resid 934 through 938 Processing helix chain 'A' and resid 984 through 986 No H-bonds generated for 'chain 'A' and resid 984 through 986' Processing helix chain 'B' and resid 322 through 329 removed outlier: 4.075A pdb=" N GLN B 328 " --> pdb=" O ARG B 324 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N ASN B 329 " --> pdb=" O LYS B 325 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.684A pdb=" N ILE A 325 " --> pdb=" O ILE A 484 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLY A 486 " --> pdb=" O ILE A 325 " (cutoff:3.500A) Processing sheet with id= B, 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: 3.902A pdb=" N HIS A 752 " --> pdb=" O LEU A 785 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 988 through 990 removed outlier: 3.564A pdb=" N CYS A 915 " --> pdb=" O PHE A 905 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 920 through 923 Processing sheet with id= E, first strand: chain 'A' and resid 940 through 942 Processing sheet with id= F, first strand: chain 'A' and resid 971 through 974 removed outlier: 3.589A pdb=" N LEU A 979 " --> pdb=" O MET A 972 " (cutoff:3.500A) Processing sheet with id= G, 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= H, first strand: chain 'B' and resid 372 through 374 removed outlier: 4.029A pdb=" N ALA B 434 " --> pdb=" O GLN B 441 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLN B 441 " --> pdb=" O ALA B 434 " (cutoff:3.500A) 291 hydrogen bonds defined for protein. 796 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: 2.71 Time building geometry restraints manager: 3.39 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: 88.09 - 106.22: 349 106.22 - 124.35: 9740 124.35 - 142.48: 237 142.48 - 160.61: 0 160.61 - 178.74: 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: 4479 33.18 - 66.37: 127 66.37 - 99.55: 16 99.55 - 132.73: 2 132.73 - 165.91: 1 Dihedral angle restraints: 4625 sinusoidal: 2162 harmonic: 2463 Sorted by residual: 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 dihedral pdb=" O2A ADP A1102 " pdb=" O3A ADP A1102 " pdb=" PA ADP A1102 " pdb=" PB ADP A1102 " ideal model delta sinusoidal sigma weight residual -60.00 55.39 -115.39 1 2.00e+01 2.50e-03 3.43e+01 dihedral pdb=" O1B ADP A1102 " pdb=" O3A ADP A1102 " pdb=" PB ADP A1102 " pdb=" PA ADP A1102 " ideal model delta sinusoidal sigma weight residual -60.00 41.70 -101.71 1 2.00e+01 2.50e-03 2.89e+01 ... (remaining 4622 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 900 0.056 - 0.113: 240 0.113 - 0.169: 32 0.169 - 0.225: 2 0.225 - 0.281: 3 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=" 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 chirality pdb=" CA ILE A 783 " pdb=" N ILE A 783 " pdb=" C ILE A 783 " pdb=" CB ILE A 783 " both_signs ideal model delta sigma weight residual False 2.43 2.17 0.26 2.00e-01 2.50e+01 1.74e+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: 5100 3.08 - 3.68: 10744 3.68 - 4.29: 15272 4.29 - 4.90: 24563 Nonbonded interactions: 55718 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 2.390 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 2.470 nonbonded pdb=" O2B ADP A1102 " pdb=" F3 ALF A1103 " model vdw 2.166 2.390 ... (remaining 55713 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 0.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 3.710 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 28.320 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 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 7552 Z= 0.507 Angle : 1.403 69.108 10328 Z= 0.628 Chirality : 0.051 0.281 1177 Planarity : 0.005 0.053 1210 Dihedral : 15.704 165.915 3023 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (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 TRP 0.011 0.002 TRP B 423 HIS 0.011 0.002 HIS A 835 PHE 0.042 0.003 PHE A 377 TYR 0.019 0.003 TYR A 311 ARG 0.011 0.001 ARG A 824 *********************** 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 fitting. rotamer outliers: 1 poor density : 182 time to evaluate : 0.826 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: 0.7859 (t) REVERT: A 391 SER cc_start: 0.8429 (p) cc_final: 0.8173 (p) REVERT: A 529 LYS cc_start: 0.8656 (mmtp) cc_final: 0.8402 (tmtt) REVERT: A 783 ILE cc_start: 0.9457 (mt) cc_final: 0.9170 (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: 0.7385 (mp0) outliers start: 1 outliers final: 0 residues processed: 183 average time/residue: 0.2536 time to fit residues: 58.1376 Evaluate side-chains 96 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 72 optimal weight: 10.0000 chunk 65 optimal weight: 0.5980 chunk 36 optimal weight: 0.4980 chunk 22 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 34 optimal weight: 0.4980 chunk 67 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 505 HIS B 343 HIS B 436 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.3147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7552 Z= 0.175 Angle : 0.900 30.161 10328 Z= 0.385 Chirality : 0.042 0.151 1177 Planarity : 0.004 0.050 1210 Dihedral : 14.030 151.429 1337 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 0.27 % Allowed : 4.10 % Favored : 95.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.28), residues: 822 helix: 1.13 (0.28), residues: 313 sheet: -0.70 (0.37), residues: 169 loop : -1.59 (0.31), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 386 HIS 0.004 0.001 HIS B 383 PHE 0.024 0.002 PHE B 335 TYR 0.018 0.001 TYR A 732 ARG 0.003 0.001 ARG B 348 *********************** 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 fitting. rotamer outliers: 2 poor density : 121 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 391 SER cc_start: 0.8644 (p) cc_final: 0.8393 (p) REVERT: A 584 GLN cc_start: 0.8205 (OUTLIER) cc_final: 0.7900 (pm20) REVERT: A 674 ARG cc_start: 0.7735 (pmt170) cc_final: 0.7437 (ptp90) REVERT: A 853 MET cc_start: 0.8667 (ttm) cc_final: 0.8019 (ttm) REVERT: A 854 MET cc_start: 0.8564 (tmm) cc_final: 0.8248 (tmm) REVERT: A 875 GLU cc_start: 0.7526 (mt-10) cc_final: 0.7074 (tp30) REVERT: A 926 MET cc_start: 0.8282 (mtp) cc_final: 0.8025 (mtp) REVERT: A 942 ARG cc_start: 0.8341 (ttp-110) cc_final: 0.7942 (tmm-80) REVERT: B 348 ARG cc_start: 0.8221 (tpp80) cc_final: 0.7154 (ttm110) REVERT: B 387 GLU cc_start: 0.7253 (mm-30) cc_final: 0.6600 (mm-30) REVERT: B 465 TYR cc_start: 0.7051 (m-10) cc_final: 0.6676 (m-10) outliers start: 2 outliers final: 0 residues processed: 123 average time/residue: 0.2319 time to fit residues: 36.8786 Evaluate side-chains 84 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 83 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 43 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 64 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 78 optimal weight: 7.9990 chunk 84 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 62 optimal weight: 6.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 524 ASN A 711 GLN ** A 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 818 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 928 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 470 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.4816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 7552 Z= 0.449 Angle : 1.047 30.433 10328 Z= 0.475 Chirality : 0.048 0.194 1177 Planarity : 0.005 0.050 1210 Dihedral : 14.604 177.114 1337 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.28), residues: 822 helix: 0.61 (0.28), residues: 309 sheet: -0.64 (0.42), residues: 146 loop : -1.58 (0.30), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP B 327 HIS 0.010 0.002 HIS A 974 PHE 0.026 0.003 PHE B 335 TYR 0.022 0.003 TYR A 732 ARG 0.006 0.001 ARG A 689 *********************** 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 100 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 0.767 Fit side-chains revert: symmetry clash REVERT: A 354 SER cc_start: 0.8933 (m) cc_final: 0.8551 (p) REVERT: A 793 GLU cc_start: 0.8289 (pt0) cc_final: 0.7904 (pt0) REVERT: A 853 MET cc_start: 0.8630 (ttm) cc_final: 0.7899 (ttm) REVERT: A 875 GLU cc_start: 0.7902 (mt-10) cc_final: 0.7335 (tp30) REVERT: A 942 ARG cc_start: 0.8544 (ttp-110) cc_final: 0.8145 (tmm-80) outliers start: 0 outliers final: 0 residues processed: 100 average time/residue: 0.1961 time to fit residues: 26.6858 Evaluate side-chains 73 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 77 optimal weight: 9.9990 chunk 58 optimal weight: 3.9990 chunk 40 optimal weight: 0.5980 chunk 8 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 78 optimal weight: 8.9990 chunk 83 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 chunk 74 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 802 ASN A 818 GLN A 877 GLN A 928 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.5171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7552 Z= 0.164 Angle : 0.887 29.884 10328 Z= 0.373 Chirality : 0.041 0.166 1177 Planarity : 0.004 0.042 1210 Dihedral : 13.853 164.222 1337 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.29), residues: 822 helix: 1.20 (0.29), residues: 318 sheet: -0.30 (0.39), residues: 175 loop : -1.37 (0.33), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 386 HIS 0.005 0.001 HIS B 355 PHE 0.013 0.001 PHE B 464 TYR 0.019 0.001 TYR B 475 ARG 0.006 0.001 ARG B 348 *********************** 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 108 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 0.875 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 354 SER cc_start: 0.8881 (m) cc_final: 0.8432 (p) REVERT: A 793 GLU cc_start: 0.8118 (pt0) cc_final: 0.7796 (pt0) REVERT: A 853 MET cc_start: 0.8748 (ttm) cc_final: 0.8080 (ttm) REVERT: A 875 GLU cc_start: 0.7723 (mt-10) cc_final: 0.7175 (tp30) REVERT: A 879 GLN cc_start: 0.7533 (tt0) cc_final: 0.6587 (tp40) REVERT: A 926 MET cc_start: 0.8637 (mtp) cc_final: 0.8348 (mtm) REVERT: A 942 ARG cc_start: 0.8472 (ttp-110) cc_final: 0.8173 (tmm-80) REVERT: B 453 MET cc_start: 0.4618 (mmp) cc_final: 0.3263 (mmp) outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.1992 time to fit residues: 29.1063 Evaluate side-chains 79 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 69 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 chunk 34 optimal weight: 9.9990 chunk 70 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 42 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 752 HIS A 771 GLN B 478 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.5562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 7552 Z= 0.383 Angle : 0.985 30.088 10328 Z= 0.435 Chirality : 0.046 0.174 1177 Planarity : 0.005 0.042 1210 Dihedral : 14.217 174.201 1337 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.29), residues: 822 helix: 0.87 (0.29), residues: 306 sheet: -0.19 (0.42), residues: 161 loop : -1.31 (0.32), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 386 HIS 0.007 0.002 HIS A 835 PHE 0.017 0.002 PHE B 335 TYR 0.018 0.002 TYR A 732 ARG 0.005 0.001 ARG A 689 *********************** 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 91 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 354 SER cc_start: 0.8974 (m) cc_final: 0.8594 (p) REVERT: A 853 MET cc_start: 0.8673 (ttm) cc_final: 0.7942 (ttm) REVERT: A 875 GLU cc_start: 0.7875 (mt-10) cc_final: 0.7627 (tp30) REVERT: A 942 ARG cc_start: 0.8480 (ttp-110) cc_final: 0.8114 (tmm-80) REVERT: B 331 ARG cc_start: 0.6665 (mmt90) cc_final: 0.4963 (mmm160) REVERT: B 335 PHE cc_start: 0.6778 (m-10) cc_final: 0.6484 (m-10) REVERT: B 453 MET cc_start: 0.4459 (mmp) cc_final: 0.3722 (mmp) outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.1919 time to fit residues: 24.3178 Evaluate side-chains 75 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 27 optimal weight: 4.9990 chunk 74 optimal weight: 10.0000 chunk 16 optimal weight: 3.9990 chunk 48 optimal weight: 0.6980 chunk 20 optimal weight: 3.9990 chunk 83 optimal weight: 0.9980 chunk 69 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 chunk 43 optimal weight: 0.3980 chunk 80 optimal weight: 4.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.5817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7552 Z= 0.168 Angle : 0.875 29.821 10328 Z= 0.367 Chirality : 0.042 0.177 1177 Planarity : 0.004 0.040 1210 Dihedral : 13.795 162.498 1337 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.30), residues: 822 helix: 1.29 (0.29), residues: 310 sheet: -0.18 (0.40), residues: 173 loop : -1.08 (0.34), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B 386 HIS 0.004 0.001 HIS A 603 PHE 0.017 0.001 PHE A 763 TYR 0.015 0.001 TYR A 732 ARG 0.006 0.000 ARG B 348 *********************** 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 104 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 354 SER cc_start: 0.8828 (m) cc_final: 0.8415 (p) REVERT: A 678 THR cc_start: 0.7773 (m) cc_final: 0.7567 (t) REVERT: A 793 GLU cc_start: 0.8161 (pt0) cc_final: 0.7701 (pt0) REVERT: A 853 MET cc_start: 0.8815 (ttm) cc_final: 0.8206 (ttm) REVERT: A 854 MET cc_start: 0.8741 (tmm) cc_final: 0.8300 (tmm) REVERT: A 879 GLN cc_start: 0.7514 (tt0) cc_final: 0.6557 (tp40) REVERT: A 942 ARG cc_start: 0.8506 (ttp-110) cc_final: 0.8187 (tmm-80) REVERT: B 470 GLN cc_start: 0.8222 (mm110) cc_final: 0.7689 (pp30) outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.1784 time to fit residues: 25.5868 Evaluate side-chains 80 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 9 optimal weight: 0.8980 chunk 47 optimal weight: 0.4980 chunk 60 optimal weight: 6.9990 chunk 70 optimal weight: 0.7980 chunk 46 optimal weight: 0.7980 chunk 82 optimal weight: 10.0000 chunk 51 optimal weight: 0.6980 chunk 50 optimal weight: 4.9990 chunk 38 optimal weight: 0.6980 chunk 33 optimal weight: 5.9990 chunk 49 optimal weight: 0.1980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 999 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.5996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 7552 Z= 0.147 Angle : 0.866 29.767 10328 Z= 0.359 Chirality : 0.041 0.152 1177 Planarity : 0.004 0.038 1210 Dihedral : 13.652 150.516 1337 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.30), residues: 822 helix: 1.39 (0.30), residues: 311 sheet: -0.07 (0.39), residues: 179 loop : -0.99 (0.34), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 386 HIS 0.006 0.001 HIS B 355 PHE 0.007 0.001 PHE B 477 TYR 0.012 0.001 TYR A 732 ARG 0.005 0.000 ARG B 348 *********************** 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 105 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 0.829 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 354 SER cc_start: 0.8780 (m) cc_final: 0.8357 (p) REVERT: A 793 GLU cc_start: 0.8078 (pt0) cc_final: 0.7660 (pt0) REVERT: A 853 MET cc_start: 0.8781 (ttm) cc_final: 0.8142 (ttm) REVERT: A 854 MET cc_start: 0.8758 (tmm) cc_final: 0.8354 (tmm) REVERT: A 926 MET cc_start: 0.8868 (mtp) cc_final: 0.8519 (mtm) REVERT: A 942 ARG cc_start: 0.8500 (ttp-110) cc_final: 0.8195 (tmm-80) REVERT: B 335 PHE cc_start: 0.6878 (m-10) cc_final: 0.6670 (m-10) REVERT: B 377 GLN cc_start: 0.4737 (mp10) cc_final: 0.3817 (mm-40) REVERT: B 470 GLN cc_start: 0.8198 (mm110) cc_final: 0.7664 (pp30) REVERT: B 496 THR cc_start: 0.9006 (m) cc_final: 0.8497 (p) outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.2072 time to fit residues: 29.3683 Evaluate side-chains 77 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 24 optimal weight: 4.9990 chunk 16 optimal weight: 0.0980 chunk 52 optimal weight: 0.7980 chunk 56 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 75 optimal weight: 9.9990 chunk 79 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 chunk 77 optimal weight: 10.0000 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.6085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7552 Z= 0.179 Angle : 0.881 29.679 10328 Z= 0.366 Chirality : 0.041 0.142 1177 Planarity : 0.004 0.043 1210 Dihedral : 13.534 130.760 1337 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.29), residues: 822 helix: 1.49 (0.29), residues: 312 sheet: 0.03 (0.39), residues: 172 loop : -1.09 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 386 HIS 0.007 0.001 HIS B 355 PHE 0.025 0.001 PHE B 477 TYR 0.014 0.001 TYR A 732 ARG 0.005 0.000 ARG B 348 *********************** 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 103 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 0.829 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 354 SER cc_start: 0.8744 (m) cc_final: 0.8348 (p) REVERT: A 678 THR cc_start: 0.7862 (m) cc_final: 0.7617 (t) REVERT: A 793 GLU cc_start: 0.8112 (pt0) cc_final: 0.7651 (pt0) REVERT: A 853 MET cc_start: 0.8765 (ttm) cc_final: 0.8114 (ttm) REVERT: A 942 ARG cc_start: 0.8504 (ttp-110) cc_final: 0.8186 (tmm-80) REVERT: B 435 TRP cc_start: 0.7269 (m100) cc_final: 0.6506 (m-10) REVERT: B 470 GLN cc_start: 0.8220 (mm110) cc_final: 0.7659 (pp30) REVERT: B 496 THR cc_start: 0.9019 (m) cc_final: 0.8487 (p) outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.1946 time to fit residues: 27.3312 Evaluate side-chains 77 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 79 optimal weight: 0.0050 chunk 46 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 60 optimal weight: 0.9990 chunk 23 optimal weight: 5.9990 chunk 69 optimal weight: 10.0000 chunk 73 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 50 optimal weight: 6.9990 chunk 81 optimal weight: 10.0000 chunk 49 optimal weight: 0.0770 overall best weight: 1.0158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.6193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7552 Z= 0.187 Angle : 0.891 29.747 10328 Z= 0.371 Chirality : 0.041 0.155 1177 Planarity : 0.004 0.043 1210 Dihedral : 13.343 124.837 1337 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.29), residues: 822 helix: 1.54 (0.29), residues: 312 sheet: 0.09 (0.39), residues: 169 loop : -1.08 (0.33), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 386 HIS 0.003 0.001 HIS A 835 PHE 0.009 0.001 PHE A 550 TYR 0.013 0.001 TYR A 732 ARG 0.005 0.000 ARG B 348 *********************** 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 100 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 354 SER cc_start: 0.8748 (m) cc_final: 0.8357 (p) REVERT: A 637 LYS cc_start: 0.7024 (tttt) cc_final: 0.6770 (ptmt) REVERT: A 793 GLU cc_start: 0.8113 (pt0) cc_final: 0.7680 (pt0) REVERT: A 853 MET cc_start: 0.8782 (ttm) cc_final: 0.8162 (ttm) REVERT: A 854 MET cc_start: 0.8699 (tmm) cc_final: 0.8384 (tmm) REVERT: A 865 LYS cc_start: 0.8872 (tppt) cc_final: 0.8572 (mmmm) REVERT: A 926 MET cc_start: 0.8795 (mtp) cc_final: 0.8464 (mtm) REVERT: A 942 ARG cc_start: 0.8475 (ttp-110) cc_final: 0.8165 (tmm-80) REVERT: B 331 ARG cc_start: 0.7176 (mpt180) cc_final: 0.5247 (mmt180) REVERT: B 435 TRP cc_start: 0.7627 (m100) cc_final: 0.6494 (m-10) REVERT: B 470 GLN cc_start: 0.7784 (mm110) cc_final: 0.7562 (pp30) REVERT: B 496 THR cc_start: 0.8994 (m) cc_final: 0.8549 (p) outliers start: 0 outliers final: 0 residues processed: 100 average time/residue: 0.1943 time to fit residues: 26.5516 Evaluate side-chains 79 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 38 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 chunk 85 optimal weight: 6.9990 chunk 78 optimal weight: 9.9990 chunk 68 optimal weight: 0.0470 chunk 7 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 54 optimal weight: 0.6980 chunk 72 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 overall best weight: 0.7280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.6259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7552 Z= 0.161 Angle : 0.878 30.067 10328 Z= 0.361 Chirality : 0.041 0.167 1177 Planarity : 0.004 0.043 1210 Dihedral : 13.027 109.626 1337 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.30), residues: 822 helix: 1.56 (0.29), residues: 322 sheet: 0.32 (0.40), residues: 163 loop : -1.14 (0.34), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 386 HIS 0.007 0.001 HIS B 355 PHE 0.009 0.001 PHE B 335 TYR 0.013 0.001 TYR A 732 ARG 0.006 0.000 ARG B 408 ********************** 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 103 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 0.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 354 SER cc_start: 0.8757 (m) cc_final: 0.8345 (p) REVERT: A 637 LYS cc_start: 0.6920 (tttt) cc_final: 0.6662 (ptmt) REVERT: A 793 GLU cc_start: 0.8116 (pt0) cc_final: 0.7648 (pt0) REVERT: A 853 MET cc_start: 0.8796 (ttm) cc_final: 0.8149 (ttm) REVERT: A 854 MET cc_start: 0.8746 (tmm) cc_final: 0.8415 (tmm) REVERT: A 926 MET cc_start: 0.8840 (mtp) cc_final: 0.8525 (mtm) REVERT: A 942 ARG cc_start: 0.8464 (ttp-110) cc_final: 0.8165 (tmm-80) REVERT: B 331 ARG cc_start: 0.7118 (mpt180) cc_final: 0.5354 (mmt180) REVERT: B 350 ASP cc_start: 0.7467 (m-30) cc_final: 0.7224 (m-30) REVERT: B 453 MET cc_start: 0.4480 (mmp) cc_final: 0.4089 (mmp) REVERT: B 496 THR cc_start: 0.8997 (m) cc_final: 0.8532 (p) outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.1980 time to fit residues: 27.7009 Evaluate side-chains 82 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 62 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 18 optimal weight: 0.0010 chunk 68 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 70 optimal weight: 6.9990 chunk 8 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 59 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 overall best weight: 0.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.097433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.078263 restraints weight = 42611.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.080746 restraints weight = 29832.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.081272 restraints weight = 18448.861| |-----------------------------------------------------------------------------| r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3083 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3083 r_free = 0.3083 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 = 0.3083 r_free = 0.3083 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3083 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.6350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7552 Z= 0.164 Angle : 0.875 30.059 10328 Z= 0.362 Chirality : 0.041 0.149 1177 Planarity : 0.004 0.042 1210 Dihedral : 12.998 111.665 1337 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.30), residues: 822 helix: 1.60 (0.29), residues: 318 sheet: 0.39 (0.40), residues: 162 loop : -1.19 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 386 HIS 0.009 0.001 HIS B 355 PHE 0.015 0.001 PHE B 464 TYR 0.011 0.001 TYR A 939 ARG 0.005 0.000 ARG B 348 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1646.84 seconds wall clock time: 30 minutes 37.90 seconds (1837.90 seconds total)