Starting phenix.real_space_refine on Thu May 15 02:19:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8txv_41706/05_2025/8txv_41706.cif Found real_map, /net/cci-nas-00/data/ceres_data/8txv_41706/05_2025/8txv_41706.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8txv_41706/05_2025/8txv_41706.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8txv_41706/05_2025/8txv_41706.map" model { file = "/net/cci-nas-00/data/ceres_data/8txv_41706/05_2025/8txv_41706.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8txv_41706/05_2025/8txv_41706.cif" } resolution = 3.8 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 Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 294 5.49 5 S 15 5.16 5 C 7144 2.51 5 N 2407 2.21 5 O 2976 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 12836 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 815 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "B" Number of atoms: 661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 661 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "D" Number of atoms: 740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 740 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 815 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "F" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "H" Number of atoms: 743 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 93, 731 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Conformer: "B" Number of residues, atoms: 93, 731 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} bond proxies already assigned to first conformer: 728 Chain: "I" Number of atoms: 2996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2996 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 3031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3031 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "K" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 117 Classifications: {'peptide': 14} Link IDs: {'PTRANS': 1, 'TRANS': 12} Chain: "M" Number of atoms: 602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 602 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "C" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 827 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "G" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 836 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N LEU M 73 " occ=0.45 ... (6 atoms not shown) pdb=" CD2 LEU M 73 " occ=0.45 residue: pdb=" N ARG M 74 " occ=0.45 ... (9 atoms not shown) pdb=" NH2 ARG M 74 " occ=0.45 residue: pdb=" N GLY M 75 " occ=0.25 ... (2 atoms not shown) pdb=" O GLY M 75 " occ=0.25 residue: pdb=" N GLY M 76 " occ=0.25 ... (3 atoms not shown) pdb=" OXT GLY M 76 " occ=0.25 Time building chain proxies: 8.25, per 1000 atoms: 0.64 Number of scatterers: 12836 At special positions: 0 Unit cell: (94.288, 124.832, 120.848, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 15 16.00 P 294 15.00 O 2976 8.00 N 2407 7.00 C 7144 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 Links applied TRANS " SER C 11 " - " SER D 123 " " SER G 11 " - " SER H 123 " Time building additional restraints: 3.16 Conformation dependent library (CDL) restraints added in 1.1 seconds 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1600 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 10 sheets defined 66.7% alpha, 4.4% beta 135 base pairs and 243 stacking pairs defined. Time for finding SS restraints: 6.01 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.527A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.576A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.010A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 Processing helix chain 'D' and resid 37 through 49 removed outlier: 3.596A pdb=" N GLN D 47 " --> pdb=" O LYS D 43 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL D 48 " --> pdb=" O VAL D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.567A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 104 through 123 removed outlier: 3.881A pdb=" N SER D 112 " --> pdb=" O LYS D 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 55 removed outlier: 3.793A pdb=" N LEU E 48 " --> pdb=" O GLY E 44 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ARG E 49 " --> pdb=" O THR E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.523A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.601A pdb=" N ALA E 114 " --> pdb=" O CYS E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 131 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.014A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.504A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.629A pdb=" N ASN H 84 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.615A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 123 removed outlier: 3.712A pdb=" N SER H 123 " --> pdb=" O THR H 119 " (cutoff:3.500A) Processing helix chain 'M' and resid 22 through 35 Processing helix chain 'M' and resid 37 through 39 No H-bonds generated for 'chain 'M' and resid 37 through 39' Processing helix chain 'M' and resid 56 through 60 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 73 Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.640A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 27 through 37 Processing helix chain 'G' and resid 46 through 73 Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 91 through 97 Processing helix chain 'G' and resid 112 through 116 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.825A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 removed outlier: 3.603A pdb=" N ILE A 119 " --> pdb=" O ARG B 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 Processing sheet with id=AA4, first strand: chain 'D' and resid 53 through 54 removed outlier: 7.528A pdb=" N GLY D 53 " --> pdb=" O ILE C 78 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'D' and resid 88 through 89 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.709A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA8, first strand: chain 'F' and resid 97 through 98 Processing sheet with id=AA9, first strand: chain 'H' and resid 88 through 89 Processing sheet with id=AB1, first strand: chain 'M' and resid 12 through 16 removed outlier: 8.825A pdb=" N LEU M 67 " --> pdb=" O GLN M 2 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N PHE M 4 " --> pdb=" O LEU M 67 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N LEU M 69 " --> pdb=" O PHE M 4 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LYS M 6 " --> pdb=" O LEU M 69 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N LEU M 71 " --> pdb=" O LYS M 6 " (cutoff:3.500A) 420 hydrogen bonds defined for protein. 1228 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 348 hydrogen bonds 692 hydrogen bond angles 0 basepair planarities 135 basepair parallelities 243 stacking parallelities Total time for adding SS restraints: 4.87 Time building geometry restraints manager: 3.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2529 1.33 - 1.45: 4339 1.45 - 1.57: 6179 1.57 - 1.69: 586 1.69 - 1.81: 26 Bond restraints: 13659 Sorted by residual: bond pdb=" CG1 ILE A 112 " pdb=" CD1 ILE A 112 " ideal model delta sigma weight residual 1.513 1.464 0.049 3.90e-02 6.57e+02 1.59e+00 bond pdb=" CG LEU A 126 " pdb=" CD1 LEU A 126 " ideal model delta sigma weight residual 1.521 1.486 0.035 3.30e-02 9.18e+02 1.13e+00 bond pdb=" CB CYS E 96 " pdb=" SG CYS E 96 " ideal model delta sigma weight residual 1.808 1.774 0.034 3.30e-02 9.18e+02 1.06e+00 bond pdb=" CB ASP C 72 " pdb=" CG ASP C 72 " ideal model delta sigma weight residual 1.516 1.541 -0.025 2.50e-02 1.60e+03 1.01e+00 bond pdb=" CB ASP E 81 " pdb=" CG ASP E 81 " ideal model delta sigma weight residual 1.516 1.541 -0.025 2.50e-02 1.60e+03 9.98e-01 ... (remaining 13654 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.44: 19072 1.44 - 2.87: 566 2.87 - 4.31: 41 4.31 - 5.74: 14 5.74 - 7.18: 5 Bond angle restraints: 19698 Sorted by residual: angle pdb=" C ARG B 23 " pdb=" N ASP B 24 " pdb=" CA ASP B 24 " ideal model delta sigma weight residual 121.54 128.48 -6.94 1.91e+00 2.74e-01 1.32e+01 angle pdb=" C ARG F 23 " pdb=" N ASP F 24 " pdb=" CA ASP F 24 " ideal model delta sigma weight residual 121.54 127.71 -6.17 1.91e+00 2.74e-01 1.04e+01 angle pdb=" CB ARG B 67 " pdb=" CG ARG B 67 " pdb=" CD ARG B 67 " ideal model delta sigma weight residual 111.30 118.48 -7.18 2.30e+00 1.89e-01 9.74e+00 angle pdb=" CA ARG B 67 " pdb=" CB ARG B 67 " pdb=" CG ARG B 67 " ideal model delta sigma weight residual 114.10 119.28 -5.18 2.00e+00 2.50e-01 6.72e+00 angle pdb=" N GLN A 125 " pdb=" CA GLN A 125 " pdb=" CB GLN A 125 " ideal model delta sigma weight residual 110.28 113.84 -3.56 1.55e+00 4.16e-01 5.28e+00 ... (remaining 19693 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.37: 5861 29.37 - 58.74: 1527 58.74 - 88.12: 105 88.12 - 117.49: 2 117.49 - 146.86: 2 Dihedral angle restraints: 7497 sinusoidal: 5012 harmonic: 2485 Sorted by residual: dihedral pdb=" C4' DG J 20 " pdb=" C3' DG J 20 " pdb=" O3' DG J 20 " pdb=" P DG J 21 " ideal model delta sinusoidal sigma weight residual 220.00 73.14 146.86 1 3.50e+01 8.16e-04 1.44e+01 dihedral pdb=" C4' DT J -17 " pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " pdb=" P DT J -16 " ideal model delta sinusoidal sigma weight residual 220.00 75.89 144.11 1 3.50e+01 8.16e-04 1.42e+01 dihedral pdb=" CB GLU C 56 " pdb=" CG GLU C 56 " pdb=" CD GLU C 56 " pdb=" OE1 GLU C 56 " ideal model delta sinusoidal sigma weight residual 0.00 89.75 -89.75 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 7494 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1558 0.028 - 0.055: 471 0.055 - 0.083: 135 0.083 - 0.110: 62 0.110 - 0.138: 14 Chirality restraints: 2240 Sorted by residual: chirality pdb=" CA ASP B 24 " pdb=" N ASP B 24 " pdb=" C ASP B 24 " pdb=" CB ASP B 24 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.76e-01 chirality pdb=" CA ASP F 24 " pdb=" N ASP F 24 " pdb=" C ASP F 24 " pdb=" CB ASP F 24 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.14 2.00e-01 2.50e+01 4.58e-01 chirality pdb=" CA ILE C 111 " pdb=" N ILE C 111 " pdb=" C ILE C 111 " pdb=" CB ILE C 111 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.98e-01 ... (remaining 2237 not shown) Planarity restraints: 1480 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA I -35 " 0.021 2.00e-02 2.50e+03 8.92e-03 2.19e+00 pdb=" N9 DA I -35 " -0.018 2.00e-02 2.50e+03 pdb=" C8 DA I -35 " -0.005 2.00e-02 2.50e+03 pdb=" N7 DA I -35 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DA I -35 " 0.003 2.00e-02 2.50e+03 pdb=" C6 DA I -35 " -0.001 2.00e-02 2.50e+03 pdb=" N6 DA I -35 " 0.008 2.00e-02 2.50e+03 pdb=" N1 DA I -35 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DA I -35 " -0.002 2.00e-02 2.50e+03 pdb=" N3 DA I -35 " -0.005 2.00e-02 2.50e+03 pdb=" C4 DA I -35 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 47 " 0.021 2.00e-02 2.50e+03 8.33e-03 2.08e+00 pdb=" N9 DG I 47 " -0.017 2.00e-02 2.50e+03 pdb=" C8 DG I 47 " -0.006 2.00e-02 2.50e+03 pdb=" N7 DG I 47 " -0.002 2.00e-02 2.50e+03 pdb=" C5 DG I 47 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DG I 47 " 0.003 2.00e-02 2.50e+03 pdb=" O6 DG I 47 " 0.007 2.00e-02 2.50e+03 pdb=" N1 DG I 47 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DG I 47 " -0.000 2.00e-02 2.50e+03 pdb=" N2 DG I 47 " -0.003 2.00e-02 2.50e+03 pdb=" N3 DG I 47 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DG I 47 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 26 " 0.018 2.00e-02 2.50e+03 7.34e-03 1.61e+00 pdb=" N9 DG I 26 " -0.015 2.00e-02 2.50e+03 pdb=" C8 DG I 26 " -0.004 2.00e-02 2.50e+03 pdb=" N7 DG I 26 " -0.002 2.00e-02 2.50e+03 pdb=" C5 DG I 26 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DG I 26 " 0.003 2.00e-02 2.50e+03 pdb=" O6 DG I 26 " 0.005 2.00e-02 2.50e+03 pdb=" N1 DG I 26 " 0.003 2.00e-02 2.50e+03 pdb=" C2 DG I 26 " 0.002 2.00e-02 2.50e+03 pdb=" N2 DG I 26 " -0.005 2.00e-02 2.50e+03 pdb=" N3 DG I 26 " -0.002 2.00e-02 2.50e+03 pdb=" C4 DG I 26 " -0.001 2.00e-02 2.50e+03 ... (remaining 1477 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 493 2.70 - 3.25: 11464 3.25 - 3.80: 23895 3.80 - 4.35: 28492 4.35 - 4.90: 41650 Nonbonded interactions: 105994 Sorted by model distance: nonbonded pdb=" O2 DC I 21 " pdb=" N2 DG J -21 " model vdw 2.151 2.496 nonbonded pdb=" OG1 THR H 90 " pdb=" OE1 GLU H 93 " model vdw 2.219 3.040 nonbonded pdb=" NH2 ARG F 35 " pdb=" OP2 DC I 8 " model vdw 2.263 3.120 nonbonded pdb=" OH TYR A 99 " pdb=" OE1 GLU A 133 " model vdw 2.271 3.040 nonbonded pdb=" NH2 ARG D 31 " pdb=" OP1 DG J 51 " model vdw 2.297 3.120 ... (remaining 105989 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 21 through 102) selection = (chain 'F' and (resid 21 through 101 or (resid 102 and (name N or name CA or nam \ e C or name O )))) } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 11 through 118) } ncs_group { reference = (chain 'D' and (resid 31 through 107 or resid 109 through 115 or resid 117 throu \ gh 123)) selection = (chain 'H' and (resid 31 through 107 or resid 109 through 115 or resid 117 throu \ gh 123)) } 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=0.25 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: 0.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.540 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 35.870 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.060 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:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 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 : 0.003 0.049 13661 Z= 0.151 Angle : 0.557 7.178 19704 Z= 0.330 Chirality : 0.033 0.138 2240 Planarity : 0.003 0.038 1478 Dihedral : 26.649 146.860 5891 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.14 % Allowed : 0.00 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.47 (0.30), residues: 839 helix: 2.61 (0.22), residues: 544 sheet: 1.56 (1.19), residues: 26 loop : -0.45 (0.37), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 113 PHE 0.009 0.001 PHE E 78 TYR 0.020 0.001 TYR H 40 ARG 0.013 0.000 ARG B 67 Details of bonding type rmsd link_TRANS : bond 0.00080 ( 2) link_TRANS : angle 0.53035 ( 6) hydrogen bonds : bond 0.10334 ( 768) hydrogen bonds : angle 3.99937 ( 1920) covalent geometry : bond 0.00321 (13659) covalent geometry : angle 0.55738 (19698) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 229 time to evaluate : 1.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.8392 (m-30) cc_final: 0.7864 (t70) REVERT: B 31 LYS cc_start: 0.9018 (ttmt) cc_final: 0.8770 (ttpp) REVERT: B 91 LYS cc_start: 0.9420 (ttmm) cc_final: 0.9160 (ttmt) REVERT: D 51 ASP cc_start: 0.9279 (p0) cc_final: 0.8711 (p0) REVERT: D 116 LYS cc_start: 0.9197 (mtmt) cc_final: 0.8989 (ttmt) REVERT: D 120 LYS cc_start: 0.8988 (ttpt) cc_final: 0.8735 (tttt) REVERT: E 57 SER cc_start: 0.9388 (p) cc_final: 0.8894 (p) REVERT: E 59 GLU cc_start: 0.8782 (pm20) cc_final: 0.7941 (pm20) REVERT: E 82 LEU cc_start: 0.9341 (mt) cc_final: 0.9119 (mm) REVERT: E 94 GLU cc_start: 0.8653 (mm-30) cc_final: 0.8359 (mm-30) REVERT: E 110 CYS cc_start: 0.7931 (m) cc_final: 0.7656 (m) REVERT: E 129 ARG cc_start: 0.8949 (tpt90) cc_final: 0.8743 (tpt-90) REVERT: F 91 LYS cc_start: 0.9101 (tttp) cc_final: 0.8743 (ttmt) REVERT: H 59 MET cc_start: 0.8960 (tpt) cc_final: 0.8643 (tpp) REVERT: H 85 LYS cc_start: 0.9341 (mttm) cc_final: 0.8923 (mttp) REVERT: M 44 ILE cc_start: 0.5531 (mm) cc_final: 0.4842 (mp) REVERT: C 64 GLU cc_start: 0.9011 (tm-30) cc_final: 0.8415 (tm-30) REVERT: G 41 GLU cc_start: 0.8634 (tm-30) cc_final: 0.8178 (tm-30) REVERT: G 64 GLU cc_start: 0.8913 (tm-30) cc_final: 0.8684 (tm-30) outliers start: 0 outliers final: 0 residues processed: 229 average time/residue: 0.3077 time to fit residues: 94.2898 Evaluate side-chains 179 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.8980 chunk 81 optimal weight: 10.0000 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 32 optimal weight: 0.5980 chunk 51 optimal weight: 0.6980 chunk 63 optimal weight: 4.9990 chunk 98 optimal weight: 8.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.086555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2638 r_free = 0.2638 target = 0.054957 restraints weight = 48981.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2688 r_free = 0.2688 target = 0.057170 restraints weight = 21539.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.058582 restraints weight = 13640.253| |-----------------------------------------------------------------------------| r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2693 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2693 r_free = 0.2693 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2691 r_free = 0.2691 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2691 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.1216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 13661 Z= 0.219 Angle : 0.603 7.407 19704 Z= 0.352 Chirality : 0.036 0.149 2240 Planarity : 0.004 0.043 1478 Dihedral : 29.676 148.629 4171 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.36 % Allowed : 11.51 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.46 (0.29), residues: 839 helix: 2.58 (0.22), residues: 555 sheet: 2.08 (1.30), residues: 18 loop : -0.51 (0.36), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 113 PHE 0.013 0.001 PHE A 78 TYR 0.013 0.002 TYR B 88 ARG 0.013 0.000 ARG M 42 Details of bonding type rmsd link_TRANS : bond 0.00034 ( 2) link_TRANS : angle 0.43106 ( 6) hydrogen bonds : bond 0.04957 ( 768) hydrogen bonds : angle 3.35835 ( 1920) covalent geometry : bond 0.00499 (13659) covalent geometry : angle 0.60314 (19698) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 185 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.8170 (m-30) cc_final: 0.7915 (t70) REVERT: B 25 ASN cc_start: 0.8675 (m-40) cc_final: 0.8051 (m110) REVERT: B 31 LYS cc_start: 0.9231 (ttmt) cc_final: 0.9006 (ttpp) REVERT: B 91 LYS cc_start: 0.9478 (ttmm) cc_final: 0.9176 (ttmt) REVERT: D 51 ASP cc_start: 0.9078 (p0) cc_final: 0.8407 (p0) REVERT: D 85 LYS cc_start: 0.9384 (mttm) cc_final: 0.9119 (mmtt) REVERT: E 57 SER cc_start: 0.9386 (p) cc_final: 0.8892 (p) REVERT: E 59 GLU cc_start: 0.8823 (pm20) cc_final: 0.7986 (pm20) REVERT: E 82 LEU cc_start: 0.9511 (mt) cc_final: 0.9274 (mm) REVERT: E 105 GLU cc_start: 0.8551 (tp30) cc_final: 0.8233 (tp30) REVERT: F 85 ASP cc_start: 0.8804 (m-30) cc_final: 0.8329 (m-30) REVERT: F 88 TYR cc_start: 0.8461 (m-10) cc_final: 0.8064 (m-10) REVERT: F 91 LYS cc_start: 0.9349 (tttp) cc_final: 0.8989 (ttmt) REVERT: H 83 TYR cc_start: 0.8825 (m-10) cc_final: 0.8501 (m-80) REVERT: H 85 LYS cc_start: 0.9332 (mttm) cc_final: 0.8955 (mttp) REVERT: H 105 GLU cc_start: 0.7112 (OUTLIER) cc_final: 0.6827 (pm20) REVERT: C 64 GLU cc_start: 0.9140 (tm-30) cc_final: 0.8484 (tm-30) REVERT: G 41 GLU cc_start: 0.8367 (tm-30) cc_final: 0.8073 (tm-30) outliers start: 16 outliers final: 13 residues processed: 191 average time/residue: 0.2969 time to fit residues: 76.8561 Evaluate side-chains 186 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 172 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain H residue 105 GLU Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 79 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 20 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 88 optimal weight: 7.9990 chunk 19 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 95 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.084976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2604 r_free = 0.2604 target = 0.053594 restraints weight = 40111.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2651 r_free = 0.2651 target = 0.055613 restraints weight = 19737.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.056838 restraints weight = 13267.747| |-----------------------------------------------------------------------------| r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2659 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2659 r_free = 0.2659 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2658 r_free = 0.2658 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2658 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 13661 Z= 0.244 Angle : 0.626 8.319 19704 Z= 0.362 Chirality : 0.037 0.167 2240 Planarity : 0.004 0.064 1478 Dihedral : 29.776 149.316 4171 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.47 % Allowed : 14.70 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.33 (0.29), residues: 839 helix: 2.53 (0.22), residues: 555 sheet: 2.13 (1.29), residues: 18 loop : -0.70 (0.36), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS H 49 PHE 0.021 0.002 PHE A 78 TYR 0.026 0.002 TYR B 88 ARG 0.007 0.001 ARG M 42 Details of bonding type rmsd link_TRANS : bond 0.00116 ( 2) link_TRANS : angle 0.39827 ( 6) hydrogen bonds : bond 0.05214 ( 768) hydrogen bonds : angle 3.33279 ( 1920) covalent geometry : bond 0.00561 (13659) covalent geometry : angle 0.62590 (19698) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 182 time to evaluate : 0.952 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8542 (OUTLIER) cc_final: 0.8236 (pm20) REVERT: A 81 ASP cc_start: 0.7973 (m-30) cc_final: 0.7753 (t70) REVERT: A 123 ASP cc_start: 0.9338 (m-30) cc_final: 0.9133 (m-30) REVERT: B 25 ASN cc_start: 0.8673 (m-40) cc_final: 0.7964 (m110) REVERT: B 88 TYR cc_start: 0.8508 (m-10) cc_final: 0.7858 (m-10) REVERT: B 91 LYS cc_start: 0.9472 (ttmm) cc_final: 0.9166 (ttmt) REVERT: D 46 LYS cc_start: 0.9465 (tppt) cc_final: 0.9207 (tppt) REVERT: D 51 ASP cc_start: 0.9058 (p0) cc_final: 0.8567 (p0) REVERT: D 83 TYR cc_start: 0.8348 (m-10) cc_final: 0.7468 (m-10) REVERT: D 85 LYS cc_start: 0.9384 (mttm) cc_final: 0.9176 (mmtt) REVERT: D 120 LYS cc_start: 0.9141 (ttmt) cc_final: 0.8912 (tttt) REVERT: E 57 SER cc_start: 0.9369 (p) cc_final: 0.8624 (p) REVERT: E 59 GLU cc_start: 0.8827 (pm20) cc_final: 0.8087 (pm20) REVERT: E 105 GLU cc_start: 0.8636 (tp30) cc_final: 0.8355 (tp30) REVERT: F 88 TYR cc_start: 0.8818 (m-10) cc_final: 0.8248 (m-10) REVERT: F 91 LYS cc_start: 0.9401 (tttp) cc_final: 0.9150 (ttmt) REVERT: H 85 LYS cc_start: 0.9321 (mttm) cc_final: 0.8856 (mtmm) REVERT: C 64 GLU cc_start: 0.9142 (tm-30) cc_final: 0.8458 (tm-30) REVERT: G 41 GLU cc_start: 0.8470 (tm-30) cc_final: 0.8069 (tm-30) outliers start: 24 outliers final: 20 residues processed: 193 average time/residue: 0.2831 time to fit residues: 74.7047 Evaluate side-chains 195 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 174 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain M residue 25 ASN Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 79 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 0.8980 chunk 41 optimal weight: 0.3980 chunk 60 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 73 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 40 GLN ** 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 = 0.3253 r_free = 0.3253 target = 0.085473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2624 r_free = 0.2624 target = 0.054561 restraints weight = 38654.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2669 r_free = 0.2669 target = 0.056541 restraints weight = 19065.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.057789 restraints weight = 12840.985| |-----------------------------------------------------------------------------| r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2676 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2676 r_free = 0.2676 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2676 r_free = 0.2676 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2676 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 13661 Z= 0.212 Angle : 0.610 8.129 19704 Z= 0.354 Chirality : 0.036 0.153 2240 Planarity : 0.004 0.036 1478 Dihedral : 29.734 149.093 4171 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.33 % Allowed : 16.09 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.33 (0.29), residues: 839 helix: 2.55 (0.22), residues: 555 sheet: 1.90 (1.22), residues: 18 loop : -0.74 (0.36), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS H 109 PHE 0.017 0.001 PHE A 78 TYR 0.020 0.002 TYR B 88 ARG 0.008 0.000 ARG H 33 Details of bonding type rmsd link_TRANS : bond 0.00087 ( 2) link_TRANS : angle 0.31139 ( 6) hydrogen bonds : bond 0.04817 ( 768) hydrogen bonds : angle 3.17199 ( 1920) covalent geometry : bond 0.00484 (13659) covalent geometry : angle 0.60967 (19698) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 184 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.8228 (pm20) REVERT: A 123 ASP cc_start: 0.9333 (m-30) cc_final: 0.8809 (m-30) REVERT: A 125 GLN cc_start: 0.8250 (mt0) cc_final: 0.7436 (mp10) REVERT: B 25 ASN cc_start: 0.8655 (m-40) cc_final: 0.7973 (m110) REVERT: B 88 TYR cc_start: 0.8623 (m-10) cc_final: 0.7881 (m-10) REVERT: B 91 LYS cc_start: 0.9468 (ttmm) cc_final: 0.9160 (ttmt) REVERT: D 33 ARG cc_start: 0.8268 (ttm-80) cc_final: 0.7913 (ttm-80) REVERT: D 46 LYS cc_start: 0.9451 (tppt) cc_final: 0.9210 (tppt) REVERT: D 51 ASP cc_start: 0.9038 (p0) cc_final: 0.8580 (p0) REVERT: D 83 TYR cc_start: 0.8334 (m-10) cc_final: 0.7497 (m-10) REVERT: E 57 SER cc_start: 0.9350 (p) cc_final: 0.8500 (p) REVERT: E 59 GLU cc_start: 0.8793 (pm20) cc_final: 0.8060 (pm20) REVERT: F 88 TYR cc_start: 0.8757 (m-10) cc_final: 0.8300 (m-10) REVERT: F 91 LYS cc_start: 0.9395 (tttp) cc_final: 0.9168 (ttmt) REVERT: H 85 LYS cc_start: 0.9320 (mttm) cc_final: 0.8858 (mtmm) REVERT: C 64 GLU cc_start: 0.9133 (tm-30) cc_final: 0.8442 (tm-30) REVERT: G 41 GLU cc_start: 0.8488 (tm-30) cc_final: 0.8046 (tm-30) outliers start: 23 outliers final: 20 residues processed: 193 average time/residue: 0.2876 time to fit residues: 75.4794 Evaluate side-chains 193 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 172 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain M residue 25 ASN Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 79 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 78 optimal weight: 4.9990 chunk 67 optimal weight: 5.9990 chunk 92 optimal weight: 1.9990 chunk 11 optimal weight: 0.0770 chunk 0 optimal weight: 4.9990 chunk 20 optimal weight: 0.7980 chunk 96 optimal weight: 0.6980 chunk 57 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 overall best weight: 1.3142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 40 GLN M 62 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.085750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2619 r_free = 0.2619 target = 0.054330 restraints weight = 42965.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2666 r_free = 0.2666 target = 0.056416 restraints weight = 20308.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.057730 restraints weight = 13395.511| |-----------------------------------------------------------------------------| r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2674 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2674 r_free = 0.2674 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2674 r_free = 0.2674 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2674 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 13661 Z= 0.204 Angle : 0.603 7.911 19704 Z= 0.350 Chirality : 0.035 0.163 2240 Planarity : 0.004 0.036 1478 Dihedral : 29.730 149.313 4171 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 4.72 % Allowed : 16.09 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.35 (0.29), residues: 839 helix: 2.60 (0.22), residues: 555 sheet: 1.66 (1.20), residues: 18 loop : -0.78 (0.36), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS H 109 PHE 0.019 0.001 PHE A 78 TYR 0.015 0.002 TYR B 88 ARG 0.007 0.000 ARG H 33 Details of bonding type rmsd link_TRANS : bond 0.00079 ( 2) link_TRANS : angle 0.30470 ( 6) hydrogen bonds : bond 0.04762 ( 768) hydrogen bonds : angle 3.12544 ( 1920) covalent geometry : bond 0.00463 (13659) covalent geometry : angle 0.60318 (19698) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 179 time to evaluate : 0.976 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.8172 (pm20) REVERT: A 123 ASP cc_start: 0.9326 (m-30) cc_final: 0.8821 (m-30) REVERT: A 125 GLN cc_start: 0.8258 (mt0) cc_final: 0.7476 (mt0) REVERT: B 25 ASN cc_start: 0.8662 (m-40) cc_final: 0.7936 (m110) REVERT: B 88 TYR cc_start: 0.8656 (m-10) cc_final: 0.7868 (m-10) REVERT: B 91 LYS cc_start: 0.9468 (ttmm) cc_final: 0.9237 (ttmt) REVERT: D 33 ARG cc_start: 0.8329 (ttm-80) cc_final: 0.7985 (ttm-80) REVERT: D 34 LYS cc_start: 0.9136 (mtpp) cc_final: 0.8907 (mmmm) REVERT: D 46 LYS cc_start: 0.9432 (tppt) cc_final: 0.9168 (tppt) REVERT: D 51 ASP cc_start: 0.9012 (p0) cc_final: 0.8553 (p0) REVERT: D 83 TYR cc_start: 0.8374 (m-10) cc_final: 0.7513 (m-10) REVERT: E 57 SER cc_start: 0.9362 (p) cc_final: 0.8481 (p) REVERT: E 59 GLU cc_start: 0.8769 (pm20) cc_final: 0.8073 (pm20) REVERT: F 88 TYR cc_start: 0.8719 (m-10) cc_final: 0.8308 (m-10) REVERT: F 91 LYS cc_start: 0.9394 (tttp) cc_final: 0.9176 (ttmt) REVERT: H 85 LYS cc_start: 0.9322 (mttm) cc_final: 0.8861 (mtmm) REVERT: C 64 GLU cc_start: 0.9140 (tm-30) cc_final: 0.8435 (tm-30) REVERT: G 41 GLU cc_start: 0.8371 (tm-30) cc_final: 0.8013 (tm-30) outliers start: 33 outliers final: 26 residues processed: 194 average time/residue: 0.2769 time to fit residues: 74.1083 Evaluate side-chains 202 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 175 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain M residue 25 ASN Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 79 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 25 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 chunk 103 optimal weight: 0.7980 chunk 76 optimal weight: 4.9990 chunk 95 optimal weight: 0.9990 chunk 107 optimal weight: 0.6980 chunk 80 optimal weight: 0.1980 chunk 8 optimal weight: 0.9990 chunk 32 optimal weight: 0.5980 chunk 54 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN F 25 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.087606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2674 r_free = 0.2674 target = 0.056539 restraints weight = 38860.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.058618 restraints weight = 18890.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.059883 restraints weight = 12614.250| |-----------------------------------------------------------------------------| r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2726 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2726 r_free = 0.2726 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2726 r_free = 0.2726 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2726 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13661 Z= 0.157 Angle : 0.582 8.414 19704 Z= 0.338 Chirality : 0.034 0.156 2240 Planarity : 0.004 0.036 1478 Dihedral : 29.593 148.500 4171 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.64 % Allowed : 18.59 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.55 (0.29), residues: 839 helix: 2.76 (0.22), residues: 554 sheet: 1.67 (1.20), residues: 18 loop : -0.69 (0.36), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS H 109 PHE 0.016 0.001 PHE A 78 TYR 0.010 0.001 TYR C 50 ARG 0.009 0.000 ARG H 33 Details of bonding type rmsd link_TRANS : bond 0.00030 ( 2) link_TRANS : angle 0.40965 ( 6) hydrogen bonds : bond 0.04197 ( 768) hydrogen bonds : angle 2.91222 ( 1920) covalent geometry : bond 0.00342 (13659) covalent geometry : angle 0.58247 (19698) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 193 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.8098 (pm20) REVERT: A 123 ASP cc_start: 0.9246 (m-30) cc_final: 0.8720 (m-30) REVERT: A 125 GLN cc_start: 0.8237 (mt0) cc_final: 0.7390 (mt0) REVERT: B 25 ASN cc_start: 0.8603 (m-40) cc_final: 0.7778 (m110) REVERT: B 67 ARG cc_start: 0.7394 (mmp80) cc_final: 0.7075 (tpp80) REVERT: B 88 TYR cc_start: 0.8606 (m-10) cc_final: 0.7903 (m-10) REVERT: B 91 LYS cc_start: 0.9462 (ttmm) cc_final: 0.9214 (ttmt) REVERT: D 33 ARG cc_start: 0.8338 (ttm-80) cc_final: 0.7983 (ttm-80) REVERT: D 51 ASP cc_start: 0.8964 (p0) cc_final: 0.8447 (p0) REVERT: D 83 TYR cc_start: 0.8284 (m-10) cc_final: 0.7522 (m-10) REVERT: E 57 SER cc_start: 0.9322 (p) cc_final: 0.8903 (p) REVERT: E 59 GLU cc_start: 0.8723 (pm20) cc_final: 0.8077 (pm20) REVERT: F 85 ASP cc_start: 0.8889 (m-30) cc_final: 0.8373 (m-30) REVERT: F 88 TYR cc_start: 0.8651 (m-10) cc_final: 0.8295 (m-10) REVERT: H 85 LYS cc_start: 0.9302 (mttm) cc_final: 0.8845 (mtmm) REVERT: C 64 GLU cc_start: 0.9126 (tm-30) cc_final: 0.8645 (tm-30) REVERT: G 41 GLU cc_start: 0.8295 (tm-30) cc_final: 0.7943 (tm-30) outliers start: 18 outliers final: 14 residues processed: 199 average time/residue: 0.2834 time to fit residues: 77.4785 Evaluate side-chains 194 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 179 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 79 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 0.9980 chunk 6 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 32 optimal weight: 0.6980 chunk 83 optimal weight: 10.0000 chunk 63 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 64 optimal weight: 4.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN M 40 GLN M 62 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.085741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2621 r_free = 0.2621 target = 0.054434 restraints weight = 40158.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2667 r_free = 0.2667 target = 0.056461 restraints weight = 19572.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.057730 restraints weight = 13126.492| |-----------------------------------------------------------------------------| r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2676 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2676 r_free = 0.2676 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2676 r_free = 0.2676 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2676 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 13661 Z= 0.219 Angle : 0.626 13.701 19704 Z= 0.357 Chirality : 0.036 0.158 2240 Planarity : 0.004 0.036 1478 Dihedral : 29.758 149.746 4171 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 4.16 % Allowed : 18.45 % Favored : 77.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.43 (0.29), residues: 839 helix: 2.65 (0.22), residues: 555 sheet: 1.58 (1.17), residues: 18 loop : -0.72 (0.36), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS H 109 PHE 0.015 0.001 PHE A 78 TYR 0.014 0.002 TYR C 57 ARG 0.009 0.000 ARG M 42 Details of bonding type rmsd link_TRANS : bond 0.00128 ( 2) link_TRANS : angle 0.32696 ( 6) hydrogen bonds : bond 0.04861 ( 768) hydrogen bonds : angle 3.14354 ( 1920) covalent geometry : bond 0.00500 (13659) covalent geometry : angle 0.62624 (19698) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 175 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 ASP cc_start: 0.9276 (m-30) cc_final: 0.8808 (m-30) REVERT: A 125 GLN cc_start: 0.8283 (mt0) cc_final: 0.7556 (mt0) REVERT: B 25 ASN cc_start: 0.8672 (m-40) cc_final: 0.7900 (m110) REVERT: B 67 ARG cc_start: 0.7618 (mmp80) cc_final: 0.7262 (tpp80) REVERT: B 88 TYR cc_start: 0.8692 (m-10) cc_final: 0.7860 (m-10) REVERT: B 91 LYS cc_start: 0.9479 (ttmm) cc_final: 0.9245 (ttmt) REVERT: D 33 ARG cc_start: 0.8402 (ttm-80) cc_final: 0.8022 (ttm-80) REVERT: D 51 ASP cc_start: 0.9055 (p0) cc_final: 0.8574 (p0) REVERT: D 83 TYR cc_start: 0.8410 (m-10) cc_final: 0.7540 (m-10) REVERT: E 57 SER cc_start: 0.9290 (p) cc_final: 0.8851 (p) REVERT: E 59 GLU cc_start: 0.8764 (pm20) cc_final: 0.8199 (pm20) REVERT: F 85 ASP cc_start: 0.8898 (m-30) cc_final: 0.8485 (m-30) REVERT: F 88 TYR cc_start: 0.8749 (m-10) cc_final: 0.8445 (m-10) REVERT: H 85 LYS cc_start: 0.9331 (mttm) cc_final: 0.8868 (mtmm) REVERT: C 64 GLU cc_start: 0.9168 (tm-30) cc_final: 0.8488 (tm-30) REVERT: G 41 GLU cc_start: 0.8359 (tm-30) cc_final: 0.7996 (tm-30) outliers start: 29 outliers final: 23 residues processed: 186 average time/residue: 0.2814 time to fit residues: 72.6730 Evaluate side-chains 196 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 173 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain M residue 25 ASN Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 79 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 105 optimal weight: 0.0040 chunk 40 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 34 optimal weight: 0.4980 chunk 25 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 18 optimal weight: 0.1980 chunk 89 optimal weight: 0.6980 chunk 69 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN M 40 GLN M 62 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.087740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2656 r_free = 0.2656 target = 0.055942 restraints weight = 51788.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2707 r_free = 0.2707 target = 0.058240 restraints weight = 22122.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.059692 restraints weight = 13835.105| |-----------------------------------------------------------------------------| r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2717 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2717 r_free = 0.2717 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2717 r_free = 0.2717 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2717 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13661 Z= 0.159 Angle : 0.590 9.451 19704 Z= 0.340 Chirality : 0.034 0.157 2240 Planarity : 0.004 0.037 1478 Dihedral : 29.604 148.278 4171 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.64 % Allowed : 19.42 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.59 (0.29), residues: 839 helix: 2.79 (0.22), residues: 554 sheet: 1.52 (1.16), residues: 18 loop : -0.66 (0.36), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 109 PHE 0.010 0.001 PHE A 78 TYR 0.010 0.001 TYR C 57 ARG 0.009 0.000 ARG M 42 Details of bonding type rmsd link_TRANS : bond 0.00013 ( 2) link_TRANS : angle 0.41389 ( 6) hydrogen bonds : bond 0.04185 ( 768) hydrogen bonds : angle 2.87559 ( 1920) covalent geometry : bond 0.00347 (13659) covalent geometry : angle 0.59035 (19698) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 181 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 ASP cc_start: 0.9253 (m-30) cc_final: 0.8774 (m-30) REVERT: A 125 GLN cc_start: 0.8247 (mt0) cc_final: 0.7364 (mt0) REVERT: B 25 ASN cc_start: 0.8614 (m-40) cc_final: 0.7862 (m110) REVERT: B 88 TYR cc_start: 0.8572 (m-10) cc_final: 0.7845 (m-10) REVERT: B 91 LYS cc_start: 0.9467 (ttmm) cc_final: 0.9213 (ttmt) REVERT: D 33 ARG cc_start: 0.8403 (ttm-80) cc_final: 0.8049 (ttm-80) REVERT: D 51 ASP cc_start: 0.8968 (p0) cc_final: 0.8502 (p0) REVERT: D 83 TYR cc_start: 0.8356 (m-10) cc_final: 0.7574 (m-10) REVERT: E 57 SER cc_start: 0.9235 (p) cc_final: 0.8776 (p) REVERT: E 59 GLU cc_start: 0.8711 (pm20) cc_final: 0.8177 (pm20) REVERT: F 85 ASP cc_start: 0.8877 (m-30) cc_final: 0.8380 (m-30) REVERT: F 88 TYR cc_start: 0.8677 (m-10) cc_final: 0.8372 (m-10) REVERT: H 85 LYS cc_start: 0.9298 (mttm) cc_final: 0.8845 (mtmm) REVERT: C 64 GLU cc_start: 0.9150 (tm-30) cc_final: 0.8626 (tm-30) REVERT: G 41 GLU cc_start: 0.8302 (tm-30) cc_final: 0.7945 (tm-30) outliers start: 18 outliers final: 15 residues processed: 188 average time/residue: 0.2877 time to fit residues: 74.8015 Evaluate side-chains 191 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 176 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 79 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 80 optimal weight: 8.9990 chunk 61 optimal weight: 4.9990 chunk 64 optimal weight: 4.9990 chunk 81 optimal weight: 9.9990 chunk 20 optimal weight: 0.5980 chunk 52 optimal weight: 5.9990 chunk 42 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.086402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2625 r_free = 0.2625 target = 0.054663 restraints weight = 51283.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2676 r_free = 0.2676 target = 0.056903 restraints weight = 22221.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.058326 restraints weight = 13991.537| |-----------------------------------------------------------------------------| r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2688 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2688 r_free = 0.2688 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2688 r_free = 0.2688 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2688 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 13661 Z= 0.202 Angle : 0.613 7.873 19704 Z= 0.353 Chirality : 0.035 0.161 2240 Planarity : 0.004 0.037 1478 Dihedral : 29.693 149.298 4171 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.64 % Allowed : 19.69 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.56 (0.29), residues: 839 helix: 2.74 (0.22), residues: 555 sheet: 1.28 (1.05), residues: 26 loop : -0.69 (0.36), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS H 109 PHE 0.009 0.001 PHE E 78 TYR 0.010 0.002 TYR B 88 ARG 0.017 0.000 ARG M 42 Details of bonding type rmsd link_TRANS : bond 0.00115 ( 2) link_TRANS : angle 0.36492 ( 6) hydrogen bonds : bond 0.04591 ( 768) hydrogen bonds : angle 3.04243 ( 1920) covalent geometry : bond 0.00460 (13659) covalent geometry : angle 0.61323 (19698) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 172 time to evaluate : 1.049 Fit side-chains revert: symmetry clash REVERT: A 123 ASP cc_start: 0.9273 (m-30) cc_final: 0.8799 (m-30) REVERT: A 125 GLN cc_start: 0.8271 (mt0) cc_final: 0.7504 (mt0) REVERT: B 25 ASN cc_start: 0.8702 (m-40) cc_final: 0.7992 (m110) REVERT: B 88 TYR cc_start: 0.8624 (m-10) cc_final: 0.7789 (m-10) REVERT: B 91 LYS cc_start: 0.9463 (ttmm) cc_final: 0.9224 (ttmt) REVERT: D 33 ARG cc_start: 0.8362 (ttm-80) cc_final: 0.8000 (ttm-80) REVERT: D 51 ASP cc_start: 0.8999 (p0) cc_final: 0.8539 (p0) REVERT: D 83 TYR cc_start: 0.8414 (m-10) cc_final: 0.7561 (m-10) REVERT: D 100 LEU cc_start: 0.9458 (mt) cc_final: 0.9243 (mt) REVERT: E 57 SER cc_start: 0.9218 (p) cc_final: 0.8799 (p) REVERT: E 59 GLU cc_start: 0.8738 (pm20) cc_final: 0.8192 (pm20) REVERT: F 85 ASP cc_start: 0.8886 (m-30) cc_final: 0.8451 (m-30) REVERT: F 88 TYR cc_start: 0.8722 (m-10) cc_final: 0.8429 (m-10) REVERT: H 85 LYS cc_start: 0.9315 (mttm) cc_final: 0.8849 (mtmm) REVERT: C 64 GLU cc_start: 0.9162 (tm-30) cc_final: 0.8482 (tm-30) REVERT: G 41 GLU cc_start: 0.8322 (tm-30) cc_final: 0.7958 (tm-30) outliers start: 18 outliers final: 16 residues processed: 181 average time/residue: 0.2726 time to fit residues: 68.6630 Evaluate side-chains 185 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 169 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 79 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 22 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 30 optimal weight: 0.5980 chunk 76 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 73 optimal weight: 3.9990 chunk 82 optimal weight: 0.0270 chunk 4 optimal weight: 2.9990 overall best weight: 0.6640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN M 40 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.088092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2656 r_free = 0.2656 target = 0.056087 restraints weight = 54443.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.058459 restraints weight = 22814.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.060004 restraints weight = 14026.687| |-----------------------------------------------------------------------------| r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2721 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2721 r_free = 0.2721 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2721 r_free = 0.2721 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2721 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13661 Z= 0.159 Angle : 0.594 8.245 19704 Z= 0.342 Chirality : 0.033 0.159 2240 Planarity : 0.004 0.037 1478 Dihedral : 29.561 148.151 4171 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.64 % Allowed : 20.25 % Favored : 77.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.71 (0.29), residues: 839 helix: 2.85 (0.22), residues: 554 sheet: 1.31 (1.03), residues: 26 loop : -0.60 (0.36), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS H 109 PHE 0.009 0.001 PHE E 78 TYR 0.010 0.001 TYR C 50 ARG 0.011 0.000 ARG M 42 Details of bonding type rmsd link_TRANS : bond 0.00013 ( 2) link_TRANS : angle 0.44220 ( 6) hydrogen bonds : bond 0.04069 ( 768) hydrogen bonds : angle 2.83303 ( 1920) covalent geometry : bond 0.00349 (13659) covalent geometry : angle 0.59393 (19698) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 175 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8031 (tt0) cc_final: 0.7415 (tt0) REVERT: A 123 ASP cc_start: 0.9234 (m-30) cc_final: 0.8745 (m-30) REVERT: A 125 GLN cc_start: 0.8267 (mt0) cc_final: 0.7425 (mt0) REVERT: B 25 ASN cc_start: 0.8658 (m-40) cc_final: 0.7890 (m110) REVERT: B 88 TYR cc_start: 0.8544 (m-10) cc_final: 0.7867 (m-10) REVERT: B 91 LYS cc_start: 0.9455 (ttmm) cc_final: 0.9208 (ttmt) REVERT: D 33 ARG cc_start: 0.8319 (ttm-80) cc_final: 0.7963 (ttm-80) REVERT: D 51 ASP cc_start: 0.8967 (p0) cc_final: 0.8445 (p0) REVERT: D 83 TYR cc_start: 0.8313 (m-10) cc_final: 0.7562 (m-10) REVERT: D 92 ARG cc_start: 0.8870 (ttt-90) cc_final: 0.8659 (ttm170) REVERT: D 100 LEU cc_start: 0.9454 (mt) cc_final: 0.9248 (mt) REVERT: E 57 SER cc_start: 0.9222 (p) cc_final: 0.8763 (p) REVERT: E 59 GLU cc_start: 0.8647 (pm20) cc_final: 0.8084 (pm20) REVERT: F 59 LYS cc_start: 0.9154 (ttmm) cc_final: 0.8718 (ttpt) REVERT: F 85 ASP cc_start: 0.8797 (m-30) cc_final: 0.8341 (m-30) REVERT: F 88 TYR cc_start: 0.8650 (m-10) cc_final: 0.8438 (m-10) REVERT: H 83 TYR cc_start: 0.8655 (m-10) cc_final: 0.7707 (m-80) REVERT: H 85 LYS cc_start: 0.9339 (mttm) cc_final: 0.8889 (mtmm) REVERT: C 64 GLU cc_start: 0.9138 (tm-30) cc_final: 0.8611 (tm-30) REVERT: G 41 GLU cc_start: 0.8278 (tm-30) cc_final: 0.7932 (tm-30) outliers start: 18 outliers final: 16 residues processed: 183 average time/residue: 0.2722 time to fit residues: 69.0125 Evaluate side-chains 190 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 174 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 79 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 16 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 82 optimal weight: 10.0000 chunk 38 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 13 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN ** M 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.087410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2637 r_free = 0.2637 target = 0.055270 restraints weight = 56521.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.057626 restraints weight = 23321.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.059159 restraints weight = 14275.762| |-----------------------------------------------------------------------------| r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2703 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2703 r_free = 0.2703 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2703 r_free = 0.2703 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2703 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13661 Z= 0.186 Angle : 0.601 8.336 19704 Z= 0.346 Chirality : 0.034 0.161 2240 Planarity : 0.004 0.037 1478 Dihedral : 29.596 148.665 4171 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.77 % Allowed : 19.69 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.65 (0.29), residues: 839 helix: 2.81 (0.22), residues: 555 sheet: 1.32 (1.03), residues: 26 loop : -0.65 (0.36), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS H 109 PHE 0.007 0.001 PHE E 78 TYR 0.010 0.001 TYR C 50 ARG 0.011 0.000 ARG M 42 Details of bonding type rmsd link_TRANS : bond 0.00076 ( 2) link_TRANS : angle 0.38481 ( 6) hydrogen bonds : bond 0.04256 ( 768) hydrogen bonds : angle 2.90186 ( 1920) covalent geometry : bond 0.00419 (13659) covalent geometry : angle 0.60105 (19698) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4047.00 seconds wall clock time: 71 minutes 57.85 seconds (4317.85 seconds total)