Starting phenix.real_space_refine on Fri Jul 3 06:52:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8txx_41708/07_2026/8txx_41708.cif Found real_map, /net/cci-nas-00/data/ceres_data/8txx_41708/07_2026/8txx_41708.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8txx_41708/07_2026/8txx_41708.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8txx_41708/07_2026/8txx_41708.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8txx_41708/07_2026/8txx_41708.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8txx_41708/07_2026/8txx_41708.map" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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 7227 2.51 5 N 2431 2.21 5 O 3002 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12969 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: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 251 Classifications: {'peptide': 30} Link IDs: {'PTRANS': 1, 'TRANS': 28} Chain breaks: 1 Chain: "M" Number of atoms: 601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 601 Classifications: {'peptide': 76} 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: 1 residue: pdb=" N LEU M 73 " occ=0.45 ... (6 atoms not shown) pdb=" CD2 LEU M 73 " occ=0.45 Time building chain proxies: 2.94, per 1000 atoms: 0.23 Number of scatterers: 12969 At special positions: 0 Unit cell: (99.6, 124.832, 123.504, 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 3002 8.00 N 2431 7.00 C 7227 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=1, symmetry=0 Links applied TRANS " SER C 11 " - " SER D 123 " " SER G 11 " - " SER H 123 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.10 Conformation dependent library (CDL) restraints added in 414.2 milliseconds 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1632 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 12 sheets defined 67.9% alpha, 3.7% beta 135 base pairs and 242 stacking pairs defined. Time for finding SS restraints: 1.94 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 79 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.724A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 removed outlier: 4.169A pdb=" N GLN B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.090A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.572A 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: 3.647A pdb=" N GLN D 47 " --> pdb=" O LYS D 43 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL D 48 " --> pdb=" O VAL D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.668A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.581A pdb=" N ILE D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 123 removed outlier: 3.687A pdb=" N SER D 112 " --> pdb=" O LYS D 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 55 Processing helix chain 'E' and resid 63 through 79 Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.538A pdb=" N ALA E 114 " --> pdb=" O CYS E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 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: 4.121A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.506A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 122 Processing helix chain 'K' and resid 447 through 461 Processing helix chain 'M' and resid 22 through 35 Processing helix chain 'M' and resid 37 through 41 Processing helix chain 'M' and resid 56 through 60 Processing helix chain 'M' and resid 71 through 75 removed outlier: 3.745A pdb=" N ARG M 74 " --> pdb=" O LEU M 71 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N GLY M 75 " --> pdb=" O ARG M 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 71 through 75' Processing helix chain 'C' and resid 16 through 21 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: 3.521A 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 38 removed outlier: 3.608A pdb=" N ASN G 38 " --> pdb=" O LEU G 34 " (cutoff:3.500A) 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: 6.681A 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 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'D' and resid 53 through 54 removed outlier: 7.477A 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: 6.597A 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 53 through 54 removed outlier: 7.297A pdb=" N GLY H 53 " --> pdb=" O ILE G 78 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'H' and resid 88 through 89 Processing sheet with id=AB2, first strand: chain 'M' and resid 12 through 15 Processing sheet with id=AB3, first strand: chain 'M' and resid 44 through 45 435 hydrogen bonds defined for protein. 1267 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 348 hydrogen bonds 692 hydrogen bond angles 0 basepair planarities 135 basepair parallelities 242 stacking parallelities Total time for adding SS restraints: 2.51 Time building geometry restraints manager: 1.48 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: 2733 1.33 - 1.45: 4234 1.45 - 1.57: 6212 1.57 - 1.69: 586 1.69 - 1.81: 26 Bond restraints: 13791 Sorted by residual: bond pdb=" C3' DT J -67 " pdb=" C2' DT J -67 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.22e+01 bond pdb=" C3' DT I -17 " pdb=" C2' DT I -17 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.14e+01 bond pdb=" C3' DG I -40 " pdb=" C2' DG I -40 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.32e+00 bond pdb=" C3' DC I 0 " pdb=" C2' DC I 0 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.16e+00 bond pdb=" C3' DA I 29 " pdb=" C2' DA I 29 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.94e+00 ... (remaining 13786 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.39: 18459 1.39 - 2.77: 1318 2.77 - 4.16: 75 4.16 - 5.54: 16 5.54 - 6.93: 4 Bond angle restraints: 19872 Sorted by residual: angle pdb=" O4' DG I 26 " pdb=" C4' DG I 26 " pdb=" C3' DG I 26 " ideal model delta sigma weight residual 106.00 102.91 3.09 6.00e-01 2.78e+00 2.65e+01 angle pdb=" O4' DG I 71 " pdb=" C4' DG I 71 " pdb=" C3' DG I 71 " ideal model delta sigma weight residual 106.00 102.98 3.02 6.00e-01 2.78e+00 2.54e+01 angle pdb=" O4' DG I 47 " pdb=" C4' DG I 47 " pdb=" C3' DG I 47 " ideal model delta sigma weight residual 106.00 103.07 2.93 6.00e-01 2.78e+00 2.38e+01 angle pdb=" N3 DT J 9 " pdb=" C4 DT J 9 " pdb=" O4 DT J 9 " ideal model delta sigma weight residual 119.90 122.60 -2.70 6.00e-01 2.78e+00 2.02e+01 angle pdb=" N3 DT I 1 " pdb=" C4 DT I 1 " pdb=" O4 DT I 1 " ideal model delta sigma weight residual 119.90 122.54 -2.64 6.00e-01 2.78e+00 1.94e+01 ... (remaining 19867 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.52: 6039 31.52 - 63.04: 1499 63.04 - 94.56: 43 94.56 - 126.09: 1 126.09 - 157.61: 2 Dihedral angle restraints: 7584 sinusoidal: 5052 harmonic: 2532 Sorted by residual: dihedral pdb=" CA TYR K 474 " pdb=" C TYR K 474 " pdb=" N HIS K 475 " pdb=" CA HIS K 475 " ideal model delta harmonic sigma weight residual 180.00 156.78 23.22 0 5.00e+00 4.00e-02 2.16e+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 62.39 157.61 1 3.50e+01 8.16e-04 1.51e+01 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 78.91 141.09 1 3.50e+01 8.16e-04 1.39e+01 ... (remaining 7581 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1327 0.031 - 0.061: 579 0.061 - 0.092: 229 0.092 - 0.123: 114 0.123 - 0.154: 12 Chirality restraints: 2261 Sorted by residual: chirality pdb=" CA ASN C 38 " pdb=" N ASN C 38 " pdb=" C ASN C 38 " pdb=" CB ASN C 38 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.91e-01 chirality pdb=" CA GLN A 125 " pdb=" N GLN A 125 " pdb=" C GLN A 125 " pdb=" CB GLN A 125 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.13e-01 chirality pdb=" C3' DT J -17 " pdb=" C4' DT J -17 " pdb=" O3' DT J -17 " pdb=" C2' DT J -17 " both_signs ideal model delta sigma weight residual False -2.73 -2.59 -0.14 2.00e-01 2.50e+01 4.73e-01 ... (remaining 2258 not shown) Planarity restraints: 1502 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 83 " -0.010 2.00e-02 2.50e+03 1.17e-02 2.74e+00 pdb=" CG TYR D 83 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR D 83 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR D 83 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR D 83 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR D 83 " -0.009 2.00e-02 2.50e+03 pdb=" CZ TYR D 83 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR D 83 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 47 " 0.022 2.00e-02 2.50e+03 8.95e-03 2.40e+00 pdb=" N9 DG I 47 " -0.017 2.00e-02 2.50e+03 pdb=" C8 DG I 47 " -0.007 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 " 0.008 2.00e-02 2.50e+03 pdb=" N1 DG I 47 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DG I 47 " -0.001 2.00e-02 2.50e+03 pdb=" N2 DG I 47 " -0.004 2.00e-02 2.50e+03 pdb=" N3 DG I 47 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DG I 47 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I -35 " 0.021 2.00e-02 2.50e+03 8.94e-03 2.20e+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 " 0.000 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 " -0.001 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 ... (remaining 1499 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 146 2.64 - 3.20: 10939 3.20 - 3.77: 23313 3.77 - 4.33: 29611 4.33 - 4.90: 43114 Nonbonded interactions: 107123 Sorted by model distance: nonbonded pdb=" OG SER A 57 " pdb=" OE1 GLU A 59 " model vdw 2.074 3.040 nonbonded pdb=" OH TYR D 40 " pdb=" OP1 DG J 48 " model vdw 2.102 3.040 nonbonded pdb=" O2 DC I 21 " pdb=" N2 DG J -21 " model vdw 2.140 2.496 nonbonded pdb=" NZ LYS B 79 " pdb=" OP1 DG J 27 " model vdw 2.215 3.120 nonbonded pdb=" OH TYR A 99 " pdb=" OE1 GLU A 133 " model vdw 2.250 3.040 ... (remaining 107118 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=0.45 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: 0.010 Normalize map: mean=0, sd=1: 1.290 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: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.420 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 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 : 0.006 0.063 13794 Z= 0.503 Angle : 0.713 6.929 19878 Z= 0.631 Chirality : 0.044 0.154 2261 Planarity : 0.003 0.036 1500 Dihedral : 26.694 157.607 5946 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.62 (0.29), residues: 853 helix: 2.67 (0.22), residues: 560 sheet: 1.12 (1.38), residues: 17 loop : -0.21 (0.37), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 29 TYR 0.028 0.002 TYR D 83 PHE 0.010 0.001 PHE E 104 HIS 0.013 0.001 HIS H 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00559 / 0.50 (13791) covalent geometry : angle 0.71278 / 0.63 (19872) hydrogen bonds : bond 0.11674 / 7.64 ( 783) hydrogen bonds : angle 3.83172 / 2.84 ( 1959) Misc. bond : bond 0.06282 / 3.31 ( 1) link_TRANS : bond 0.00047 / 0.02 ( 2) link_TRANS : angle 0.46968 / 0.26 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 0.364 Fit side-chains revert: symmetry clash REVERT: A 90 MET cc_start: 0.8504 (mmm) cc_final: 0.8053 (tpp) REVERT: A 123 ASP cc_start: 0.8817 (m-30) cc_final: 0.8567 (m-30) REVERT: B 27 GLN cc_start: 0.9204 (mm-40) cc_final: 0.8914 (mp10) REVERT: B 88 TYR cc_start: 0.8607 (m-80) cc_final: 0.8082 (m-10) REVERT: D 51 ASP cc_start: 0.8750 (p0) cc_final: 0.8199 (p0) REVERT: D 57 LYS cc_start: 0.8894 (mmmm) cc_final: 0.8581 (mmtp) REVERT: D 86 ARG cc_start: 0.9070 (mmt-90) cc_final: 0.8801 (mtt-85) REVERT: E 59 GLU cc_start: 0.8380 (pm20) cc_final: 0.7987 (pm20) REVERT: E 76 GLN cc_start: 0.8724 (tm-30) cc_final: 0.8467 (tm-30) REVERT: F 88 TYR cc_start: 0.8759 (m-80) cc_final: 0.8445 (m-80) REVERT: H 33 ARG cc_start: 0.8429 (mtp85) cc_final: 0.7810 (mtp-110) REVERT: H 42 TYR cc_start: 0.8941 (t80) cc_final: 0.8679 (t80) REVERT: C 64 GLU cc_start: 0.8766 (tm-30) cc_final: 0.8445 (tm-30) REVERT: C 95 LYS cc_start: 0.9398 (ttmt) cc_final: 0.9191 (ttmt) REVERT: C 110 ASN cc_start: 0.8949 (t0) cc_final: 0.8344 (p0) REVERT: G 74 LYS cc_start: 0.9412 (mttp) cc_final: 0.9152 (mmtp) REVERT: G 76 THR cc_start: 0.9096 (p) cc_final: 0.8666 (t) outliers start: 0 outliers final: 0 residues processed: 218 average time/residue: 0.1428 time to fit residues: 42.1364 Evaluate side-chains 160 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 0.0870 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 20.0000 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 8.9990 chunk 106 optimal weight: 0.3980 overall best weight: 0.8762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 ASN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 ASN ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.099370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.063296 restraints weight = 59299.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.066118 restraints weight = 24472.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.066619 restraints weight = 13578.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.066846 restraints weight = 11643.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.067073 restraints weight = 10794.861| |-----------------------------------------------------------------------------| r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2836 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2836 r_free = 0.2836 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2835 r_free = 0.2835 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2835 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8814 moved from start: 0.0919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13794 Z= 0.164 Angle : 0.598 5.946 19878 Z= 0.366 Chirality : 0.041 0.219 2261 Planarity : 0.004 0.041 1500 Dihedral : 29.948 160.758 4186 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.04 % Allowed : 11.55 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.69 (0.29), residues: 853 helix: 2.71 (0.22), residues: 576 sheet: 1.19 (1.38), residues: 17 loop : -0.36 (0.38), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 99 TYR 0.020 0.001 TYR H 40 PHE 0.010 0.001 PHE H 70 HIS 0.008 0.001 HIS H 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.16 (13791) covalent geometry : angle 0.59779 / 0.37 (19872) hydrogen bonds : bond 0.05612 / 3.66 ( 783) hydrogen bonds : angle 3.17516 / 2.34 ( 1959) Misc. bond : bond 0.00813 / 0.43 ( 1) link_TRANS : bond 0.00176 / 0.09 ( 2) link_TRANS : angle 0.29867 / 0.15 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 165 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.8461 (mmm) cc_final: 0.7856 (tpp) REVERT: D 42 TYR cc_start: 0.8166 (t80) cc_final: 0.7119 (t80) REVERT: D 47 GLN cc_start: 0.8550 (mt0) cc_final: 0.8303 (mt0) REVERT: D 51 ASP cc_start: 0.8284 (p0) cc_final: 0.7808 (p0) REVERT: D 105 GLU cc_start: 0.8396 (tp30) cc_final: 0.8153 (mm-30) REVERT: D 108 LYS cc_start: 0.9290 (ttpt) cc_final: 0.9024 (ttpt) REVERT: E 59 GLU cc_start: 0.8310 (pm20) cc_final: 0.7987 (pm20) REVERT: E 76 GLN cc_start: 0.8652 (tm-30) cc_final: 0.8385 (tm-30) REVERT: H 33 ARG cc_start: 0.8357 (mtp85) cc_final: 0.7816 (mtp-110) REVERT: H 42 TYR cc_start: 0.9036 (t80) cc_final: 0.8777 (t80) REVERT: H 68 ASP cc_start: 0.8897 (t0) cc_final: 0.8648 (t0) REVERT: H 90 THR cc_start: 0.9260 (p) cc_final: 0.8813 (p) REVERT: C 64 GLU cc_start: 0.8764 (tm-30) cc_final: 0.8463 (tm-30) REVERT: C 95 LYS cc_start: 0.9384 (ttmt) cc_final: 0.9178 (ttmt) REVERT: C 110 ASN cc_start: 0.8896 (t0) cc_final: 0.8327 (p0) REVERT: G 76 THR cc_start: 0.9095 (p) cc_final: 0.8686 (t) outliers start: 15 outliers final: 10 residues processed: 176 average time/residue: 0.1326 time to fit residues: 32.6157 Evaluate side-chains 172 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 162 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain G residue 18 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 30 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 29 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 71 optimal weight: 10.0000 chunk 100 optimal weight: 8.9990 chunk 52 optimal weight: 20.0000 chunk 78 optimal weight: 9.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 47 GLN H 84 ASN ** H 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.098694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.062654 restraints weight = 35437.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.064742 restraints weight = 18325.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.066090 restraints weight = 12790.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.066803 restraints weight = 10604.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.067127 restraints weight = 9647.667| |-----------------------------------------------------------------------------| r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2832 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2832 r_free = 0.2832 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2832 r_free = 0.2832 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2832 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8812 moved from start: 0.1170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13794 Z= 0.168 Angle : 0.583 6.770 19878 Z= 0.352 Chirality : 0.041 0.237 2261 Planarity : 0.004 0.042 1500 Dihedral : 30.092 161.791 4186 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.31 % Allowed : 13.04 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.74 (0.29), residues: 853 helix: 2.80 (0.22), residues: 575 sheet: 1.14 (1.37), residues: 17 loop : -0.46 (0.38), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 31 TYR 0.034 0.002 TYR H 40 PHE 0.010 0.001 PHE H 70 HIS 0.007 0.001 HIS H 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.17 (13791) covalent geometry : angle 0.58356 / 0.35 (19872) hydrogen bonds : bond 0.05215 / 3.44 ( 783) hydrogen bonds : angle 2.99778 / 2.19 ( 1959) Misc. bond : bond 0.00267 / 0.14 ( 1) link_TRANS : bond 0.00019 / 0.01 ( 2) link_TRANS : angle 0.26618 / 0.13 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 170 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 42 TYR cc_start: 0.8188 (t80) cc_final: 0.7153 (t80) REVERT: D 51 ASP cc_start: 0.8258 (p0) cc_final: 0.7800 (p0) REVERT: E 59 GLU cc_start: 0.8416 (pm20) cc_final: 0.8056 (pm20) REVERT: H 33 ARG cc_start: 0.8564 (mtp85) cc_final: 0.7964 (mtp-110) REVERT: H 120 LYS cc_start: 0.9092 (tptm) cc_final: 0.8763 (tptm) REVERT: C 110 ASN cc_start: 0.8905 (t0) cc_final: 0.8376 (p0) REVERT: G 64 GLU cc_start: 0.9291 (tm-30) cc_final: 0.8962 (tm-30) REVERT: G 76 THR cc_start: 0.9149 (p) cc_final: 0.8681 (t) outliers start: 17 outliers final: 14 residues processed: 179 average time/residue: 0.1291 time to fit residues: 32.3524 Evaluate side-chains 175 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 161 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain G residue 13 SER Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 40 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 90 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 81 optimal weight: 9.9990 chunk 60 optimal weight: 10.0000 chunk 108 optimal weight: 0.9980 chunk 53 optimal weight: 20.0000 chunk 78 optimal weight: 10.0000 chunk 83 optimal weight: 7.9990 chunk 4 optimal weight: 0.6980 chunk 56 optimal weight: 9.9990 chunk 100 optimal weight: 3.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN D 47 GLN D 49 HIS H 109 HIS C 24 GLN ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.096612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.2693 r_free = 0.2693 target = 0.059109 restraints weight = 54166.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.061500 restraints weight = 23607.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 63)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.063096 restraints weight = 14982.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.063993 restraints weight = 11758.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.064422 restraints weight = 10397.240| |-----------------------------------------------------------------------------| r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2784 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2784 r_free = 0.2784 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2784 r_free = 0.2784 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2784 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8854 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13794 Z= 0.212 Angle : 0.632 6.543 19878 Z= 0.368 Chirality : 0.042 0.253 2261 Planarity : 0.004 0.045 1500 Dihedral : 30.281 163.655 4186 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.72 % Allowed : 14.95 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.53 (0.29), residues: 853 helix: 2.65 (0.21), residues: 577 sheet: 0.97 (1.33), residues: 17 loop : -0.59 (0.38), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 31 TYR 0.037 0.002 TYR H 40 PHE 0.010 0.001 PHE H 70 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.21 (13791) covalent geometry : angle 0.63161 / 0.37 (19872) hydrogen bonds : bond 0.05666 / 3.75 ( 783) hydrogen bonds : angle 3.13560 / 2.27 ( 1959) Misc. bond : bond 0.00192 / 0.10 ( 1) link_TRANS : bond 0.00088 / 0.04 ( 2) link_TRANS : angle 0.34010 / 0.16 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 171 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.8713 (mmm) cc_final: 0.8379 (tpp) REVERT: A 108 ASN cc_start: 0.9372 (t0) cc_final: 0.9104 (t0) REVERT: D 47 GLN cc_start: 0.8595 (mt0) cc_final: 0.8323 (mt0) REVERT: D 51 ASP cc_start: 0.8375 (p0) cc_final: 0.7726 (p0) REVERT: D 105 GLU cc_start: 0.8492 (mm-30) cc_final: 0.8163 (mm-30) REVERT: E 59 GLU cc_start: 0.8415 (pm20) cc_final: 0.8025 (pm20) REVERT: E 105 GLU cc_start: 0.7958 (tt0) cc_final: 0.7734 (tt0) REVERT: F 35 ARG cc_start: 0.8907 (mtp85) cc_final: 0.8595 (mtp85) REVERT: H 33 ARG cc_start: 0.8631 (mtp85) cc_final: 0.8011 (mtp-110) REVERT: H 120 LYS cc_start: 0.9133 (tptm) cc_final: 0.8820 (tptm) REVERT: C 24 GLN cc_start: 0.8841 (OUTLIER) cc_final: 0.8609 (mp10) REVERT: C 56 GLU cc_start: 0.8855 (tm-30) cc_final: 0.8269 (tm-30) REVERT: C 110 ASN cc_start: 0.8896 (t0) cc_final: 0.8356 (p0) REVERT: G 76 THR cc_start: 0.9153 (p) cc_final: 0.8727 (t) outliers start: 20 outliers final: 19 residues processed: 182 average time/residue: 0.1219 time to fit residues: 31.2613 Evaluate side-chains 182 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 162 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain C residue 24 GLN Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain G residue 13 SER Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 107 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 96 optimal weight: 0.9990 chunk 62 optimal weight: 9.9990 chunk 78 optimal weight: 10.0000 chunk 4 optimal weight: 0.8980 chunk 73 optimal weight: 9.9990 chunk 10 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 83 optimal weight: 9.9990 chunk 20 optimal weight: 0.9990 chunk 101 optimal weight: 0.0040 overall best weight: 0.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 ASN ** G 38 ASN ** 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 = 0.3432 r_free = 0.3432 target = 0.098236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.062253 restraints weight = 58168.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.064951 restraints weight = 24530.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.065447 restraints weight = 13902.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.065835 restraints weight = 11927.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.065843 restraints weight = 10864.268| |-----------------------------------------------------------------------------| r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2796 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2796 r_free = 0.2796 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2796 r_free = 0.2796 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2796 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8833 moved from start: 0.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13794 Z= 0.152 Angle : 0.579 6.198 19878 Z= 0.348 Chirality : 0.041 0.241 2261 Planarity : 0.004 0.043 1500 Dihedral : 30.190 163.070 4186 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.12 % Allowed : 15.90 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.63 (0.29), residues: 853 helix: 2.76 (0.22), residues: 576 sheet: 0.94 (1.34), residues: 17 loop : -0.64 (0.38), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 116 TYR 0.028 0.001 TYR H 40 PHE 0.007 0.001 PHE A 67 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.15 (13791) covalent geometry : angle 0.57905 / 0.35 (19872) hydrogen bonds : bond 0.05041 / 3.30 ( 783) hydrogen bonds : angle 2.88017 / 2.08 ( 1959) Misc. bond : bond 0.00095 / 0.05 ( 1) link_TRANS : bond 0.00043 / 0.02 ( 2) link_TRANS : angle 0.26687 / 0.13 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 172 time to evaluate : 0.271 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 42 TYR cc_start: 0.8154 (t80) cc_final: 0.7313 (t80) REVERT: D 46 LYS cc_start: 0.9336 (mmtt) cc_final: 0.8903 (mmtp) REVERT: D 47 GLN cc_start: 0.8653 (mt0) cc_final: 0.8305 (mt0) REVERT: D 51 ASP cc_start: 0.8297 (p0) cc_final: 0.7696 (p0) REVERT: E 59 GLU cc_start: 0.8486 (pm20) cc_final: 0.8222 (pm20) REVERT: F 35 ARG cc_start: 0.8885 (mtp85) cc_final: 0.8669 (mtp85) REVERT: H 33 ARG cc_start: 0.8626 (mtp85) cc_final: 0.8009 (mtp-110) REVERT: H 71 GLU cc_start: 0.8392 (tm-30) cc_final: 0.8024 (tm-30) REVERT: H 120 LYS cc_start: 0.9124 (tptm) cc_final: 0.8799 (tptm) REVERT: C 56 GLU cc_start: 0.8809 (tm-30) cc_final: 0.8229 (tm-30) REVERT: C 110 ASN cc_start: 0.8874 (t0) cc_final: 0.8300 (p0) REVERT: G 64 GLU cc_start: 0.9282 (tm-30) cc_final: 0.8969 (tm-30) REVERT: G 76 THR cc_start: 0.9128 (p) cc_final: 0.8624 (t) REVERT: G 91 GLU cc_start: 0.8063 (tp30) cc_final: 0.7806 (tp30) outliers start: 23 outliers final: 16 residues processed: 185 average time/residue: 0.1158 time to fit residues: 29.9806 Evaluate side-chains 183 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 167 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 62 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 103 optimal weight: 0.0270 chunk 28 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 71 optimal weight: 9.9990 chunk 3 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 107 optimal weight: 0.3980 chunk 106 optimal weight: 0.2980 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN D 47 GLN H 84 ASN ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.099059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.061722 restraints weight = 56068.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.064210 restraints weight = 23592.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 71)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.065922 restraints weight = 14686.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 68)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.066949 restraints weight = 11397.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.067395 restraints weight = 10002.483| |-----------------------------------------------------------------------------| r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2840 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2840 r_free = 0.2840 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2840 r_free = 0.2840 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2840 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 13794 Z= 0.140 Angle : 0.562 6.021 19878 Z= 0.341 Chirality : 0.040 0.242 2261 Planarity : 0.004 0.042 1500 Dihedral : 30.150 163.304 4186 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.85 % Allowed : 16.17 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.74 (0.29), residues: 853 helix: 2.88 (0.22), residues: 574 sheet: 0.90 (1.34), residues: 17 loop : -0.65 (0.38), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 86 TYR 0.022 0.002 TYR H 40 PHE 0.007 0.001 PHE A 67 HIS 0.002 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.14 (13791) covalent geometry : angle 0.56187 / 0.34 (19872) hydrogen bonds : bond 0.04748 / 3.09 ( 783) hydrogen bonds : angle 2.77557 / 2.01 ( 1959) Misc. bond : bond 0.00020 / 0.01 ( 1) link_TRANS : bond 0.00087 / 0.04 ( 2) link_TRANS : angle 0.25456 / 0.12 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 179 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 LEU cc_start: 0.9250 (OUTLIER) cc_final: 0.9043 (mt) REVERT: B 25 ASN cc_start: 0.8802 (OUTLIER) cc_final: 0.8550 (t0) REVERT: D 42 TYR cc_start: 0.8125 (t80) cc_final: 0.7230 (t80) REVERT: D 47 GLN cc_start: 0.8528 (mt0) cc_final: 0.8160 (mt0) REVERT: D 51 ASP cc_start: 0.8230 (p0) cc_final: 0.7799 (p0) REVERT: E 59 GLU cc_start: 0.8450 (pm20) cc_final: 0.8160 (pm20) REVERT: F 35 ARG cc_start: 0.8876 (mtp85) cc_final: 0.8656 (mtp85) REVERT: H 33 ARG cc_start: 0.8620 (mtp85) cc_final: 0.7976 (mtp-110) REVERT: H 71 GLU cc_start: 0.8469 (tm-30) cc_final: 0.8149 (tm-30) REVERT: H 120 LYS cc_start: 0.9086 (tptm) cc_final: 0.8576 (ttpp) REVERT: C 56 GLU cc_start: 0.8771 (tm-30) cc_final: 0.8176 (tm-30) REVERT: C 110 ASN cc_start: 0.8854 (t0) cc_final: 0.8310 (p0) REVERT: G 64 GLU cc_start: 0.9278 (tm-30) cc_final: 0.8969 (tm-30) REVERT: G 76 THR cc_start: 0.9137 (p) cc_final: 0.8624 (t) REVERT: G 91 GLU cc_start: 0.8059 (tp30) cc_final: 0.7751 (tp30) outliers start: 21 outliers final: 14 residues processed: 190 average time/residue: 0.1284 time to fit residues: 33.9613 Evaluate side-chains 186 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 170 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain G residue 15 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 56 optimal weight: 10.0000 chunk 97 optimal weight: 0.7980 chunk 63 optimal weight: 9.9990 chunk 105 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 chunk 62 optimal weight: 9.9990 chunk 0 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN ** G 38 ASN ** 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 = 0.3441 r_free = 0.3441 target = 0.098722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.063115 restraints weight = 59991.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.065713 restraints weight = 24573.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.066214 restraints weight = 14856.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.066486 restraints weight = 11481.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.066595 restraints weight = 10712.799| |-----------------------------------------------------------------------------| r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2824 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2824 r_free = 0.2824 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2824 r_free = 0.2824 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2824 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8815 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13794 Z= 0.153 Angle : 0.575 9.095 19878 Z= 0.344 Chirality : 0.040 0.246 2261 Planarity : 0.004 0.042 1500 Dihedral : 30.185 163.751 4186 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.72 % Allowed : 16.98 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.71 (0.29), residues: 853 helix: 2.85 (0.21), residues: 575 sheet: 0.88 (1.34), residues: 17 loop : -0.66 (0.38), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 116 TYR 0.021 0.001 TYR H 40 PHE 0.007 0.001 PHE A 67 HIS 0.002 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.15 (13791) covalent geometry : angle 0.57485 / 0.34 (19872) hydrogen bonds : bond 0.04813 / 3.14 ( 783) hydrogen bonds : angle 2.81649 / 2.04 ( 1959) Misc. bond : bond 0.00013 / 0.01 ( 1) link_TRANS : bond 0.00020 / 0.01 ( 2) link_TRANS : angle 0.29539 / 0.15 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 168 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 42 TYR cc_start: 0.8191 (t80) cc_final: 0.7238 (t80) REVERT: D 47 GLN cc_start: 0.8482 (mt0) cc_final: 0.8114 (mt0) REVERT: D 51 ASP cc_start: 0.8248 (p0) cc_final: 0.7637 (p0) REVERT: F 35 ARG cc_start: 0.8896 (mtp85) cc_final: 0.8659 (mtp85) REVERT: H 33 ARG cc_start: 0.8637 (mtp85) cc_final: 0.7999 (mtp-110) REVERT: H 71 GLU cc_start: 0.8440 (tm-30) cc_final: 0.8138 (tm-30) REVERT: H 120 LYS cc_start: 0.9104 (tptm) cc_final: 0.8556 (ttpp) REVERT: C 56 GLU cc_start: 0.8789 (tm-30) cc_final: 0.8188 (tm-30) REVERT: C 110 ASN cc_start: 0.8847 (t0) cc_final: 0.8321 (p0) REVERT: G 76 THR cc_start: 0.9151 (p) cc_final: 0.8637 (t) REVERT: G 91 GLU cc_start: 0.8092 (tp30) cc_final: 0.7743 (tp30) outliers start: 20 outliers final: 16 residues processed: 180 average time/residue: 0.1360 time to fit residues: 34.0185 Evaluate side-chains 181 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 165 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 59 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 32 optimal weight: 2.9990 chunk 53 optimal weight: 20.0000 chunk 106 optimal weight: 0.0980 chunk 108 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 56 optimal weight: 10.0000 chunk 58 optimal weight: 10.0000 chunk 24 optimal weight: 0.0030 chunk 50 optimal weight: 1.9990 chunk 94 optimal weight: 0.7980 chunk 6 optimal weight: 0.7980 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.099810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.063444 restraints weight = 46356.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 69)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.065626 restraints weight = 22338.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 73)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.067103 restraints weight = 14904.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.067903 restraints weight = 12017.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.068432 restraints weight = 10782.201| |-----------------------------------------------------------------------------| r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2866 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2866 r_free = 0.2866 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2866 r_free = 0.2866 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2866 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 13794 Z= 0.137 Angle : 0.560 8.700 19878 Z= 0.338 Chirality : 0.039 0.243 2261 Planarity : 0.003 0.040 1500 Dihedral : 30.160 163.699 4186 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.04 % Allowed : 17.66 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.79 (0.29), residues: 853 helix: 2.90 (0.21), residues: 575 sheet: 0.90 (1.33), residues: 17 loop : -0.60 (0.38), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 86 TYR 0.018 0.001 TYR H 40 PHE 0.006 0.001 PHE E 67 HIS 0.002 0.000 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.14 (13791) covalent geometry : angle 0.55989 / 0.34 (19872) hydrogen bonds : bond 0.04548 / 2.96 ( 783) hydrogen bonds : angle 2.71188 / 1.96 ( 1959) Misc. bond : bond 0.00009 / 0.00 ( 1) link_TRANS : bond 0.00072 / 0.04 ( 2) link_TRANS : angle 0.27984 / 0.13 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 182 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 42 TYR cc_start: 0.8167 (t80) cc_final: 0.7276 (t80) REVERT: D 47 GLN cc_start: 0.8498 (mt0) cc_final: 0.8136 (mt0) REVERT: D 51 ASP cc_start: 0.8110 (p0) cc_final: 0.7509 (p0) REVERT: E 59 GLU cc_start: 0.8587 (pm20) cc_final: 0.8096 (pm20) REVERT: E 105 GLU cc_start: 0.7888 (tt0) cc_final: 0.7623 (tt0) REVERT: F 35 ARG cc_start: 0.8869 (mtp85) cc_final: 0.8646 (mtp85) REVERT: H 33 ARG cc_start: 0.8687 (mtp85) cc_final: 0.8145 (mtp-110) REVERT: H 59 MET cc_start: 0.9293 (tpp) cc_final: 0.9007 (tpp) REVERT: H 71 GLU cc_start: 0.8323 (tm-30) cc_final: 0.8046 (tm-30) REVERT: H 120 LYS cc_start: 0.9099 (tptm) cc_final: 0.8589 (ttpp) REVERT: C 110 ASN cc_start: 0.8840 (t0) cc_final: 0.8412 (p0) REVERT: G 64 GLU cc_start: 0.9261 (tm-30) cc_final: 0.9018 (tm-30) REVERT: G 76 THR cc_start: 0.9149 (p) cc_final: 0.8615 (t) REVERT: G 91 GLU cc_start: 0.8054 (tp30) cc_final: 0.7702 (tp30) outliers start: 15 outliers final: 12 residues processed: 190 average time/residue: 0.1376 time to fit residues: 36.1278 Evaluate side-chains 183 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 171 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain K residue 449 LEU Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain G residue 15 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 38 optimal weight: 0.7980 chunk 88 optimal weight: 0.0570 chunk 55 optimal weight: 9.9990 chunk 77 optimal weight: 9.9990 chunk 57 optimal weight: 9.9990 chunk 63 optimal weight: 9.9990 chunk 36 optimal weight: 0.1980 chunk 82 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 overall best weight: 0.5700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.099969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.063583 restraints weight = 47552.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.065712 restraints weight = 22617.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 66)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.067260 restraints weight = 15027.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.068037 restraints weight = 12060.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.068553 restraints weight = 10821.322| |-----------------------------------------------------------------------------| r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2866 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2866 r_free = 0.2866 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2866 r_free = 0.2866 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2866 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13794 Z= 0.139 Angle : 0.568 9.274 19878 Z= 0.339 Chirality : 0.039 0.248 2261 Planarity : 0.004 0.041 1500 Dihedral : 30.176 164.068 4186 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.63 % Allowed : 18.21 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.73 (0.29), residues: 853 helix: 2.84 (0.21), residues: 575 sheet: 0.87 (1.32), residues: 17 loop : -0.57 (0.38), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 67 TYR 0.023 0.001 TYR D 40 PHE 0.007 0.001 PHE A 67 HIS 0.002 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.14 (13791) covalent geometry : angle 0.56828 / 0.34 (19872) hydrogen bonds : bond 0.04547 / 2.95 ( 783) hydrogen bonds : angle 2.71911 / 1.97 ( 1959) Misc. bond : bond 0.00002 / 0.00 ( 1) link_TRANS : bond 0.00050 / 0.02 ( 2) link_TRANS : angle 0.27440 / 0.13 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 177 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 42 TYR cc_start: 0.8132 (t80) cc_final: 0.7303 (t80) REVERT: D 47 GLN cc_start: 0.8462 (mt0) cc_final: 0.8096 (mt0) REVERT: D 51 ASP cc_start: 0.8102 (p0) cc_final: 0.7516 (p0) REVERT: E 59 GLU cc_start: 0.8641 (pm20) cc_final: 0.8171 (pm20) REVERT: E 105 GLU cc_start: 0.7892 (tt0) cc_final: 0.7623 (tt0) REVERT: F 35 ARG cc_start: 0.8874 (mtp85) cc_final: 0.8651 (mtp85) REVERT: H 33 ARG cc_start: 0.8686 (mtp85) cc_final: 0.8145 (mtp-110) REVERT: H 71 GLU cc_start: 0.8315 (tm-30) cc_final: 0.8051 (tm-30) REVERT: H 120 LYS cc_start: 0.9089 (tptm) cc_final: 0.8759 (tptm) REVERT: C 110 ASN cc_start: 0.8836 (t0) cc_final: 0.8418 (p0) REVERT: G 64 GLU cc_start: 0.9259 (tm-30) cc_final: 0.8999 (tm-30) REVERT: G 76 THR cc_start: 0.9159 (p) cc_final: 0.8618 (t) REVERT: G 91 GLU cc_start: 0.8075 (tp30) cc_final: 0.7738 (tp30) outliers start: 12 outliers final: 12 residues processed: 183 average time/residue: 0.1353 time to fit residues: 34.2602 Evaluate side-chains 185 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 173 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain K residue 449 LEU Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain G residue 15 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 87 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 75 optimal weight: 9.9990 chunk 50 optimal weight: 0.4980 chunk 39 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 61 optimal weight: 10.0000 chunk 35 optimal weight: 0.8980 chunk 102 optimal weight: 0.1980 chunk 32 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.099936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.066142 restraints weight = 54102.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.068311 restraints weight = 26054.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.069436 restraints weight = 14186.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.069154 restraints weight = 12812.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.069387 restraints weight = 12229.888| |-----------------------------------------------------------------------------| r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2870 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2870 r_free = 0.2870 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2870 r_free = 0.2870 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2870 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 13794 Z= 0.141 Angle : 0.569 9.369 19878 Z= 0.339 Chirality : 0.039 0.250 2261 Planarity : 0.004 0.042 1500 Dihedral : 30.194 164.331 4186 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.77 % Allowed : 18.07 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.75 (0.29), residues: 853 helix: 2.85 (0.21), residues: 575 sheet: 0.87 (1.31), residues: 17 loop : -0.56 (0.38), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 86 TYR 0.023 0.001 TYR D 40 PHE 0.006 0.001 PHE E 67 HIS 0.002 0.000 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.14 (13791) covalent geometry : angle 0.56943 / 0.34 (19872) hydrogen bonds : bond 0.04552 / 2.96 ( 783) hydrogen bonds : angle 2.72487 / 1.98 ( 1959) Misc. bond : bond 0.00000 / 0.00 ( 1) link_TRANS : bond 0.00047 / 0.02 ( 2) link_TRANS : angle 0.27001 / 0.13 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 176 time to evaluate : 0.225 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 42 TYR cc_start: 0.8143 (t80) cc_final: 0.7766 (t80) REVERT: D 47 GLN cc_start: 0.8459 (mt0) cc_final: 0.8084 (mt0) REVERT: D 51 ASP cc_start: 0.8088 (p0) cc_final: 0.7501 (p0) REVERT: E 59 GLU cc_start: 0.8620 (pm20) cc_final: 0.7978 (pm20) REVERT: E 105 GLU cc_start: 0.7954 (tt0) cc_final: 0.7687 (tt0) REVERT: F 35 ARG cc_start: 0.8870 (mtp85) cc_final: 0.8650 (mtp85) REVERT: H 33 ARG cc_start: 0.8693 (mtp85) cc_final: 0.8141 (mtp-110) REVERT: H 59 MET cc_start: 0.9284 (tpp) cc_final: 0.8930 (tpp) REVERT: H 71 GLU cc_start: 0.8290 (tm-30) cc_final: 0.8021 (tm-30) REVERT: H 120 LYS cc_start: 0.9105 (tptm) cc_final: 0.8765 (tptm) REVERT: C 110 ASN cc_start: 0.8814 (t0) cc_final: 0.8411 (p0) REVERT: G 64 GLU cc_start: 0.9255 (tm-30) cc_final: 0.9006 (tm-30) REVERT: G 76 THR cc_start: 0.9173 (p) cc_final: 0.8641 (t) REVERT: G 91 GLU cc_start: 0.8075 (tp30) cc_final: 0.7692 (tp30) outliers start: 13 outliers final: 12 residues processed: 183 average time/residue: 0.1243 time to fit residues: 31.4871 Evaluate side-chains 181 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 169 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain K residue 449 LEU Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain G residue 15 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 79 optimal weight: 10.0000 chunk 14 optimal weight: 1.9990 chunk 77 optimal weight: 10.0000 chunk 84 optimal weight: 7.9990 chunk 56 optimal weight: 9.9990 chunk 60 optimal weight: 9.9990 chunk 99 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 109 optimal weight: 0.6980 chunk 46 optimal weight: 0.6980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 ASN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 ASN ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.099029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.063499 restraints weight = 55876.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.065144 restraints weight = 23816.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.066161 restraints weight = 16359.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.066768 restraints weight = 12219.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.067399 restraints weight = 10419.317| |-----------------------------------------------------------------------------| r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2840 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2840 r_free = 0.2840 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2840 r_free = 0.2840 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2840 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13794 Z= 0.160 Angle : 0.589 9.581 19878 Z= 0.345 Chirality : 0.040 0.257 2261 Planarity : 0.004 0.040 1500 Dihedral : 30.270 165.069 4186 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.90 % Allowed : 18.21 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.72 (0.29), residues: 853 helix: 2.84 (0.21), residues: 575 sheet: 0.83 (1.30), residues: 17 loop : -0.62 (0.38), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 116 TYR 0.023 0.001 TYR H 40 PHE 0.007 0.001 PHE C 25 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.16 (13791) covalent geometry : angle 0.58941 / 0.35 (19872) hydrogen bonds : bond 0.04804 / 3.14 ( 783) hydrogen bonds : angle 2.80685 / 2.03 ( 1959) Misc. bond : bond 0.00000 / 0.00 ( 1) link_TRANS : bond 0.00013 / 0.01 ( 2) link_TRANS : angle 0.26883 / 0.14 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2303.82 seconds wall clock time: 40 minutes 19.02 seconds (2419.02 seconds total)