Starting phenix.real_space_refine on Sat Aug 23 14:32:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8txx_41708/08_2025/8txx_41708.cif Found real_map, /net/cci-nas-00/data/ceres_data/8txx_41708/08_2025/8txx_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8txx_41708/08_2025/8txx_41708.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8txx_41708/08_2025/8txx_41708.map" model { file = "/net/cci-nas-00/data/ceres_data/8txx_41708/08_2025/8txx_41708.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8txx_41708/08_2025/8txx_41708.cif" } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 2.66, per 1000 atoms: 0.21 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: 0.70 Conformation dependent library (CDL) restraints added in 265.2 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 1.93 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: 1.80 Time building geometry restraints manager: 0.96 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 -17 " pdb=" O3' DT J -17 " ideal model delta sigma weight residual 1.422 1.457 -0.035 3.00e-02 1.11e+03 1.38e+00 bond pdb=" CG GLN A 125 " pdb=" CD GLN A 125 " ideal model delta sigma weight residual 1.516 1.491 0.025 2.50e-02 1.60e+03 1.03e+00 bond pdb=" CB CYS A 96 " pdb=" SG CYS A 96 " ideal model delta sigma weight residual 1.808 1.776 0.032 3.30e-02 9.18e+02 9.25e-01 bond pdb=" CD LYS B 79 " pdb=" CE LYS B 79 " ideal model delta sigma weight residual 1.520 1.491 0.029 3.00e-02 1.11e+03 9.13e-01 bond pdb=" CB GLN A 76 " pdb=" CG GLN A 76 " ideal model delta sigma weight residual 1.520 1.548 -0.028 3.00e-02 1.11e+03 8.99e-01 ... (remaining 13786 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.39: 19232 1.39 - 2.77: 579 2.77 - 4.16: 41 4.16 - 5.54: 16 5.54 - 6.93: 4 Bond angle restraints: 19872 Sorted by residual: angle pdb=" C ILE A 124 " pdb=" N GLN A 125 " pdb=" CA GLN A 125 " ideal model delta sigma weight residual 120.72 115.00 5.72 1.67e+00 3.59e-01 1.17e+01 angle pdb=" C ARG B 23 " pdb=" N ASP B 24 " pdb=" CA ASP B 24 " ideal model delta sigma weight residual 121.54 127.34 -5.80 1.91e+00 2.74e-01 9.23e+00 angle pdb=" N GLY D 104 " pdb=" CA GLY D 104 " pdb=" C GLY D 104 " ideal model delta sigma weight residual 110.77 116.37 -5.60 1.93e+00 2.68e-01 8.43e+00 angle pdb=" N GLN A 125 " pdb=" CA GLN A 125 " pdb=" CB GLN A 125 " ideal model delta sigma weight residual 110.39 114.91 -4.52 1.66e+00 3.63e-01 7.40e+00 angle pdb=" CA GLN A 76 " pdb=" CB GLN A 76 " pdb=" CG GLN A 76 " ideal model delta sigma weight residual 114.10 119.51 -5.41 2.00e+00 2.50e-01 7.31e+00 ... (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: 1640 0.031 - 0.061: 464 0.061 - 0.092: 109 0.092 - 0.123: 40 0.123 - 0.154: 8 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=" CA LEU E 65 " pdb=" N LEU E 65 " pdb=" C LEU E 65 " pdb=" CB LEU E 65 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.48e-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: 0.000 Normalize map: mean=0, sd=1: 0.960 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: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.490 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 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 : 0.004 0.063 13794 Z= 0.173 Angle : 0.551 6.929 19878 Z= 0.327 Chirality : 0.033 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 aren 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 covalent geometry : bond 0.00357 (13791) covalent geometry : angle 0.55138 (19872) hydrogen bonds : bond 0.11674 ( 783) hydrogen bonds : angle 3.83172 ( 1959) Misc. bond : bond 0.06282 ( 1) link_TRANS : bond 0.00047 ( 2) link_TRANS : angle 0.46968 ( 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 : 0.318 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: 0.8345 (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: 0.1306 time to fit residues: 38.1336 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 : 0.315 ------------------------------------------------------------------------------- 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: 6.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 8.9990 chunk 106 optimal weight: 0.2980 overall best weight: 0.8562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 ASN H 109 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.099617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.064949 restraints weight = 62853.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.067043 restraints weight = 28992.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.067933 restraints weight = 15721.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.068094 restraints weight = 13441.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.068208 restraints weight = 12824.478| |-----------------------------------------------------------------------------| r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2849 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2849 r_free = 0.2849 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 = 0.2849 r_free = 0.2849 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2849 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.1136 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= 0.169 Angle : 0.549 5.904 19878 Z= 0.327 Chirality : 0.034 0.155 2261 Planarity : 0.004 0.040 1500 Dihedral : 29.585 158.030 4186 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.77 % Allowed : 11.55 % Favored : 86.68 % 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 aren not related in a simple way. whole: 2.76 (0.29), residues: 853 helix: 2.77 (0.22), residues: 574 sheet: 1.25 (1.39), residues: 17 loop : -0.34 (0.38), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 29 TYR 0.023 0.001 TYR H 40 PHE 0.008 0.001 PHE E 67 HIS 0.010 0.001 HIS H 109 Details of bonding type rmsd covalent geometry : bond 0.00369 (13791) covalent geometry : angle 0.54901 (19872) hydrogen bonds : bond 0.04526 ( 783) hydrogen bonds : angle 2.90471 ( 1959) Misc. bond : bond 0.00023 ( 1) link_TRANS : bond 0.00133 ( 2) link_TRANS : angle 0.60031 ( 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 190 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 177 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.8517 (mmm) cc_final: 0.7919 (tpp) REVERT: B 27 GLN cc_start: 0.9231 (mm-40) cc_final: 0.8983 (mp10) REVERT: B 85 ASP cc_start: 0.8792 (m-30) cc_final: 0.8581 (m-30) REVERT: D 42 TYR cc_start: 0.8162 (t80) cc_final: 0.7193 (t80) REVERT: D 47 GLN cc_start: 0.8565 (mt0) cc_final: 0.8277 (mt0) REVERT: D 51 ASP cc_start: 0.8169 (p0) cc_final: 0.7711 (p0) REVERT: D 86 ARG cc_start: 0.8963 (mmt-90) cc_final: 0.8746 (mtt-85) REVERT: D 108 LYS cc_start: 0.9238 (ttpt) cc_final: 0.9025 (ttpt) REVERT: E 59 GLU cc_start: 0.8205 (pm20) cc_final: 0.7902 (pm20) REVERT: H 33 ARG cc_start: 0.8575 (mtp85) cc_final: 0.8000 (mtp-110) REVERT: C 56 GLU cc_start: 0.8808 (tm-30) cc_final: 0.8233 (tm-30) REVERT: C 64 GLU cc_start: 0.8782 (tm-30) cc_final: 0.8576 (tm-30) REVERT: C 110 ASN cc_start: 0.8860 (t0) cc_final: 0.8361 (p0) REVERT: G 76 THR cc_start: 0.9128 (p) cc_final: 0.8670 (t) outliers start: 13 outliers final: 9 residues processed: 185 average time/residue: 0.1197 time to fit residues: 30.8283 Evaluate side-chains 177 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 168 time to evaluate : 0.284 ------------------------------------------------------------------------------- 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 112 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 30 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 32 optimal weight: 0.5980 chunk 4 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 chunk 100 optimal weight: 6.9990 chunk 52 optimal weight: 6.9990 chunk 78 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN 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 = 0.3449 r_free = 0.3449 target = 0.099288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.063181 restraints weight = 35822.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 72)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.065289 restraints weight = 18546.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 65)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.066683 restraints weight = 12969.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.067384 restraints weight = 10735.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.067748 restraints weight = 9786.152| |-----------------------------------------------------------------------------| r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2853 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2853 r_free = 0.2853 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 = 0.2853 r_free = 0.2853 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2853 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.1388 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= 0.165 Angle : 0.539 8.327 19878 Z= 0.320 Chirality : 0.033 0.147 2261 Planarity : 0.003 0.038 1500 Dihedral : 29.618 158.122 4186 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.45 % Allowed : 13.86 % Favored : 83.70 % 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 aren not related in a simple way. whole: 2.83 (0.29), residues: 853 helix: 2.86 (0.22), residues: 574 sheet: 1.27 (1.38), residues: 17 loop : -0.40 (0.38), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 99 TYR 0.015 0.001 TYR H 40 PHE 0.006 0.001 PHE E 67 HIS 0.004 0.001 HIS H 82 Details of bonding type rmsd covalent geometry : bond 0.00362 (13791) covalent geometry : angle 0.53878 (19872) hydrogen bonds : bond 0.04423 ( 783) hydrogen bonds : angle 2.78570 ( 1959) Misc. bond : bond 0.00013 ( 1) link_TRANS : bond 0.00033 ( 2) link_TRANS : angle 0.39574 ( 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 194 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 176 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.8660 (mmm) cc_final: 0.8061 (tpp) REVERT: B 27 GLN cc_start: 0.9218 (mm-40) cc_final: 0.8977 (mp10) REVERT: B 85 ASP cc_start: 0.8796 (m-30) cc_final: 0.8513 (m-30) REVERT: D 42 TYR cc_start: 0.8145 (t80) cc_final: 0.7325 (t80) REVERT: D 46 LYS cc_start: 0.9321 (mmtt) cc_final: 0.8917 (mmtp) REVERT: D 47 GLN cc_start: 0.8461 (mt0) cc_final: 0.8176 (mt0) REVERT: D 51 ASP cc_start: 0.8303 (p0) cc_final: 0.7813 (p0) REVERT: D 86 ARG cc_start: 0.8977 (mmt-90) cc_final: 0.8711 (mtt-85) REVERT: E 59 GLU cc_start: 0.8335 (pm20) cc_final: 0.7976 (pm20) REVERT: E 76 GLN cc_start: 0.8768 (tm-30) cc_final: 0.8506 (tm-30) REVERT: F 24 ASP cc_start: 0.7761 (t0) cc_final: 0.7480 (t0) REVERT: H 33 ARG cc_start: 0.8637 (mtp85) cc_final: 0.8035 (mtp-110) REVERT: H 120 LYS cc_start: 0.9150 (tptm) cc_final: 0.8817 (tptm) REVERT: C 64 GLU cc_start: 0.8740 (tm-30) cc_final: 0.8451 (tm-30) REVERT: C 110 ASN cc_start: 0.8907 (t0) cc_final: 0.8369 (p0) REVERT: G 64 GLU cc_start: 0.9303 (tm-30) cc_final: 0.8997 (tm-30) REVERT: G 76 THR cc_start: 0.9086 (p) cc_final: 0.8579 (t) outliers start: 18 outliers final: 16 residues processed: 187 average time/residue: 0.1051 time to fit residues: 27.4652 Evaluate side-chains 182 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 166 time to evaluate : 0.203 ------------------------------------------------------------------------------- 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 26 ILE Chi-restraints excluded: chain B residue 30 THR 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 F residue 63 GLU Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 101 LEU 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 90 optimal weight: 0.0980 chunk 38 optimal weight: 0.5980 chunk 81 optimal weight: 8.9990 chunk 60 optimal weight: 3.9990 chunk 108 optimal weight: 0.0060 chunk 53 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 chunk 83 optimal weight: 8.9990 chunk 4 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 chunk 100 optimal weight: 0.9980 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3467 r_free = 0.3467 target = 0.100418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.066738 restraints weight = 54356.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.068986 restraints weight = 28080.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.069261 restraints weight = 14953.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.069517 restraints weight = 14204.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.069577 restraints weight = 13678.529| |-----------------------------------------------------------------------------| r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2875 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2875 r_free = 0.2875 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2875 r_free = 0.2875 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2875 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13794 Z= 0.146 Angle : 0.523 8.369 19878 Z= 0.312 Chirality : 0.033 0.148 2261 Planarity : 0.003 0.040 1500 Dihedral : 29.529 157.741 4186 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.45 % Allowed : 15.62 % Favored : 81.93 % 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 aren not related in a simple way. whole: 2.89 (0.29), residues: 853 helix: 2.92 (0.21), residues: 575 sheet: 1.26 (1.36), residues: 17 loop : -0.42 (0.38), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 116 TYR 0.016 0.001 TYR H 40 PHE 0.007 0.001 PHE A 67 HIS 0.002 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00310 (13791) covalent geometry : angle 0.52280 (19872) hydrogen bonds : bond 0.04071 ( 783) hydrogen bonds : angle 2.64452 ( 1959) Misc. bond : bond 0.00001 ( 1) link_TRANS : bond 0.00074 ( 2) link_TRANS : angle 0.32891 ( 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 199 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 181 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.7941 (tt0) cc_final: 0.7693 (tt0) REVERT: B 85 ASP cc_start: 0.8762 (m-30) cc_final: 0.8500 (m-30) REVERT: D 42 TYR cc_start: 0.8066 (t80) cc_final: 0.7269 (t80) REVERT: D 46 LYS cc_start: 0.9308 (mmtt) cc_final: 0.8875 (mmtp) REVERT: D 47 GLN cc_start: 0.8367 (mt0) cc_final: 0.8077 (mt0) REVERT: D 51 ASP cc_start: 0.8233 (p0) cc_final: 0.7796 (p0) REVERT: D 86 ARG cc_start: 0.8917 (mmt-90) cc_final: 0.8668 (mtt-85) REVERT: D 105 GLU cc_start: 0.8286 (mm-30) cc_final: 0.8082 (mm-30) REVERT: E 59 GLU cc_start: 0.8332 (pm20) cc_final: 0.8047 (pm20) REVERT: E 105 GLU cc_start: 0.8013 (tt0) cc_final: 0.7807 (tt0) REVERT: F 24 ASP cc_start: 0.7981 (t0) cc_final: 0.7660 (t0) REVERT: H 33 ARG cc_start: 0.8631 (mtp85) cc_final: 0.8001 (mtp-110) REVERT: H 120 LYS cc_start: 0.9090 (tptm) cc_final: 0.8756 (tptm) REVERT: C 64 GLU cc_start: 0.8714 (tm-30) cc_final: 0.8488 (tm-30) REVERT: C 110 ASN cc_start: 0.8841 (t0) cc_final: 0.8408 (p0) REVERT: G 76 THR cc_start: 0.9114 (p) cc_final: 0.8609 (t) outliers start: 18 outliers final: 14 residues processed: 189 average time/residue: 0.1138 time to fit residues: 29.8909 Evaluate side-chains 178 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 164 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 26 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 112 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 13 SER Chi-restraints excluded: chain G residue 15 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 96 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 83 optimal weight: 10.0000 chunk 20 optimal weight: 0.7980 chunk 101 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN D 47 GLN D 95 GLN C 24 GLN ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.096556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.061117 restraints weight = 58480.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.063599 restraints weight = 26834.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.064745 restraints weight = 14093.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.064511 restraints weight = 12133.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.064793 restraints weight = 11858.536| |-----------------------------------------------------------------------------| r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2782 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2782 r_free = 0.2782 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 = 0.2782 r_free = 0.2782 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2782 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 13794 Z= 0.227 Angle : 0.587 9.402 19878 Z= 0.343 Chirality : 0.035 0.161 2261 Planarity : 0.004 0.038 1500 Dihedral : 29.870 159.085 4186 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.26 % Allowed : 15.90 % Favored : 80.84 % 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 aren not related in a simple way. whole: 2.70 (0.29), residues: 853 helix: 2.81 (0.22), residues: 575 sheet: 0.99 (1.32), residues: 17 loop : -0.58 (0.38), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 67 TYR 0.018 0.002 TYR H 40 PHE 0.007 0.001 PHE A 67 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00518 (13791) covalent geometry : angle 0.58710 (19872) hydrogen bonds : bond 0.05197 ( 783) hydrogen bonds : angle 2.99637 ( 1959) Misc. bond : bond 0.00005 ( 1) link_TRANS : bond 0.00120 ( 2) link_TRANS : angle 0.39521 ( 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 196 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 172 time to evaluate : 0.211 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.8734 (mmm) cc_final: 0.8167 (tpp) REVERT: A 129 ARG cc_start: 0.8686 (tpt90) cc_final: 0.8285 (tpt90) REVERT: B 50 ILE cc_start: 0.9441 (OUTLIER) cc_final: 0.9140 (tp) REVERT: B 85 ASP cc_start: 0.8808 (m-30) cc_final: 0.8539 (m-30) REVERT: D 47 GLN cc_start: 0.8551 (mt0) cc_final: 0.8214 (mt0) REVERT: D 51 ASP cc_start: 0.8156 (p0) cc_final: 0.7564 (p0) REVERT: D 57 LYS cc_start: 0.9019 (mmmt) cc_final: 0.8341 (mmtp) REVERT: E 59 GLU cc_start: 0.8426 (pm20) cc_final: 0.8221 (pm20) REVERT: E 105 GLU cc_start: 0.7973 (tt0) cc_final: 0.7754 (tt0) REVERT: H 33 ARG cc_start: 0.8653 (mtp85) cc_final: 0.8035 (mtp-110) REVERT: H 120 LYS cc_start: 0.9118 (tptm) cc_final: 0.8561 (ttpp) REVERT: C 56 GLU cc_start: 0.8853 (tm-30) cc_final: 0.8500 (tm-30) REVERT: C 110 ASN cc_start: 0.8863 (t0) cc_final: 0.8369 (p0) REVERT: G 76 THR cc_start: 0.9162 (p) cc_final: 0.8752 (t) REVERT: G 91 GLU cc_start: 0.8165 (tm-30) cc_final: 0.7947 (tp30) outliers start: 24 outliers final: 19 residues processed: 187 average time/residue: 0.1033 time to fit residues: 26.6827 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 : 0.210 ------------------------------------------------------------------------------- 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 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 112 ILE Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 78 ILE 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 103 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 107 optimal weight: 0.5980 chunk 106 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.098339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.063917 restraints weight = 55899.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.066208 restraints weight = 26170.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.067264 restraints weight = 14558.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.067094 restraints weight = 11656.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.067460 restraints weight = 11893.640| |-----------------------------------------------------------------------------| r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2825 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2825 r_free = 0.2825 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2825 r_free = 0.2825 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2825 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13794 Z= 0.165 Angle : 0.551 8.213 19878 Z= 0.326 Chirality : 0.033 0.157 2261 Planarity : 0.004 0.036 1500 Dihedral : 29.672 158.969 4186 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.85 % Allowed : 16.58 % Favored : 80.57 % 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 aren not related in a simple way. whole: 2.75 (0.29), residues: 853 helix: 2.87 (0.22), residues: 575 sheet: 0.94 (1.31), residues: 17 loop : -0.60 (0.37), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 86 TYR 0.019 0.001 TYR H 40 PHE 0.006 0.001 PHE G 25 HIS 0.002 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00364 (13791) covalent geometry : angle 0.55073 (19872) hydrogen bonds : bond 0.04386 ( 783) hydrogen bonds : angle 2.76136 ( 1959) Misc. bond : bond 0.00008 ( 1) link_TRANS : bond 0.00038 ( 2) link_TRANS : angle 0.34736 ( 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 198 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 177 time to evaluate : 0.211 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.8640 (mmm) cc_final: 0.8002 (tpp) REVERT: A 129 ARG cc_start: 0.8604 (tpt90) cc_final: 0.8121 (tpt90) REVERT: B 85 ASP cc_start: 0.8781 (m-30) cc_final: 0.8493 (m-30) REVERT: D 42 TYR cc_start: 0.8171 (t80) cc_final: 0.7716 (t80) REVERT: D 46 LYS cc_start: 0.9282 (mmtt) cc_final: 0.8939 (mmtm) REVERT: D 47 GLN cc_start: 0.8349 (mt0) cc_final: 0.7996 (mt0) REVERT: D 51 ASP cc_start: 0.8163 (p0) cc_final: 0.7745 (p0) REVERT: D 57 LYS cc_start: 0.8939 (mmmt) cc_final: 0.8427 (mmtp) REVERT: E 105 GLU cc_start: 0.7923 (tt0) cc_final: 0.7661 (tt0) REVERT: E 120 MET cc_start: 0.8173 (tpp) cc_final: 0.7521 (mmt) REVERT: H 33 ARG cc_start: 0.8619 (mtp85) cc_final: 0.7997 (mtp-110) REVERT: H 59 MET cc_start: 0.9326 (tpp) cc_final: 0.8995 (tpp) REVERT: H 120 LYS cc_start: 0.9130 (tptm) cc_final: 0.8770 (tptm) REVERT: C 56 GLU cc_start: 0.8797 (tm-30) cc_final: 0.8175 (tm-30) REVERT: C 110 ASN cc_start: 0.8821 (t0) cc_final: 0.8383 (p0) REVERT: G 24 GLN cc_start: 0.8915 (mm-40) cc_final: 0.8613 (mm-40) REVERT: G 64 GLU cc_start: 0.9271 (tm-30) cc_final: 0.9009 (tm-30) REVERT: G 76 THR cc_start: 0.9160 (p) cc_final: 0.8657 (t) REVERT: G 91 GLU cc_start: 0.8082 (tm-30) cc_final: 0.7865 (tp30) outliers start: 21 outliers final: 14 residues processed: 187 average time/residue: 0.1183 time to fit residues: 30.7359 Evaluate side-chains 188 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 174 time to evaluate : 0.345 ------------------------------------------------------------------------------- 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 30 THR 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 112 ILE Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 101 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 Chi-restraints excluded: chain G residue 18 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 56 optimal weight: 4.9990 chunk 97 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 45 optimal weight: 0.0370 chunk 16 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 chunk 62 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 overall best weight: 0.6860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 HIS D 95 GLN H 84 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.098779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.064498 restraints weight = 60016.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.066271 restraints weight = 29365.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.067315 restraints weight = 15962.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.067316 restraints weight = 13361.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.067463 restraints weight = 12874.694| |-----------------------------------------------------------------------------| r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2828 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2828 r_free = 0.2828 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2828 r_free = 0.2828 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2828 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13794 Z= 0.158 Angle : 0.548 8.448 19878 Z= 0.325 Chirality : 0.033 0.166 2261 Planarity : 0.004 0.037 1500 Dihedral : 29.661 159.036 4186 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.45 % Allowed : 16.71 % Favored : 80.84 % 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 aren not related in a simple way. whole: 2.75 (0.29), residues: 853 helix: 2.87 (0.21), residues: 575 sheet: 0.98 (1.31), residues: 17 loop : -0.62 (0.37), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 116 TYR 0.015 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 covalent geometry : bond 0.00345 (13791) covalent geometry : angle 0.54781 (19872) hydrogen bonds : bond 0.04296 ( 783) hydrogen bonds : angle 2.72391 ( 1959) Misc. bond : bond 0.00011 ( 1) link_TRANS : bond 0.00044 ( 2) link_TRANS : angle 0.32563 ( 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 194 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 176 time to evaluate : 0.219 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 THR cc_start: 0.9617 (OUTLIER) cc_final: 0.9393 (t) REVERT: A 129 ARG cc_start: 0.8604 (tpt90) cc_final: 0.8116 (tpt90) REVERT: B 85 ASP cc_start: 0.8798 (m-30) cc_final: 0.8508 (m-30) REVERT: D 42 TYR cc_start: 0.8135 (t80) cc_final: 0.7685 (t80) REVERT: D 46 LYS cc_start: 0.9287 (mmtt) cc_final: 0.9005 (mmtm) REVERT: D 47 GLN cc_start: 0.8298 (mt0) cc_final: 0.8089 (mt0) REVERT: D 51 ASP cc_start: 0.8098 (p0) cc_final: 0.7653 (p0) REVERT: E 59 GLU cc_start: 0.8576 (pm20) cc_final: 0.8097 (pm20) REVERT: E 105 GLU cc_start: 0.7925 (tt0) cc_final: 0.7670 (tt0) REVERT: E 120 MET cc_start: 0.8122 (tpp) cc_final: 0.7465 (mmt) REVERT: H 33 ARG cc_start: 0.8646 (mtp85) cc_final: 0.7989 (mtp-110) REVERT: H 120 LYS cc_start: 0.9114 (tptm) cc_final: 0.8772 (tptm) REVERT: C 110 ASN cc_start: 0.8830 (t0) cc_final: 0.8401 (p0) REVERT: G 24 GLN cc_start: 0.8877 (mm-40) cc_final: 0.8586 (mm-40) REVERT: G 64 GLU cc_start: 0.9306 (tm-30) cc_final: 0.9007 (tm-30) REVERT: G 76 THR cc_start: 0.9175 (p) cc_final: 0.8666 (t) outliers start: 18 outliers final: 15 residues processed: 183 average time/residue: 0.1139 time to fit residues: 28.7899 Evaluate side-chains 184 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 168 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 107 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 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 112 ILE Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain H residue 101 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 Chi-restraints excluded: chain G residue 18 SER 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: 6.9990 chunk 106 optimal weight: 2.9990 chunk 108 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 24 optimal weight: 0.5980 chunk 50 optimal weight: 0.7980 chunk 94 optimal weight: 0.5980 chunk 6 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.099044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.063986 restraints weight = 46468.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.065626 restraints weight = 22404.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.066767 restraints weight = 15381.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.067128 restraints weight = 12508.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.067465 restraints weight = 10934.341| |-----------------------------------------------------------------------------| r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2831 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2831 r_free = 0.2831 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2831 r_free = 0.2831 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2831 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13794 Z= 0.158 Angle : 0.550 9.411 19878 Z= 0.325 Chirality : 0.033 0.157 2261 Planarity : 0.004 0.037 1500 Dihedral : 29.645 159.145 4186 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.72 % Allowed : 17.12 % 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 aren not related in a simple way. whole: 2.74 (0.29), residues: 853 helix: 2.86 (0.21), residues: 575 sheet: 1.07 (1.33), residues: 17 loop : -0.62 (0.37), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 67 TYR 0.014 0.001 TYR H 40 PHE 0.007 0.001 PHE H 70 HIS 0.002 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00346 (13791) covalent geometry : angle 0.54960 (19872) hydrogen bonds : bond 0.04244 ( 783) hydrogen bonds : angle 2.69702 ( 1959) Misc. bond : bond 0.00012 ( 1) link_TRANS : bond 0.00043 ( 2) link_TRANS : angle 0.32230 ( 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 191 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 171 time to evaluate : 0.258 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 THR cc_start: 0.9622 (OUTLIER) cc_final: 0.9393 (t) REVERT: A 129 ARG cc_start: 0.8533 (tpt90) cc_final: 0.8040 (tpt90) REVERT: B 85 ASP cc_start: 0.8814 (m-30) cc_final: 0.8512 (m-30) REVERT: D 42 TYR cc_start: 0.8139 (t80) cc_final: 0.7331 (t80) REVERT: D 46 LYS cc_start: 0.9296 (mmtt) cc_final: 0.8881 (mmtp) REVERT: D 47 GLN cc_start: 0.8297 (mt0) cc_final: 0.8094 (mt0) REVERT: D 51 ASP cc_start: 0.8101 (p0) cc_final: 0.7516 (p0) REVERT: E 56 LYS cc_start: 0.9445 (ttpp) cc_final: 0.9190 (ttpp) REVERT: E 59 GLU cc_start: 0.8579 (pm20) cc_final: 0.7931 (pm20) REVERT: E 105 GLU cc_start: 0.7894 (tt0) cc_final: 0.7672 (tt0) REVERT: E 120 MET cc_start: 0.8157 (tpp) cc_final: 0.7480 (mmt) REVERT: F 67 ARG cc_start: 0.8952 (ttm-80) cc_final: 0.8741 (ttm-80) REVERT: H 33 ARG cc_start: 0.8620 (mtp85) cc_final: 0.7997 (mtp-110) REVERT: H 59 MET cc_start: 0.9294 (tpp) cc_final: 0.8940 (tpp) REVERT: H 120 LYS cc_start: 0.9126 (tptm) cc_final: 0.8786 (tptm) REVERT: C 110 ASN cc_start: 0.8850 (t0) cc_final: 0.8419 (p0) REVERT: G 24 GLN cc_start: 0.8867 (mm-40) cc_final: 0.8575 (mm-40) REVERT: G 76 THR cc_start: 0.9163 (p) cc_final: 0.8636 (t) outliers start: 20 outliers final: 19 residues processed: 180 average time/residue: 0.1008 time to fit residues: 25.1027 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 : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 107 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 48 VAL Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 101 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 38 optimal weight: 0.8980 chunk 88 optimal weight: 6.9990 chunk 55 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 82 optimal weight: 10.0000 chunk 43 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 48 optimal weight: 0.1980 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.094822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2663 r_free = 0.2663 target = 0.057854 restraints weight = 47783.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.060111 restraints weight = 21656.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 77)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.061606 restraints weight = 14157.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.062422 restraints weight = 11292.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.062805 restraints weight = 10092.369| |-----------------------------------------------------------------------------| r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2743 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2743 r_free = 0.2743 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2743 r_free = 0.2743 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2743 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.040 13794 Z= 0.290 Angle : 0.641 9.965 19878 Z= 0.371 Chirality : 0.038 0.151 2261 Planarity : 0.004 0.044 1500 Dihedral : 30.080 161.359 4186 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.99 % Allowed : 16.85 % 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 aren not related in a simple way. whole: 2.44 (0.29), residues: 853 helix: 2.61 (0.21), residues: 577 sheet: 0.98 (1.32), residues: 17 loop : -0.73 (0.38), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 29 TYR 0.025 0.002 TYR H 40 PHE 0.008 0.001 PHE G 25 HIS 0.004 0.001 HIS D 82 Details of bonding type rmsd covalent geometry : bond 0.00669 (13791) covalent geometry : angle 0.64065 (19872) hydrogen bonds : bond 0.05689 ( 783) hydrogen bonds : angle 3.18461 ( 1959) Misc. bond : bond 0.00013 ( 1) link_TRANS : bond 0.00184 ( 2) link_TRANS : angle 0.55937 ( 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: 22 poor density : 167 time to evaluate : 0.235 Fit side-chains revert: symmetry clash REVERT: A 90 MET cc_start: 0.8816 (mmm) cc_final: 0.8274 (tpp) REVERT: A 120 MET cc_start: 0.9033 (mtm) cc_final: 0.8478 (ptp) REVERT: B 53 GLU cc_start: 0.8705 (mm-30) cc_final: 0.8483 (tp30) REVERT: B 85 ASP cc_start: 0.8910 (m-30) cc_final: 0.8588 (m-30) REVERT: D 47 GLN cc_start: 0.8558 (mt0) cc_final: 0.8317 (mt0) REVERT: D 51 ASP cc_start: 0.8365 (p0) cc_final: 0.7847 (p0) REVERT: D 57 LYS cc_start: 0.9029 (mmmt) cc_final: 0.8465 (mmtp) REVERT: E 59 GLU cc_start: 0.8728 (pm20) cc_final: 0.8123 (pm20) REVERT: E 105 GLU cc_start: 0.8130 (tt0) cc_final: 0.7856 (tt0) REVERT: E 120 MET cc_start: 0.8279 (tpp) cc_final: 0.7799 (mtp) REVERT: H 33 ARG cc_start: 0.8697 (mtp85) cc_final: 0.7989 (mtp-110) REVERT: H 40 TYR cc_start: 0.8824 (m-10) cc_final: 0.8602 (m-10) REVERT: H 120 LYS cc_start: 0.9161 (tptm) cc_final: 0.8735 (ttmm) REVERT: C 56 GLU cc_start: 0.8991 (tm-30) cc_final: 0.8636 (tm-30) REVERT: C 110 ASN cc_start: 0.8954 (t0) cc_final: 0.8371 (p0) REVERT: G 64 GLU cc_start: 0.9345 (tm-30) cc_final: 0.9118 (tm-30) REVERT: G 76 THR cc_start: 0.9276 (p) cc_final: 0.8851 (t) outliers start: 22 outliers final: 18 residues processed: 181 average time/residue: 0.1086 time to fit residues: 27.3311 Evaluate side-chains 179 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 161 time to evaluate : 0.303 ------------------------------------------------------------------------------- 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 B residue 30 THR 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 F residue 50 ILE Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain M residue 7 THR 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 87 optimal weight: 4.9990 chunk 30 optimal weight: 0.9980 chunk 75 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 61 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 102 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.097539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.060597 restraints weight = 54190.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.062892 restraints weight = 22593.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.064645 restraints weight = 14280.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.065519 restraints weight = 11098.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.066149 restraints weight = 9819.741| |-----------------------------------------------------------------------------| r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2815 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2815 r_free = 0.2815 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 = 0.2815 r_free = 0.2815 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2815 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13794 Z= 0.169 Angle : 0.573 9.476 19878 Z= 0.337 Chirality : 0.034 0.151 2261 Planarity : 0.004 0.040 1500 Dihedral : 29.799 161.418 4186 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.04 % Allowed : 18.07 % 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 aren not related in a simple way. whole: 2.63 (0.29), residues: 853 helix: 2.79 (0.22), residues: 575 sheet: 0.85 (1.29), residues: 17 loop : -0.69 (0.38), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 67 TYR 0.013 0.001 TYR H 40 PHE 0.007 0.001 PHE A 67 HIS 0.003 0.001 HIS H 82 Details of bonding type rmsd covalent geometry : bond 0.00373 (13791) covalent geometry : angle 0.57333 (19872) hydrogen bonds : bond 0.04462 ( 783) hydrogen bonds : angle 2.80554 ( 1959) Misc. bond : bond 0.00016 ( 1) link_TRANS : bond 0.00017 ( 2) link_TRANS : angle 0.38149 ( 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 186 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 171 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 THR cc_start: 0.9535 (OUTLIER) cc_final: 0.9328 (t) REVERT: A 129 ARG cc_start: 0.8743 (tpt90) cc_final: 0.8271 (tpt90) REVERT: B 85 ASP cc_start: 0.8815 (m-30) cc_final: 0.8526 (m-30) REVERT: D 46 LYS cc_start: 0.9155 (mmtt) cc_final: 0.8740 (mmtm) REVERT: D 51 ASP cc_start: 0.8298 (p0) cc_final: 0.7745 (p0) REVERT: E 56 LYS cc_start: 0.9500 (ttpp) cc_final: 0.9271 (ttpp) REVERT: E 59 GLU cc_start: 0.8665 (pm20) cc_final: 0.8071 (pm20) REVERT: E 105 GLU cc_start: 0.8035 (tt0) cc_final: 0.7704 (tt0) REVERT: H 33 ARG cc_start: 0.8674 (mtp85) cc_final: 0.7965 (mtp-110) REVERT: H 59 MET cc_start: 0.9333 (tpp) cc_final: 0.9036 (tpp) REVERT: H 120 LYS cc_start: 0.9136 (tptm) cc_final: 0.8668 (ttmm) REVERT: C 56 GLU cc_start: 0.8913 (tm-30) cc_final: 0.8290 (tm-30) REVERT: C 110 ASN cc_start: 0.8970 (t0) cc_final: 0.8438 (p0) REVERT: G 24 GLN cc_start: 0.8984 (mm-40) cc_final: 0.8733 (mm-40) REVERT: G 64 GLU cc_start: 0.9377 (tm-30) cc_final: 0.9139 (tm-30) REVERT: G 76 THR cc_start: 0.9227 (p) cc_final: 0.8711 (t) outliers start: 15 outliers final: 14 residues processed: 179 average time/residue: 0.1104 time to fit residues: 27.3223 Evaluate side-chains 182 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 167 time to evaluate : 0.336 ------------------------------------------------------------------------------- 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 B residue 30 THR 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 F residue 50 ILE Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 101 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 79 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 84 optimal weight: 6.9990 chunk 56 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 99 optimal weight: 0.9980 chunk 24 optimal weight: 0.3980 chunk 7 optimal weight: 2.9990 chunk 109 optimal weight: 0.8980 chunk 46 optimal weight: 0.7980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.097483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.060436 restraints weight = 55861.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.062892 restraints weight = 23030.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 69)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.064544 restraints weight = 14296.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.065436 restraints weight = 11117.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.066062 restraints weight = 9817.658| |-----------------------------------------------------------------------------| r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2810 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2810 r_free = 0.2810 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2810 r_free = 0.2810 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2810 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13794 Z= 0.184 Angle : 0.579 9.476 19878 Z= 0.340 Chirality : 0.034 0.160 2261 Planarity : 0.004 0.040 1500 Dihedral : 29.802 161.533 4186 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.04 % Allowed : 18.34 % Favored : 79.62 % 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 aren not related in a simple way. whole: 2.61 (0.29), residues: 853 helix: 2.77 (0.21), residues: 575 sheet: 0.90 (1.30), residues: 17 loop : -0.71 (0.38), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 71 TYR 0.033 0.001 TYR D 40 PHE 0.006 0.001 PHE A 67 HIS 0.003 0.001 HIS D 82 Details of bonding type rmsd covalent geometry : bond 0.00413 (13791) covalent geometry : angle 0.57892 (19872) hydrogen bonds : bond 0.04517 ( 783) hydrogen bonds : angle 2.82150 ( 1959) Misc. bond : bond 0.00040 ( 1) link_TRANS : bond 0.00018 ( 2) link_TRANS : angle 0.37692 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1912.48 seconds wall clock time: 33 minutes 37.44 seconds (2017.44 seconds total)