Starting phenix.real_space_refine on Thu Aug 6 07:44:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dwg_47243/08_2026/9dwg_47243.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dwg_47243/08_2026/9dwg_47243.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dwg_47243/08_2026/9dwg_47243.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dwg_47243/08_2026/9dwg_47243.map" model { file = "/net/cci-nas-00/data/ceres_data/9dwg_47243/08_2026/9dwg_47243.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dwg_47243/08_2026/9dwg_47243.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 1.005 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 293 5.49 5 S 19 5.16 5 C 8237 2.51 5 N 2692 2.21 5 O 3294 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14535 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 800 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "B" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 641 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "C" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 848 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "D" Number of atoms: 725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 725 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "E" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 789 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "F" Number of atoms: 668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 668 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "G" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 784 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 5, 'TRANS': 96} Chain: "H" Number of atoms: 702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 702 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "I" Number of atoms: 2383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 2383 Classifications: {'DNA': 117} Link IDs: {'rna3p': 116} 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: 595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 595 Classifications: {'DNA': 29} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 28} Chain: "L" Number of atoms: 2569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2569 Classifications: {'peptide': 323} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'CIS': 1, 'PTRANS': 13, 'TRANS': 308} Chain breaks: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 18 Time building chain proxies: 2.31, per 1000 atoms: 0.16 Number of scatterers: 14535 At special positions: 0 Unit cell: (97.468, 149.919, 137.529, 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 19 16.00 P 293 15.00 O 3294 8.00 N 2692 7.00 C 8237 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.15 Conformation dependent library (CDL) restraints added in 509.5 milliseconds 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2004 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 11 sheets defined 69.5% alpha, 4.6% beta 143 base pairs and 243 stacking pairs defined. Time for finding SS restraints: 2.22 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 removed outlier: 3.898A pdb=" N SER A 57 " --> pdb=" O ARG A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.676A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.528A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.583A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.712A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 45 through 72 removed outlier: 4.360A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.746A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.698A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 104 through 124 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.632A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.617A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY E 132 " --> pdb=" O ARG E 128 " (cutoff:3.500A) 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 75 removed outlier: 4.351A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 76 through 78 No H-bonds generated for 'chain 'F' and resid 76 through 78' Processing helix chain 'F' and resid 82 through 93 removed outlier: 4.045A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 17 through 21 Processing helix chain 'G' and resid 26 through 38 removed outlier: 3.882A pdb=" N ASN G 38 " --> pdb=" O LEU G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 72 removed outlier: 4.509A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASP G 72 " --> pdb=" O ASN G 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 75 No H-bonds generated for 'chain 'G' and resid 73 through 75' Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 91 through 97 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 Processing helix chain 'H' and resid 103 through 123 removed outlier: 3.662A pdb=" N SER H 123 " --> pdb=" O THR H 119 " (cutoff:3.500A) Processing helix chain 'L' and resid 12 through 29 Processing helix chain 'L' and resid 32 through 48 Processing helix chain 'L' and resid 55 through 62 removed outlier: 3.545A pdb=" N ALA L 59 " --> pdb=" O SER L 55 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N LEU L 62 " --> pdb=" O GLU L 58 " (cutoff:3.500A) Processing helix chain 'L' and resid 66 through 80 Processing helix chain 'L' and resid 82 through 90 Processing helix chain 'L' and resid 91 through 101 Processing helix chain 'L' and resid 107 through 117 Processing helix chain 'L' and resid 121 through 128 Processing helix chain 'L' and resid 129 through 132 Processing helix chain 'L' and resid 133 through 142 Processing helix chain 'L' and resid 142 through 147 Processing helix chain 'L' and resid 152 through 170 Processing helix chain 'L' and resid 209 through 221 removed outlier: 4.308A pdb=" N VAL L 214 " --> pdb=" O LEU L 210 " (cutoff:3.500A) Processing helix chain 'L' and resid 261 through 274 removed outlier: 4.517A pdb=" N TYR L 266 " --> pdb=" O LYS L 262 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N CYS L 267 " --> pdb=" O ASP L 263 " (cutoff:3.500A) Processing helix chain 'L' and resid 275 through 289 Processing helix chain 'L' and resid 315 through 323 removed outlier: 3.513A pdb=" N ILE L 323 " --> pdb=" O ILE L 319 " (cutoff:3.500A) Processing helix chain 'L' and resid 329 through 333 Processing sheet with id=AA1, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA2, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.836A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 42 through 43 removed outlier: 6.952A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA5, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.835A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 118 through 119 removed outlier: 4.061A pdb=" N ILE E 119 " --> pdb=" O ARG F 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.312A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AA9, first strand: chain 'L' and resid 150 through 151 Processing sheet with id=AB1, first strand: chain 'L' and resid 174 through 177 removed outlier: 6.601A pdb=" N VAL L 238 " --> pdb=" O THR L 227 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N THR L 227 " --> pdb=" O VAL L 238 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 291 through 293 534 hydrogen bonds defined for protein. 1563 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 366 hydrogen bonds 732 hydrogen bond angles 0 basepair planarities 143 basepair parallelities 243 stacking parallelities Total time for adding SS restraints: 2.73 Time building geometry restraints manager: 1.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 1668 1.28 - 1.41: 4813 1.41 - 1.55: 8291 1.55 - 1.68: 586 1.68 - 1.82: 35 Bond restraints: 15393 Sorted by residual: bond pdb=" C TYR D 83 " pdb=" O TYR D 83 " ideal model delta sigma weight residual 1.236 1.144 0.092 1.19e-02 7.06e+03 5.97e+01 bond pdb=" P DC K 119 " pdb=" OP3 DC K 119 " ideal model delta sigma weight residual 1.480 1.611 -0.131 2.00e-02 2.50e+03 4.26e+01 bond pdb=" C HIS D 82 " pdb=" N TYR D 83 " ideal model delta sigma weight residual 1.334 1.264 0.070 1.41e-02 5.03e+03 2.45e+01 bond pdb=" C TYR D 83 " pdb=" N ASN D 84 " ideal model delta sigma weight residual 1.333 1.252 0.081 1.73e-02 3.34e+03 2.18e+01 bond pdb=" C ARG A 131 " pdb=" O ARG A 131 " ideal model delta sigma weight residual 1.235 1.175 0.060 1.38e-02 5.25e+03 1.87e+01 ... (remaining 15388 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 21081 2.09 - 4.19: 859 4.19 - 6.28: 67 6.28 - 8.38: 14 8.38 - 10.47: 9 Bond angle restraints: 22030 Sorted by residual: angle pdb=" N TYR D 40 " pdb=" CA TYR D 40 " pdb=" C TYR D 40 " ideal model delta sigma weight residual 111.11 121.58 -10.47 1.20e+00 6.94e-01 7.62e+01 angle pdb=" N ASN B 25 " pdb=" CA ASN B 25 " pdb=" C ASN B 25 " ideal model delta sigma weight residual 111.71 104.22 7.49 1.15e+00 7.56e-01 4.24e+01 angle pdb=" N ARG B 23 " pdb=" CA ARG B 23 " pdb=" C ARG B 23 " ideal model delta sigma weight residual 111.02 120.86 -9.84 1.52e+00 4.33e-01 4.19e+01 angle pdb=" C LYS A 122 " pdb=" CA LYS A 122 " pdb=" CB LYS A 122 " ideal model delta sigma weight residual 110.81 101.56 9.25 1.60e+00 3.91e-01 3.34e+01 angle pdb=" O4' DA I 39 " pdb=" C4' DA I 39 " pdb=" C3' DA I 39 " ideal model delta sigma weight residual 106.00 102.54 3.46 6.00e-01 2.78e+00 3.32e+01 ... (remaining 22025 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.40: 7122 35.40 - 70.81: 1382 70.81 - 106.21: 21 106.21 - 141.61: 1 141.61 - 177.01: 4 Dihedral angle restraints: 8530 sinusoidal: 5420 harmonic: 3110 Sorted by residual: dihedral pdb=" CD ARG D 33 " pdb=" NE ARG D 33 " pdb=" CZ ARG D 33 " pdb=" NH1 ARG D 33 " ideal model delta sinusoidal sigma weight residual 0.00 -75.64 75.64 1 1.00e+01 1.00e-02 7.22e+01 dihedral pdb=" C TYR D 83 " pdb=" N TYR D 83 " pdb=" CA TYR D 83 " pdb=" CB TYR D 83 " ideal model delta harmonic sigma weight residual -122.60 -109.49 -13.11 0 2.50e+00 1.60e-01 2.75e+01 dihedral pdb=" C LYS A 122 " pdb=" N LYS A 122 " pdb=" CA LYS A 122 " pdb=" CB LYS A 122 " ideal model delta harmonic sigma weight residual -122.60 -112.39 -10.21 0 2.50e+00 1.60e-01 1.67e+01 ... (remaining 8527 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.126: 2439 0.126 - 0.251: 51 0.251 - 0.377: 2 0.377 - 0.503: 0 0.503 - 0.628: 2 Chirality restraints: 2494 Sorted by residual: chirality pdb=" P DC K 119 " pdb=" OP1 DC K 119 " pdb=" OP2 DC K 119 " pdb=" O5' DC K 119 " both_signs ideal model delta sigma weight residual True 2.34 2.96 -0.63 2.00e-01 2.50e+01 9.88e+00 chirality pdb=" P DA K 120 " pdb=" OP1 DA K 120 " pdb=" OP2 DA K 120 " pdb=" O5' DA K 120 " both_signs ideal model delta sigma weight residual True 2.34 -2.92 -0.59 2.00e-01 2.50e+01 8.65e+00 chirality pdb=" CB VAL E 46 " pdb=" CA VAL E 46 " pdb=" CG1 VAL E 46 " pdb=" CG2 VAL E 46 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.80e+00 ... (remaining 2491 not shown) Planarity restraints: 1779 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 33 " 1.073 9.50e-02 1.11e+02 4.81e-01 1.40e+02 pdb=" NE ARG D 33 " -0.064 2.00e-02 2.50e+03 pdb=" CZ ARG D 33 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG D 33 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG D 33 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 25 " 0.021 2.00e-02 2.50e+03 4.22e-02 1.78e+01 pdb=" C ASN B 25 " -0.073 2.00e-02 2.50e+03 pdb=" O ASN B 25 " 0.027 2.00e-02 2.50e+03 pdb=" N ILE B 26 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 23 " -0.017 2.00e-02 2.50e+03 3.47e-02 1.20e+01 pdb=" C ARG B 23 " 0.060 2.00e-02 2.50e+03 pdb=" O ARG B 23 " -0.022 2.00e-02 2.50e+03 pdb=" N ASP B 24 " -0.021 2.00e-02 2.50e+03 ... (remaining 1776 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 3032 2.79 - 3.32: 13012 3.32 - 3.85: 28584 3.85 - 4.37: 31555 4.37 - 4.90: 46144 Nonbonded interactions: 122327 Sorted by model distance: nonbonded pdb=" ND2 ASN A 108 " pdb=" O GLY B 42 " model vdw 2.268 3.120 nonbonded pdb=" OH TYR C 39 " pdb=" OE1 GLU D 71 " model vdw 2.298 3.040 nonbonded pdb=" O TYR C 39 " pdb=" OG SER D 78 " model vdw 2.300 3.040 nonbonded pdb=" O VAL L 29 " pdb=" NH2 ARG L 112 " model vdw 2.303 3.120 nonbonded pdb=" OG SER G 18 " pdb=" O LEU G 23 " model vdw 2.313 3.040 ... (remaining 122322 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' and resid 38 through 133) selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 22 through 101) } ncs_group { reference = (chain 'C' and resid 16 through 117) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 34 through 123) selection = chain 'H' } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 19.490 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: 0.020 Extract box with map and model: 0.940 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 14.460 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 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:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 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 : 0.007 0.131 15393 Z= 0.524 Angle : 0.887 10.473 22030 Z= 0.705 Chirality : 0.054 0.628 2494 Planarity : 0.013 0.481 1779 Dihedral : 26.774 177.014 6526 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.89 % Allowed : 1.11 % Favored : 98.01 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.26), residues: 1054 helix: 1.14 (0.20), residues: 701 sheet: 0.71 (0.84), residues: 30 loop : -0.12 (0.34), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 49 TYR 0.030 0.002 TYR L 322 PHE 0.016 0.002 PHE A 84 TRP 0.005 0.001 TRP L 325 HIS 0.011 0.002 HIS L 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00662 / 0.52 (15393) covalent geometry : angle 0.88677 / 0.71 (22030) hydrogen bonds : bond 0.11718 / 7.66 ( 900) hydrogen bonds : angle 4.49393 / 3.20 ( 2295) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 174 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 LEU cc_start: 0.8565 (mm) cc_final: 0.8304 (mm) REVERT: A 120 MET cc_start: 0.9246 (mtm) cc_final: 0.8696 (mtm) REVERT: B 78 ARG cc_start: 0.8696 (ptt90) cc_final: 0.8144 (ptt90) REVERT: C 92 GLU cc_start: 0.8890 (pp20) cc_final: 0.8285 (pp20) REVERT: D 35 GLU cc_start: 0.8519 (mt-10) cc_final: 0.8314 (mt-10) REVERT: E 59 GLU cc_start: 0.7878 (pm20) cc_final: 0.7551 (pm20) REVERT: E 81 ASP cc_start: 0.8810 (t70) cc_final: 0.8349 (t70) REVERT: E 97 GLU cc_start: 0.8505 (mm-30) cc_final: 0.8214 (tt0) REVERT: E 125 GLN cc_start: 0.8864 (mp10) cc_final: 0.8648 (mp10) REVERT: F 84 MET cc_start: 0.8857 (tpt) cc_final: 0.8476 (tpp) REVERT: F 88 TYR cc_start: 0.8753 (m-80) cc_final: 0.8506 (m-80) REVERT: G 36 LYS cc_start: 0.9155 (mmmt) cc_final: 0.8913 (ttpt) REVERT: G 72 ASP cc_start: 0.9110 (m-30) cc_final: 0.8870 (t0) REVERT: G 90 ASP cc_start: 0.8854 (t70) cc_final: 0.7842 (t70) REVERT: G 104 GLN cc_start: 0.8603 (pm20) cc_final: 0.8270 (pm20) REVERT: H 68 ASP cc_start: 0.8992 (t0) cc_final: 0.8727 (t0) REVERT: H 84 ASN cc_start: 0.9188 (t0) cc_final: 0.8869 (t0) REVERT: L 217 GLN cc_start: 0.7217 (mt0) cc_final: 0.6975 (pp30) outliers start: 8 outliers final: 4 residues processed: 177 average time/residue: 0.1387 time to fit residues: 34.1773 Evaluate side-chains 131 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 127 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain D residue 33 ARG Chi-restraints excluded: chain D residue 116 LYS Chi-restraints excluded: chain E residue 46 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 98 optimal weight: 40.0000 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 50.0000 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 20.0000 chunk 55 optimal weight: 1.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 GLN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 113 HIS G 82 HIS H 82 HIS H 84 ASN L 159 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.094930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.055982 restraints weight = 56092.523| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 3.45 r_work: 0.2833 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.1170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 15393 Z= 0.239 Angle : 0.687 7.757 22030 Z= 0.388 Chirality : 0.045 0.309 2494 Planarity : 0.005 0.053 1779 Dihedral : 30.284 177.740 4401 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.77 % Allowed : 10.41 % Favored : 87.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.26), residues: 1054 helix: 1.41 (0.19), residues: 718 sheet: 0.75 (0.70), residues: 42 loop : -0.41 (0.36), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 32 TYR 0.026 0.002 TYR L 322 PHE 0.020 0.002 PHE L 181 TRP 0.004 0.001 TRP L 325 HIS 0.008 0.001 HIS L 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00512 / 0.24 (15393) covalent geometry : angle 0.68663 / 0.39 (22030) hydrogen bonds : bond 0.05056 / 3.37 ( 900) hydrogen bonds : angle 3.59872 / 2.58 ( 2295) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 131 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.9216 (mtm) cc_final: 0.8820 (mtm) REVERT: B 25 ASN cc_start: 0.8624 (m110) cc_final: 0.8070 (m-40) REVERT: E 59 GLU cc_start: 0.7946 (pm20) cc_final: 0.7521 (pm20) REVERT: E 81 ASP cc_start: 0.8815 (t70) cc_final: 0.8361 (t70) REVERT: E 97 GLU cc_start: 0.8626 (mm-30) cc_final: 0.8246 (tt0) REVERT: E 125 GLN cc_start: 0.8962 (mp10) cc_final: 0.8722 (mm-40) REVERT: F 88 TYR cc_start: 0.8727 (m-10) cc_final: 0.8505 (m-80) REVERT: G 72 ASP cc_start: 0.9250 (m-30) cc_final: 0.9002 (m-30) REVERT: G 90 ASP cc_start: 0.8454 (t70) cc_final: 0.8066 (t0) REVERT: G 92 GLU cc_start: 0.8655 (pm20) cc_final: 0.8432 (pm20) REVERT: H 68 ASP cc_start: 0.9015 (t0) cc_final: 0.8678 (t0) REVERT: H 84 ASN cc_start: 0.9002 (t0) cc_final: 0.8571 (t0) REVERT: H 86 ARG cc_start: 0.8214 (ttm-80) cc_final: 0.7974 (mtm-85) REVERT: L 158 MET cc_start: 0.5160 (ptp) cc_final: 0.4906 (ptt) outliers start: 16 outliers final: 12 residues processed: 142 average time/residue: 0.1337 time to fit residues: 26.8901 Evaluate side-chains 131 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 119 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain D residue 116 LYS Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain L residue 213 GLN Chi-restraints excluded: chain L residue 291 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 57 optimal weight: 0.9990 chunk 102 optimal weight: 30.0000 chunk 73 optimal weight: 40.0000 chunk 110 optimal weight: 9.9990 chunk 88 optimal weight: 50.0000 chunk 86 optimal weight: 50.0000 chunk 15 optimal weight: 1.9990 chunk 114 optimal weight: 7.9990 chunk 113 optimal weight: 30.0000 chunk 46 optimal weight: 9.9990 chunk 82 optimal weight: 20.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 HIS ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.093112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.053677 restraints weight = 56570.935| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 3.44 r_work: 0.2770 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 15393 Z= 0.339 Angle : 0.761 9.674 22030 Z= 0.423 Chirality : 0.049 0.332 2494 Planarity : 0.005 0.039 1779 Dihedral : 30.409 178.457 4393 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.88 % Allowed : 12.51 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.26), residues: 1054 helix: 1.32 (0.19), residues: 714 sheet: 0.93 (0.65), residues: 41 loop : -0.56 (0.36), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 116 TYR 0.022 0.002 TYR B 88 PHE 0.024 0.002 PHE L 181 TRP 0.004 0.001 TRP L 325 HIS 0.007 0.001 HIS L 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00747 / 0.34 (15393) covalent geometry : angle 0.76134 / 0.42 (22030) hydrogen bonds : bond 0.05907 / 3.99 ( 900) hydrogen bonds : angle 3.75966 / 2.69 ( 2295) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 120 time to evaluate : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.9208 (mtm) cc_final: 0.8875 (mtm) REVERT: B 88 TYR cc_start: 0.8788 (m-80) cc_final: 0.8366 (m-80) REVERT: C 92 GLU cc_start: 0.8724 (pp20) cc_final: 0.8061 (pp20) REVERT: D 93 GLU cc_start: 0.8853 (OUTLIER) cc_final: 0.8548 (mp0) REVERT: E 57 SER cc_start: 0.8687 (p) cc_final: 0.8433 (p) REVERT: E 59 GLU cc_start: 0.7971 (pm20) cc_final: 0.7062 (pm20) REVERT: E 81 ASP cc_start: 0.8787 (t70) cc_final: 0.8363 (t70) REVERT: E 97 GLU cc_start: 0.8660 (mm-30) cc_final: 0.8295 (tt0) REVERT: G 90 ASP cc_start: 0.8688 (t70) cc_final: 0.7998 (t70) REVERT: H 68 ASP cc_start: 0.9063 (t0) cc_final: 0.8713 (t0) REVERT: H 76 GLU cc_start: 0.9001 (tp30) cc_final: 0.8794 (tp30) REVERT: H 84 ASN cc_start: 0.9084 (t0) cc_final: 0.8669 (t0) REVERT: H 86 ARG cc_start: 0.8345 (ttm-80) cc_final: 0.7969 (ttm-80) outliers start: 26 outliers final: 21 residues processed: 138 average time/residue: 0.1160 time to fit residues: 23.5036 Evaluate side-chains 142 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 120 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 47 GLN Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain L residue 213 GLN Chi-restraints excluded: chain L residue 291 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 125 optimal weight: 50.0000 chunk 27 optimal weight: 0.2980 chunk 67 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 121 optimal weight: 50.0000 chunk 76 optimal weight: 20.0000 chunk 64 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 120 optimal weight: 30.0000 chunk 106 optimal weight: 40.0000 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 39 HIS ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.094647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.056384 restraints weight = 56286.897| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 3.22 r_work: 0.2848 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15393 Z= 0.142 Angle : 0.604 7.203 22030 Z= 0.351 Chirality : 0.043 0.332 2494 Planarity : 0.004 0.042 1779 Dihedral : 30.321 178.942 4389 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.33 % Allowed : 14.51 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.64 (0.26), residues: 1054 helix: 1.74 (0.20), residues: 711 sheet: 1.09 (0.62), residues: 41 loop : -0.42 (0.36), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 32 TYR 0.017 0.002 TYR B 88 PHE 0.012 0.001 PHE L 76 TRP 0.005 0.001 TRP L 325 HIS 0.006 0.001 HIS L 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.14 (15393) covalent geometry : angle 0.60387 / 0.35 (22030) hydrogen bonds : bond 0.04143 / 2.83 ( 900) hydrogen bonds : angle 3.24831 / 2.33 ( 2295) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 138 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.9194 (mtm) cc_final: 0.8834 (mtm) REVERT: B 25 ASN cc_start: 0.8579 (m110) cc_final: 0.8064 (m-40) REVERT: C 36 LYS cc_start: 0.9038 (pttt) cc_final: 0.8822 (mptt) REVERT: C 90 ASP cc_start: 0.8226 (t0) cc_final: 0.7908 (t0) REVERT: C 92 GLU cc_start: 0.8648 (pp20) cc_final: 0.8228 (pp20) REVERT: E 81 ASP cc_start: 0.8757 (t70) cc_final: 0.8323 (t70) REVERT: E 97 GLU cc_start: 0.8566 (mm-30) cc_final: 0.8276 (tt0) REVERT: E 107 THR cc_start: 0.9431 (m) cc_final: 0.9159 (t) REVERT: E 125 GLN cc_start: 0.9175 (mm-40) cc_final: 0.8960 (mm-40) REVERT: F 53 GLU cc_start: 0.8159 (tp30) cc_final: 0.7846 (tp30) REVERT: H 68 ASP cc_start: 0.8974 (t0) cc_final: 0.8626 (t0) REVERT: H 71 GLU cc_start: 0.9269 (tm-30) cc_final: 0.8982 (tm-30) REVERT: H 84 ASN cc_start: 0.8968 (t0) cc_final: 0.8556 (t0) REVERT: H 86 ARG cc_start: 0.8287 (ttm-80) cc_final: 0.7873 (ttm-80) REVERT: L 158 MET cc_start: 0.4566 (ptt) cc_final: 0.4040 (ptt) outliers start: 21 outliers final: 13 residues processed: 150 average time/residue: 0.1174 time to fit residues: 25.7985 Evaluate side-chains 139 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 126 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain L residue 213 GLN Chi-restraints excluded: chain L residue 291 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 101 optimal weight: 40.0000 chunk 116 optimal weight: 10.0000 chunk 100 optimal weight: 6.9990 chunk 88 optimal weight: 40.0000 chunk 112 optimal weight: 7.9990 chunk 48 optimal weight: 3.9990 chunk 117 optimal weight: 30.0000 chunk 105 optimal weight: 40.0000 chunk 95 optimal weight: 20.0000 chunk 67 optimal weight: 3.9990 chunk 50 optimal weight: 0.4980 overall best weight: 4.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 GLN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 ASN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.092869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.053961 restraints weight = 56303.153| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 3.39 r_work: 0.2764 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 15393 Z= 0.269 Angle : 0.685 8.623 22030 Z= 0.383 Chirality : 0.045 0.330 2494 Planarity : 0.004 0.041 1779 Dihedral : 30.392 179.864 4389 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.10 % Allowed : 14.73 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.26), residues: 1054 helix: 1.65 (0.20), residues: 711 sheet: 1.21 (0.64), residues: 41 loop : -0.46 (0.36), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 116 TYR 0.024 0.002 TYR D 83 PHE 0.014 0.001 PHE A 104 TRP 0.004 0.001 TRP L 325 HIS 0.005 0.001 HIS L 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00587 / 0.27 (15393) covalent geometry : angle 0.68463 / 0.38 (22030) hydrogen bonds : bond 0.05082 / 3.44 ( 900) hydrogen bonds : angle 3.43620 / 2.46 ( 2295) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 117 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 ARG cc_start: 0.8279 (OUTLIER) cc_final: 0.7568 (mmm-85) REVERT: A 94 GLU cc_start: 0.9236 (mm-30) cc_final: 0.9025 (tp30) REVERT: B 25 ASN cc_start: 0.8670 (m110) cc_final: 0.8168 (m-40) REVERT: C 92 GLU cc_start: 0.8640 (pp20) cc_final: 0.8156 (pp20) REVERT: E 81 ASP cc_start: 0.8806 (t70) cc_final: 0.8369 (t70) REVERT: E 97 GLU cc_start: 0.8638 (mm-30) cc_final: 0.8333 (tt0) REVERT: E 125 GLN cc_start: 0.9263 (mm-40) cc_final: 0.9005 (mm-40) REVERT: H 68 ASP cc_start: 0.9045 (t0) cc_final: 0.8706 (t0) REVERT: H 83 TYR cc_start: 0.8381 (m-10) cc_final: 0.8078 (m-10) REVERT: H 84 ASN cc_start: 0.9056 (t0) cc_final: 0.8652 (t0) REVERT: H 86 ARG cc_start: 0.8359 (ttm-80) cc_final: 0.7961 (ttm-80) REVERT: L 158 MET cc_start: 0.5031 (ptt) cc_final: 0.3799 (ptt) outliers start: 28 outliers final: 21 residues processed: 140 average time/residue: 0.1156 time to fit residues: 23.6954 Evaluate side-chains 136 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 114 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 83 ARG Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain L residue 213 GLN Chi-restraints excluded: chain L residue 291 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 105 optimal weight: 6.9990 chunk 114 optimal weight: 8.9990 chunk 91 optimal weight: 20.0000 chunk 128 optimal weight: 0.9980 chunk 47 optimal weight: 4.9990 chunk 42 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 99 optimal weight: 40.0000 chunk 32 optimal weight: 1.9990 chunk 28 optimal weight: 0.1980 chunk 2 optimal weight: 5.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.094662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.056342 restraints weight = 55809.480| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 3.43 r_work: 0.2853 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 15393 Z= 0.136 Angle : 0.588 6.068 22030 Z= 0.342 Chirality : 0.042 0.334 2494 Planarity : 0.004 0.042 1779 Dihedral : 30.297 178.235 4389 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.99 % Allowed : 15.50 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.83 (0.26), residues: 1054 helix: 1.90 (0.20), residues: 711 sheet: 1.33 (0.63), residues: 41 loop : -0.43 (0.36), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 42 TYR 0.021 0.001 TYR D 83 PHE 0.009 0.001 PHE E 67 TRP 0.005 0.001 TRP L 325 HIS 0.005 0.001 HIS L 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.14 (15393) covalent geometry : angle 0.58834 / 0.34 (22030) hydrogen bonds : bond 0.04054 / 2.77 ( 900) hydrogen bonds : angle 3.14541 / 2.26 ( 2295) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 136 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.9211 (mm-30) cc_final: 0.8992 (tp30) REVERT: A 120 MET cc_start: 0.9213 (mtm) cc_final: 0.8868 (mtm) REVERT: C 90 ASP cc_start: 0.7873 (t0) cc_final: 0.7447 (t0) REVERT: C 92 GLU cc_start: 0.8580 (pp20) cc_final: 0.8267 (pp20) REVERT: C 111 ILE cc_start: 0.9289 (OUTLIER) cc_final: 0.8924 (mm) REVERT: E 59 GLU cc_start: 0.7869 (pt0) cc_final: 0.7658 (pt0) REVERT: E 81 ASP cc_start: 0.8782 (t70) cc_final: 0.8340 (t70) REVERT: E 97 GLU cc_start: 0.8567 (mm-30) cc_final: 0.8319 (tt0) REVERT: E 107 THR cc_start: 0.9429 (m) cc_final: 0.9145 (t) REVERT: E 125 GLN cc_start: 0.9221 (mm-40) cc_final: 0.9006 (mm-40) REVERT: F 53 GLU cc_start: 0.8234 (tp30) cc_final: 0.7981 (tp30) REVERT: G 92 GLU cc_start: 0.8656 (mp0) cc_final: 0.8354 (mp0) REVERT: H 68 ASP cc_start: 0.8974 (t0) cc_final: 0.8599 (t0) REVERT: H 84 ASN cc_start: 0.8993 (t0) cc_final: 0.8602 (t0) REVERT: H 86 ARG cc_start: 0.8307 (ttm-80) cc_final: 0.7889 (ttm-80) REVERT: L 155 MET cc_start: 0.0185 (OUTLIER) cc_final: -0.1112 (ttt) REVERT: L 236 MET cc_start: 0.7238 (ttp) cc_final: 0.7027 (tmm) outliers start: 27 outliers final: 20 residues processed: 154 average time/residue: 0.1101 time to fit residues: 24.8566 Evaluate side-chains 147 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 125 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain L residue 155 MET Chi-restraints excluded: chain L residue 213 GLN Chi-restraints excluded: chain L residue 291 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 74 optimal weight: 30.0000 chunk 85 optimal weight: 40.0000 chunk 58 optimal weight: 0.9980 chunk 44 optimal weight: 6.9990 chunk 118 optimal weight: 50.0000 chunk 116 optimal weight: 8.9990 chunk 83 optimal weight: 30.0000 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.094638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.056171 restraints weight = 55771.755| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 3.24 r_work: 0.2853 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15393 Z= 0.138 Angle : 0.600 10.244 22030 Z= 0.343 Chirality : 0.042 0.329 2494 Planarity : 0.004 0.043 1779 Dihedral : 30.267 177.380 4389 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.10 % Allowed : 16.61 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.91 (0.26), residues: 1054 helix: 1.94 (0.20), residues: 711 sheet: 1.53 (0.71), residues: 36 loop : -0.34 (0.36), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 42 TYR 0.019 0.001 TYR D 40 PHE 0.008 0.001 PHE A 67 TRP 0.005 0.001 TRP L 325 HIS 0.004 0.001 HIS L 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.14 (15393) covalent geometry : angle 0.60000 / 0.34 (22030) hydrogen bonds : bond 0.04033 / 2.75 ( 900) hydrogen bonds : angle 3.13604 / 2.25 ( 2295) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 129 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.9214 (OUTLIER) cc_final: 0.8828 (mtm) REVERT: B 25 ASN cc_start: 0.8615 (m-40) cc_final: 0.8088 (m110) REVERT: C 90 ASP cc_start: 0.7812 (t0) cc_final: 0.7288 (t0) REVERT: C 92 GLU cc_start: 0.8562 (pp20) cc_final: 0.8275 (pp20) REVERT: C 111 ILE cc_start: 0.9258 (OUTLIER) cc_final: 0.8911 (mm) REVERT: E 59 GLU cc_start: 0.7937 (pt0) cc_final: 0.7718 (pt0) REVERT: E 81 ASP cc_start: 0.8814 (t70) cc_final: 0.8362 (t70) REVERT: E 97 GLU cc_start: 0.8588 (mm-30) cc_final: 0.8385 (tt0) REVERT: E 107 THR cc_start: 0.9430 (m) cc_final: 0.9127 (t) REVERT: E 125 GLN cc_start: 0.9245 (mm-40) cc_final: 0.9024 (mm-40) REVERT: F 53 GLU cc_start: 0.8256 (tp30) cc_final: 0.7995 (tp30) REVERT: G 92 GLU cc_start: 0.8632 (mp0) cc_final: 0.8407 (mp0) REVERT: H 68 ASP cc_start: 0.8957 (t0) cc_final: 0.8691 (t0) REVERT: H 84 ASN cc_start: 0.8968 (t0) cc_final: 0.8582 (t0) REVERT: H 86 ARG cc_start: 0.8286 (ttm-80) cc_final: 0.7848 (ttm-80) REVERT: L 155 MET cc_start: 0.0332 (OUTLIER) cc_final: -0.0753 (ppp) outliers start: 28 outliers final: 20 residues processed: 148 average time/residue: 0.1046 time to fit residues: 22.9811 Evaluate side-chains 147 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 124 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain L residue 155 MET Chi-restraints excluded: chain L residue 213 GLN Chi-restraints excluded: chain L residue 291 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 68 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 93 optimal weight: 20.0000 chunk 88 optimal weight: 50.0000 chunk 78 optimal weight: 20.0000 chunk 11 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 75 optimal weight: 20.0000 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.094230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.055583 restraints weight = 55569.528| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 3.25 r_work: 0.2815 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 15393 Z= 0.171 Angle : 0.623 9.328 22030 Z= 0.352 Chirality : 0.042 0.331 2494 Planarity : 0.004 0.044 1779 Dihedral : 30.295 177.791 4389 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.99 % Allowed : 16.83 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.92 (0.26), residues: 1054 helix: 1.94 (0.20), residues: 711 sheet: 1.48 (0.70), residues: 36 loop : -0.31 (0.36), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 42 TYR 0.021 0.002 TYR B 88 PHE 0.010 0.001 PHE A 104 TRP 0.004 0.001 TRP L 325 HIS 0.004 0.001 HIS L 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.17 (15393) covalent geometry : angle 0.62328 / 0.35 (22030) hydrogen bonds : bond 0.04241 / 2.89 ( 900) hydrogen bonds : angle 3.20274 / 2.30 ( 2295) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 123 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.9187 (OUTLIER) cc_final: 0.8787 (mtm) REVERT: B 25 ASN cc_start: 0.8664 (m-40) cc_final: 0.8110 (m110) REVERT: C 90 ASP cc_start: 0.7824 (t0) cc_final: 0.7273 (t0) REVERT: C 92 GLU cc_start: 0.8535 (pp20) cc_final: 0.8234 (pp20) REVERT: C 111 ILE cc_start: 0.9250 (OUTLIER) cc_final: 0.8908 (mm) REVERT: E 81 ASP cc_start: 0.8829 (t70) cc_final: 0.8363 (t70) REVERT: E 97 GLU cc_start: 0.8643 (mm-30) cc_final: 0.8375 (tt0) REVERT: E 107 THR cc_start: 0.9413 (m) cc_final: 0.9108 (t) REVERT: E 125 GLN cc_start: 0.9236 (mm-40) cc_final: 0.9020 (mm-40) REVERT: G 92 GLU cc_start: 0.8658 (mp0) cc_final: 0.8408 (mp0) REVERT: G 95 LYS cc_start: 0.9181 (tmmt) cc_final: 0.8826 (tmmt) REVERT: H 68 ASP cc_start: 0.8991 (t0) cc_final: 0.8702 (t0) REVERT: H 84 ASN cc_start: 0.8982 (t0) cc_final: 0.8599 (t0) REVERT: H 86 ARG cc_start: 0.8271 (ttm-80) cc_final: 0.7826 (ttm-80) REVERT: L 155 MET cc_start: 0.0396 (OUTLIER) cc_final: -0.0515 (tmm) REVERT: L 236 MET cc_start: 0.7136 (ptt) cc_final: 0.6909 (ttp) outliers start: 27 outliers final: 21 residues processed: 140 average time/residue: 0.1111 time to fit residues: 23.0615 Evaluate side-chains 145 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 121 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain L residue 155 MET Chi-restraints excluded: chain L residue 213 GLN Chi-restraints excluded: chain L residue 291 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 30 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 chunk 125 optimal weight: 40.0000 chunk 102 optimal weight: 30.0000 chunk 112 optimal weight: 10.0000 chunk 121 optimal weight: 10.0000 chunk 59 optimal weight: 6.9990 chunk 80 optimal weight: 20.0000 chunk 99 optimal weight: 30.0000 overall best weight: 2.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.093923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.054982 restraints weight = 56187.966| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 3.47 r_work: 0.2822 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 15393 Z= 0.194 Angle : 0.647 11.664 22030 Z= 0.362 Chirality : 0.043 0.333 2494 Planarity : 0.004 0.043 1779 Dihedral : 30.335 178.251 4389 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.65 % Allowed : 16.17 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.84 (0.26), residues: 1054 helix: 1.88 (0.20), residues: 711 sheet: 1.46 (0.71), residues: 36 loop : -0.33 (0.36), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 42 TYR 0.025 0.002 TYR H 83 PHE 0.011 0.001 PHE A 104 TRP 0.004 0.001 TRP L 325 HIS 0.004 0.001 HIS L 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.19 (15393) covalent geometry : angle 0.64651 / 0.36 (22030) hydrogen bonds : bond 0.04438 / 3.02 ( 900) hydrogen bonds : angle 3.27139 / 2.35 ( 2295) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 123 time to evaluate : 0.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 ARG cc_start: 0.8230 (OUTLIER) cc_final: 0.7549 (mmm-85) REVERT: A 120 MET cc_start: 0.9199 (OUTLIER) cc_final: 0.8816 (mtm) REVERT: B 25 ASN cc_start: 0.8693 (m-40) cc_final: 0.8111 (m-40) REVERT: C 90 ASP cc_start: 0.8029 (t0) cc_final: 0.7493 (t0) REVERT: C 92 GLU cc_start: 0.8586 (pp20) cc_final: 0.8269 (pp20) REVERT: C 111 ILE cc_start: 0.9307 (OUTLIER) cc_final: 0.8962 (mm) REVERT: E 81 ASP cc_start: 0.8814 (t70) cc_final: 0.8355 (t70) REVERT: G 92 GLU cc_start: 0.8669 (mp0) cc_final: 0.8392 (mp0) REVERT: G 95 LYS cc_start: 0.9275 (tmmt) cc_final: 0.8844 (tmmt) REVERT: H 68 ASP cc_start: 0.9028 (t0) cc_final: 0.8741 (t0) REVERT: H 84 ASN cc_start: 0.8931 (t0) cc_final: 0.8570 (t0) REVERT: H 86 ARG cc_start: 0.8296 (ttm-80) cc_final: 0.7881 (ttm-80) REVERT: L 155 MET cc_start: 0.0885 (OUTLIER) cc_final: -0.0498 (ttt) outliers start: 33 outliers final: 20 residues processed: 146 average time/residue: 0.1276 time to fit residues: 27.2126 Evaluate side-chains 144 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 120 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 83 ARG Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain L residue 155 MET Chi-restraints excluded: chain L residue 213 GLN Chi-restraints excluded: chain L residue 291 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 112 optimal weight: 10.0000 chunk 46 optimal weight: 8.9990 chunk 76 optimal weight: 20.0000 chunk 19 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 83 optimal weight: 30.0000 chunk 93 optimal weight: 20.0000 chunk 61 optimal weight: 5.9990 chunk 81 optimal weight: 20.0000 chunk 37 optimal weight: 7.9990 chunk 107 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.092374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.053364 restraints weight = 56514.945| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 3.43 r_work: 0.2776 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 15393 Z= 0.294 Angle : 0.749 13.222 22030 Z= 0.408 Chirality : 0.047 0.339 2494 Planarity : 0.005 0.042 1779 Dihedral : 30.459 179.857 4389 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.77 % Allowed : 17.05 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.48 (0.26), residues: 1054 helix: 1.60 (0.20), residues: 711 sheet: 0.94 (0.76), residues: 36 loop : -0.40 (0.36), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 32 TYR 0.073 0.003 TYR H 83 PHE 0.017 0.002 PHE A 104 TRP 0.005 0.001 TRP L 325 HIS 0.007 0.002 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00650 / 0.29 (15393) covalent geometry : angle 0.74870 / 0.41 (22030) hydrogen bonds : bond 0.05437 / 3.68 ( 900) hydrogen bonds : angle 3.57870 / 2.56 ( 2295) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 114 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 ARG cc_start: 0.8333 (OUTLIER) cc_final: 0.7634 (mmm-85) REVERT: A 120 MET cc_start: 0.9180 (OUTLIER) cc_final: 0.8820 (mtm) REVERT: B 25 ASN cc_start: 0.8762 (m-40) cc_final: 0.7958 (m110) REVERT: C 90 ASP cc_start: 0.8297 (t0) cc_final: 0.8012 (t0) REVERT: C 92 GLU cc_start: 0.8646 (pp20) cc_final: 0.8246 (pp20) REVERT: C 111 ILE cc_start: 0.9353 (OUTLIER) cc_final: 0.8983 (mm) REVERT: E 81 ASP cc_start: 0.8799 (t70) cc_final: 0.8351 (t70) REVERT: F 88 TYR cc_start: 0.8603 (m-80) cc_final: 0.8120 (m-80) REVERT: G 92 GLU cc_start: 0.8698 (mp0) cc_final: 0.8496 (mp0) REVERT: H 68 ASP cc_start: 0.9081 (t0) cc_final: 0.8751 (t0) REVERT: H 84 ASN cc_start: 0.9080 (t0) cc_final: 0.8838 (t0) REVERT: L 236 MET cc_start: 0.8223 (ttp) cc_final: 0.7693 (mmm) outliers start: 25 outliers final: 19 residues processed: 133 average time/residue: 0.1277 time to fit residues: 24.8585 Evaluate side-chains 133 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 111 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 83 ARG Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain L residue 213 GLN Chi-restraints excluded: chain L residue 291 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 32 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 72 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 chunk 119 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 chunk 112 optimal weight: 20.0000 chunk 85 optimal weight: 40.0000 chunk 29 optimal weight: 1.9990 chunk 37 optimal weight: 10.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 93 GLN H 84 ASN ** L 34 HIS ** 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 = 0.3936 r_free = 0.3936 target = 0.093039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.054256 restraints weight = 55765.472| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 3.42 r_work: 0.2777 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 15393 Z= 0.220 Angle : 0.684 12.164 22030 Z= 0.381 Chirality : 0.045 0.342 2494 Planarity : 0.004 0.043 1779 Dihedral : 30.438 179.508 4389 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.77 % Allowed : 17.17 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.61 (0.26), residues: 1054 helix: 1.72 (0.20), residues: 708 sheet: 0.76 (0.74), residues: 36 loop : -0.37 (0.36), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 86 TYR 0.093 0.003 TYR H 83 PHE 0.011 0.001 PHE A 104 TRP 0.004 0.001 TRP L 325 HIS 0.005 0.001 HIS L 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.22 (15393) covalent geometry : angle 0.68432 / 0.38 (22030) hydrogen bonds : bond 0.04716 / 3.20 ( 900) hydrogen bonds : angle 3.43072 / 2.46 ( 2295) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4841.35 seconds wall clock time: 83 minutes 16.76 seconds (4996.76 seconds total)