Starting phenix.real_space_refine on Mon Aug 25 20:44:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j04_35883/08_2025/8j04_35883_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j04_35883/08_2025/8j04_35883.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8j04_35883/08_2025/8j04_35883_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j04_35883/08_2025/8j04_35883_neut_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8j04_35883/08_2025/8j04_35883.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j04_35883/08_2025/8j04_35883.map" } resolution = 2.7 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= 0.003 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: 6 Type Number sf(0) Gaussians S 88 5.16 5 C 10068 2.51 5 N 2616 2.21 5 O 2800 1.98 5 F 8 1.80 5 H 15244 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s 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: 30824 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 5478 Classifications: {'peptide': 332} Link IDs: {'PTRANS': 6, 'TRANS': 325} Chain breaks: 2 Chain: "B" Number of atoms: 5478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 5478 Classifications: {'peptide': 332} Link IDs: {'PTRANS': 6, 'TRANS': 325} Chain breaks: 2 Chain: "C" Number of atoms: 2178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2178 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Chain: "D" Number of atoms: 5478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 5478 Classifications: {'peptide': 332} Link IDs: {'PTRANS': 6, 'TRANS': 325} Chain breaks: 2 Chain: "E" Number of atoms: 2178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2178 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Chain: "F" Number of atoms: 2178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2178 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Chain: "G" Number of atoms: 5478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 5478 Classifications: {'peptide': 332} Link IDs: {'PTRANS': 6, 'TRANS': 325} Chain breaks: 2 Chain: "H" Number of atoms: 2178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2178 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Chain: "A" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 50 Unusual residues: {'9MF': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 50 Unusual residues: {'9MF': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 50 Unusual residues: {'9MF': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 50 Unusual residues: {'9MF': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.58, per 1000 atoms: 0.15 Number of scatterers: 30824 At special positions: 0 Unit cell: (121.83, 121.83, 106.02, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 88 16.00 F 8 9.00 O 2800 8.00 N 2616 7.00 C 10068 6.00 H 15244 1.00 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: 2.87 Conformation dependent library (CDL) restraints added in 749.4 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 3736 Ramachandran restraints generated. 1868 Oldfield, 0 Emsley, 1868 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3536 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 7 sheets defined 82.0% alpha, 0.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'A' and resid 70 through 86 removed outlier: 3.690A pdb=" N TYR A 74 " --> pdb=" O ARG A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 114 removed outlier: 4.098A pdb=" N TYR A 95 " --> pdb=" O TRP A 91 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N HIS A 96 " --> pdb=" O ALA A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 148 removed outlier: 3.897A pdb=" N ILE A 128 " --> pdb=" O GLY A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 154 removed outlier: 4.377A pdb=" N CYS A 152 " --> pdb=" O GLY A 149 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N ARG A 153 " --> pdb=" O CYS A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 165 Processing helix chain 'A' and resid 166 through 184 Processing helix chain 'A' and resid 196 through 210 Processing helix chain 'A' and resid 215 through 228 Processing helix chain 'A' and resid 228 through 255 Processing helix chain 'A' and resid 263 through 276 Processing helix chain 'A' and resid 287 through 329 removed outlier: 3.790A pdb=" N LEU A 299 " --> pdb=" O ALA A 295 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ILE A 300 " --> pdb=" O THR A 296 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER A 303 " --> pdb=" O LEU A 299 " (cutoff:3.500A) Proline residue: A 308 - end of helix Processing helix chain 'A' and resid 332 through 350 Processing helix chain 'A' and resid 357 through 366 Processing helix chain 'A' and resid 536 through 558 Processing helix chain 'A' and resid 563 through 578 removed outlier: 3.840A pdb=" N VAL A 567 " --> pdb=" O ASP A 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 86 Processing helix chain 'B' and resid 91 through 114 removed outlier: 4.100A pdb=" N TYR B 95 " --> pdb=" O TRP B 91 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N HIS B 96 " --> pdb=" O ALA B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 148 removed outlier: 3.899A pdb=" N ILE B 128 " --> pdb=" O GLY B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 154 removed outlier: 4.378A pdb=" N CYS B 152 " --> pdb=" O GLY B 149 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ARG B 153 " --> pdb=" O CYS B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 165 Processing helix chain 'B' and resid 166 through 184 Processing helix chain 'B' and resid 196 through 210 Processing helix chain 'B' and resid 215 through 228 Processing helix chain 'B' and resid 228 through 255 Processing helix chain 'B' and resid 263 through 276 Processing helix chain 'B' and resid 287 through 329 removed outlier: 3.784A pdb=" N LEU B 299 " --> pdb=" O ALA B 295 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ILE B 300 " --> pdb=" O THR B 296 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER B 303 " --> pdb=" O LEU B 299 " (cutoff:3.500A) Proline residue: B 308 - end of helix Processing helix chain 'B' and resid 332 through 350 Processing helix chain 'B' and resid 357 through 366 Processing helix chain 'B' and resid 536 through 558 Processing helix chain 'B' and resid 563 through 578 removed outlier: 3.840A pdb=" N VAL B 567 " --> pdb=" O ASP B 563 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 21 Processing helix chain 'C' and resid 29 through 41 Processing helix chain 'C' and resid 45 through 57 Processing helix chain 'C' and resid 66 through 75 Processing helix chain 'C' and resid 76 through 80 Processing helix chain 'C' and resid 82 through 94 Processing helix chain 'C' and resid 103 through 111 removed outlier: 3.650A pdb=" N THR C 111 " --> pdb=" O ARG C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 130 Processing helix chain 'C' and resid 138 through 146 removed outlier: 3.977A pdb=" N MET C 146 " --> pdb=" O PHE C 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 86 Processing helix chain 'D' and resid 91 through 114 removed outlier: 4.091A pdb=" N TYR D 95 " --> pdb=" O TRP D 91 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N HIS D 96 " --> pdb=" O ALA D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 148 removed outlier: 3.896A pdb=" N ILE D 128 " --> pdb=" O GLY D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 154 removed outlier: 4.376A pdb=" N CYS D 152 " --> pdb=" O GLY D 149 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ARG D 153 " --> pdb=" O CYS D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 165 Processing helix chain 'D' and resid 166 through 184 Processing helix chain 'D' and resid 196 through 210 Processing helix chain 'D' and resid 215 through 228 Processing helix chain 'D' and resid 228 through 255 Processing helix chain 'D' and resid 263 through 276 Processing helix chain 'D' and resid 287 through 329 removed outlier: 3.781A pdb=" N LEU D 299 " --> pdb=" O ALA D 295 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ILE D 300 " --> pdb=" O THR D 296 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER D 303 " --> pdb=" O LEU D 299 " (cutoff:3.500A) Proline residue: D 308 - end of helix Processing helix chain 'D' and resid 332 through 350 Processing helix chain 'D' and resid 357 through 366 Processing helix chain 'D' and resid 536 through 558 Processing helix chain 'D' and resid 563 through 578 removed outlier: 3.845A pdb=" N VAL D 567 " --> pdb=" O ASP D 563 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 21 Processing helix chain 'E' and resid 29 through 41 Processing helix chain 'E' and resid 45 through 57 Processing helix chain 'E' and resid 66 through 75 Processing helix chain 'E' and resid 76 through 80 Processing helix chain 'E' and resid 82 through 94 Processing helix chain 'E' and resid 103 through 111 removed outlier: 3.649A pdb=" N THR E 111 " --> pdb=" O ARG E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 130 Processing helix chain 'E' and resid 138 through 146 removed outlier: 3.977A pdb=" N MET E 146 " --> pdb=" O PHE E 142 " (cutoff:3.500A) Processing helix chain 'F' and resid 7 through 21 Processing helix chain 'F' and resid 29 through 41 Processing helix chain 'F' and resid 45 through 57 Processing helix chain 'F' and resid 66 through 75 Processing helix chain 'F' and resid 76 through 80 Processing helix chain 'F' and resid 82 through 94 Processing helix chain 'F' and resid 103 through 111 removed outlier: 3.653A pdb=" N THR F 111 " --> pdb=" O ARG F 107 " (cutoff:3.500A) Processing helix chain 'F' and resid 118 through 130 Processing helix chain 'F' and resid 138 through 146 removed outlier: 3.975A pdb=" N MET F 146 " --> pdb=" O PHE F 142 " (cutoff:3.500A) Processing helix chain 'G' and resid 71 through 86 Processing helix chain 'G' and resid 91 through 114 removed outlier: 4.101A pdb=" N TYR G 95 " --> pdb=" O TRP G 91 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N HIS G 96 " --> pdb=" O ALA G 92 " (cutoff:3.500A) Processing helix chain 'G' and resid 118 through 148 removed outlier: 3.910A pdb=" N ILE G 128 " --> pdb=" O GLY G 124 " (cutoff:3.500A) Processing helix chain 'G' and resid 149 through 154 removed outlier: 4.376A pdb=" N CYS G 152 " --> pdb=" O GLY G 149 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N ARG G 153 " --> pdb=" O CYS G 150 " (cutoff:3.500A) Processing helix chain 'G' and resid 155 through 165 Processing helix chain 'G' and resid 166 through 184 Processing helix chain 'G' and resid 196 through 210 Processing helix chain 'G' and resid 215 through 228 Processing helix chain 'G' and resid 228 through 255 Processing helix chain 'G' and resid 263 through 276 Processing helix chain 'G' and resid 287 through 329 removed outlier: 3.789A pdb=" N LEU G 299 " --> pdb=" O ALA G 295 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ILE G 300 " --> pdb=" O THR G 296 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER G 303 " --> pdb=" O LEU G 299 " (cutoff:3.500A) Proline residue: G 308 - end of helix Processing helix chain 'G' and resid 332 through 350 Processing helix chain 'G' and resid 357 through 366 Processing helix chain 'G' and resid 536 through 558 Processing helix chain 'G' and resid 563 through 578 removed outlier: 3.841A pdb=" N VAL G 567 " --> pdb=" O ASP G 563 " (cutoff:3.500A) Processing helix chain 'H' and resid 7 through 21 Processing helix chain 'H' and resid 29 through 41 Processing helix chain 'H' and resid 45 through 57 Processing helix chain 'H' and resid 65 through 75 removed outlier: 3.535A pdb=" N PHE H 69 " --> pdb=" O ASP H 65 " (cutoff:3.500A) Processing helix chain 'H' and resid 76 through 80 Processing helix chain 'H' and resid 82 through 94 Processing helix chain 'H' and resid 103 through 111 removed outlier: 3.652A pdb=" N THR H 111 " --> pdb=" O ARG H 107 " (cutoff:3.500A) Processing helix chain 'H' and resid 118 through 130 Processing helix chain 'H' and resid 138 through 146 removed outlier: 3.977A pdb=" N MET H 146 " --> pdb=" O PHE H 142 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 27 through 28 Processing sheet with id=AA2, first strand: chain 'C' and resid 101 through 102 Processing sheet with id=AA3, first strand: chain 'E' and resid 27 through 28 Processing sheet with id=AA4, first strand: chain 'E' and resid 101 through 102 Processing sheet with id=AA5, first strand: chain 'F' and resid 27 through 28 Processing sheet with id=AA6, first strand: chain 'F' and resid 101 through 102 Processing sheet with id=AA7, first strand: chain 'H' and resid 101 through 102 1138 hydrogen bonds defined for protein. 3357 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.59 Time building geometry restraints manager: 3.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 15216 1.03 - 1.23: 52 1.23 - 1.42: 6920 1.42 - 1.62: 8828 1.62 - 1.81: 148 Bond restraints: 31164 Sorted by residual: bond pdb=" C09 9MF G 801 " pdb=" N08 9MF G 801 " ideal model delta sigma weight residual 1.352 1.452 -0.100 2.00e-02 2.50e+03 2.51e+01 bond pdb=" C09 9MF D 801 " pdb=" N08 9MF D 801 " ideal model delta sigma weight residual 1.352 1.452 -0.100 2.00e-02 2.50e+03 2.50e+01 bond pdb=" C09 9MF B 801 " pdb=" N08 9MF B 801 " ideal model delta sigma weight residual 1.352 1.452 -0.100 2.00e-02 2.50e+03 2.50e+01 bond pdb=" C09 9MF A 802 " pdb=" N08 9MF A 802 " ideal model delta sigma weight residual 1.352 1.451 -0.099 2.00e-02 2.50e+03 2.46e+01 bond pdb=" C09 9MF A 801 " pdb=" N08 9MF A 801 " ideal model delta sigma weight residual 1.352 1.449 -0.097 2.00e-02 2.50e+03 2.36e+01 ... (remaining 31159 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 55593 2.04 - 4.08: 310 4.08 - 6.12: 41 6.12 - 8.16: 12 8.16 - 10.21: 8 Bond angle restraints: 55964 Sorted by residual: angle pdb=" N08 9MF D 802 " pdb=" C09 9MF D 802 " pdb=" O11 9MF D 802 " ideal model delta sigma weight residual 110.34 120.55 -10.21 3.00e+00 1.11e-01 1.16e+01 angle pdb=" N08 9MF A 801 " pdb=" C09 9MF A 801 " pdb=" O11 9MF A 801 " ideal model delta sigma weight residual 110.34 120.52 -10.18 3.00e+00 1.11e-01 1.15e+01 angle pdb=" N08 9MF B 802 " pdb=" C09 9MF B 802 " pdb=" O11 9MF B 802 " ideal model delta sigma weight residual 110.34 120.51 -10.17 3.00e+00 1.11e-01 1.15e+01 angle pdb=" N08 9MF G 802 " pdb=" C09 9MF G 802 " pdb=" O11 9MF G 802 " ideal model delta sigma weight residual 110.34 120.46 -10.12 3.00e+00 1.11e-01 1.14e+01 angle pdb=" N08 9MF B 801 " pdb=" C09 9MF B 801 " pdb=" O11 9MF B 801 " ideal model delta sigma weight residual 110.34 120.33 -9.99 3.00e+00 1.11e-01 1.11e+01 ... (remaining 55959 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.91: 12587 16.91 - 33.83: 1272 33.83 - 50.74: 462 50.74 - 67.66: 167 67.66 - 84.57: 28 Dihedral angle restraints: 14516 sinusoidal: 7740 harmonic: 6776 Sorted by residual: dihedral pdb=" CA ASP H 81 " pdb=" CB ASP H 81 " pdb=" CG ASP H 81 " pdb=" OD1 ASP H 81 " ideal model delta sinusoidal sigma weight residual -30.00 -89.14 59.14 1 2.00e+01 2.50e-03 1.17e+01 dihedral pdb=" CA ASP F 81 " pdb=" CB ASP F 81 " pdb=" CG ASP F 81 " pdb=" OD1 ASP F 81 " ideal model delta sinusoidal sigma weight residual -30.00 -89.10 59.10 1 2.00e+01 2.50e-03 1.17e+01 dihedral pdb=" CA ASP E 81 " pdb=" CB ASP E 81 " pdb=" CG ASP E 81 " pdb=" OD1 ASP E 81 " ideal model delta sinusoidal sigma weight residual -30.00 -89.06 59.06 1 2.00e+01 2.50e-03 1.17e+01 ... (remaining 14513 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 1486 0.025 - 0.050: 522 0.050 - 0.075: 224 0.075 - 0.100: 59 0.100 - 0.125: 25 Chirality restraints: 2316 Sorted by residual: chirality pdb=" CA ILE F 64 " pdb=" N ILE F 64 " pdb=" C ILE F 64 " pdb=" CB ILE F 64 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.91e-01 chirality pdb=" CA ILE C 64 " pdb=" N ILE C 64 " pdb=" C ILE C 64 " pdb=" CB ILE C 64 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.84e-01 chirality pdb=" CA ILE H 64 " pdb=" N ILE H 64 " pdb=" C ILE H 64 " pdb=" CB ILE H 64 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.76e-01 ... (remaining 2313 not shown) Planarity restraints: 4560 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C04 9MF A 801 " 0.010 2.00e-02 2.50e+03 1.69e-02 2.85e+00 pdb=" C15 9MF A 801 " 0.010 2.00e-02 2.50e+03 pdb=" C18 9MF A 801 " 0.010 2.00e-02 2.50e+03 pdb=" N14 9MF A 801 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C04 9MF G 802 " 0.010 2.00e-02 2.50e+03 1.67e-02 2.80e+00 pdb=" C15 9MF G 802 " 0.010 2.00e-02 2.50e+03 pdb=" C18 9MF G 802 " 0.010 2.00e-02 2.50e+03 pdb=" N14 9MF G 802 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C04 9MF B 802 " 0.009 2.00e-02 2.50e+03 1.61e-02 2.61e+00 pdb=" C15 9MF B 802 " 0.009 2.00e-02 2.50e+03 pdb=" C18 9MF B 802 " 0.009 2.00e-02 2.50e+03 pdb=" N14 9MF B 802 " -0.028 2.00e-02 2.50e+03 ... (remaining 4557 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.21: 2342 2.21 - 2.81: 64989 2.81 - 3.40: 88081 3.40 - 4.00: 110831 4.00 - 4.60: 171192 Nonbonded interactions: 437435 Sorted by model distance: nonbonded pdb=" O VAL F 143 " pdb=" HG1 THR F 147 " model vdw 1.609 2.450 nonbonded pdb=" O VAL C 143 " pdb=" HG1 THR C 147 " model vdw 1.609 2.450 nonbonded pdb=" O VAL E 143 " pdb=" HG1 THR E 147 " model vdw 1.610 2.450 nonbonded pdb=" O VAL H 143 " pdb=" HG1 THR H 147 " model vdw 1.611 2.450 nonbonded pdb=" OE1 GLU D 254 " pdb="HD22 ASN D 258 " model vdw 1.665 2.450 ... (remaining 437430 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'D' selection = chain 'G' } ncs_group { reference = chain 'C' selection = chain 'E' selection = chain 'F' 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: 0.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.130 Extract box with map and model: 0.350 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 24.800 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6716 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 : 0.005 0.100 15920 Z= 0.235 Angle : 0.586 10.205 21480 Z= 0.288 Chirality : 0.033 0.125 2316 Planarity : 0.003 0.040 2708 Dihedral : 17.293 84.574 5776 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.93 % Allowed : 24.26 % Favored : 74.81 % 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: 2.30 (0.20), residues: 1868 helix: 1.93 (0.14), residues: 1484 sheet: None (None), residues: 0 loop : 0.01 (0.38), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 207 TYR 0.011 0.001 TYR D 571 PHE 0.012 0.001 PHE G 304 TRP 0.009 0.001 TRP G 288 HIS 0.001 0.000 HIS B 328 Details of bonding type rmsd covalent geometry : bond 0.00482 (15920) covalent geometry : angle 0.58554 (21480) hydrogen bonds : bond 0.10759 ( 1138) hydrogen bonds : angle 5.27662 ( 3357) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3736 Ramachandran restraints generated. 1868 Oldfield, 0 Emsley, 1868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3736 Ramachandran restraints generated. 1868 Oldfield, 0 Emsley, 1868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 180 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 ARG cc_start: 0.3126 (ptm-80) cc_final: 0.1659 (tpm170) REVERT: A 152 CYS cc_start: 0.6194 (m) cc_final: 0.5793 (t) REVERT: A 198 ARG cc_start: 0.4769 (mtt180) cc_final: 0.4435 (tpt-90) REVERT: A 298 THR cc_start: 0.9026 (OUTLIER) cc_final: 0.8684 (m) REVERT: A 327 LYS cc_start: 0.8014 (tmmm) cc_final: 0.7808 (tttt) REVERT: B 116 LYS cc_start: 0.8937 (tppp) cc_final: 0.8733 (mmtm) REVERT: B 161 LEU cc_start: 0.8048 (tt) cc_final: 0.7724 (tm) REVERT: B 289 ASN cc_start: 0.8064 (m-40) cc_final: 0.7714 (m-40) REVERT: B 298 THR cc_start: 0.9093 (OUTLIER) cc_final: 0.8858 (m) REVERT: B 578 MET cc_start: 0.2671 (ttt) cc_final: 0.2469 (ttt) REVERT: C 110 MET cc_start: 0.3829 (tpp) cc_final: 0.2776 (mmp) REVERT: D 80 PHE cc_start: 0.8343 (t80) cc_final: 0.8060 (t80) REVERT: D 130 GLU cc_start: 0.7716 (tt0) cc_final: 0.7430 (tt0) REVERT: E 110 MET cc_start: 0.4048 (tpp) cc_final: 0.2846 (mmp) REVERT: F 76 LYS cc_start: -0.1698 (OUTLIER) cc_final: -0.2514 (tttm) REVERT: F 110 MET cc_start: 0.3968 (tpp) cc_final: 0.2558 (mmp) REVERT: G 198 ARG cc_start: 0.5272 (mtt180) cc_final: 0.4979 (tpt-90) REVERT: G 298 THR cc_start: 0.8852 (OUTLIER) cc_final: 0.8597 (m) REVERT: G 344 TRP cc_start: 0.4236 (t-100) cc_final: 0.3947 (t-100) REVERT: H 110 MET cc_start: 0.4008 (tpp) cc_final: 0.2393 (mmp) outliers start: 15 outliers final: 3 residues processed: 193 average time/residue: 1.2197 time to fit residues: 259.0144 Evaluate side-chains 166 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 159 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain C residue 76 LYS Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain F residue 76 LYS Chi-restraints excluded: chain G residue 298 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 30.0000 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 30.0000 chunk 130 optimal weight: 40.0000 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 40.0000 chunk 91 optimal weight: 9.9990 chunk 149 optimal weight: 9.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 350 ASN ** H 50 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 = 0.4767 r_free = 0.4767 target = 0.244273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.123885 restraints weight = 52598.662| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 2.22 r_work: 0.3157 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7100 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.080 15920 Z= 0.429 Angle : 0.643 7.427 21480 Z= 0.345 Chirality : 0.044 0.171 2316 Planarity : 0.006 0.085 2708 Dihedral : 6.939 60.521 2187 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.47 % Allowed : 23.51 % Favored : 73.02 % 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: 2.04 (0.20), residues: 1868 helix: 1.75 (0.13), residues: 1484 sheet: None (None), residues: 0 loop : -0.10 (0.38), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 144 TYR 0.020 0.002 TYR A 237 PHE 0.025 0.002 PHE B 304 TRP 0.013 0.002 TRP A 344 HIS 0.005 0.001 HIS B 228 Details of bonding type rmsd covalent geometry : bond 0.00977 (15920) covalent geometry : angle 0.64319 (21480) hydrogen bonds : bond 0.04994 ( 1138) hydrogen bonds : angle 4.58163 ( 3357) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3736 Ramachandran restraints generated. 1868 Oldfield, 0 Emsley, 1868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3736 Ramachandran restraints generated. 1868 Oldfield, 0 Emsley, 1868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 153 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 CYS cc_start: 0.6494 (m) cc_final: 0.6098 (t) REVERT: A 198 ARG cc_start: 0.5422 (mtt180) cc_final: 0.4808 (tpt-90) REVERT: A 257 GLU cc_start: 0.8825 (pm20) cc_final: 0.8604 (pm20) REVERT: A 360 TRP cc_start: -0.1415 (m100) cc_final: -0.1862 (m-10) REVERT: B 214 ARG cc_start: 0.8741 (OUTLIER) cc_final: 0.7993 (ttp80) REVERT: B 289 ASN cc_start: 0.8627 (OUTLIER) cc_final: 0.7942 (m-40) REVERT: C 110 MET cc_start: 0.4087 (tpp) cc_final: 0.2919 (mmp) REVERT: C 141 GLU cc_start: 0.4645 (OUTLIER) cc_final: 0.3889 (pp20) REVERT: D 257 GLU cc_start: 0.8884 (pm20) cc_final: 0.8649 (pm20) REVERT: E 110 MET cc_start: 0.4276 (tpp) cc_final: 0.3057 (mmp) REVERT: E 141 GLU cc_start: 0.3961 (OUTLIER) cc_final: 0.3164 (tm-30) REVERT: F 110 MET cc_start: 0.3990 (tpp) cc_final: 0.2621 (mmp) REVERT: F 141 GLU cc_start: 0.4817 (OUTLIER) cc_final: 0.4016 (pp20) REVERT: G 198 ARG cc_start: 0.5858 (mtt180) cc_final: 0.5383 (tpt-90) REVERT: G 257 GLU cc_start: 0.8863 (pm20) cc_final: 0.8634 (pm20) REVERT: H 110 MET cc_start: 0.4169 (tpp) cc_final: 0.2678 (mmp) REVERT: H 141 GLU cc_start: 0.4366 (OUTLIER) cc_final: 0.3586 (tm-30) outliers start: 56 outliers final: 15 residues processed: 186 average time/residue: 1.0731 time to fit residues: 222.8340 Evaluate side-chains 166 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 145 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 289 ASN Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 289 ASN Chi-restraints excluded: chain C residue 141 GLU Chi-restraints excluded: chain D residue 122 SER Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain E residue 141 GLU Chi-restraints excluded: chain F residue 82 SER Chi-restraints excluded: chain F residue 141 GLU Chi-restraints excluded: chain G residue 133 THR Chi-restraints excluded: chain G residue 161 LEU Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain G residue 575 HIS Chi-restraints excluded: chain H residue 141 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 171 optimal weight: 20.0000 chunk 80 optimal weight: 10.0000 chunk 96 optimal weight: 0.6980 chunk 166 optimal weight: 5.9990 chunk 121 optimal weight: 9.9990 chunk 125 optimal weight: 20.0000 chunk 59 optimal weight: 8.9990 chunk 138 optimal weight: 5.9990 chunk 160 optimal weight: 0.5980 chunk 145 optimal weight: 0.6980 chunk 26 optimal weight: 5.9990 overall best weight: 2.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4789 r_free = 0.4789 target = 0.247205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.134957 restraints weight = 51850.034| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 4.35 r_work: 0.3201 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 15920 Z= 0.212 Angle : 0.532 6.147 21480 Z= 0.283 Chirality : 0.035 0.127 2316 Planarity : 0.004 0.046 2708 Dihedral : 6.422 58.318 2172 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.54 % Allowed : 25.19 % Favored : 72.28 % 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: 2.40 (0.20), residues: 1868 helix: 2.03 (0.13), residues: 1468 sheet: None (None), residues: 0 loop : 0.02 (0.37), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 144 TYR 0.011 0.001 TYR A 237 PHE 0.016 0.001 PHE A 304 TRP 0.013 0.001 TRP A 344 HIS 0.002 0.001 HIS D 228 Details of bonding type rmsd covalent geometry : bond 0.00472 (15920) covalent geometry : angle 0.53176 (21480) hydrogen bonds : bond 0.04086 ( 1138) hydrogen bonds : angle 4.35104 ( 3357) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3736 Ramachandran restraints generated. 1868 Oldfield, 0 Emsley, 1868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3736 Ramachandran restraints generated. 1868 Oldfield, 0 Emsley, 1868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 160 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 ARG cc_start: 0.5299 (mtt180) cc_final: 0.4746 (tpt-90) REVERT: A 289 ASN cc_start: 0.8671 (m-40) cc_final: 0.8150 (m-40) REVERT: B 161 LEU cc_start: 0.8150 (tt) cc_final: 0.7759 (tt) REVERT: B 214 ARG cc_start: 0.8739 (OUTLIER) cc_final: 0.8194 (mtp85) REVERT: B 289 ASN cc_start: 0.8662 (OUTLIER) cc_final: 0.8090 (OUTLIER) REVERT: B 332 ARG cc_start: 0.4048 (OUTLIER) cc_final: 0.3757 (mtm180) REVERT: C 110 MET cc_start: 0.4045 (tpp) cc_final: 0.2917 (mmp) REVERT: C 141 GLU cc_start: 0.4645 (OUTLIER) cc_final: 0.4007 (tm-30) REVERT: D 257 GLU cc_start: 0.8884 (pm20) cc_final: 0.8581 (pm20) REVERT: D 289 ASN cc_start: 0.8466 (m-40) cc_final: 0.8160 (m110) REVERT: D 578 MET cc_start: 0.3156 (ttt) cc_final: 0.2873 (ttt) REVERT: E 110 MET cc_start: 0.4402 (tpp) cc_final: 0.3113 (mmp) REVERT: E 141 GLU cc_start: 0.4023 (OUTLIER) cc_final: 0.3365 (tm-30) REVERT: F 110 MET cc_start: 0.4064 (tpp) cc_final: 0.2643 (mmp) REVERT: G 198 ARG cc_start: 0.5664 (mtt180) cc_final: 0.5206 (tpt-90) REVERT: G 257 GLU cc_start: 0.8909 (pm20) cc_final: 0.8650 (pm20) REVERT: G 289 ASN cc_start: 0.8664 (OUTLIER) cc_final: 0.7889 (m-40) REVERT: H 110 MET cc_start: 0.4512 (tpp) cc_final: 0.3045 (mmp) REVERT: H 141 GLU cc_start: 0.4459 (OUTLIER) cc_final: 0.3707 (tm-30) outliers start: 41 outliers final: 21 residues processed: 191 average time/residue: 1.3106 time to fit residues: 279.2157 Evaluate side-chains 182 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 155 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 575 HIS Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 289 ASN Chi-restraints excluded: chain B residue 332 ARG Chi-restraints excluded: chain B residue 575 HIS Chi-restraints excluded: chain C residue 90 PHE Chi-restraints excluded: chain C residue 141 GLU Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain E residue 90 PHE Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 141 GLU Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain G residue 133 THR Chi-restraints excluded: chain G residue 161 LEU Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain G residue 289 ASN Chi-restraints excluded: chain G residue 575 HIS Chi-restraints excluded: chain H residue 90 PHE Chi-restraints excluded: chain H residue 141 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 122 optimal weight: 50.0000 chunk 76 optimal weight: 20.0000 chunk 138 optimal weight: 20.0000 chunk 115 optimal weight: 7.9990 chunk 154 optimal weight: 4.9990 chunk 73 optimal weight: 20.0000 chunk 117 optimal weight: 50.0000 chunk 177 optimal weight: 20.0000 chunk 61 optimal weight: 20.0000 chunk 33 optimal weight: 10.0000 chunk 131 optimal weight: 50.0000 overall best weight: 12.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4723 r_free = 0.4723 target = 0.238713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.118866 restraints weight = 53044.431| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 2.20 r_work: 0.3105 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.019 0.143 15920 Z= 0.803 Angle : 0.838 9.779 21480 Z= 0.459 Chirality : 0.066 0.266 2316 Planarity : 0.009 0.159 2708 Dihedral : 7.928 83.076 2172 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 5.32 % Allowed : 24.26 % Favored : 70.42 % 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: 0.67 (0.19), residues: 1868 helix: 0.78 (0.13), residues: 1480 sheet: None (None), residues: 0 loop : -0.52 (0.36), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 201 TYR 0.026 0.004 TYR A 237 PHE 0.033 0.003 PHE G 304 TRP 0.019 0.004 TRP G 146 HIS 0.007 0.002 HIS A 228 Details of bonding type rmsd covalent geometry : bond 0.01854 (15920) covalent geometry : angle 0.83828 (21480) hydrogen bonds : bond 0.06066 ( 1138) hydrogen bonds : angle 5.01042 ( 3357) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3736 Ramachandran restraints generated. 1868 Oldfield, 0 Emsley, 1868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3736 Ramachandran restraints generated. 1868 Oldfield, 0 Emsley, 1868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 150 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 ARG cc_start: 0.7737 (OUTLIER) cc_final: 0.7468 (ttp80) REVERT: A 214 ARG cc_start: 0.8766 (OUTLIER) cc_final: 0.8357 (tpp80) REVERT: B 214 ARG cc_start: 0.8790 (OUTLIER) cc_final: 0.8371 (tpp80) REVERT: B 578 MET cc_start: 0.3084 (ttt) cc_final: 0.2801 (ttt) REVERT: C 110 MET cc_start: 0.4247 (tpp) cc_final: 0.3031 (mmp) REVERT: C 141 GLU cc_start: 0.4269 (OUTLIER) cc_final: 0.3515 (tm-30) REVERT: D 120 LYS cc_start: 0.8151 (OUTLIER) cc_final: 0.7923 (mptt) REVERT: D 123 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7498 (pt0) REVERT: D 158 ARG cc_start: 0.6887 (tpm170) cc_final: 0.6619 (mmm-85) REVERT: D 214 ARG cc_start: 0.8656 (tpp80) cc_final: 0.8072 (mtt90) REVERT: E 141 GLU cc_start: 0.4165 (OUTLIER) cc_final: 0.3413 (tm-30) REVERT: F 110 MET cc_start: 0.4159 (tpp) cc_final: 0.2890 (mmp) REVERT: F 141 GLU cc_start: 0.4672 (pt0) cc_final: 0.4230 (tm-30) REVERT: G 123 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7607 (pt0) REVERT: G 210 ARG cc_start: 0.7461 (OUTLIER) cc_final: 0.7204 (ttp80) REVERT: G 214 ARG cc_start: 0.8637 (tpp80) cc_final: 0.8101 (mtt90) REVERT: H 145 MET cc_start: 0.0355 (ttp) cc_final: 0.0144 (ttp) outliers start: 86 outliers final: 41 residues processed: 208 average time/residue: 1.2040 time to fit residues: 278.9957 Evaluate side-chains 202 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 152 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 289 ASN Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 257 GLU Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 289 ASN Chi-restraints excluded: chain B residue 358 SER Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain C residue 90 PHE Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 141 GLU Chi-restraints excluded: chain D residue 120 LYS Chi-restraints excluded: chain D residue 122 SER Chi-restraints excluded: chain D residue 123 GLU Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 210 ARG Chi-restraints excluded: chain D residue 277 THR Chi-restraints excluded: chain D residue 358 SER Chi-restraints excluded: chain D residue 359 THR Chi-restraints excluded: chain E residue 90 PHE Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 141 GLU Chi-restraints excluded: chain F residue 6 THR Chi-restraints excluded: chain G residue 122 SER Chi-restraints excluded: chain G residue 123 GLU Chi-restraints excluded: chain G residue 133 THR Chi-restraints excluded: chain G residue 161 LEU Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain G residue 177 ILE Chi-restraints excluded: chain G residue 210 ARG Chi-restraints excluded: chain G residue 277 THR Chi-restraints excluded: chain G residue 289 ASN Chi-restraints excluded: chain G residue 358 SER Chi-restraints excluded: chain G residue 359 THR Chi-restraints excluded: chain H residue 90 PHE Chi-restraints excluded: chain H residue 109 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 170 optimal weight: 6.9990 chunk 140 optimal weight: 20.0000 chunk 149 optimal weight: 5.9990 chunk 155 optimal weight: 0.5980 chunk 26 optimal weight: 10.0000 chunk 166 optimal weight: 4.9990 chunk 184 optimal weight: 7.9990 chunk 79 optimal weight: 6.9990 chunk 52 optimal weight: 0.7980 chunk 106 optimal weight: 7.9990 chunk 67 optimal weight: 50.0000 overall best weight: 3.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4763 r_free = 0.4763 target = 0.244364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.125172 restraints weight = 52553.998| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 2.19 r_work: 0.3187 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 moved from start: 0.3151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 15920 Z= 0.285 Angle : 0.585 6.609 21480 Z= 0.315 Chirality : 0.037 0.132 2316 Planarity : 0.005 0.054 2708 Dihedral : 6.731 63.266 2172 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 3.40 % Allowed : 26.55 % Favored : 70.05 % 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: 1.23 (0.19), residues: 1868 helix: 1.21 (0.13), residues: 1480 sheet: None (None), residues: 0 loop : -0.46 (0.36), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 165 TYR 0.013 0.002 TYR D 571 PHE 0.018 0.001 PHE G 304 TRP 0.014 0.002 TRP A 344 HIS 0.003 0.001 HIS A 228 Details of bonding type rmsd covalent geometry : bond 0.00641 (15920) covalent geometry : angle 0.58469 (21480) hydrogen bonds : bond 0.04473 ( 1138) hydrogen bonds : angle 4.57301 ( 3357) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3736 Ramachandran restraints generated. 1868 Oldfield, 0 Emsley, 1868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3736 Ramachandran restraints generated. 1868 Oldfield, 0 Emsley, 1868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 158 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 CYS cc_start: 0.6906 (m) cc_final: 0.6247 (t) REVERT: A 210 ARG cc_start: 0.7545 (OUTLIER) cc_final: 0.7236 (ttp80) REVERT: A 214 ARG cc_start: 0.8706 (OUTLIER) cc_final: 0.8104 (mtp85) REVERT: A 289 ASN cc_start: 0.8722 (OUTLIER) cc_final: 0.7875 (m-40) REVERT: B 214 ARG cc_start: 0.8780 (OUTLIER) cc_final: 0.8154 (mtp85) REVERT: B 289 ASN cc_start: 0.8688 (OUTLIER) cc_final: 0.8020 (p0) REVERT: B 578 MET cc_start: 0.3168 (ttt) cc_final: 0.2855 (ttt) REVERT: C 110 MET cc_start: 0.4225 (tpp) cc_final: 0.3021 (mmp) REVERT: C 145 MET cc_start: -0.0698 (pp-130) cc_final: -0.1341 (ttp) REVERT: D 158 ARG cc_start: 0.6886 (tpm170) cc_final: 0.6668 (mmm-85) REVERT: D 214 ARG cc_start: 0.8637 (tpp80) cc_final: 0.8091 (mtp85) REVERT: E 141 GLU cc_start: 0.4074 (OUTLIER) cc_final: 0.3441 (tm-30) REVERT: F 110 MET cc_start: 0.4247 (tpp) cc_final: 0.2848 (mmp) REVERT: G 214 ARG cc_start: 0.8620 (tpp80) cc_final: 0.8003 (mtt90) REVERT: G 289 ASN cc_start: 0.8742 (OUTLIER) cc_final: 0.7942 (p0) outliers start: 55 outliers final: 20 residues processed: 192 average time/residue: 1.2049 time to fit residues: 256.4199 Evaluate side-chains 179 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 152 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 174 MET Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 289 ASN Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 289 ASN Chi-restraints excluded: chain B residue 358 SER Chi-restraints excluded: chain C residue 90 PHE Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 361 GLN Chi-restraints excluded: chain E residue 90 PHE Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 141 GLU Chi-restraints excluded: chain G residue 133 THR Chi-restraints excluded: chain G residue 161 LEU Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain G residue 171 ILE Chi-restraints excluded: chain G residue 289 ASN Chi-restraints excluded: chain G residue 358 SER Chi-restraints excluded: chain H residue 90 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 71 optimal weight: 10.0000 chunk 182 optimal weight: 20.0000 chunk 98 optimal weight: 0.5980 chunk 86 optimal weight: 0.8980 chunk 94 optimal weight: 1.9990 chunk 130 optimal weight: 8.9990 chunk 139 optimal weight: 6.9990 chunk 49 optimal weight: 0.8980 chunk 132 optimal weight: 50.0000 chunk 32 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4790 r_free = 0.4790 target = 0.247517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.130507 restraints weight = 52001.630| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 2.12 r_work: 0.3213 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7103 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 15920 Z= 0.150 Angle : 0.516 7.261 21480 Z= 0.274 Chirality : 0.034 0.127 2316 Planarity : 0.004 0.047 2708 Dihedral : 6.378 58.126 2172 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.23 % Allowed : 27.97 % Favored : 69.80 % 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: 1.96 (0.20), residues: 1868 helix: 1.74 (0.13), residues: 1480 sheet: None (None), residues: 0 loop : -0.30 (0.36), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 165 TYR 0.015 0.001 TYR D 571 PHE 0.009 0.001 PHE A 304 TRP 0.013 0.001 TRP A 344 HIS 0.003 0.001 HIS G 357 Details of bonding type rmsd covalent geometry : bond 0.00326 (15920) covalent geometry : angle 0.51626 (21480) hydrogen bonds : bond 0.03812 ( 1138) hydrogen bonds : angle 4.30347 ( 3357) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3736 Ramachandran restraints generated. 1868 Oldfield, 0 Emsley, 1868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3736 Ramachandran restraints generated. 1868 Oldfield, 0 Emsley, 1868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 165 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 CYS cc_start: 0.7020 (m) cc_final: 0.6340 (t) REVERT: A 198 ARG cc_start: 0.5529 (mtt180) cc_final: 0.4928 (tpt-90) REVERT: A 214 ARG cc_start: 0.8679 (tpp80) cc_final: 0.8042 (mtp85) REVERT: B 214 ARG cc_start: 0.8754 (tpp80) cc_final: 0.8176 (mtp85) REVERT: B 578 MET cc_start: 0.3242 (ttt) cc_final: 0.2912 (ttt) REVERT: D 214 ARG cc_start: 0.8659 (tpp80) cc_final: 0.8098 (mtp85) REVERT: E 141 GLU cc_start: 0.4121 (OUTLIER) cc_final: 0.3452 (tm-30) REVERT: F 110 MET cc_start: 0.4167 (tpp) cc_final: 0.2770 (mmp) REVERT: G 198 ARG cc_start: 0.5682 (mtt180) cc_final: 0.5193 (tpt-90) REVERT: G 214 ARG cc_start: 0.8627 (tpp80) cc_final: 0.8027 (mtt90) outliers start: 36 outliers final: 20 residues processed: 184 average time/residue: 1.3633 time to fit residues: 278.3330 Evaluate side-chains 181 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 160 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 289 ASN Chi-restraints excluded: chain A residue 575 HIS Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 165 ARG Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 289 ASN Chi-restraints excluded: chain B residue 575 HIS Chi-restraints excluded: chain C residue 90 PHE Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain E residue 90 PHE Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 141 GLU Chi-restraints excluded: chain G residue 133 THR Chi-restraints excluded: chain G residue 161 LEU Chi-restraints excluded: chain G residue 289 ASN Chi-restraints excluded: chain G residue 575 HIS Chi-restraints excluded: chain H residue 90 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 20 optimal weight: 0.9980 chunk 113 optimal weight: 50.0000 chunk 25 optimal weight: 10.0000 chunk 2 optimal weight: 4.9990 chunk 26 optimal weight: 20.0000 chunk 70 optimal weight: 30.0000 chunk 74 optimal weight: 10.0000 chunk 64 optimal weight: 20.0000 chunk 90 optimal weight: 2.9990 chunk 166 optimal weight: 20.0000 chunk 182 optimal weight: 20.0000 overall best weight: 5.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4762 r_free = 0.4762 target = 0.244079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.125365 restraints weight = 52434.641| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 2.13 r_work: 0.3166 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7208 moved from start: 0.3304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.070 15920 Z= 0.388 Angle : 0.613 7.296 21480 Z= 0.329 Chirality : 0.042 0.158 2316 Planarity : 0.005 0.059 2708 Dihedral : 6.833 63.240 2172 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 3.16 % Allowed : 27.10 % Favored : 69.74 % 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: 1.60 (0.19), residues: 1868 helix: 1.51 (0.13), residues: 1476 sheet: None (None), residues: 0 loop : -0.52 (0.35), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 165 TYR 0.016 0.002 TYR D 571 PHE 0.021 0.002 PHE D 304 TRP 0.013 0.002 TRP G 344 HIS 0.004 0.001 HIS A 228 Details of bonding type rmsd covalent geometry : bond 0.00886 (15920) covalent geometry : angle 0.61338 (21480) hydrogen bonds : bond 0.04565 ( 1138) hydrogen bonds : angle 4.51391 ( 3357) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3736 Ramachandran restraints generated. 1868 Oldfield, 0 Emsley, 1868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3736 Ramachandran restraints generated. 1868 Oldfield, 0 Emsley, 1868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 155 time to evaluate : 0.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 CYS cc_start: 0.6995 (m) cc_final: 0.6348 (t) REVERT: A 198 ARG cc_start: 0.5619 (mtt180) cc_final: 0.5115 (tpt-90) REVERT: B 214 ARG cc_start: 0.8775 (OUTLIER) cc_final: 0.8149 (mtp85) REVERT: B 578 MET cc_start: 0.3276 (ttt) cc_final: 0.2954 (ttt) REVERT: C 141 GLU cc_start: 0.4082 (OUTLIER) cc_final: 0.3605 (tm-30) REVERT: C 145 MET cc_start: -0.0922 (pp-130) cc_final: -0.1484 (ttp) REVERT: D 123 GLU cc_start: 0.7555 (OUTLIER) cc_final: 0.7333 (pt0) REVERT: D 214 ARG cc_start: 0.8660 (tpp80) cc_final: 0.8025 (mtt90) REVERT: E 141 GLU cc_start: 0.4043 (OUTLIER) cc_final: 0.3383 (tm-30) REVERT: F 110 MET cc_start: 0.4042 (tpp) cc_final: 0.2766 (mmp) REVERT: G 214 ARG cc_start: 0.8655 (tpp80) cc_final: 0.8061 (mtt90) outliers start: 51 outliers final: 30 residues processed: 187 average time/residue: 1.3365 time to fit residues: 278.1134 Evaluate side-chains 185 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 151 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 174 MET Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 289 ASN Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 289 ASN Chi-restraints excluded: chain C residue 90 PHE Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 141 GLU Chi-restraints excluded: chain D residue 123 GLU Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 210 ARG Chi-restraints excluded: chain D residue 277 THR Chi-restraints excluded: chain D residue 358 SER Chi-restraints excluded: chain D residue 361 GLN Chi-restraints excluded: chain E residue 90 PHE Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 141 GLU Chi-restraints excluded: chain F residue 6 THR Chi-restraints excluded: chain F residue 141 GLU Chi-restraints excluded: chain G residue 133 THR Chi-restraints excluded: chain G residue 161 LEU Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain G residue 171 ILE Chi-restraints excluded: chain G residue 277 THR Chi-restraints excluded: chain G residue 289 ASN Chi-restraints excluded: chain G residue 358 SER Chi-restraints excluded: chain H residue 90 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 182 optimal weight: 20.0000 chunk 183 optimal weight: 10.0000 chunk 92 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 28 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 15 optimal weight: 0.6980 chunk 71 optimal weight: 50.0000 chunk 157 optimal weight: 0.5980 chunk 166 optimal weight: 7.9990 chunk 179 optimal weight: 40.0000 overall best weight: 2.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4769 r_free = 0.4769 target = 0.244892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.127473 restraints weight = 52632.901| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 2.11 r_work: 0.3218 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7118 moved from start: 0.3355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 15920 Z= 0.212 Angle : 0.557 7.867 21480 Z= 0.295 Chirality : 0.036 0.129 2316 Planarity : 0.004 0.054 2708 Dihedral : 6.565 59.099 2172 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 1.98 % Allowed : 28.40 % Favored : 69.62 % 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: 1.82 (0.20), residues: 1868 helix: 1.67 (0.13), residues: 1472 sheet: None (None), residues: 0 loop : -0.44 (0.35), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 165 TYR 0.015 0.001 TYR D 571 PHE 0.014 0.001 PHE D 304 TRP 0.014 0.001 TRP A 344 HIS 0.002 0.001 HIS G 357 Details of bonding type rmsd covalent geometry : bond 0.00471 (15920) covalent geometry : angle 0.55709 (21480) hydrogen bonds : bond 0.04103 ( 1138) hydrogen bonds : angle 4.39388 ( 3357) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3736 Ramachandran restraints generated. 1868 Oldfield, 0 Emsley, 1868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3736 Ramachandran restraints generated. 1868 Oldfield, 0 Emsley, 1868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 167 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 CYS cc_start: 0.6989 (m) cc_final: 0.6342 (t) REVERT: A 198 ARG cc_start: 0.5489 (mtt180) cc_final: 0.5009 (tpt-90) REVERT: A 214 ARG cc_start: 0.8698 (tpp80) cc_final: 0.8108 (mtp85) REVERT: A 289 ASN cc_start: 0.8604 (OUTLIER) cc_final: 0.7960 (m-40) REVERT: B 214 ARG cc_start: 0.8737 (tpp80) cc_final: 0.8102 (mtp85) REVERT: B 578 MET cc_start: 0.3255 (ttt) cc_final: 0.2952 (ttt) REVERT: C 145 MET cc_start: -0.0892 (pp-130) cc_final: -0.1480 (ttp) REVERT: D 210 ARG cc_start: 0.7039 (OUTLIER) cc_final: 0.6418 (ttt90) REVERT: D 214 ARG cc_start: 0.8654 (tpp80) cc_final: 0.8081 (mtp85) REVERT: E 141 GLU cc_start: 0.3998 (OUTLIER) cc_final: 0.3362 (tm-30) REVERT: F 110 MET cc_start: 0.3981 (tpp) cc_final: 0.2739 (mmp) REVERT: G 198 ARG cc_start: 0.5647 (mtt180) cc_final: 0.5179 (tpt-90) REVERT: G 214 ARG cc_start: 0.8626 (tpp80) cc_final: 0.8002 (mtt90) REVERT: G 289 ASN cc_start: 0.8633 (OUTLIER) cc_final: 0.7794 (m-40) outliers start: 32 outliers final: 21 residues processed: 186 average time/residue: 1.1732 time to fit residues: 241.6582 Evaluate side-chains 184 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 159 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 289 ASN Chi-restraints excluded: chain A residue 575 HIS Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 165 ARG Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 289 ASN Chi-restraints excluded: chain C residue 90 PHE Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 210 ARG Chi-restraints excluded: chain D residue 361 GLN Chi-restraints excluded: chain E residue 90 PHE Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 141 GLU Chi-restraints excluded: chain G residue 133 THR Chi-restraints excluded: chain G residue 161 LEU Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain G residue 289 ASN Chi-restraints excluded: chain G residue 358 SER Chi-restraints excluded: chain G residue 575 HIS Chi-restraints excluded: chain H residue 90 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 10 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 108 optimal weight: 30.0000 chunk 121 optimal weight: 7.9990 chunk 1 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 143 optimal weight: 3.9990 chunk 114 optimal weight: 50.0000 chunk 64 optimal weight: 7.9990 chunk 122 optimal weight: 30.0000 chunk 66 optimal weight: 20.0000 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4783 r_free = 0.4783 target = 0.246723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.129413 restraints weight = 52243.181| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 2.17 r_work: 0.3247 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7156 moved from start: 0.3360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 15920 Z= 0.177 Angle : 0.547 8.517 21480 Z= 0.288 Chirality : 0.035 0.162 2316 Planarity : 0.004 0.050 2708 Dihedral : 6.505 58.414 2172 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 2.17 % Allowed : 28.34 % Favored : 69.49 % 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: 2.02 (0.20), residues: 1868 helix: 1.81 (0.13), residues: 1476 sheet: None (None), residues: 0 loop : -0.37 (0.36), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 165 TYR 0.014 0.001 TYR D 571 PHE 0.012 0.001 PHE D 304 TRP 0.016 0.001 TRP G 344 HIS 0.002 0.001 HIS G 357 Details of bonding type rmsd covalent geometry : bond 0.00392 (15920) covalent geometry : angle 0.54742 (21480) hydrogen bonds : bond 0.03947 ( 1138) hydrogen bonds : angle 4.33007 ( 3357) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3736 Ramachandran restraints generated. 1868 Oldfield, 0 Emsley, 1868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3736 Ramachandran restraints generated. 1868 Oldfield, 0 Emsley, 1868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 165 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 CYS cc_start: 0.6805 (m) cc_final: 0.6163 (t) REVERT: A 198 ARG cc_start: 0.5551 (mtt180) cc_final: 0.4952 (tpt-90) REVERT: A 214 ARG cc_start: 0.8685 (tpp80) cc_final: 0.8094 (mtp85) REVERT: A 289 ASN cc_start: 0.8616 (OUTLIER) cc_final: 0.7869 (m-40) REVERT: B 214 ARG cc_start: 0.8759 (tpp80) cc_final: 0.8132 (mtp85) REVERT: B 578 MET cc_start: 0.3356 (ttt) cc_final: 0.3046 (ttt) REVERT: C 145 MET cc_start: -0.0934 (pp-130) cc_final: -0.1528 (ttp) REVERT: D 214 ARG cc_start: 0.8656 (tpp80) cc_final: 0.8080 (mtp85) REVERT: E 141 GLU cc_start: 0.4076 (OUTLIER) cc_final: 0.3427 (tm-30) REVERT: F 110 MET cc_start: 0.4017 (tpp) cc_final: 0.2715 (mmp) REVERT: G 198 ARG cc_start: 0.5709 (mtt180) cc_final: 0.5231 (tpt-90) REVERT: G 214 ARG cc_start: 0.8622 (tpp80) cc_final: 0.8021 (mtt90) REVERT: G 578 MET cc_start: 0.3039 (ttt) cc_final: 0.2706 (ttt) outliers start: 35 outliers final: 24 residues processed: 184 average time/residue: 1.3790 time to fit residues: 281.5495 Evaluate side-chains 187 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 161 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 289 ASN Chi-restraints excluded: chain A residue 575 HIS Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 289 ASN Chi-restraints excluded: chain B residue 575 HIS Chi-restraints excluded: chain C residue 90 PHE Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 361 GLN Chi-restraints excluded: chain E residue 90 PHE Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 141 GLU Chi-restraints excluded: chain F residue 6 THR Chi-restraints excluded: chain G residue 133 THR Chi-restraints excluded: chain G residue 161 LEU Chi-restraints excluded: chain G residue 289 ASN Chi-restraints excluded: chain G residue 358 SER Chi-restraints excluded: chain G residue 575 HIS Chi-restraints excluded: chain H residue 90 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 121 optimal weight: 10.0000 chunk 81 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 86 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 118 optimal weight: 6.9990 chunk 34 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4799 r_free = 0.4799 target = 0.248549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.131653 restraints weight = 51812.985| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 2.10 r_work: 0.3235 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7087 moved from start: 0.3378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15920 Z= 0.118 Angle : 0.525 8.589 21480 Z= 0.274 Chirality : 0.034 0.127 2316 Planarity : 0.004 0.078 2708 Dihedral : 6.294 57.522 2172 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.24 % Allowed : 29.21 % Favored : 69.55 % 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: 2.36 (0.20), residues: 1868 helix: 2.02 (0.13), residues: 1480 sheet: None (None), residues: 0 loop : -0.17 (0.36), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG B 165 TYR 0.013 0.001 TYR G 571 PHE 0.009 0.001 PHE B 100 TRP 0.018 0.001 TRP G 344 HIS 0.002 0.001 HIS G 357 Details of bonding type rmsd covalent geometry : bond 0.00253 (15920) covalent geometry : angle 0.52534 (21480) hydrogen bonds : bond 0.03586 ( 1138) hydrogen bonds : angle 4.21703 ( 3357) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3736 Ramachandran restraints generated. 1868 Oldfield, 0 Emsley, 1868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3736 Ramachandran restraints generated. 1868 Oldfield, 0 Emsley, 1868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 160 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 CYS cc_start: 0.6728 (m) cc_final: 0.6136 (t) REVERT: A 198 ARG cc_start: 0.5422 (mtt180) cc_final: 0.4944 (tpt-90) REVERT: A 214 ARG cc_start: 0.8666 (tpp80) cc_final: 0.8063 (mtp85) REVERT: B 214 ARG cc_start: 0.8751 (tpp80) cc_final: 0.8124 (mtp85) REVERT: B 578 MET cc_start: 0.3285 (ttt) cc_final: 0.2992 (ttt) REVERT: C 145 MET cc_start: -0.0997 (pp-130) cc_final: -0.1591 (ttp) REVERT: D 214 ARG cc_start: 0.8645 (tpp80) cc_final: 0.8060 (mtp85) REVERT: E 141 GLU cc_start: 0.4147 (OUTLIER) cc_final: 0.3507 (tm-30) REVERT: F 110 MET cc_start: 0.3955 (tpp) cc_final: 0.2683 (mmp) REVERT: G 198 ARG cc_start: 0.5498 (mtt180) cc_final: 0.5084 (tpt-90) REVERT: G 214 ARG cc_start: 0.8584 (tpp80) cc_final: 0.8050 (mtp85) REVERT: G 578 MET cc_start: 0.3052 (ttt) cc_final: 0.2720 (ttt) outliers start: 20 outliers final: 19 residues processed: 169 average time/residue: 1.2236 time to fit residues: 229.6010 Evaluate side-chains 178 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 158 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 174 MET Chi-restraints excluded: chain A residue 289 ASN Chi-restraints excluded: chain A residue 575 HIS Chi-restraints excluded: chain B residue 289 ASN Chi-restraints excluded: chain B residue 575 HIS Chi-restraints excluded: chain C residue 90 PHE Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain E residue 90 PHE Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 141 GLU Chi-restraints excluded: chain F residue 6 THR Chi-restraints excluded: chain G residue 161 LEU Chi-restraints excluded: chain G residue 171 ILE Chi-restraints excluded: chain G residue 289 ASN Chi-restraints excluded: chain G residue 358 SER Chi-restraints excluded: chain G residue 575 HIS Chi-restraints excluded: chain H residue 90 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 105 optimal weight: 7.9990 chunk 17 optimal weight: 2.9990 chunk 153 optimal weight: 5.9990 chunk 184 optimal weight: 20.0000 chunk 172 optimal weight: 8.9990 chunk 111 optimal weight: 5.9990 chunk 55 optimal weight: 0.0980 chunk 83 optimal weight: 1.9990 chunk 29 optimal weight: 20.0000 chunk 131 optimal weight: 40.0000 chunk 52 optimal weight: 0.9990 overall best weight: 2.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 570 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4791 r_free = 0.4791 target = 0.247547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 92)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.128788 restraints weight = 52151.849| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 2.22 r_work: 0.3247 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 moved from start: 0.3387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15920 Z= 0.186 Angle : 0.549 10.888 21480 Z= 0.285 Chirality : 0.035 0.127 2316 Planarity : 0.004 0.065 2708 Dihedral : 6.382 57.015 2172 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.30 % Allowed : 29.15 % Favored : 69.55 % 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: 2.35 (0.20), residues: 1868 helix: 2.05 (0.13), residues: 1476 sheet: None (None), residues: 0 loop : -0.28 (0.36), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 165 TYR 0.014 0.001 TYR G 571 PHE 0.013 0.001 PHE D 304 TRP 0.017 0.001 TRP G 344 HIS 0.002 0.001 HIS G 357 Details of bonding type rmsd covalent geometry : bond 0.00415 (15920) covalent geometry : angle 0.54871 (21480) hydrogen bonds : bond 0.03738 ( 1138) hydrogen bonds : angle 4.24320 ( 3357) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17334.71 seconds wall clock time: 292 minutes 45.28 seconds (17565.28 seconds total)