Starting phenix.real_space_refine on Thu Jun 26 15:23:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j04_35883/06_2025/8j04_35883_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j04_35883/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8j04_35883/06_2025/8j04_35883.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j04_35883/06_2025/8j04_35883.map" model { file = "/net/cci-nas-00/data/ceres_data/8j04_35883/06_2025/8j04_35883_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j04_35883/06_2025/8j04_35883_neut_trim.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 14.48, per 1000 atoms: 0.47 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: 8.70 Conformation dependent library (CDL) restraints added in 2.3 seconds 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: 2.69 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: 11.53 Time building geometry restraints manager: 10.43 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: 0.13 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: 0.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.520 Extract box with map and model: 1.180 Check model and map are aligned: 0.220 Set scattering table: 0.300 Process input model: 64.680 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.110 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:12.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.330 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.30 (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 TRP 0.009 0.001 TRP G 288 HIS 0.001 0.000 HIS B 328 PHE 0.012 0.001 PHE G 304 TYR 0.011 0.001 TYR D 571 ARG 0.002 0.000 ARG B 207 Details of bonding type rmsd hydrogen bonds : bond 0.10759 ( 1138) hydrogen bonds : angle 5.27662 ( 3357) covalent geometry : bond 0.00482 (15920) covalent geometry : angle 0.58554 (21480) *********************** 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 : 2.361 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: 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: 0.5794 (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: 0.8685 (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: 0.8857 (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: 0.8598 (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: 2.6507 time to fit residues: 570.0671 Evaluate side-chains 167 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 160 time to evaluate : 2.244 ------------------------------------------------------------------------------- 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 158 optimal weight: 1.9990 chunk 142 optimal weight: 3.9990 chunk 79 optimal weight: 20.0000 chunk 48 optimal weight: 0.6980 chunk 96 optimal weight: 1.9990 chunk 76 optimal weight: 20.0000 chunk 147 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 89 optimal weight: 8.9990 chunk 109 optimal weight: 20.0000 chunk 170 optimal weight: 30.0000 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 350 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4803 r_free = 0.4803 target = 0.248587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.130077 restraints weight = 51959.367| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 2.24 r_work: 0.3248 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7102 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 15920 Z= 0.188 Angle : 0.530 6.183 21480 Z= 0.281 Chirality : 0.034 0.125 2316 Planarity : 0.004 0.071 2708 Dihedral : 6.603 59.862 2187 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.54 % Allowed : 23.64 % Favored : 73.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.61 (0.20), residues: 1868 helix: 2.19 (0.13), residues: 1488 sheet: None (None), residues: 0 loop : -0.09 (0.37), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 344 HIS 0.002 0.001 HIS D 228 PHE 0.020 0.001 PHE A 163 TYR 0.015 0.001 TYR A 237 ARG 0.011 0.000 ARG A 144 Details of bonding type rmsd hydrogen bonds : bond 0.03896 ( 1138) hydrogen bonds : angle 4.24802 ( 3357) covalent geometry : bond 0.00417 (15920) covalent geometry : angle 0.53043 (21480) *********************** 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 208 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 167 time to evaluate : 2.272 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: 0.6524 (m) cc_final: 0.6079 (t) REVERT: A 198 ARG cc_start: 0.5084 (mtt180) cc_final: 0.4477 (tpt-90) REVERT: A 257 GLU cc_start: 0.8780 (pm20) cc_final: 0.8516 (pm20) REVERT: A 322 GLU cc_start: 0.7342 (pp20) cc_final: 0.7093 (pp20) REVERT: B 161 LEU cc_start: 0.7985 (tt) cc_final: 0.7580 (tm) REVERT: B 177 ILE cc_start: 0.8639 (OUTLIER) cc_final: 0.8148 (pp) REVERT: C 110 MET cc_start: 0.4078 (tpp) cc_final: 0.3000 (mmp) REVERT: C 141 GLU cc_start: 0.4605 (OUTLIER) cc_final: 0.3921 (pp20) REVERT: D 80 PHE cc_start: 0.8318 (t80) cc_final: 0.8082 (t80) REVERT: E 141 GLU cc_start: 0.3952 (OUTLIER) cc_final: 0.3174 (tm-30) REVERT: F 72 MET cc_start: -0.4548 (tmt) cc_final: -0.4768 (tmt) REVERT: F 110 MET cc_start: 0.4129 (tpp) cc_final: 0.2681 (mmp) REVERT: G 198 ARG cc_start: 0.5586 (mtt180) cc_final: 0.5063 (tpt-90) REVERT: G 257 GLU cc_start: 0.8817 (pm20) cc_final: 0.8586 (pm20) REVERT: G 289 ASN cc_start: 0.8410 (m-40) cc_final: 0.8099 (m110) REVERT: H 110 MET cc_start: 0.4475 (tpp) cc_final: 0.2898 (mmp) REVERT: H 141 GLU cc_start: 0.4465 (OUTLIER) cc_final: 0.3584 (OUTLIER) outliers start: 41 outliers final: 16 residues processed: 195 average time/residue: 2.2895 time to fit residues: 505.6532 Evaluate side-chains 174 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 155 time to evaluate : 2.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 575 HIS Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 289 ASN Chi-restraints excluded: chain B residue 575 HIS 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 171 ILE Chi-restraints excluded: chain E residue 90 PHE 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 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 183 optimal weight: 50.0000 chunk 166 optimal weight: 20.0000 chunk 155 optimal weight: 0.6980 chunk 109 optimal weight: 20.0000 chunk 47 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 119 optimal weight: 20.0000 chunk 168 optimal weight: 20.0000 chunk 153 optimal weight: 6.9990 chunk 62 optimal weight: 20.0000 chunk 177 optimal weight: 30.0000 overall best weight: 6.1390 ------------------------------------------------------------------------------- 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 = 0.4782 r_free = 0.4782 target = 0.249234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.131063 restraints weight = 52150.035| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 2.03 r_work: 0.3200 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7204 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.074 15920 Z= 0.416 Angle : 0.640 7.693 21480 Z= 0.342 Chirality : 0.043 0.171 2316 Planarity : 0.006 0.090 2708 Dihedral : 7.082 75.047 2174 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.90 % Allowed : 23.21 % Favored : 72.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.20), residues: 1868 helix: 1.75 (0.13), residues: 1464 sheet: None (None), residues: 0 loop : -0.17 (0.37), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 344 HIS 0.005 0.001 HIS D 228 PHE 0.027 0.002 PHE A 304 TYR 0.018 0.002 TYR A 237 ARG 0.004 0.001 ARG D 144 Details of bonding type rmsd hydrogen bonds : bond 0.04818 ( 1138) hydrogen bonds : angle 4.52706 ( 3357) covalent geometry : bond 0.00951 (15920) covalent geometry : angle 0.63980 (21480) *********************** 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 220 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 157 time to evaluate : 2.503 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: 0.6504 (m) cc_final: 0.5856 (t) REVERT: A 198 ARG cc_start: 0.5334 (mtt180) cc_final: 0.4807 (tpt-90) REVERT: B 120 LYS cc_start: 0.7896 (OUTLIER) cc_final: 0.7644 (mptt) REVERT: B 214 ARG cc_start: 0.8785 (OUTLIER) cc_final: 0.8223 (mtp85) REVERT: B 332 ARG cc_start: 0.4101 (OUTLIER) cc_final: 0.3794 (mtm180) REVERT: B 578 MET cc_start: 0.2705 (ttt) cc_final: 0.2447 (ttt) REVERT: C 110 MET cc_start: 0.4090 (tpp) cc_final: 0.3007 (mmp) REVERT: C 141 GLU cc_start: 0.4632 (OUTLIER) cc_final: 0.3951 (tm-30) REVERT: D 214 ARG cc_start: 0.8658 (tpp80) cc_final: 0.7998 (mtt90) REVERT: D 578 MET cc_start: 0.3129 (ttt) cc_final: 0.2811 (ttt) REVERT: E 110 MET cc_start: 0.4448 (tpp) cc_final: 0.3205 (mmp) REVERT: E 141 GLU cc_start: 0.4067 (OUTLIER) cc_final: 0.3357 (tm-30) REVERT: F 110 MET cc_start: 0.3993 (tpp) cc_final: 0.2591 (mmp) REVERT: G 123 GLU cc_start: 0.7564 (OUTLIER) cc_final: 0.7361 (pt0) REVERT: G 198 ARG cc_start: 0.5596 (mtt180) cc_final: 0.5245 (tpt-90) REVERT: G 257 GLU cc_start: 0.8832 (pm20) cc_final: 0.8552 (pm20) REVERT: H 110 MET cc_start: 0.4461 (tpp) cc_final: 0.2973 (mmp) REVERT: H 141 GLU cc_start: 0.4374 (OUTLIER) cc_final: 0.3716 (tm-30) outliers start: 63 outliers final: 25 residues processed: 198 average time/residue: 2.5199 time to fit residues: 557.4654 Evaluate side-chains 182 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 150 time to evaluate : 2.236 ------------------------------------------------------------------------------- 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 277 THR Chi-restraints excluded: chain B residue 120 LYS Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 171 ILE 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 B residue 332 ARG 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 133 THR Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 277 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 141 GLU 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 277 THR 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 152 optimal weight: 10.0000 chunk 32 optimal weight: 8.9990 chunk 155 optimal weight: 0.6980 chunk 112 optimal weight: 8.9990 chunk 137 optimal weight: 30.0000 chunk 33 optimal weight: 10.0000 chunk 100 optimal weight: 0.5980 chunk 182 optimal weight: 20.0000 chunk 14 optimal weight: 0.5980 chunk 40 optimal weight: 0.8980 chunk 128 optimal weight: 50.0000 overall best weight: 2.3582 ------------------------------------------------------------------------------- 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 = 0.4792 r_free = 0.4792 target = 0.247557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.129548 restraints weight = 52261.828| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 2.09 r_work: 0.3194 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 15920 Z= 0.182 Angle : 0.515 6.255 21480 Z= 0.275 Chirality : 0.034 0.128 2316 Planarity : 0.004 0.044 2708 Dihedral : 6.422 57.795 2172 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.60 % Allowed : 25.37 % Favored : 72.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.30 (0.20), residues: 1868 helix: 1.99 (0.13), residues: 1464 sheet: None (None), residues: 0 loop : -0.14 (0.37), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 344 HIS 0.002 0.000 HIS A 228 PHE 0.015 0.001 PHE B 163 TYR 0.011 0.001 TYR B 571 ARG 0.003 0.000 ARG A 214 Details of bonding type rmsd hydrogen bonds : bond 0.03935 ( 1138) hydrogen bonds : angle 4.28754 ( 3357) covalent geometry : bond 0.00402 (15920) covalent geometry : angle 0.51525 (21480) *********************** 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 201 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 159 time to evaluate : 2.431 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: symmetry clash REVERT: A 198 ARG cc_start: 0.5260 (mtt180) cc_final: 0.4710 (tpt-90) REVERT: A 214 ARG cc_start: 0.8604 (tpp80) cc_final: 0.7997 (mtp85) REVERT: B 214 ARG cc_start: 0.8755 (OUTLIER) cc_final: 0.8126 (mtp85) REVERT: B 289 ASN cc_start: 0.8553 (OUTLIER) cc_final: 0.7996 (p0) REVERT: B 578 MET cc_start: 0.2815 (ttt) cc_final: 0.2563 (ttt) REVERT: C 110 MET cc_start: 0.4221 (tpp) cc_final: 0.3174 (mmp) REVERT: C 141 GLU cc_start: 0.4542 (OUTLIER) cc_final: 0.3950 (tm-30) REVERT: D 364 GLU cc_start: 0.2065 (OUTLIER) cc_final: 0.1783 (mp0) REVERT: D 578 MET cc_start: 0.3247 (ttt) cc_final: 0.2974 (ttt) REVERT: E 141 GLU cc_start: 0.3983 (OUTLIER) cc_final: 0.3274 (tm-30) REVERT: F 110 MET cc_start: 0.4164 (tpp) cc_final: 0.2812 (mmp) REVERT: G 198 ARG cc_start: 0.5624 (mtt180) cc_final: 0.5170 (tpt-90) REVERT: G 289 ASN cc_start: 0.8591 (OUTLIER) cc_final: 0.7805 (m-40) REVERT: H 110 MET cc_start: 0.4291 (tpp) cc_final: 0.2958 (mmp) REVERT: H 141 GLU cc_start: 0.4421 (OUTLIER) cc_final: 0.3602 (tm-30) outliers start: 42 outliers final: 19 residues processed: 189 average time/residue: 2.3961 time to fit residues: 510.3307 Evaluate side-chains 178 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 152 time to evaluate : 2.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 THR 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 214 ARG 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 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 358 SER Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain E residue 90 PHE 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 134 ILE 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 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 Chi-restraints excluded: chain H residue 141 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 28 optimal weight: 30.0000 chunk 40 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 126 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 178 optimal weight: 20.0000 chunk 157 optimal weight: 1.9990 chunk 37 optimal weight: 0.0370 chunk 106 optimal weight: 6.9990 overall best weight: 2.4066 ------------------------------------------------------------------------------- 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 = 0.4792 r_free = 0.4792 target = 0.247514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.129315 restraints weight = 52055.492| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.17 r_work: 0.3250 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 moved from start: 0.2607 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= 0.189 Angle : 0.515 6.909 21480 Z= 0.274 Chirality : 0.034 0.128 2316 Planarity : 0.004 0.043 2708 Dihedral : 6.453 58.962 2172 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.78 % Allowed : 25.87 % Favored : 71.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.43 (0.20), residues: 1868 helix: 2.09 (0.13), residues: 1464 sheet: None (None), residues: 0 loop : -0.13 (0.37), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 344 HIS 0.002 0.001 HIS A 228 PHE 0.016 0.001 PHE B 163 TYR 0.013 0.001 TYR A 571 ARG 0.007 0.000 ARG B 165 Details of bonding type rmsd hydrogen bonds : bond 0.03888 ( 1138) hydrogen bonds : angle 4.23367 ( 3357) covalent geometry : bond 0.00422 (15920) covalent geometry : angle 0.51492 (21480) *********************** 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 203 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 158 time to evaluate : 2.287 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 123 GLU cc_start: 0.7336 (OUTLIER) cc_final: 0.7107 (pt0) REVERT: A 198 ARG cc_start: 0.5182 (mtt180) cc_final: 0.4722 (tpt-90) REVERT: A 214 ARG cc_start: 0.8598 (tpp80) cc_final: 0.7984 (mtp85) REVERT: B 214 ARG cc_start: 0.8762 (tpp80) cc_final: 0.8129 (mtp85) REVERT: B 332 ARG cc_start: 0.4046 (OUTLIER) cc_final: 0.3663 (mtm180) REVERT: B 578 MET cc_start: 0.2854 (ttt) cc_final: 0.2591 (ttt) REVERT: C 110 MET cc_start: 0.4244 (tpp) cc_final: 0.3195 (mmp) REVERT: C 141 GLU cc_start: 0.4525 (OUTLIER) cc_final: 0.3955 (tm-30) REVERT: D 364 GLU cc_start: 0.1943 (OUTLIER) cc_final: 0.1637 (mp0) REVERT: D 578 MET cc_start: 0.3364 (ttt) cc_final: 0.3076 (ttt) REVERT: E 141 GLU cc_start: 0.4310 (OUTLIER) cc_final: 0.3619 (tm-30) REVERT: F 110 MET cc_start: 0.4261 (tpp) cc_final: 0.2917 (mmp) REVERT: G 198 ARG cc_start: 0.5557 (mtt180) cc_final: 0.5155 (tpt-90) REVERT: G 214 ARG cc_start: 0.8599 (tpp80) cc_final: 0.7740 (mtp-110) REVERT: G 289 ASN cc_start: 0.8607 (OUTLIER) cc_final: 0.7895 (m-40) REVERT: H 110 MET cc_start: 0.4338 (tpp) cc_final: 0.2994 (mmp) REVERT: H 141 GLU cc_start: 0.4262 (OUTLIER) cc_final: 0.3563 (tm-30) outliers start: 45 outliers final: 26 residues processed: 189 average time/residue: 2.5161 time to fit residues: 534.8469 Evaluate side-chains 186 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 153 time to evaluate : 2.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 575 HIS 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 171 ILE 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 171 ILE Chi-restraints excluded: chain D residue 358 SER Chi-restraints excluded: chain D residue 364 GLU 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 171 ILE Chi-restraints excluded: chain G residue 177 ILE Chi-restraints excluded: chain G residue 289 ASN Chi-restraints excluded: chain G residue 358 SER Chi-restraints excluded: chain G residue 364 GLU Chi-restraints excluded: chain G residue 575 HIS Chi-restraints excluded: chain H residue 90 PHE Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 141 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 133 optimal weight: 40.0000 chunk 143 optimal weight: 2.9990 chunk 108 optimal weight: 30.0000 chunk 139 optimal weight: 10.0000 chunk 74 optimal weight: 20.0000 chunk 141 optimal weight: 10.0000 chunk 66 optimal weight: 4.9990 chunk 62 optimal weight: 20.0000 chunk 101 optimal weight: 1.9990 chunk 183 optimal weight: 50.0000 chunk 176 optimal weight: 10.0000 overall best weight: 5.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 ASN 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 = 0.244247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.124232 restraints weight = 52446.338| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 2.19 r_work: 0.3120 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.072 15920 Z= 0.408 Angle : 0.628 7.260 21480 Z= 0.336 Chirality : 0.042 0.166 2316 Planarity : 0.006 0.082 2708 Dihedral : 6.816 63.672 2172 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.96 % Allowed : 24.63 % Favored : 71.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.20), residues: 1868 helix: 1.71 (0.13), residues: 1456 sheet: None (None), residues: 0 loop : -0.41 (0.35), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 344 HIS 0.005 0.001 HIS B 228 PHE 0.024 0.002 PHE A 304 TYR 0.016 0.002 TYR A 237 ARG 0.007 0.001 ARG B 165 Details of bonding type rmsd hydrogen bonds : bond 0.04675 ( 1138) hydrogen bonds : angle 4.46979 ( 3357) covalent geometry : bond 0.00939 (15920) covalent geometry : angle 0.62829 (21480) *********************** 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 219 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 155 time to evaluate : 2.476 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: 0.5470 (mtt180) cc_final: 0.4985 (tpt-90) REVERT: A 210 ARG cc_start: 0.7355 (OUTLIER) cc_final: 0.7040 (ttp80) REVERT: B 214 ARG cc_start: 0.8775 (OUTLIER) cc_final: 0.8191 (mtp85) REVERT: B 332 ARG cc_start: 0.4017 (OUTLIER) cc_final: 0.3622 (mtm180) REVERT: B 578 MET cc_start: 0.3077 (ttt) cc_final: 0.2810 (ttt) REVERT: C 141 GLU cc_start: 0.4356 (OUTLIER) cc_final: 0.3694 (pp20) REVERT: D 123 GLU cc_start: 0.7534 (OUTLIER) cc_final: 0.7305 (pt0) REVERT: D 214 ARG cc_start: 0.8663 (tpp80) cc_final: 0.8078 (mtt90) REVERT: D 578 MET cc_start: 0.3317 (ttt) cc_final: 0.3067 (ttt) REVERT: E 141 GLU cc_start: 0.4154 (OUTLIER) cc_final: 0.3442 (tm-30) REVERT: F 110 MET cc_start: 0.4080 (tpp) cc_final: 0.2745 (mmp) REVERT: G 198 ARG cc_start: 0.5611 (mtt180) cc_final: 0.5236 (tpt-90) REVERT: G 214 ARG cc_start: 0.8640 (tpp80) cc_final: 0.8066 (mtt90) REVERT: H 141 GLU cc_start: 0.4280 (OUTLIER) cc_final: 0.3666 (tm-30) outliers start: 64 outliers final: 36 residues processed: 199 average time/residue: 2.5610 time to fit residues: 567.9029 Evaluate side-chains 194 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 151 time to evaluate : 2.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 GLU 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 277 THR Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 567 VAL 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 171 ILE 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 B residue 332 ARG 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 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 161 LEU 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 332 ARG Chi-restraints excluded: chain D residue 358 SER 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 77 MET 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 92 optimal weight: 3.9990 chunk 178 optimal weight: 40.0000 chunk 180 optimal weight: 30.0000 chunk 20 optimal weight: 0.3980 chunk 33 optimal weight: 10.0000 chunk 94 optimal weight: 0.5980 chunk 155 optimal weight: 0.7980 chunk 140 optimal weight: 30.0000 chunk 130 optimal weight: 20.0000 chunk 160 optimal weight: 0.7980 chunk 106 optimal weight: 9.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- 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 = 0.4796 r_free = 0.4796 target = 0.248170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.136629 restraints weight = 52033.761| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 5.82 r_work: 0.3175 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 moved from start: 0.2962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15920 Z= 0.130 Angle : 0.504 7.310 21480 Z= 0.267 Chirality : 0.034 0.126 2316 Planarity : 0.004 0.042 2708 Dihedral : 6.335 56.178 2172 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.92 % Allowed : 26.79 % Favored : 71.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.40 (0.20), residues: 1868 helix: 2.07 (0.13), residues: 1472 sheet: None (None), residues: 0 loop : -0.17 (0.36), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 344 HIS 0.001 0.000 HIS D 260 PHE 0.014 0.001 PHE B 163 TYR 0.013 0.001 TYR D 571 ARG 0.005 0.000 ARG B 165 Details of bonding type rmsd hydrogen bonds : bond 0.03680 ( 1138) hydrogen bonds : angle 4.19748 ( 3357) covalent geometry : bond 0.00279 (15920) covalent geometry : angle 0.50355 (21480) *********************** 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 192 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 161 time to evaluate : 1.995 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: A 198 ARG cc_start: 0.5538 (mtt180) cc_final: 0.4946 (tpt-90) REVERT: A 214 ARG cc_start: 0.8640 (tpp80) cc_final: 0.8009 (mtp85) REVERT: B 214 ARG cc_start: 0.8787 (tpp80) cc_final: 0.8180 (mtp85) REVERT: B 578 MET cc_start: 0.3247 (ttt) cc_final: 0.2924 (ttt) REVERT: D 214 ARG cc_start: 0.8673 (tpp80) cc_final: 0.8102 (mtp85) REVERT: D 578 MET cc_start: 0.3349 (ttt) cc_final: 0.3137 (ttt) REVERT: E 141 GLU cc_start: 0.4267 (OUTLIER) cc_final: 0.3500 (tm-30) REVERT: F 110 MET cc_start: 0.4053 (tpp) cc_final: 0.2672 (mmp) REVERT: G 198 ARG cc_start: 0.5769 (mtt180) cc_final: 0.5178 (tpt-90) REVERT: G 214 ARG cc_start: 0.8656 (tpp80) cc_final: 0.7720 (mtp-110) REVERT: H 110 MET cc_start: 0.4390 (tpp) cc_final: 0.3225 (mmp) outliers start: 31 outliers final: 23 residues processed: 178 average time/residue: 2.5342 time to fit residues: 505.8632 Evaluate side-chains 182 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 158 time to evaluate : 2.143 ------------------------------------------------------------------------------- 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 575 HIS Chi-restraints excluded: chain B residue 161 LEU 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 332 ARG Chi-restraints excluded: chain B residue 358 SER 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 D residue 332 ARG Chi-restraints excluded: chain D residue 358 SER 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 358 SER Chi-restraints excluded: chain G residue 575 HIS 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 24 optimal weight: 3.9990 chunk 161 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 131 optimal weight: 30.0000 chunk 81 optimal weight: 0.8980 chunk 163 optimal weight: 0.9980 chunk 46 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 153 optimal weight: 8.9990 chunk 61 optimal weight: 30.0000 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 570 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4801 r_free = 0.4801 target = 0.248554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.139550 restraints weight = 52297.401| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 5.39 r_work: 0.3216 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.2972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15920 Z= 0.124 Angle : 0.505 8.277 21480 Z= 0.265 Chirality : 0.034 0.208 2316 Planarity : 0.003 0.057 2708 Dihedral : 6.259 57.699 2172 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.17 % Allowed : 26.55 % Favored : 71.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.60 (0.20), residues: 1868 helix: 2.22 (0.13), residues: 1468 sheet: None (None), residues: 0 loop : -0.13 (0.36), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP G 344 HIS 0.002 0.000 HIS A 96 PHE 0.012 0.001 PHE B 163 TYR 0.014 0.001 TYR D 571 ARG 0.006 0.000 ARG B 165 Details of bonding type rmsd hydrogen bonds : bond 0.03625 ( 1138) hydrogen bonds : angle 4.14794 ( 3357) covalent geometry : bond 0.00266 (15920) covalent geometry : angle 0.50475 (21480) *********************** 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 193 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 158 time to evaluate : 2.702 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: 0.5501 (mtt180) cc_final: 0.4930 (tpt-90) REVERT: A 214 ARG cc_start: 0.8634 (tpp80) cc_final: 0.8008 (mtp85) REVERT: A 330 GLU cc_start: 0.5939 (pt0) cc_final: 0.5692 (tt0) REVERT: B 214 ARG cc_start: 0.8794 (tpp80) cc_final: 0.8197 (mtp85) REVERT: B 578 MET cc_start: 0.3243 (ttt) cc_final: 0.2919 (ttt) REVERT: D 214 ARG cc_start: 0.8653 (tpp80) cc_final: 0.8107 (mtp85) REVERT: D 578 MET cc_start: 0.3312 (ttt) cc_final: 0.3089 (ttt) REVERT: E 141 GLU cc_start: 0.4288 (OUTLIER) cc_final: 0.3558 (tm-30) REVERT: F 110 MET cc_start: 0.4047 (tpp) cc_final: 0.2645 (mmp) REVERT: G 198 ARG cc_start: 0.5709 (mtt180) cc_final: 0.5155 (tpt-90) REVERT: G 214 ARG cc_start: 0.8653 (tpp80) cc_final: 0.7776 (mtp-110) REVERT: H 141 GLU cc_start: 0.4362 (OUTLIER) cc_final: 0.3575 (tm-30) outliers start: 35 outliers final: 23 residues processed: 179 average time/residue: 2.6311 time to fit residues: 530.6097 Evaluate side-chains 180 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 155 time to evaluate : 2.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 575 HIS 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 358 SER 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 332 ARG Chi-restraints excluded: chain D residue 358 SER Chi-restraints excluded: chain E residue 76 LYS 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 77 MET 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 Chi-restraints excluded: chain H residue 141 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 31 optimal weight: 9.9990 chunk 166 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 chunk 152 optimal weight: 0.4980 chunk 2 optimal weight: 4.9990 chunk 28 optimal weight: 20.0000 chunk 108 optimal weight: 30.0000 chunk 171 optimal weight: 8.9990 chunk 114 optimal weight: 50.0000 chunk 36 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- 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 = 0.247317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.136592 restraints weight = 52051.886| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 4.99 r_work: 0.3173 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 0.3037 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= 0.201 Angle : 0.533 9.129 21480 Z= 0.279 Chirality : 0.035 0.127 2316 Planarity : 0.004 0.046 2708 Dihedral : 6.409 57.625 2172 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.79 % Allowed : 26.73 % Favored : 71.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.54 (0.20), residues: 1868 helix: 2.20 (0.13), residues: 1464 sheet: None (None), residues: 0 loop : -0.24 (0.36), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 344 HIS 0.002 0.001 HIS B 228 PHE 0.014 0.001 PHE A 304 TYR 0.014 0.001 TYR D 571 ARG 0.007 0.000 ARG B 165 Details of bonding type rmsd hydrogen bonds : bond 0.03808 ( 1138) hydrogen bonds : angle 4.19407 ( 3357) covalent geometry : bond 0.00452 (15920) covalent geometry : angle 0.53269 (21480) *********************** 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 186 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 157 time to evaluate : 2.329 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: A 198 ARG cc_start: 0.5449 (mtt180) cc_final: 0.4955 (tpt-90) REVERT: A 214 ARG cc_start: 0.8674 (tpp80) cc_final: 0.8055 (mtp85) REVERT: A 330 GLU cc_start: 0.6008 (pt0) cc_final: 0.5770 (tt0) REVERT: B 214 ARG cc_start: 0.8807 (tpp80) cc_final: 0.8226 (mtp85) REVERT: B 578 MET cc_start: 0.3254 (ttt) cc_final: 0.2956 (ttt) REVERT: D 214 ARG cc_start: 0.8662 (tpp80) cc_final: 0.8114 (mtp85) REVERT: D 578 MET cc_start: 0.3290 (ttt) cc_final: 0.3080 (ttt) REVERT: E 141 GLU cc_start: 0.4310 (OUTLIER) cc_final: 0.3555 (tm-30) REVERT: F 110 MET cc_start: 0.3921 (tpp) cc_final: 0.2555 (mmp) REVERT: G 198 ARG cc_start: 0.5611 (mtt180) cc_final: 0.5144 (tpt-90) REVERT: G 214 ARG cc_start: 0.8666 (tpp80) cc_final: 0.7783 (mtp-110) REVERT: G 289 ASN cc_start: 0.8667 (OUTLIER) cc_final: 0.7998 (m-40) REVERT: H 141 GLU cc_start: 0.4358 (OUTLIER) cc_final: 0.3590 (tm-30) outliers start: 29 outliers final: 19 residues processed: 175 average time/residue: 2.5139 time to fit residues: 492.3643 Evaluate side-chains 177 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 155 time to evaluate : 2.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 575 HIS 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 358 SER 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 332 ARG Chi-restraints excluded: chain D residue 358 SER 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 Chi-restraints excluded: chain H residue 141 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 164 optimal weight: 1.9990 chunk 33 optimal weight: 10.0000 chunk 167 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 84 optimal weight: 0.5980 chunk 154 optimal weight: 4.9990 chunk 44 optimal weight: 9.9990 chunk 92 optimal weight: 6.9990 chunk 1 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 110 optimal weight: 20.0000 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 289 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4805 r_free = 0.4805 target = 0.248664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.136554 restraints weight = 52330.744| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 4.46 r_work: 0.3229 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.3034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 15920 Z= 0.120 Angle : 0.511 9.983 21480 Z= 0.267 Chirality : 0.033 0.126 2316 Planarity : 0.003 0.043 2708 Dihedral : 6.287 57.343 2172 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.61 % Allowed : 26.86 % Favored : 71.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.64 (0.20), residues: 1868 helix: 2.27 (0.13), residues: 1464 sheet: None (None), residues: 0 loop : -0.17 (0.36), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP G 344 HIS 0.001 0.000 HIS A 96 PHE 0.012 0.001 PHE B 163 TYR 0.014 0.001 TYR G 571 ARG 0.006 0.000 ARG B 165 Details of bonding type rmsd hydrogen bonds : bond 0.03553 ( 1138) hydrogen bonds : angle 4.12758 ( 3357) covalent geometry : bond 0.00258 (15920) covalent geometry : angle 0.51061 (21480) ********************** 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 186 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 160 time to evaluate : 2.292 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: A 198 ARG cc_start: 0.5467 (mtt180) cc_final: 0.4930 (tpt-90) REVERT: A 214 ARG cc_start: 0.8628 (tpp80) cc_final: 0.8000 (mtp85) REVERT: B 214 ARG cc_start: 0.8741 (tpp80) cc_final: 0.8164 (mtp85) REVERT: B 578 MET cc_start: 0.3262 (ttt) cc_final: 0.2955 (ttt) REVERT: D 214 ARG cc_start: 0.8622 (tpp80) cc_final: 0.8071 (mtp85) REVERT: E 141 GLU cc_start: 0.4247 (OUTLIER) cc_final: 0.3572 (tm-30) REVERT: F 110 MET cc_start: 0.3940 (tpp) cc_final: 0.2584 (mmp) REVERT: G 198 ARG cc_start: 0.5677 (mtt180) cc_final: 0.5171 (tpt170) REVERT: G 214 ARG cc_start: 0.8631 (tpp80) cc_final: 0.8074 (mtp85) REVERT: H 141 GLU cc_start: 0.4311 (OUTLIER) cc_final: 0.3578 (tm-30) outliers start: 26 outliers final: 22 residues processed: 176 average time/residue: 2.6941 time to fit residues: 528.9110 Evaluate side-chains 183 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 159 time to evaluate : 2.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 575 HIS 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 358 SER 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 D residue 289 ASN Chi-restraints excluded: chain D residue 358 SER Chi-restraints excluded: chain E residue 90 PHE Chi-restraints excluded: chain E residue 141 GLU Chi-restraints excluded: chain F residue 6 THR Chi-restraints excluded: chain F residue 77 MET Chi-restraints excluded: chain G residue 133 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 Chi-restraints excluded: chain H residue 141 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 142 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 61 optimal weight: 20.0000 chunk 144 optimal weight: 2.9990 chunk 163 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 41 optimal weight: 9.9990 chunk 138 optimal weight: 9.9990 chunk 105 optimal weight: 8.9990 chunk 182 optimal weight: 20.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 289 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4792 r_free = 0.4792 target = 0.247019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.131657 restraints weight = 52403.352| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 2.07 r_work: 0.3284 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7135 moved from start: 0.3060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.215 15920 Z= 0.200 Angle : 0.727 59.199 21480 Z= 0.414 Chirality : 0.035 0.157 2316 Planarity : 0.003 0.043 2708 Dihedral : 6.457 57.505 2172 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.42 % Allowed : 26.86 % Favored : 71.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.62 (0.20), residues: 1868 helix: 2.22 (0.13), residues: 1468 sheet: None (None), residues: 0 loop : -0.08 (0.36), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 344 HIS 0.002 0.000 HIS G 260 PHE 0.010 0.001 PHE B 163 TYR 0.013 0.001 TYR G 571 ARG 0.017 0.000 ARG A 332 Details of bonding type rmsd hydrogen bonds : bond 0.03626 ( 1138) hydrogen bonds : angle 4.13144 ( 3357) covalent geometry : bond 0.00442 (15920) covalent geometry : angle 0.72743 (21480) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 34973.45 seconds wall clock time: 592 minutes 2.71 seconds (35522.71 seconds total)