Starting phenix.real_space_refine on Wed Mar 4 20:34:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7cr7_30448/03_2026/7cr7_30448_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cr7_30448/03_2026/7cr7_30448.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7cr7_30448/03_2026/7cr7_30448.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cr7_30448/03_2026/7cr7_30448.map" model { file = "/net/cci-nas-00/data/ceres_data/7cr7_30448/03_2026/7cr7_30448_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cr7_30448/03_2026/7cr7_30448_trim.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 88 5.16 5 C 10384 2.51 5 N 2748 2.21 5 O 2912 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16136 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2886 Classifications: {'peptide': 354} Link IDs: {'PTRANS': 7, 'TRANS': 346} Chain breaks: 2 Chain: "F" Number of atoms: 1126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1126 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'FBX': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B, D, G, C, E, H Time building chain proxies: 2.48, per 1000 atoms: 0.15 Number of scatterers: 16136 At special positions: 0 Unit cell: (130.806, 130.806, 129.792, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 88 16.00 F 4 9.00 O 2912 8.00 N 2748 7.00 C 10384 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.42 Conformation dependent library (CDL) restraints added in 671.1 milliseconds 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3696 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 8 sheets defined 81.5% alpha, 1.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 70 through 86 Processing helix chain 'A' and resid 91 through 113 removed outlier: 4.380A pdb=" N TYR A 95 " --> pdb=" O TRP A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 148 removed outlier: 4.568A pdb=" N ILE A 128 " --> pdb=" O GLY A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 151 No H-bonds generated for 'chain 'A' and resid 149 through 151' Processing helix chain 'A' and resid 156 through 161 Processing helix chain 'A' and resid 162 through 165 removed outlier: 3.906A pdb=" N ARG A 165 " --> pdb=" O LYS A 162 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 162 through 165' Processing helix chain 'A' and resid 166 through 183 Processing helix chain 'A' and resid 196 through 211 Processing helix chain 'A' and resid 215 through 228 Processing helix chain 'A' and resid 228 through 252 Processing helix chain 'A' and resid 263 through 276 Processing helix chain 'A' and resid 287 through 348 removed outlier: 3.867A pdb=" N THR A 296 " --> pdb=" O LEU A 292 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N LEU A 299 " --> pdb=" O ALA A 295 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N SER A 303 " --> pdb=" O LEU A 299 " (cutoff:3.500A) Proline residue: A 308 - end of helix removed outlier: 3.901A pdb=" N PHE A 329 " --> pdb=" O ARG A 325 " (cutoff:3.500A) Proline residue: A 335 - end of helix removed outlier: 3.943A pdb=" N ILE A 340 " --> pdb=" O ALA A 336 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N GLN A 341 " --> pdb=" O ALA A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 367 removed outlier: 4.561A pdb=" N TRP A 360 " --> pdb=" O LEU A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 557 Processing helix chain 'A' and resid 562 through 599 Proline residue: A 597 - end of helix Processing helix chain 'F' and resid 7 through 21 Processing helix chain 'F' and resid 30 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 removed outlier: 4.607A pdb=" N PHE F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'F' and resid 103 through 112 Processing helix chain 'F' and resid 118 through 130 Processing helix chain 'F' and resid 139 through 148 removed outlier: 3.550A pdb=" N ALA F 148 " --> pdb=" O GLN F 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 86 Processing helix chain 'B' and resid 91 through 113 removed outlier: 4.380A pdb=" N TYR B 95 " --> pdb=" O TRP B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 148 removed outlier: 4.567A pdb=" N ILE B 128 " --> pdb=" O GLY B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 151 No H-bonds generated for 'chain 'B' and resid 149 through 151' Processing helix chain 'B' and resid 156 through 161 Processing helix chain 'B' and resid 162 through 165 removed outlier: 3.906A pdb=" N ARG B 165 " --> pdb=" O LYS B 162 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 162 through 165' Processing helix chain 'B' and resid 166 through 183 Processing helix chain 'B' and resid 196 through 211 Processing helix chain 'B' and resid 215 through 228 Processing helix chain 'B' and resid 228 through 252 Processing helix chain 'B' and resid 263 through 276 Processing helix chain 'B' and resid 287 through 348 removed outlier: 3.867A pdb=" N THR B 296 " --> pdb=" O LEU B 292 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N LEU B 299 " --> pdb=" O ALA B 295 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N SER B 303 " --> pdb=" O LEU B 299 " (cutoff:3.500A) Proline residue: B 308 - end of helix removed outlier: 3.901A pdb=" N PHE B 329 " --> pdb=" O ARG B 325 " (cutoff:3.500A) Proline residue: B 335 - end of helix removed outlier: 3.944A pdb=" N ILE B 340 " --> pdb=" O ALA B 336 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N GLN B 341 " --> pdb=" O ALA B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 367 removed outlier: 4.561A pdb=" N TRP B 360 " --> pdb=" O LEU B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 557 Processing helix chain 'B' and resid 562 through 599 Proline residue: B 597 - end of helix Processing helix chain 'C' and resid 7 through 21 Processing helix chain 'C' and resid 30 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 removed outlier: 4.605A pdb=" N PHE C 93 " --> pdb=" O ALA C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 112 Processing helix chain 'C' and resid 118 through 130 Processing helix chain 'C' and resid 139 through 148 removed outlier: 3.551A pdb=" N ALA C 148 " --> pdb=" O GLN C 144 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 86 Processing helix chain 'D' and resid 91 through 113 removed outlier: 4.380A pdb=" N TYR D 95 " --> pdb=" O TRP D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 148 removed outlier: 4.568A pdb=" N ILE D 128 " --> pdb=" O GLY D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 151 No H-bonds generated for 'chain 'D' and resid 149 through 151' Processing helix chain 'D' and resid 156 through 161 Processing helix chain 'D' and resid 162 through 165 removed outlier: 3.906A pdb=" N ARG D 165 " --> pdb=" O LYS D 162 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 162 through 165' Processing helix chain 'D' and resid 166 through 183 Processing helix chain 'D' and resid 196 through 211 Processing helix chain 'D' and resid 215 through 228 Processing helix chain 'D' and resid 228 through 252 Processing helix chain 'D' and resid 263 through 276 Processing helix chain 'D' and resid 287 through 348 removed outlier: 3.867A pdb=" N THR D 296 " --> pdb=" O LEU D 292 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N LEU D 299 " --> pdb=" O ALA D 295 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N SER D 303 " --> pdb=" O LEU D 299 " (cutoff:3.500A) Proline residue: D 308 - end of helix removed outlier: 3.902A pdb=" N PHE D 329 " --> pdb=" O ARG D 325 " (cutoff:3.500A) Proline residue: D 335 - end of helix removed outlier: 3.944A pdb=" N ILE D 340 " --> pdb=" O ALA D 336 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N GLN D 341 " --> pdb=" O ALA D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 356 through 367 removed outlier: 4.561A pdb=" N TRP D 360 " --> pdb=" O LEU D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 536 through 557 Processing helix chain 'D' and resid 562 through 599 Proline residue: D 597 - end of helix Processing helix chain 'E' and resid 7 through 21 Processing helix chain 'E' and resid 30 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 removed outlier: 4.606A pdb=" N PHE E 93 " --> pdb=" O ALA E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 112 Processing helix chain 'E' and resid 118 through 130 Processing helix chain 'E' and resid 139 through 148 removed outlier: 3.550A pdb=" N ALA E 148 " --> pdb=" O GLN E 144 " (cutoff:3.500A) Processing helix chain 'G' and resid 71 through 86 Processing helix chain 'G' and resid 91 through 113 removed outlier: 4.380A pdb=" N TYR G 95 " --> pdb=" O TRP G 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 118 through 148 removed outlier: 4.568A pdb=" N ILE G 128 " --> pdb=" O GLY G 124 " (cutoff:3.500A) Processing helix chain 'G' and resid 149 through 151 No H-bonds generated for 'chain 'G' and resid 149 through 151' Processing helix chain 'G' and resid 156 through 161 Processing helix chain 'G' and resid 162 through 165 removed outlier: 3.905A pdb=" N ARG G 165 " --> pdb=" O LYS G 162 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 162 through 165' Processing helix chain 'G' and resid 166 through 183 Processing helix chain 'G' and resid 196 through 211 Processing helix chain 'G' and resid 215 through 228 Processing helix chain 'G' and resid 228 through 252 Processing helix chain 'G' and resid 263 through 276 Processing helix chain 'G' and resid 287 through 348 removed outlier: 3.867A pdb=" N THR G 296 " --> pdb=" O LEU G 292 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N LEU G 299 " --> pdb=" O ALA G 295 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N SER G 303 " --> pdb=" O LEU G 299 " (cutoff:3.500A) Proline residue: G 308 - end of helix removed outlier: 3.901A pdb=" N PHE G 329 " --> pdb=" O ARG G 325 " (cutoff:3.500A) Proline residue: G 335 - end of helix removed outlier: 3.944A pdb=" N ILE G 340 " --> pdb=" O ALA G 336 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N GLN G 341 " --> pdb=" O ALA G 337 " (cutoff:3.500A) Processing helix chain 'G' and resid 356 through 367 removed outlier: 4.562A pdb=" N TRP G 360 " --> pdb=" O LEU G 356 " (cutoff:3.500A) Processing helix chain 'G' and resid 536 through 557 Processing helix chain 'G' and resid 562 through 599 Proline residue: G 597 - end of helix Processing helix chain 'H' and resid 7 through 21 Processing helix chain 'H' and resid 30 through 41 Processing helix chain 'H' and resid 45 through 57 Processing helix chain 'H' and resid 66 through 75 Processing helix chain 'H' and resid 76 through 80 Processing helix chain 'H' and resid 82 through 94 removed outlier: 4.606A pdb=" N PHE H 93 " --> pdb=" O ALA H 89 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 112 Processing helix chain 'H' and resid 118 through 130 Processing helix chain 'H' and resid 139 through 148 removed outlier: 3.551A pdb=" N ALA H 148 " --> pdb=" O GLN H 144 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'F' and resid 27 through 29 Processing sheet with id=AA2, first strand: chain 'F' and resid 100 through 102 Processing sheet with id=AA3, first strand: chain 'C' and resid 27 through 29 Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA5, first strand: chain 'E' and resid 27 through 29 Processing sheet with id=AA6, first strand: chain 'E' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'H' and resid 27 through 29 Processing sheet with id=AA8, first strand: chain 'H' and resid 100 through 102 1181 hydrogen bonds defined for protein. 3519 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: 2.63 Time building geometry restraints manager: 1.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2609 1.31 - 1.43: 4630 1.43 - 1.56: 9085 1.56 - 1.69: 4 1.69 - 1.81: 148 Bond restraints: 16476 Sorted by residual: bond pdb=" C17 FBX D1001 " pdb=" C19 FBX D1001 " ideal model delta sigma weight residual 1.381 1.522 -0.141 2.00e-02 2.50e+03 5.00e+01 bond pdb=" C17 FBX A1001 " pdb=" C19 FBX A1001 " ideal model delta sigma weight residual 1.381 1.522 -0.141 2.00e-02 2.50e+03 4.99e+01 bond pdb=" C17 FBX B1001 " pdb=" C19 FBX B1001 " ideal model delta sigma weight residual 1.381 1.521 -0.140 2.00e-02 2.50e+03 4.93e+01 bond pdb=" C17 FBX G1001 " pdb=" C19 FBX G1001 " ideal model delta sigma weight residual 1.381 1.521 -0.140 2.00e-02 2.50e+03 4.92e+01 bond pdb=" C16 FBX A1001 " pdb=" C18 FBX A1001 " ideal model delta sigma weight residual 1.388 1.518 -0.130 2.00e-02 2.50e+03 4.23e+01 ... (remaining 16471 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.96: 22016 2.96 - 5.92: 165 5.92 - 8.88: 39 8.88 - 11.85: 0 11.85 - 14.81: 4 Bond angle restraints: 22224 Sorted by residual: angle pdb=" C LEU D 559 " pdb=" N ARG D 560 " pdb=" CA ARG D 560 " ideal model delta sigma weight residual 121.80 106.99 14.81 2.44e+00 1.68e-01 3.68e+01 angle pdb=" C LEU A 559 " pdb=" N ARG A 560 " pdb=" CA ARG A 560 " ideal model delta sigma weight residual 121.80 107.00 14.80 2.44e+00 1.68e-01 3.68e+01 angle pdb=" C LEU G 559 " pdb=" N ARG G 560 " pdb=" CA ARG G 560 " ideal model delta sigma weight residual 121.80 107.00 14.80 2.44e+00 1.68e-01 3.68e+01 angle pdb=" C LEU B 559 " pdb=" N ARG B 560 " pdb=" CA ARG B 560 " ideal model delta sigma weight residual 121.80 107.04 14.76 2.44e+00 1.68e-01 3.66e+01 angle pdb=" CA PRO D 561 " pdb=" N PRO D 561 " pdb=" CD PRO D 561 " ideal model delta sigma weight residual 112.00 106.50 5.50 1.40e+00 5.10e-01 1.54e+01 ... (remaining 22219 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.74: 9445 32.74 - 65.47: 219 65.47 - 98.21: 20 98.21 - 130.94: 0 130.94 - 163.68: 4 Dihedral angle restraints: 9688 sinusoidal: 3936 harmonic: 5752 Sorted by residual: dihedral pdb=" C8 FBX D1001 " pdb=" C7 FBX D1001 " pdb=" N4 FBX D1001 " pdb=" C9 FBX D1001 " ideal model delta sinusoidal sigma weight residual -75.46 88.22 -163.68 1 3.00e+01 1.11e-03 2.09e+01 dihedral pdb=" C8 FBX G1001 " pdb=" C7 FBX G1001 " pdb=" N4 FBX G1001 " pdb=" C9 FBX G1001 " ideal model delta sinusoidal sigma weight residual -75.46 88.19 -163.65 1 3.00e+01 1.11e-03 2.09e+01 dihedral pdb=" C8 FBX A1001 " pdb=" C7 FBX A1001 " pdb=" N4 FBX A1001 " pdb=" C9 FBX A1001 " ideal model delta sinusoidal sigma weight residual -75.46 88.17 -163.63 1 3.00e+01 1.11e-03 2.09e+01 ... (remaining 9685 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1572 0.034 - 0.068: 630 0.068 - 0.102: 149 0.102 - 0.136: 72 0.136 - 0.169: 5 Chirality restraints: 2428 Sorted by residual: chirality pdb=" CG LEU A 559 " pdb=" CB LEU A 559 " pdb=" CD1 LEU A 559 " pdb=" CD2 LEU A 559 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.18e-01 chirality pdb=" CG LEU G 559 " pdb=" CB LEU G 559 " pdb=" CD1 LEU G 559 " pdb=" CD2 LEU G 559 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 6.97e-01 chirality pdb=" CG LEU B 559 " pdb=" CB LEU B 559 " pdb=" CD1 LEU B 559 " pdb=" CD2 LEU B 559 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 6.86e-01 ... (remaining 2425 not shown) Planarity restraints: 2804 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG D 560 " -0.042 5.00e-02 4.00e+02 6.23e-02 6.22e+00 pdb=" N PRO D 561 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO D 561 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO D 561 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG G 560 " 0.042 5.00e-02 4.00e+02 6.22e-02 6.19e+00 pdb=" N PRO G 561 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO G 561 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO G 561 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 560 " 0.042 5.00e-02 4.00e+02 6.22e-02 6.18e+00 pdb=" N PRO A 561 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO A 561 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 561 " 0.034 5.00e-02 4.00e+02 ... (remaining 2801 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 355 2.55 - 3.14: 17121 3.14 - 3.72: 28153 3.72 - 4.31: 40282 4.31 - 4.90: 58057 Nonbonded interactions: 143968 Sorted by model distance: nonbonded pdb=" O VAL D 111 " pdb=" OG1 THR D 114 " model vdw 1.962 3.040 nonbonded pdb=" O VAL A 111 " pdb=" OG1 THR A 114 " model vdw 1.962 3.040 nonbonded pdb=" O VAL G 111 " pdb=" OG1 THR G 114 " model vdw 1.963 3.040 nonbonded pdb=" O VAL B 111 " pdb=" OG1 THR B 114 " model vdw 1.963 3.040 nonbonded pdb=" O TYR A 347 " pdb=" NH1 ARG A 353 " model vdw 1.985 3.120 ... (remaining 143963 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'D' selection = chain 'G' } ncs_group { reference = chain 'F' selection = chain 'C' selection = chain 'E' 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.640 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7011 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 : 0.008 0.141 16476 Z= 0.398 Angle : 0.789 14.807 22224 Z= 0.440 Chirality : 0.041 0.169 2428 Planarity : 0.005 0.062 2804 Dihedral : 14.627 163.679 5992 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 92.60 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.57 % Favored : 94.22 % Rotamer: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.89 (0.15), residues: 1956 helix: -2.41 (0.10), residues: 1448 sheet: None (None), residues: 0 loop : -2.39 (0.28), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 353 TYR 0.024 0.003 TYR G 280 PHE 0.026 0.002 PHE F 142 TRP 0.019 0.002 TRP G 360 HIS 0.004 0.002 HIS G 96 Details of bonding type rmsd covalent geometry : bond 0.00822 (16476) covalent geometry : angle 0.78917 (22224) hydrogen bonds : bond 0.19932 ( 1181) hydrogen bonds : angle 8.29998 ( 3519) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 386 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 ILE cc_start: 0.8347 (mm) cc_final: 0.8082 (mm) REVERT: A 266 ASP cc_start: 0.7526 (m-30) cc_final: 0.7247 (m-30) REVERT: F 13 PHE cc_start: 0.3397 (m-10) cc_final: 0.2517 (m-80) REVERT: F 73 MET cc_start: 0.5990 (mmm) cc_final: 0.5556 (mmp) REVERT: B 101 LEU cc_start: 0.8987 (mt) cc_final: 0.8777 (mt) REVERT: B 171 ILE cc_start: 0.8231 (mm) cc_final: 0.7966 (mm) REVERT: B 546 MET cc_start: 0.7898 (tpt) cc_final: 0.7672 (tpp) REVERT: C 54 ASN cc_start: 0.7734 (m-40) cc_final: 0.7523 (t0) REVERT: D 171 ILE cc_start: 0.8290 (mm) cc_final: 0.7974 (mm) REVERT: D 266 ASP cc_start: 0.7372 (m-30) cc_final: 0.7075 (m-30) REVERT: E 13 PHE cc_start: 0.3195 (m-10) cc_final: 0.2329 (m-80) REVERT: E 76 LYS cc_start: 0.6609 (mttt) cc_final: 0.6373 (tptt) REVERT: G 171 ILE cc_start: 0.8303 (mm) cc_final: 0.8005 (mm) REVERT: G 546 MET cc_start: 0.8035 (tpt) cc_final: 0.7802 (tpp) outliers start: 0 outliers final: 0 residues processed: 386 average time/residue: 0.1528 time to fit residues: 82.2329 Evaluate side-chains 281 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 281 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 20.0000 chunk 194 optimal weight: 0.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 20.0000 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 GLN A 96 HIS B 78 GLN B 96 HIS C 50 GLN ** C 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 78 GLN D 96 HIS ** D 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 78 GLN G 96 HIS H 50 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4650 r_free = 0.4650 target = 0.166983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.123466 restraints weight = 46313.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.126607 restraints weight = 23469.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.126264 restraints weight = 15290.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.126511 restraints weight = 15763.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.126566 restraints weight = 14681.783| |-----------------------------------------------------------------------------| r_work (final): 0.4016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.3624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 16476 Z= 0.295 Angle : 0.882 10.796 22224 Z= 0.467 Chirality : 0.048 0.185 2428 Planarity : 0.006 0.051 2804 Dihedral : 8.991 145.089 2216 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 26.53 Ramachandran Plot: Outliers : 0.41 % Allowed : 4.45 % Favored : 95.14 % Rotamer: Outliers : 2.30 % Allowed : 14.30 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.87 (0.18), residues: 1956 helix: -0.86 (0.12), residues: 1516 sheet: None (None), residues: 0 loop : -2.06 (0.31), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 553 TYR 0.025 0.003 TYR D 251 PHE 0.023 0.003 PHE F 142 TRP 0.031 0.002 TRP A 288 HIS 0.005 0.002 HIS B 96 Details of bonding type rmsd covalent geometry : bond 0.00648 (16476) covalent geometry : angle 0.88236 (22224) hydrogen bonds : bond 0.07863 ( 1181) hydrogen bonds : angle 6.65643 ( 3519) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 329 time to evaluate : 0.465 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 ILE cc_start: 0.7833 (mm) cc_final: 0.7614 (mm) REVERT: F 13 PHE cc_start: 0.3003 (m-10) cc_final: 0.2712 (m-80) REVERT: F 73 MET cc_start: 0.6523 (mmm) cc_final: 0.6157 (mmp) REVERT: F 76 LYS cc_start: 0.3455 (tptt) cc_final: 0.2636 (tptp) REVERT: B 171 ILE cc_start: 0.7701 (mm) cc_final: 0.7459 (mm) REVERT: B 546 MET cc_start: 0.8483 (tpt) cc_final: 0.8099 (tmm) REVERT: C 52 MET cc_start: 0.8230 (tmm) cc_final: 0.7730 (ppp) REVERT: C 76 LYS cc_start: 0.4321 (tptt) cc_final: 0.4027 (tptt) REVERT: D 171 ILE cc_start: 0.7771 (mm) cc_final: 0.7558 (mm) REVERT: E 52 MET cc_start: 0.8258 (tmm) cc_final: 0.7799 (tmm) REVERT: E 126 ILE cc_start: 0.7345 (mm) cc_final: 0.7010 (mm) REVERT: G 171 ILE cc_start: 0.7690 (mm) cc_final: 0.7459 (mm) REVERT: G 209 ILE cc_start: 0.9453 (mt) cc_final: 0.9171 (mt) REVERT: G 546 MET cc_start: 0.8443 (tpt) cc_final: 0.7866 (tmm) REVERT: H 77 MET cc_start: 0.1183 (ptm) cc_final: 0.0686 (ptm) REVERT: H 125 MET cc_start: 0.5583 (tmm) cc_final: 0.5377 (tmm) REVERT: H 126 ILE cc_start: 0.7496 (OUTLIER) cc_final: 0.7104 (mm) outliers start: 39 outliers final: 18 residues processed: 341 average time/residue: 0.1276 time to fit residues: 63.1686 Evaluate side-chains 305 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 286 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain B residue 106 CYS Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain D residue 106 CYS Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 204 GLN Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 360 TRP Chi-restraints excluded: chain G residue 106 CYS Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 204 GLN Chi-restraints excluded: chain G residue 250 VAL Chi-restraints excluded: chain H residue 126 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 95 optimal weight: 10.0000 chunk 26 optimal weight: 6.9990 chunk 156 optimal weight: 0.9990 chunk 143 optimal weight: 5.9990 chunk 171 optimal weight: 3.9990 chunk 134 optimal weight: 4.9990 chunk 146 optimal weight: 10.0000 chunk 8 optimal weight: 20.0000 chunk 160 optimal weight: 9.9990 chunk 22 optimal weight: 0.9980 chunk 172 optimal weight: 5.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 591 GLN G 591 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4658 r_free = 0.4658 target = 0.167541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.122206 restraints weight = 47318.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.126704 restraints weight = 18610.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.128609 restraints weight = 11337.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.129421 restraints weight = 9121.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.129805 restraints weight = 8378.510| |-----------------------------------------------------------------------------| r_work (final): 0.4109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7094 moved from start: 0.4676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 16476 Z= 0.223 Angle : 0.765 12.430 22224 Z= 0.404 Chirality : 0.044 0.182 2428 Planarity : 0.005 0.051 2804 Dihedral : 9.217 154.162 2216 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 21.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 3.01 % Allowed : 17.61 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.18), residues: 1956 helix: -0.35 (0.12), residues: 1536 sheet: None (None), residues: 0 loop : -1.46 (0.33), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 581 TYR 0.036 0.003 TYR A 363 PHE 0.027 0.002 PHE A 240 TRP 0.023 0.002 TRP A 288 HIS 0.006 0.001 HIS A 575 Details of bonding type rmsd covalent geometry : bond 0.00487 (16476) covalent geometry : angle 0.76541 (22224) hydrogen bonds : bond 0.06789 ( 1181) hydrogen bonds : angle 5.94648 ( 3519) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 323 time to evaluate : 0.590 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 ILE cc_start: 0.8068 (mm) cc_final: 0.7850 (mm) REVERT: A 319 LYS cc_start: 0.8667 (tmtt) cc_final: 0.8385 (tmtt) REVERT: F 76 LYS cc_start: 0.3245 (tptt) cc_final: 0.2920 (tmtt) REVERT: F 145 MET cc_start: 0.5362 (ptm) cc_final: 0.5037 (ppp) REVERT: B 171 ILE cc_start: 0.7957 (mm) cc_final: 0.7697 (mm) REVERT: B 176 LEU cc_start: 0.3800 (OUTLIER) cc_final: 0.3597 (mt) REVERT: B 546 MET cc_start: 0.8573 (tpt) cc_final: 0.7976 (tmm) REVERT: C 52 MET cc_start: 0.8236 (tmm) cc_final: 0.7813 (tmm) REVERT: C 76 LYS cc_start: 0.4009 (tptt) cc_final: 0.3278 (tmtt) REVERT: D 137 PHE cc_start: 0.8080 (OUTLIER) cc_final: 0.7567 (m-80) REVERT: D 171 ILE cc_start: 0.8163 (mm) cc_final: 0.7920 (mm) REVERT: D 591 GLN cc_start: 0.8649 (OUTLIER) cc_final: 0.8426 (pp30) REVERT: D 592 ILE cc_start: 0.8139 (OUTLIER) cc_final: 0.7818 (mm) REVERT: E 73 MET cc_start: 0.7551 (OUTLIER) cc_final: 0.7166 (mmm) REVERT: E 76 LYS cc_start: 0.6976 (mttt) cc_final: 0.6551 (tptt) REVERT: E 126 ILE cc_start: 0.7515 (mm) cc_final: 0.7147 (mm) REVERT: G 137 PHE cc_start: 0.8098 (OUTLIER) cc_final: 0.7508 (m-80) REVERT: G 171 ILE cc_start: 0.8168 (mm) cc_final: 0.7909 (mm) REVERT: G 209 ILE cc_start: 0.9370 (mt) cc_final: 0.9162 (mt) REVERT: G 546 MET cc_start: 0.8433 (tpt) cc_final: 0.7801 (tmm) REVERT: H 52 MET cc_start: 0.8416 (tmm) cc_final: 0.7702 (tmm) REVERT: H 101 ILE cc_start: 0.3458 (OUTLIER) cc_final: 0.3210 (tt) REVERT: H 126 ILE cc_start: 0.7326 (mm) cc_final: 0.6965 (mm) outliers start: 51 outliers final: 27 residues processed: 348 average time/residue: 0.1252 time to fit residues: 63.3720 Evaluate side-chains 330 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 296 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 324 HIS Chi-restraints excluded: chain F residue 101 ILE Chi-restraints excluded: chain B residue 100 PHE Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain D residue 106 CYS Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 137 PHE Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 254 GLU Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 591 GLN Chi-restraints excluded: chain D residue 592 ILE Chi-restraints excluded: chain E residue 73 MET Chi-restraints excluded: chain G residue 100 PHE Chi-restraints excluded: chain G residue 106 CYS Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 137 PHE Chi-restraints excluded: chain G residue 204 GLN Chi-restraints excluded: chain G residue 232 LEU Chi-restraints excluded: chain G residue 250 VAL Chi-restraints excluded: chain G residue 268 LEU Chi-restraints excluded: chain G residue 292 LEU Chi-restraints excluded: chain H residue 101 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 130 optimal weight: 10.0000 chunk 6 optimal weight: 20.0000 chunk 50 optimal weight: 8.9990 chunk 157 optimal weight: 8.9990 chunk 133 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 46 optimal weight: 5.9990 chunk 104 optimal weight: 0.7980 chunk 100 optimal weight: 7.9990 chunk 21 optimal weight: 3.9990 chunk 123 optimal weight: 5.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 GLN B 321 GLN H 9 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4652 r_free = 0.4652 target = 0.166612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.120624 restraints weight = 47789.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.124844 restraints weight = 19373.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.126718 restraints weight = 12046.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.127419 restraints weight = 9754.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.127538 restraints weight = 8972.280| |-----------------------------------------------------------------------------| r_work (final): 0.4066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7165 moved from start: 0.5224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 16476 Z= 0.249 Angle : 0.771 12.923 22224 Z= 0.411 Chirality : 0.045 0.179 2428 Planarity : 0.005 0.054 2804 Dihedral : 9.178 156.513 2216 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 23.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 4.31 % Allowed : 18.14 % Favored : 77.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.18), residues: 1956 helix: -0.26 (0.12), residues: 1540 sheet: None (None), residues: 0 loop : -1.42 (0.33), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 75 TYR 0.027 0.003 TYR A 363 PHE 0.036 0.002 PHE D 346 TRP 0.022 0.002 TRP B 344 HIS 0.007 0.001 HIS A 575 Details of bonding type rmsd covalent geometry : bond 0.00549 (16476) covalent geometry : angle 0.77146 (22224) hydrogen bonds : bond 0.06727 ( 1181) hydrogen bonds : angle 5.86269 ( 3519) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 309 time to evaluate : 0.557 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 137 PHE cc_start: 0.7992 (OUTLIER) cc_final: 0.7691 (m-80) REVERT: A 171 ILE cc_start: 0.8044 (mm) cc_final: 0.7835 (mm) REVERT: A 323 GLN cc_start: 0.8099 (tp40) cc_final: 0.7839 (mm110) REVERT: A 546 MET cc_start: 0.8176 (tpp) cc_final: 0.7892 (tpp) REVERT: F 72 MET cc_start: 0.4421 (ptt) cc_final: 0.4055 (ptp) REVERT: F 76 LYS cc_start: 0.3548 (tptt) cc_final: 0.2937 (tptt) REVERT: B 171 ILE cc_start: 0.7921 (mm) cc_final: 0.6841 (mm) REVERT: B 325 ARG cc_start: 0.7857 (mmm160) cc_final: 0.7578 (mmp80) REVERT: B 546 MET cc_start: 0.8558 (tpt) cc_final: 0.7909 (tmm) REVERT: C 52 MET cc_start: 0.8306 (OUTLIER) cc_final: 0.7890 (tmm) REVERT: C 76 LYS cc_start: 0.3959 (tptt) cc_final: 0.3194 (tptt) REVERT: C 125 MET cc_start: 0.5808 (tmm) cc_final: 0.4981 (ptm) REVERT: C 126 ILE cc_start: 0.7187 (mm) cc_final: 0.6366 (mm) REVERT: D 137 PHE cc_start: 0.8353 (OUTLIER) cc_final: 0.8090 (m-80) REVERT: D 592 ILE cc_start: 0.8055 (OUTLIER) cc_final: 0.7850 (mm) REVERT: E 75 ARG cc_start: 0.8311 (mmp80) cc_final: 0.8007 (mmp80) REVERT: E 76 LYS cc_start: 0.7199 (mttt) cc_final: 0.6782 (tptt) REVERT: E 126 ILE cc_start: 0.7151 (mm) cc_final: 0.6781 (mm) REVERT: G 130 GLU cc_start: 0.7171 (pt0) cc_final: 0.6507 (pp20) REVERT: G 171 ILE cc_start: 0.8064 (mm) cc_final: 0.7139 (mm) REVERT: G 546 MET cc_start: 0.8468 (tpt) cc_final: 0.7759 (tmm) REVERT: H 52 MET cc_start: 0.8254 (tmm) cc_final: 0.7644 (tmm) REVERT: H 101 ILE cc_start: 0.3631 (OUTLIER) cc_final: 0.3396 (tt) outliers start: 73 outliers final: 41 residues processed: 355 average time/residue: 0.1329 time to fit residues: 67.8177 Evaluate side-chains 328 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 282 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 137 PHE Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 324 HIS Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 100 PHE Chi-restraints excluded: chain B residue 106 CYS Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 242 CYS Chi-restraints excluded: chain B residue 254 GLU Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 324 HIS Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 100 PHE Chi-restraints excluded: chain D residue 106 CYS Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 137 PHE Chi-restraints excluded: chain D residue 212 ASP Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 254 GLU Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 324 HIS Chi-restraints excluded: chain D residue 592 ILE Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 100 PHE Chi-restraints excluded: chain G residue 106 CYS Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 204 GLN Chi-restraints excluded: chain G residue 232 LEU Chi-restraints excluded: chain G residue 250 VAL Chi-restraints excluded: chain G residue 254 GLU Chi-restraints excluded: chain G residue 268 LEU Chi-restraints excluded: chain G residue 292 LEU Chi-restraints excluded: chain G residue 324 HIS Chi-restraints excluded: chain H residue 101 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 122 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 chunk 156 optimal weight: 0.0870 chunk 87 optimal weight: 0.9980 chunk 36 optimal weight: 20.0000 chunk 187 optimal weight: 8.9990 chunk 149 optimal weight: 2.9990 chunk 10 optimal weight: 9.9990 chunk 15 optimal weight: 0.8980 chunk 191 optimal weight: 5.9990 chunk 142 optimal weight: 6.9990 overall best weight: 1.5962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 HIS D 228 HIS D 591 GLN G 228 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4701 r_free = 0.4701 target = 0.171054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.126062 restraints weight = 47539.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.130686 restraints weight = 18155.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.132682 restraints weight = 10852.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.133577 restraints weight = 8660.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.133852 restraints weight = 7930.214| |-----------------------------------------------------------------------------| r_work (final): 0.4157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 moved from start: 0.6047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 16476 Z= 0.175 Angle : 0.727 9.605 22224 Z= 0.380 Chirality : 0.041 0.182 2428 Planarity : 0.004 0.049 2804 Dihedral : 9.107 161.164 2216 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 18.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.78 % Allowed : 20.15 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.19), residues: 1956 helix: 0.16 (0.12), residues: 1564 sheet: None (None), residues: 0 loop : -1.19 (0.34), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 127 TYR 0.021 0.002 TYR A 363 PHE 0.022 0.002 PHE D 240 TRP 0.028 0.002 TRP B 344 HIS 0.005 0.001 HIS B 575 Details of bonding type rmsd covalent geometry : bond 0.00379 (16476) covalent geometry : angle 0.72653 (22224) hydrogen bonds : bond 0.05744 ( 1181) hydrogen bonds : angle 5.37556 ( 3519) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 322 time to evaluate : 0.622 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 546 MET cc_start: 0.8207 (tpp) cc_final: 0.7673 (ppp) REVERT: F 52 MET cc_start: 0.7769 (ppp) cc_final: 0.6966 (ppp) REVERT: B 137 PHE cc_start: 0.7809 (OUTLIER) cc_final: 0.7409 (m-80) REVERT: B 171 ILE cc_start: 0.7716 (mm) cc_final: 0.7501 (mm) REVERT: B 546 MET cc_start: 0.8587 (tpt) cc_final: 0.7920 (ppp) REVERT: C 13 PHE cc_start: 0.2630 (m-10) cc_final: 0.2289 (m-10) REVERT: C 52 MET cc_start: 0.8077 (OUTLIER) cc_final: 0.7523 (tmm) REVERT: C 73 MET cc_start: 0.7053 (mmm) cc_final: 0.6835 (mmm) REVERT: C 76 LYS cc_start: 0.3809 (tptt) cc_final: 0.2990 (tptt) REVERT: C 125 MET cc_start: 0.5752 (tmm) cc_final: 0.5018 (ptm) REVERT: C 126 ILE cc_start: 0.6936 (mm) cc_final: 0.6114 (mm) REVERT: C 145 MET cc_start: 0.5138 (ptm) cc_final: 0.4674 (ppp) REVERT: C 146 MET cc_start: 0.4248 (mmm) cc_final: 0.3715 (mmm) REVERT: D 137 PHE cc_start: 0.8050 (OUTLIER) cc_final: 0.7832 (m-10) REVERT: E 125 MET cc_start: 0.5091 (tmm) cc_final: 0.4577 (ptm) REVERT: E 126 ILE cc_start: 0.7143 (mm) cc_final: 0.6306 (mm) REVERT: G 130 GLU cc_start: 0.6977 (pt0) cc_final: 0.6477 (pp20) REVERT: G 546 MET cc_start: 0.8301 (tpt) cc_final: 0.7958 (tpt) REVERT: H 125 MET cc_start: 0.5974 (tmm) cc_final: 0.5486 (ppp) REVERT: H 126 ILE cc_start: 0.7590 (mm) cc_final: 0.6639 (mm) REVERT: H 127 ARG cc_start: 0.7877 (tpt90) cc_final: 0.6876 (mmm160) outliers start: 47 outliers final: 28 residues processed: 350 average time/residue: 0.1302 time to fit residues: 65.7221 Evaluate side-chains 312 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 281 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain F residue 28 ILE Chi-restraints excluded: chain B residue 100 PHE Chi-restraints excluded: chain B residue 137 PHE Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 254 GLU Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 324 HIS Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain D residue 100 PHE Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 137 PHE Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 254 GLU Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 324 HIS Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain G residue 100 PHE Chi-restraints excluded: chain G residue 204 GLN Chi-restraints excluded: chain G residue 212 ASP Chi-restraints excluded: chain G residue 232 LEU Chi-restraints excluded: chain G residue 254 GLU Chi-restraints excluded: chain G residue 268 LEU Chi-restraints excluded: chain G residue 292 LEU Chi-restraints excluded: chain G residue 324 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 69 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 125 optimal weight: 20.0000 chunk 38 optimal weight: 5.9990 chunk 104 optimal weight: 2.9990 chunk 170 optimal weight: 0.7980 chunk 169 optimal weight: 0.7980 chunk 168 optimal weight: 0.8980 chunk 180 optimal weight: 0.9990 chunk 183 optimal weight: 8.9990 chunk 162 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 204 GLN ** D 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4768 r_free = 0.4768 target = 0.181907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.134887 restraints weight = 43167.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.139242 restraints weight = 18686.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.141295 restraints weight = 11959.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.142289 restraints weight = 9786.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.142289 restraints weight = 8968.650| |-----------------------------------------------------------------------------| r_work (final): 0.4213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6957 moved from start: 0.6673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 16476 Z= 0.161 Angle : 0.748 9.701 22224 Z= 0.384 Chirality : 0.041 0.265 2428 Planarity : 0.004 0.046 2804 Dihedral : 8.995 162.455 2216 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 17.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.90 % Allowed : 20.51 % Favored : 76.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.19), residues: 1956 helix: 0.45 (0.13), residues: 1548 sheet: None (None), residues: 0 loop : -1.15 (0.34), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 547 TYR 0.019 0.002 TYR A 363 PHE 0.031 0.002 PHE F 142 TRP 0.027 0.002 TRP B 344 HIS 0.005 0.001 HIS G 575 Details of bonding type rmsd covalent geometry : bond 0.00343 (16476) covalent geometry : angle 0.74800 (22224) hydrogen bonds : bond 0.05287 ( 1181) hydrogen bonds : angle 5.13717 ( 3519) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 332 time to evaluate : 0.565 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: symmetry clash REVERT: A 546 MET cc_start: 0.8278 (tpp) cc_final: 0.7405 (tpp) REVERT: F 125 MET cc_start: 0.5358 (tmm) cc_final: 0.4818 (ppp) REVERT: B 546 MET cc_start: 0.8467 (tpt) cc_final: 0.7669 (tmm) REVERT: C 13 PHE cc_start: 0.2230 (m-10) cc_final: 0.2010 (m-10) REVERT: C 52 MET cc_start: 0.7781 (OUTLIER) cc_final: 0.7352 (tmm) REVERT: C 125 MET cc_start: 0.5546 (tmm) cc_final: 0.4819 (ptm) REVERT: C 126 ILE cc_start: 0.6771 (mm) cc_final: 0.5943 (mm) REVERT: C 145 MET cc_start: 0.5172 (ptm) cc_final: 0.4794 (ppp) REVERT: C 146 MET cc_start: 0.4136 (mmm) cc_final: 0.3687 (mmm) REVERT: D 137 PHE cc_start: 0.7795 (OUTLIER) cc_final: 0.7324 (m-80) REVERT: D 546 MET cc_start: 0.8852 (ppp) cc_final: 0.8165 (ppp) REVERT: E 75 ARG cc_start: 0.8510 (mmp80) cc_final: 0.8132 (mmp80) REVERT: E 76 LYS cc_start: 0.7456 (mttt) cc_final: 0.7113 (tmtt) REVERT: E 125 MET cc_start: 0.5052 (tmm) cc_final: 0.4558 (ptm) REVERT: E 126 ILE cc_start: 0.7061 (mm) cc_final: 0.6393 (mm) REVERT: G 130 GLU cc_start: 0.7005 (pt0) cc_final: 0.6390 (pp20) REVERT: G 546 MET cc_start: 0.8318 (tpt) cc_final: 0.7747 (tpt) REVERT: H 73 MET cc_start: 0.6441 (mmm) cc_final: 0.6089 (mmm) REVERT: H 125 MET cc_start: 0.6003 (tmm) cc_final: 0.5340 (ptm) outliers start: 49 outliers final: 24 residues processed: 357 average time/residue: 0.1300 time to fit residues: 66.4838 Evaluate side-chains 312 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 286 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 324 HIS Chi-restraints excluded: chain F residue 28 ILE Chi-restraints excluded: chain B residue 106 CYS Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 324 HIS Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 100 PHE Chi-restraints excluded: chain D residue 137 PHE Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 324 HIS Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain G residue 106 CYS Chi-restraints excluded: chain G residue 204 GLN Chi-restraints excluded: chain G residue 212 ASP Chi-restraints excluded: chain G residue 254 GLU Chi-restraints excluded: chain G residue 292 LEU Chi-restraints excluded: chain G residue 324 HIS Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain H residue 93 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 85 optimal weight: 0.9980 chunk 173 optimal weight: 10.0000 chunk 167 optimal weight: 3.9990 chunk 128 optimal weight: 5.9990 chunk 29 optimal weight: 0.8980 chunk 9 optimal weight: 8.9990 chunk 110 optimal weight: 6.9990 chunk 156 optimal weight: 6.9990 chunk 73 optimal weight: 5.9990 chunk 93 optimal weight: 9.9990 chunk 120 optimal weight: 2.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4730 r_free = 0.4730 target = 0.179215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.132044 restraints weight = 42350.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.136183 restraints weight = 19083.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.137986 restraints weight = 12423.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.138988 restraints weight = 10260.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.139219 restraints weight = 9383.591| |-----------------------------------------------------------------------------| r_work (final): 0.4156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7044 moved from start: 0.6650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 16476 Z= 0.198 Angle : 0.775 13.667 22224 Z= 0.402 Chirality : 0.043 0.209 2428 Planarity : 0.004 0.056 2804 Dihedral : 8.963 160.729 2216 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 21.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 3.19 % Allowed : 21.34 % Favored : 75.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.19), residues: 1956 helix: 0.26 (0.12), residues: 1556 sheet: None (None), residues: 0 loop : -1.09 (0.35), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 553 TYR 0.017 0.002 TYR A 363 PHE 0.034 0.002 PHE F 142 TRP 0.021 0.001 TRP B 344 HIS 0.019 0.001 HIS B 96 Details of bonding type rmsd covalent geometry : bond 0.00438 (16476) covalent geometry : angle 0.77544 (22224) hydrogen bonds : bond 0.05703 ( 1181) hydrogen bonds : angle 5.34822 ( 3519) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 299 time to evaluate : 0.607 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 546 MET cc_start: 0.7856 (tpp) cc_final: 0.7189 (tpp) REVERT: F 73 MET cc_start: 0.7015 (mmm) cc_final: 0.6706 (mmm) REVERT: F 125 MET cc_start: 0.5768 (tmm) cc_final: 0.5216 (ppp) REVERT: B 546 MET cc_start: 0.8433 (tpt) cc_final: 0.7676 (tmm) REVERT: C 52 MET cc_start: 0.7615 (OUTLIER) cc_final: 0.7132 (tmm) REVERT: C 125 MET cc_start: 0.5820 (tmm) cc_final: 0.5266 (ptm) REVERT: C 126 ILE cc_start: 0.6951 (mm) cc_final: 0.6316 (mm) REVERT: C 145 MET cc_start: 0.5185 (ptm) cc_final: 0.4758 (ppp) REVERT: C 146 MET cc_start: 0.4277 (mmm) cc_final: 0.3941 (mmm) REVERT: D 210 ARG cc_start: 0.7755 (mtm110) cc_final: 0.7529 (ttt-90) REVERT: E 75 ARG cc_start: 0.8440 (mmp80) cc_final: 0.8119 (mmp80) REVERT: E 76 LYS cc_start: 0.7383 (mttt) cc_final: 0.6990 (tmtt) REVERT: E 125 MET cc_start: 0.5417 (tmm) cc_final: 0.4834 (ptm) REVERT: E 126 ILE cc_start: 0.7259 (mm) cc_final: 0.6227 (mm) REVERT: E 127 ARG cc_start: 0.7417 (tpt90) cc_final: 0.6588 (mmm160) REVERT: G 130 GLU cc_start: 0.6999 (pt0) cc_final: 0.6380 (pp20) REVERT: G 208 MET cc_start: 0.8405 (ppp) cc_final: 0.8175 (ppp) REVERT: G 546 MET cc_start: 0.8290 (tpt) cc_final: 0.7735 (ppp) REVERT: H 52 MET cc_start: 0.7766 (tmm) cc_final: 0.7165 (tmm) REVERT: H 125 MET cc_start: 0.6083 (tmm) cc_final: 0.5550 (ptm) REVERT: H 126 ILE cc_start: 0.7268 (mm) cc_final: 0.6436 (mm) outliers start: 54 outliers final: 46 residues processed: 329 average time/residue: 0.1231 time to fit residues: 59.3959 Evaluate side-chains 336 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 289 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 324 HIS Chi-restraints excluded: chain F residue 28 ILE Chi-restraints excluded: chain B residue 106 CYS Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 254 GLU Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 324 HIS Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 100 PHE Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 204 GLN Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 242 CYS Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 254 GLU Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 324 HIS Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 592 ILE Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 106 CYS Chi-restraints excluded: chain G residue 204 GLN Chi-restraints excluded: chain G residue 212 ASP Chi-restraints excluded: chain G residue 232 LEU Chi-restraints excluded: chain G residue 242 CYS Chi-restraints excluded: chain G residue 250 VAL Chi-restraints excluded: chain G residue 254 GLU Chi-restraints excluded: chain G residue 268 LEU Chi-restraints excluded: chain G residue 292 LEU Chi-restraints excluded: chain G residue 324 HIS Chi-restraints excluded: chain H residue 28 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 60 optimal weight: 0.0670 chunk 75 optimal weight: 5.9990 chunk 51 optimal weight: 8.9990 chunk 182 optimal weight: 1.9990 chunk 143 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 191 optimal weight: 20.0000 chunk 40 optimal weight: 0.0070 chunk 41 optimal weight: 20.0000 chunk 27 optimal weight: 1.9990 overall best weight: 1.2142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 591 GLN E 42 GLN ** G 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4730 r_free = 0.4730 target = 0.175016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.132739 restraints weight = 47788.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.135950 restraints weight = 20213.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.138526 restraints weight = 11877.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.138082 restraints weight = 11045.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.138001 restraints weight = 9848.603| |-----------------------------------------------------------------------------| r_work (final): 0.4161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7083 moved from start: 0.7062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 16476 Z= 0.159 Angle : 0.760 12.426 22224 Z= 0.391 Chirality : 0.042 0.213 2428 Planarity : 0.004 0.056 2804 Dihedral : 8.968 163.435 2216 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 18.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 3.01 % Allowed : 22.34 % Favored : 74.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.19), residues: 1956 helix: 0.43 (0.13), residues: 1548 sheet: None (None), residues: 0 loop : -0.86 (0.34), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 75 TYR 0.016 0.002 TYR B 237 PHE 0.042 0.002 PHE C 13 TRP 0.023 0.001 TRP B 344 HIS 0.019 0.001 HIS B 96 Details of bonding type rmsd covalent geometry : bond 0.00346 (16476) covalent geometry : angle 0.76043 (22224) hydrogen bonds : bond 0.05235 ( 1181) hydrogen bonds : angle 5.19331 ( 3519) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 307 time to evaluate : 0.568 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 546 MET cc_start: 0.8232 (tpp) cc_final: 0.7532 (tpp) REVERT: F 52 MET cc_start: 0.7227 (ppp) cc_final: 0.6953 (ppp) REVERT: F 73 MET cc_start: 0.7005 (mmm) cc_final: 0.6489 (mmm) REVERT: F 76 LYS cc_start: 0.4520 (tptt) cc_final: 0.3841 (tmtt) REVERT: F 125 MET cc_start: 0.5637 (tmm) cc_final: 0.5172 (ppp) REVERT: F 146 MET cc_start: 0.4788 (mmm) cc_final: 0.4584 (mmm) REVERT: B 210 ARG cc_start: 0.7819 (ttt-90) cc_final: 0.7509 (ttt90) REVERT: B 546 MET cc_start: 0.8643 (tpt) cc_final: 0.7779 (tmm) REVERT: C 52 MET cc_start: 0.7737 (OUTLIER) cc_final: 0.7236 (tmm) REVERT: C 76 LYS cc_start: 0.4325 (tptt) cc_final: 0.3575 (tmtt) REVERT: C 125 MET cc_start: 0.5707 (tmm) cc_final: 0.5100 (ptm) REVERT: C 126 ILE cc_start: 0.6941 (mm) cc_final: 0.6146 (mm) REVERT: C 145 MET cc_start: 0.5224 (ptm) cc_final: 0.4793 (ppp) REVERT: C 146 MET cc_start: 0.4366 (mmm) cc_final: 0.4148 (mmm) REVERT: D 145 ILE cc_start: 0.9180 (tp) cc_final: 0.8800 (pt) REVERT: E 75 ARG cc_start: 0.8589 (mmp80) cc_final: 0.8371 (ptm-80) REVERT: E 125 MET cc_start: 0.5505 (tmm) cc_final: 0.5034 (ptm) REVERT: E 126 ILE cc_start: 0.7400 (mm) cc_final: 0.6401 (mm) REVERT: E 127 ARG cc_start: 0.7508 (tpt90) cc_final: 0.6537 (mmm160) REVERT: E 142 PHE cc_start: 0.3741 (t80) cc_final: 0.3538 (t80) REVERT: G 130 GLU cc_start: 0.7135 (pt0) cc_final: 0.6466 (pp20) REVERT: G 145 ILE cc_start: 0.9159 (tp) cc_final: 0.8781 (pt) REVERT: G 546 MET cc_start: 0.8332 (tpt) cc_final: 0.7679 (ppp) REVERT: H 52 MET cc_start: 0.7878 (tmm) cc_final: 0.7227 (tmm) REVERT: H 73 MET cc_start: 0.5795 (mmm) cc_final: 0.5457 (mmm) REVERT: H 125 MET cc_start: 0.5993 (tmm) cc_final: 0.5677 (ptm) REVERT: H 126 ILE cc_start: 0.7404 (mm) cc_final: 0.6666 (mm) outliers start: 51 outliers final: 40 residues processed: 335 average time/residue: 0.1283 time to fit residues: 61.8543 Evaluate side-chains 325 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 284 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 242 CYS Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 324 HIS Chi-restraints excluded: chain F residue 28 ILE Chi-restraints excluded: chain B residue 100 PHE Chi-restraints excluded: chain B residue 106 CYS Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 254 GLU Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 324 HIS Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 100 PHE Chi-restraints excluded: chain D residue 204 GLN Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 254 GLU Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 324 HIS Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain D residue 592 ILE Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain G residue 100 PHE Chi-restraints excluded: chain G residue 106 CYS Chi-restraints excluded: chain G residue 212 ASP Chi-restraints excluded: chain G residue 232 LEU Chi-restraints excluded: chain G residue 242 CYS Chi-restraints excluded: chain G residue 254 GLU Chi-restraints excluded: chain G residue 268 LEU Chi-restraints excluded: chain G residue 292 LEU Chi-restraints excluded: chain G residue 324 HIS Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain H residue 93 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 103 optimal weight: 10.0000 chunk 154 optimal weight: 0.6980 chunk 80 optimal weight: 7.9990 chunk 86 optimal weight: 1.9990 chunk 85 optimal weight: 5.9990 chunk 144 optimal weight: 7.9990 chunk 169 optimal weight: 0.8980 chunk 6 optimal weight: 5.9990 chunk 87 optimal weight: 7.9990 chunk 124 optimal weight: 5.9990 chunk 45 optimal weight: 6.9990 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4703 r_free = 0.4703 target = 0.172326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.130586 restraints weight = 47113.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.132757 restraints weight = 25168.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.131970 restraints weight = 17810.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.132507 restraints weight = 17032.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.132603 restraints weight = 15550.981| |-----------------------------------------------------------------------------| r_work (final): 0.4089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.6994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 16476 Z= 0.203 Angle : 0.803 12.955 22224 Z= 0.419 Chirality : 0.044 0.216 2428 Planarity : 0.004 0.050 2804 Dihedral : 8.976 162.236 2216 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 22.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 3.07 % Allowed : 22.22 % Favored : 74.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.19), residues: 1956 helix: 0.23 (0.13), residues: 1552 sheet: None (None), residues: 0 loop : -0.90 (0.35), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 213 TYR 0.019 0.002 TYR B 237 PHE 0.060 0.002 PHE C 13 TRP 0.017 0.001 TRP B 344 HIS 0.014 0.002 HIS A 96 Details of bonding type rmsd covalent geometry : bond 0.00453 (16476) covalent geometry : angle 0.80304 (22224) hydrogen bonds : bond 0.05721 ( 1181) hydrogen bonds : angle 5.39482 ( 3519) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 289 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 HIS cc_start: 0.7280 (m-70) cc_final: 0.6970 (m90) REVERT: A 546 MET cc_start: 0.8175 (tpp) cc_final: 0.7801 (tpp) REVERT: F 73 MET cc_start: 0.6908 (mmm) cc_final: 0.6599 (mmm) REVERT: F 76 LYS cc_start: 0.4887 (tptt) cc_final: 0.4223 (tmtt) REVERT: F 125 MET cc_start: 0.5760 (tmm) cc_final: 0.5052 (ptm) REVERT: B 546 MET cc_start: 0.8588 (tpt) cc_final: 0.7811 (tmm) REVERT: C 52 MET cc_start: 0.7605 (OUTLIER) cc_final: 0.7087 (tmm) REVERT: C 125 MET cc_start: 0.5987 (tmm) cc_final: 0.5470 (ptm) REVERT: C 126 ILE cc_start: 0.7013 (mm) cc_final: 0.6321 (mm) REVERT: D 145 ILE cc_start: 0.9160 (tp) cc_final: 0.8761 (pt) REVERT: D 210 ARG cc_start: 0.7869 (mtp-110) cc_final: 0.7604 (ptm-80) REVERT: E 73 MET cc_start: 0.6226 (mmm) cc_final: 0.5924 (mmm) REVERT: E 76 LYS cc_start: 0.7517 (mttt) cc_final: 0.7235 (tmtt) REVERT: E 125 MET cc_start: 0.5589 (tmm) cc_final: 0.5089 (ptm) REVERT: E 126 ILE cc_start: 0.7389 (mm) cc_final: 0.6300 (mm) REVERT: E 127 ARG cc_start: 0.7567 (tpt90) cc_final: 0.6651 (mmm160) REVERT: G 130 GLU cc_start: 0.7174 (pt0) cc_final: 0.6392 (pp20) REVERT: G 145 ILE cc_start: 0.9149 (tp) cc_final: 0.8743 (pt) REVERT: G 546 MET cc_start: 0.8203 (tpt) cc_final: 0.7691 (tpt) REVERT: H 125 MET cc_start: 0.6235 (tmm) cc_final: 0.5759 (ptm) REVERT: H 126 ILE cc_start: 0.7318 (mm) cc_final: 0.6480 (mm) REVERT: H 146 MET cc_start: 0.3300 (mtm) cc_final: 0.2973 (ttm) outliers start: 52 outliers final: 48 residues processed: 319 average time/residue: 0.1305 time to fit residues: 60.3469 Evaluate side-chains 329 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 280 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 242 CYS Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 324 HIS Chi-restraints excluded: chain F residue 28 ILE Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 100 PHE Chi-restraints excluded: chain B residue 106 CYS Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 254 GLU Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 324 HIS Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 100 PHE Chi-restraints excluded: chain D residue 106 CYS Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 204 GLN Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 324 HIS Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 100 PHE Chi-restraints excluded: chain G residue 106 CYS Chi-restraints excluded: chain G residue 212 ASP Chi-restraints excluded: chain G residue 232 LEU Chi-restraints excluded: chain G residue 242 CYS Chi-restraints excluded: chain G residue 250 VAL Chi-restraints excluded: chain G residue 254 GLU Chi-restraints excluded: chain G residue 268 LEU Chi-restraints excluded: chain G residue 292 LEU Chi-restraints excluded: chain G residue 320 VAL Chi-restraints excluded: chain G residue 324 HIS Chi-restraints excluded: chain G residue 592 ILE Chi-restraints excluded: chain H residue 28 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 143 optimal weight: 5.9990 chunk 193 optimal weight: 5.9990 chunk 108 optimal weight: 5.9990 chunk 101 optimal weight: 0.9980 chunk 128 optimal weight: 0.9980 chunk 37 optimal weight: 6.9990 chunk 154 optimal weight: 30.0000 chunk 76 optimal weight: 20.0000 chunk 111 optimal weight: 0.8980 chunk 145 optimal weight: 6.9990 chunk 21 optimal weight: 0.8980 overall best weight: 1.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4742 r_free = 0.4742 target = 0.177918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.142221 restraints weight = 45027.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.140721 restraints weight = 30017.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.141272 restraints weight = 19725.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.141325 restraints weight = 16659.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.141403 restraints weight = 15697.187| |-----------------------------------------------------------------------------| r_work (final): 0.4256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6860 moved from start: 0.7299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 16476 Z= 0.174 Angle : 0.814 12.765 22224 Z= 0.419 Chirality : 0.044 0.258 2428 Planarity : 0.004 0.048 2804 Dihedral : 9.025 164.417 2216 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 19.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.72 % Allowed : 23.05 % Favored : 74.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.19), residues: 1956 helix: 0.28 (0.13), residues: 1552 sheet: None (None), residues: 0 loop : -0.76 (0.35), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 588 TYR 0.021 0.002 TYR B 237 PHE 0.061 0.002 PHE C 13 TRP 0.025 0.001 TRP B 344 HIS 0.017 0.001 HIS A 96 Details of bonding type rmsd covalent geometry : bond 0.00385 (16476) covalent geometry : angle 0.81394 (22224) hydrogen bonds : bond 0.05502 ( 1181) hydrogen bonds : angle 5.32717 ( 3519) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 283 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 546 MET cc_start: 0.7751 (tpp) cc_final: 0.7060 (tpp) REVERT: F 73 MET cc_start: 0.6654 (mmm) cc_final: 0.6188 (mmm) REVERT: F 76 LYS cc_start: 0.5564 (tptt) cc_final: 0.5039 (tmtt) REVERT: F 125 MET cc_start: 0.5501 (tmm) cc_final: 0.5207 (ppp) REVERT: F 146 MET cc_start: 0.4644 (mmm) cc_final: 0.3887 (mmm) REVERT: B 546 MET cc_start: 0.7643 (tpt) cc_final: 0.7426 (tmm) REVERT: C 52 MET cc_start: 0.6908 (OUTLIER) cc_final: 0.6546 (tmm) REVERT: D 145 ILE cc_start: 0.9009 (tp) cc_final: 0.8718 (pt) REVERT: D 210 ARG cc_start: 0.7545 (mtp-110) cc_final: 0.7162 (ptm-80) REVERT: E 125 MET cc_start: 0.5669 (tmm) cc_final: 0.4949 (ptp) REVERT: E 126 ILE cc_start: 0.7047 (mm) cc_final: 0.6246 (mm) REVERT: G 130 GLU cc_start: 0.6953 (pt0) cc_final: 0.6211 (pp20) REVERT: G 145 ILE cc_start: 0.8929 (tp) cc_final: 0.8638 (pt) REVERT: G 546 MET cc_start: 0.7328 (tpt) cc_final: 0.6916 (tpt) REVERT: G 592 ILE cc_start: 0.7706 (OUTLIER) cc_final: 0.7419 (mm) REVERT: H 110 MET cc_start: 0.6544 (ppp) cc_final: 0.6113 (ppp) REVERT: H 125 MET cc_start: 0.5846 (tmm) cc_final: 0.5436 (ptm) REVERT: H 126 ILE cc_start: 0.6952 (mm) cc_final: 0.6164 (mm) outliers start: 46 outliers final: 44 residues processed: 309 average time/residue: 0.1342 time to fit residues: 59.9435 Evaluate side-chains 316 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 270 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 324 HIS Chi-restraints excluded: chain A residue 575 HIS Chi-restraints excluded: chain F residue 28 ILE Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 100 PHE Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 254 GLU Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 324 HIS Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 100 PHE Chi-restraints excluded: chain D residue 106 CYS Chi-restraints excluded: chain D residue 204 GLN Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 242 CYS Chi-restraints excluded: chain D residue 254 GLU Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 324 HIS Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 100 PHE Chi-restraints excluded: chain G residue 106 CYS Chi-restraints excluded: chain G residue 212 ASP Chi-restraints excluded: chain G residue 232 LEU Chi-restraints excluded: chain G residue 242 CYS Chi-restraints excluded: chain G residue 250 VAL Chi-restraints excluded: chain G residue 254 GLU Chi-restraints excluded: chain G residue 268 LEU Chi-restraints excluded: chain G residue 292 LEU Chi-restraints excluded: chain G residue 324 HIS Chi-restraints excluded: chain G residue 592 ILE Chi-restraints excluded: chain H residue 28 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 87 optimal weight: 0.4980 chunk 51 optimal weight: 0.6980 chunk 171 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 46 optimal weight: 7.9990 chunk 176 optimal weight: 3.9990 chunk 40 optimal weight: 30.0000 chunk 100 optimal weight: 5.9990 chunk 60 optimal weight: 10.0000 chunk 11 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 42 GLN ** B 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 586 GLN ** D 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 591 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4730 r_free = 0.4730 target = 0.174955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.142777 restraints weight = 47895.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.139558 restraints weight = 37470.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.140390 restraints weight = 28056.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.140553 restraints weight = 21162.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.140767 restraints weight = 19268.331| |-----------------------------------------------------------------------------| r_work (final): 0.4316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6835 moved from start: 0.7537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 16476 Z= 0.165 Angle : 0.823 15.204 22224 Z= 0.422 Chirality : 0.044 0.221 2428 Planarity : 0.004 0.051 2804 Dihedral : 9.027 165.085 2216 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 18.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 3.01 % Allowed : 22.87 % Favored : 74.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.19), residues: 1956 helix: 0.29 (0.13), residues: 1564 sheet: None (None), residues: 0 loop : -0.63 (0.36), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 588 TYR 0.027 0.002 TYR B 347 PHE 0.062 0.002 PHE B 346 TRP 0.031 0.001 TRP B 344 HIS 0.014 0.001 HIS G 96 Details of bonding type rmsd covalent geometry : bond 0.00361 (16476) covalent geometry : angle 0.82308 (22224) hydrogen bonds : bond 0.05386 ( 1181) hydrogen bonds : angle 5.29009 ( 3519) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3415.95 seconds wall clock time: 59 minutes 37.73 seconds (3577.73 seconds total)