Starting phenix.real_space_refine on Thu Sep 18 06:53:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vxp_21447/09_2025/6vxp_21447.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vxp_21447/09_2025/6vxp_21447.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6vxp_21447/09_2025/6vxp_21447.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vxp_21447/09_2025/6vxp_21447.map" model { file = "/net/cci-nas-00/data/ceres_data/6vxp_21447/09_2025/6vxp_21447.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vxp_21447/09_2025/6vxp_21447.cif" } resolution = 3.39 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: 4 Type Number sf(0) Gaussians S 84 5.16 5 C 9534 2.51 5 N 2485 2.21 5 O 2716 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14819 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2117 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 8, 'TRANS': 268} Chain breaks: 2 Chain: "B" Number of atoms: 2117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2117 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 8, 'TRANS': 268} Chain breaks: 2 Chain: "C" Number of atoms: 2117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2117 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 8, 'TRANS': 268} Chain breaks: 2 Chain: "D" Number of atoms: 2117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2117 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 8, 'TRANS': 268} Chain breaks: 2 Chain: "E" Number of atoms: 2117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2117 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 8, 'TRANS': 268} Chain breaks: 2 Chain: "F" Number of atoms: 2117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2117 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 8, 'TRANS': 268} Chain breaks: 2 Chain: "G" Number of atoms: 2117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2117 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 8, 'TRANS': 268} Chain breaks: 2 Time building chain proxies: 3.69, per 1000 atoms: 0.25 Number of scatterers: 14819 At special positions: 0 Unit cell: (101.2, 102.3, 128.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 84 16.00 O 2716 8.00 N 2485 7.00 C 9534 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: 1.25 Conformation dependent library (CDL) restraints added in 773.1 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3598 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 8 sheets defined 58.8% alpha, 17.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 204 through 229 Proline residue: A 212 - end of helix removed outlier: 3.574A pdb=" N ILE A 225 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL A 229 " --> pdb=" O ILE A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 266 Processing helix chain 'A' and resid 277 through 304 Processing helix chain 'A' and resid 306 through 325 Processing helix chain 'A' and resid 325 through 341 Processing helix chain 'A' and resid 382 through 384 No H-bonds generated for 'chain 'A' and resid 382 through 384' Processing helix chain 'A' and resid 410 through 412 No H-bonds generated for 'chain 'A' and resid 410 through 412' Processing helix chain 'A' and resid 413 through 427 Processing helix chain 'A' and resid 463 through 484 removed outlier: 3.551A pdb=" N TYR A 467 " --> pdb=" O LYS A 463 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N HIS A 484 " --> pdb=" O ILE A 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 229 Proline residue: B 212 - end of helix removed outlier: 3.574A pdb=" N ILE B 225 " --> pdb=" O ALA B 221 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL B 229 " --> pdb=" O ILE B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 266 Processing helix chain 'B' and resid 277 through 304 Processing helix chain 'B' and resid 306 through 325 Processing helix chain 'B' and resid 325 through 341 Processing helix chain 'B' and resid 382 through 384 No H-bonds generated for 'chain 'B' and resid 382 through 384' Processing helix chain 'B' and resid 410 through 412 No H-bonds generated for 'chain 'B' and resid 410 through 412' Processing helix chain 'B' and resid 413 through 427 Processing helix chain 'B' and resid 463 through 484 removed outlier: 3.550A pdb=" N TYR B 467 " --> pdb=" O LYS B 463 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N HIS B 484 " --> pdb=" O ILE B 480 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 229 Proline residue: C 212 - end of helix removed outlier: 3.574A pdb=" N ILE C 225 " --> pdb=" O ALA C 221 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL C 229 " --> pdb=" O ILE C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 266 Processing helix chain 'C' and resid 277 through 304 Processing helix chain 'C' and resid 306 through 325 Processing helix chain 'C' and resid 325 through 341 Processing helix chain 'C' and resid 382 through 384 No H-bonds generated for 'chain 'C' and resid 382 through 384' Processing helix chain 'C' and resid 410 through 412 No H-bonds generated for 'chain 'C' and resid 410 through 412' Processing helix chain 'C' and resid 413 through 427 Processing helix chain 'C' and resid 463 through 484 removed outlier: 3.550A pdb=" N TYR C 467 " --> pdb=" O LYS C 463 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N HIS C 484 " --> pdb=" O ILE C 480 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 229 Proline residue: D 212 - end of helix removed outlier: 3.574A pdb=" N ILE D 225 " --> pdb=" O ALA D 221 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL D 229 " --> pdb=" O ILE D 225 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 266 Processing helix chain 'D' and resid 277 through 304 Processing helix chain 'D' and resid 306 through 325 Processing helix chain 'D' and resid 325 through 341 Processing helix chain 'D' and resid 382 through 384 No H-bonds generated for 'chain 'D' and resid 382 through 384' Processing helix chain 'D' and resid 410 through 412 No H-bonds generated for 'chain 'D' and resid 410 through 412' Processing helix chain 'D' and resid 413 through 427 Processing helix chain 'D' and resid 463 through 484 removed outlier: 3.550A pdb=" N TYR D 467 " --> pdb=" O LYS D 463 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N HIS D 484 " --> pdb=" O ILE D 480 " (cutoff:3.500A) Processing helix chain 'E' and resid 204 through 229 Proline residue: E 212 - end of helix removed outlier: 3.574A pdb=" N ILE E 225 " --> pdb=" O ALA E 221 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL E 229 " --> pdb=" O ILE E 225 " (cutoff:3.500A) Processing helix chain 'E' and resid 238 through 266 Processing helix chain 'E' and resid 277 through 304 Processing helix chain 'E' and resid 306 through 325 Processing helix chain 'E' and resid 325 through 341 Processing helix chain 'E' and resid 382 through 384 No H-bonds generated for 'chain 'E' and resid 382 through 384' Processing helix chain 'E' and resid 410 through 412 No H-bonds generated for 'chain 'E' and resid 410 through 412' Processing helix chain 'E' and resid 413 through 427 Processing helix chain 'E' and resid 463 through 484 removed outlier: 3.550A pdb=" N TYR E 467 " --> pdb=" O LYS E 463 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N HIS E 484 " --> pdb=" O ILE E 480 " (cutoff:3.500A) Processing helix chain 'F' and resid 204 through 229 Proline residue: F 212 - end of helix removed outlier: 3.574A pdb=" N ILE F 225 " --> pdb=" O ALA F 221 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL F 229 " --> pdb=" O ILE F 225 " (cutoff:3.500A) Processing helix chain 'F' and resid 238 through 266 Processing helix chain 'F' and resid 277 through 304 Processing helix chain 'F' and resid 306 through 325 Processing helix chain 'F' and resid 325 through 341 Processing helix chain 'F' and resid 382 through 384 No H-bonds generated for 'chain 'F' and resid 382 through 384' Processing helix chain 'F' and resid 410 through 412 No H-bonds generated for 'chain 'F' and resid 410 through 412' Processing helix chain 'F' and resid 413 through 427 Processing helix chain 'F' and resid 463 through 484 removed outlier: 3.550A pdb=" N TYR F 467 " --> pdb=" O LYS F 463 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N HIS F 484 " --> pdb=" O ILE F 480 " (cutoff:3.500A) Processing helix chain 'G' and resid 204 through 229 Proline residue: G 212 - end of helix removed outlier: 3.574A pdb=" N ILE G 225 " --> pdb=" O ALA G 221 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL G 229 " --> pdb=" O ILE G 225 " (cutoff:3.500A) Processing helix chain 'G' and resid 238 through 266 Processing helix chain 'G' and resid 277 through 304 Processing helix chain 'G' and resid 306 through 325 Processing helix chain 'G' and resid 325 through 341 Processing helix chain 'G' and resid 382 through 384 No H-bonds generated for 'chain 'G' and resid 382 through 384' Processing helix chain 'G' and resid 410 through 412 No H-bonds generated for 'chain 'G' and resid 410 through 412' Processing helix chain 'G' and resid 413 through 427 Processing helix chain 'G' and resid 463 through 484 removed outlier: 3.551A pdb=" N TYR G 467 " --> pdb=" O LYS G 463 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N HIS G 484 " --> pdb=" O ILE G 480 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 349 through 352 removed outlier: 6.007A pdb=" N VAL A 359 " --> pdb=" O LEU A 370 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LEU A 370 " --> pdb=" O VAL A 359 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N VAL G 359 " --> pdb=" O LEU G 370 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LEU G 370 " --> pdb=" O VAL G 359 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N VAL F 359 " --> pdb=" O LEU F 370 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LEU F 370 " --> pdb=" O VAL F 359 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N VAL E 359 " --> pdb=" O LEU E 370 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LEU E 370 " --> pdb=" O VAL E 359 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N VAL D 359 " --> pdb=" O LEU D 370 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LEU D 370 " --> pdb=" O VAL D 359 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N VAL C 359 " --> pdb=" O LEU C 370 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LEU C 370 " --> pdb=" O VAL C 359 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N VAL B 359 " --> pdb=" O LEU B 370 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LEU B 370 " --> pdb=" O VAL B 359 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 439 through 446 removed outlier: 6.839A pdb=" N GLU A 451 " --> pdb=" O SER A 443 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N VAL A 445 " --> pdb=" O PHE A 449 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N PHE A 449 " --> pdb=" O VAL A 445 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N SER A 487 " --> pdb=" O GLN A 407 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 439 through 446 removed outlier: 6.839A pdb=" N GLU B 451 " --> pdb=" O SER B 443 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N VAL B 445 " --> pdb=" O PHE B 449 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N PHE B 449 " --> pdb=" O VAL B 445 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N SER B 487 " --> pdb=" O GLN B 407 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 439 through 446 removed outlier: 6.839A pdb=" N GLU C 451 " --> pdb=" O SER C 443 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N VAL C 445 " --> pdb=" O PHE C 449 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N PHE C 449 " --> pdb=" O VAL C 445 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N SER C 487 " --> pdb=" O GLN C 407 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 439 through 446 removed outlier: 6.838A pdb=" N GLU D 451 " --> pdb=" O SER D 443 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N VAL D 445 " --> pdb=" O PHE D 449 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N PHE D 449 " --> pdb=" O VAL D 445 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N SER D 487 " --> pdb=" O GLN D 407 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 439 through 446 removed outlier: 6.838A pdb=" N GLU E 451 " --> pdb=" O SER E 443 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N VAL E 445 " --> pdb=" O PHE E 449 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N PHE E 449 " --> pdb=" O VAL E 445 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N SER E 487 " --> pdb=" O GLN E 407 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 439 through 446 removed outlier: 6.839A pdb=" N GLU F 451 " --> pdb=" O SER F 443 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N VAL F 445 " --> pdb=" O PHE F 449 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N PHE F 449 " --> pdb=" O VAL F 445 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N SER F 487 " --> pdb=" O GLN F 407 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 439 through 446 removed outlier: 6.839A pdb=" N GLU G 451 " --> pdb=" O SER G 443 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N VAL G 445 " --> pdb=" O PHE G 449 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N PHE G 449 " --> pdb=" O VAL G 445 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N SER G 487 " --> pdb=" O GLN G 407 " (cutoff:3.500A) 1071 hydrogen bonds defined for protein. 3150 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: 2.88 Time building geometry restraints manager: 1.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 4351 1.33 - 1.45: 2037 1.45 - 1.57: 8502 1.57 - 1.69: 13 1.69 - 1.80: 147 Bond restraints: 15050 Sorted by residual: bond pdb=" CA MET E 266 " pdb=" C MET E 266 " ideal model delta sigma weight residual 1.523 1.610 -0.088 1.41e-02 5.03e+03 3.88e+01 bond pdb=" CA MET F 266 " pdb=" C MET F 266 " ideal model delta sigma weight residual 1.523 1.610 -0.088 1.41e-02 5.03e+03 3.86e+01 bond pdb=" CA MET G 266 " pdb=" C MET G 266 " ideal model delta sigma weight residual 1.523 1.610 -0.087 1.41e-02 5.03e+03 3.83e+01 bond pdb=" CA MET C 266 " pdb=" C MET C 266 " ideal model delta sigma weight residual 1.523 1.610 -0.087 1.41e-02 5.03e+03 3.83e+01 bond pdb=" CA MET B 266 " pdb=" C MET B 266 " ideal model delta sigma weight residual 1.523 1.610 -0.087 1.41e-02 5.03e+03 3.83e+01 ... (remaining 15045 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.46: 19718 2.46 - 4.92: 356 4.92 - 7.38: 142 7.38 - 9.85: 91 9.85 - 12.31: 28 Bond angle restraints: 20335 Sorted by residual: angle pdb=" N VAL E 252 " pdb=" CA VAL E 252 " pdb=" C VAL E 252 " ideal model delta sigma weight residual 110.53 101.40 9.13 9.40e-01 1.13e+00 9.43e+01 angle pdb=" N VAL A 252 " pdb=" CA VAL A 252 " pdb=" C VAL A 252 " ideal model delta sigma weight residual 110.53 101.40 9.13 9.40e-01 1.13e+00 9.43e+01 angle pdb=" N VAL G 252 " pdb=" CA VAL G 252 " pdb=" C VAL G 252 " ideal model delta sigma weight residual 110.53 101.40 9.13 9.40e-01 1.13e+00 9.43e+01 angle pdb=" N VAL D 252 " pdb=" CA VAL D 252 " pdb=" C VAL D 252 " ideal model delta sigma weight residual 110.53 101.40 9.13 9.40e-01 1.13e+00 9.43e+01 angle pdb=" N VAL B 252 " pdb=" CA VAL B 252 " pdb=" C VAL B 252 " ideal model delta sigma weight residual 110.53 101.40 9.13 9.40e-01 1.13e+00 9.43e+01 ... (remaining 20330 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.14: 8203 13.14 - 26.27: 638 26.27 - 39.41: 182 39.41 - 52.54: 35 52.54 - 65.68: 14 Dihedral angle restraints: 9072 sinusoidal: 3521 harmonic: 5551 Sorted by residual: dihedral pdb=" C MET G 266 " pdb=" N MET G 266 " pdb=" CA MET G 266 " pdb=" CB MET G 266 " ideal model delta harmonic sigma weight residual -122.60 -110.75 -11.85 0 2.50e+00 1.60e-01 2.25e+01 dihedral pdb=" C MET B 266 " pdb=" N MET B 266 " pdb=" CA MET B 266 " pdb=" CB MET B 266 " ideal model delta harmonic sigma weight residual -122.60 -110.76 -11.84 0 2.50e+00 1.60e-01 2.24e+01 dihedral pdb=" C MET F 266 " pdb=" N MET F 266 " pdb=" CA MET F 266 " pdb=" CB MET F 266 " ideal model delta harmonic sigma weight residual -122.60 -110.77 -11.83 0 2.50e+00 1.60e-01 2.24e+01 ... (remaining 9069 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 1954 0.067 - 0.133: 380 0.133 - 0.200: 57 0.200 - 0.266: 17 0.266 - 0.333: 35 Chirality restraints: 2443 Sorted by residual: chirality pdb=" CA SER E 250 " pdb=" N SER E 250 " pdb=" C SER E 250 " pdb=" CB SER E 250 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.76e+00 chirality pdb=" CA ARG F 265 " pdb=" N ARG F 265 " pdb=" C ARG F 265 " pdb=" CB ARG F 265 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.76e+00 chirality pdb=" CA SER B 250 " pdb=" N SER B 250 " pdb=" C SER B 250 " pdb=" CB SER B 250 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.76e+00 ... (remaining 2440 not shown) Planarity restraints: 2520 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL E 445 " 0.011 2.00e-02 2.50e+03 2.30e-02 5.30e+00 pdb=" C VAL E 445 " -0.040 2.00e-02 2.50e+03 pdb=" O VAL E 445 " 0.015 2.00e-02 2.50e+03 pdb=" N GLU E 446 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL F 445 " 0.011 2.00e-02 2.50e+03 2.29e-02 5.26e+00 pdb=" C VAL F 445 " -0.040 2.00e-02 2.50e+03 pdb=" O VAL F 445 " 0.015 2.00e-02 2.50e+03 pdb=" N GLU F 446 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 445 " -0.011 2.00e-02 2.50e+03 2.29e-02 5.23e+00 pdb=" C VAL C 445 " 0.040 2.00e-02 2.50e+03 pdb=" O VAL C 445 " -0.015 2.00e-02 2.50e+03 pdb=" N GLU C 446 " -0.013 2.00e-02 2.50e+03 ... (remaining 2517 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2689 2.76 - 3.30: 13748 3.30 - 3.83: 23156 3.83 - 4.37: 26985 4.37 - 4.90: 49381 Nonbonded interactions: 115959 Sorted by model distance: nonbonded pdb=" OG SER G 443 " pdb=" OE1 GLU G 451 " model vdw 2.226 3.040 nonbonded pdb=" OG SER B 443 " pdb=" OE1 GLU B 451 " model vdw 2.226 3.040 nonbonded pdb=" OG SER C 443 " pdb=" OE1 GLU C 451 " model vdw 2.227 3.040 nonbonded pdb=" OG SER E 443 " pdb=" OE1 GLU E 451 " model vdw 2.227 3.040 nonbonded pdb=" OG SER A 443 " pdb=" OE1 GLU A 451 " model vdw 2.227 3.040 ... (remaining 115954 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.610 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: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.650 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 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 0.088 15050 Z= 0.371 Angle : 1.131 12.307 20335 Z= 0.792 Chirality : 0.067 0.333 2443 Planarity : 0.005 0.050 2520 Dihedral : 11.357 65.677 5474 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Cbeta Deviations : 0.78 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.30 (0.17), residues: 1897 helix: -0.26 (0.15), residues: 1092 sheet: -2.63 (0.22), residues: 315 loop : -3.43 (0.20), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 444 TYR 0.010 0.001 TYR G 441 PHE 0.011 0.002 PHE G 239 TRP 0.005 0.001 TRP G 397 HIS 0.003 0.001 HIS D 439 Details of bonding type rmsd covalent geometry : bond 0.00781 (15050) covalent geometry : angle 1.13070 (20335) hydrogen bonds : bond 0.15888 ( 1071) hydrogen bonds : angle 6.34336 ( 3150) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 270 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: A 410 ASP cc_start: 0.7648 (t0) cc_final: 0.7422 (t0) REVERT: D 410 ASP cc_start: 0.7530 (t0) cc_final: 0.7317 (t0) REVERT: F 410 ASP cc_start: 0.7378 (t0) cc_final: 0.7130 (t0) REVERT: G 410 ASP cc_start: 0.7357 (t0) cc_final: 0.7113 (t0) outliers start: 0 outliers final: 0 residues processed: 270 average time/residue: 0.1388 time to fit residues: 53.8131 Evaluate side-chains 149 residues out of total 1617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 4.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 ASN A 308 GLN A 331 ASN A 387 GLN B 261 ASN B 308 GLN B 331 ASN B 387 GLN C 261 ASN C 308 GLN C 331 ASN C 387 GLN D 261 ASN D 308 GLN D 331 ASN D 387 GLN E 261 ASN E 308 GLN E 331 ASN E 387 GLN E 428 ASN F 261 ASN F 308 GLN F 331 ASN F 387 GLN G 308 GLN G 331 ASN G 387 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.079178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.058086 restraints weight = 49518.513| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 3.87 r_work: 0.2789 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15050 Z= 0.145 Angle : 0.560 11.073 20335 Z= 0.279 Chirality : 0.039 0.144 2443 Planarity : 0.004 0.039 2520 Dihedral : 3.647 14.969 2030 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.72 % Allowed : 14.04 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.37 (0.20), residues: 1897 helix: 1.45 (0.16), residues: 1141 sheet: -2.35 (0.23), residues: 308 loop : -3.12 (0.22), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 460 TYR 0.015 0.002 TYR D 256 PHE 0.021 0.001 PHE B 222 TRP 0.008 0.001 TRP A 253 HIS 0.002 0.001 HIS G 484 Details of bonding type rmsd covalent geometry : bond 0.00317 (15050) covalent geometry : angle 0.55979 (20335) hydrogen bonds : bond 0.03944 ( 1071) hydrogen bonds : angle 4.00045 ( 3150) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 165 time to evaluate : 0.614 Fit side-chains REVERT: A 346 MET cc_start: 0.9245 (tpp) cc_final: 0.8988 (tpp) REVERT: A 348 ASP cc_start: 0.8972 (m-30) cc_final: 0.8760 (m-30) REVERT: B 348 ASP cc_start: 0.8983 (m-30) cc_final: 0.8668 (m-30) REVERT: C 348 ASP cc_start: 0.9026 (m-30) cc_final: 0.8791 (m-30) REVERT: D 348 ASP cc_start: 0.8974 (m-30) cc_final: 0.8567 (m-30) REVERT: E 228 MET cc_start: 0.0368 (ttm) cc_final: 0.0117 (ttt) REVERT: E 348 ASP cc_start: 0.9071 (m-30) cc_final: 0.8802 (m-30) REVERT: E 362 MET cc_start: 0.8626 (mtp) cc_final: 0.8394 (mtm) REVERT: F 348 ASP cc_start: 0.9062 (m-30) cc_final: 0.8823 (m-30) outliers start: 44 outliers final: 26 residues processed: 183 average time/residue: 0.0897 time to fit residues: 27.8701 Evaluate side-chains 179 residues out of total 1617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 153 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 284 ASP Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 284 ASP Chi-restraints excluded: chain E residue 252 VAL Chi-restraints excluded: chain E residue 284 ASP Chi-restraints excluded: chain E residue 388 VAL Chi-restraints excluded: chain F residue 211 ASP Chi-restraints excluded: chain F residue 284 ASP Chi-restraints excluded: chain G residue 211 ASP Chi-restraints excluded: chain G residue 284 ASP Chi-restraints excluded: chain G residue 292 PHE Chi-restraints excluded: chain G residue 310 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 76 optimal weight: 0.0040 chunk 125 optimal weight: 5.9990 chunk 121 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 108 optimal weight: 40.0000 chunk 139 optimal weight: 10.0000 chunk 92 optimal weight: 0.9980 chunk 186 optimal weight: 0.9990 chunk 104 optimal weight: 9.9990 chunk 162 optimal weight: 40.0000 overall best weight: 1.1796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 ASN B 428 ASN C 428 ASN D 428 ASN F 261 ASN F 428 ASN G 428 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.078980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.058005 restraints weight = 49952.682| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 3.85 r_work: 0.2795 rms_B_bonded: 4.88 restraints_weight: 0.5000 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.3157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 15050 Z= 0.110 Angle : 0.492 8.679 20335 Z= 0.240 Chirality : 0.037 0.133 2443 Planarity : 0.003 0.033 2520 Dihedral : 3.193 10.618 2030 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.86 % Allowed : 15.52 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.75 (0.20), residues: 1897 helix: 2.40 (0.16), residues: 1134 sheet: -2.05 (0.24), residues: 315 loop : -2.67 (0.23), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 265 TYR 0.013 0.002 TYR D 256 PHE 0.023 0.001 PHE E 222 TRP 0.004 0.000 TRP B 253 HIS 0.001 0.000 HIS A 484 Details of bonding type rmsd covalent geometry : bond 0.00240 (15050) covalent geometry : angle 0.49186 (20335) hydrogen bonds : bond 0.03269 ( 1071) hydrogen bonds : angle 3.59221 ( 3150) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 153 time to evaluate : 0.668 Fit side-chains REVERT: A 215 TYR cc_start: 0.6237 (OUTLIER) cc_final: 0.5908 (m-80) REVERT: A 348 ASP cc_start: 0.9001 (m-30) cc_final: 0.8774 (m-30) REVERT: B 215 TYR cc_start: 0.6131 (OUTLIER) cc_final: 0.5751 (m-80) REVERT: B 266 MET cc_start: 0.7132 (mmp) cc_final: 0.6727 (mmp) REVERT: B 348 ASP cc_start: 0.8980 (m-30) cc_final: 0.8741 (m-30) REVERT: C 215 TYR cc_start: 0.6127 (OUTLIER) cc_final: 0.5690 (m-80) REVERT: C 348 ASP cc_start: 0.9034 (m-30) cc_final: 0.8825 (m-30) REVERT: D 215 TYR cc_start: 0.6478 (OUTLIER) cc_final: 0.5985 (m-80) REVERT: D 266 MET cc_start: 0.7495 (mmp) cc_final: 0.7232 (mmp) REVERT: D 346 MET cc_start: 0.9108 (tpp) cc_final: 0.8753 (mmt) REVERT: D 348 ASP cc_start: 0.9013 (m-30) cc_final: 0.8548 (m-30) REVERT: E 215 TYR cc_start: 0.5975 (OUTLIER) cc_final: 0.5599 (m-80) REVERT: E 348 ASP cc_start: 0.9112 (m-30) cc_final: 0.8850 (m-30) REVERT: E 362 MET cc_start: 0.8679 (mtp) cc_final: 0.8347 (mtm) REVERT: F 215 TYR cc_start: 0.6247 (OUTLIER) cc_final: 0.5869 (m-80) REVERT: F 346 MET cc_start: 0.9181 (tpp) cc_final: 0.8791 (mmt) REVERT: F 348 ASP cc_start: 0.9093 (m-30) cc_final: 0.8801 (m-30) REVERT: G 215 TYR cc_start: 0.6098 (OUTLIER) cc_final: 0.5713 (m-80) REVERT: G 266 MET cc_start: 0.7021 (mmp) cc_final: 0.6777 (mmp) REVERT: G 348 ASP cc_start: 0.9037 (m-30) cc_final: 0.8752 (m-30) outliers start: 30 outliers final: 12 residues processed: 161 average time/residue: 0.0961 time to fit residues: 25.8976 Evaluate side-chains 162 residues out of total 1617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 143 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 215 TYR Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain B residue 215 TYR Chi-restraints excluded: chain B residue 284 ASP Chi-restraints excluded: chain C residue 215 TYR Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 215 TYR Chi-restraints excluded: chain D residue 284 ASP Chi-restraints excluded: chain E residue 215 TYR Chi-restraints excluded: chain E residue 284 ASP Chi-restraints excluded: chain F residue 211 ASP Chi-restraints excluded: chain F residue 215 TYR Chi-restraints excluded: chain F residue 284 ASP Chi-restraints excluded: chain G residue 211 ASP Chi-restraints excluded: chain G residue 215 TYR Chi-restraints excluded: chain G residue 284 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 47 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 chunk 2 optimal weight: 8.9990 chunk 166 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 179 optimal weight: 5.9990 chunk 40 optimal weight: 7.9990 chunk 89 optimal weight: 0.9990 chunk 115 optimal weight: 6.9990 chunk 171 optimal weight: 6.9990 chunk 68 optimal weight: 8.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.078129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.057274 restraints weight = 50056.361| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 3.85 r_work: 0.2782 rms_B_bonded: 4.91 restraints_weight: 0.5000 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.3557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 15050 Z= 0.107 Angle : 0.496 7.629 20335 Z= 0.237 Chirality : 0.037 0.129 2443 Planarity : 0.003 0.030 2520 Dihedral : 3.057 10.375 2030 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.23 % Allowed : 16.02 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.67 (0.20), residues: 1897 helix: 3.06 (0.16), residues: 1099 sheet: -1.37 (0.27), residues: 322 loop : -1.92 (0.24), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 342 TYR 0.014 0.001 TYR C 467 PHE 0.019 0.001 PHE E 222 TRP 0.004 0.000 TRP F 397 HIS 0.001 0.000 HIS C 484 Details of bonding type rmsd covalent geometry : bond 0.00235 (15050) covalent geometry : angle 0.49611 (20335) hydrogen bonds : bond 0.03055 ( 1071) hydrogen bonds : angle 3.38199 ( 3150) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 152 time to evaluate : 0.640 Fit side-chains REVERT: A 215 TYR cc_start: 0.6217 (OUTLIER) cc_final: 0.5856 (m-80) REVERT: A 348 ASP cc_start: 0.9022 (m-30) cc_final: 0.8804 (m-30) REVERT: B 215 TYR cc_start: 0.6136 (OUTLIER) cc_final: 0.5760 (m-80) REVERT: B 348 ASP cc_start: 0.8992 (m-30) cc_final: 0.8627 (m-30) REVERT: C 215 TYR cc_start: 0.6170 (OUTLIER) cc_final: 0.5740 (m-80) REVERT: D 215 TYR cc_start: 0.6386 (OUTLIER) cc_final: 0.5887 (m-80) REVERT: D 266 MET cc_start: 0.7459 (mmp) cc_final: 0.7217 (mmp) REVERT: D 348 ASP cc_start: 0.9039 (m-30) cc_final: 0.8636 (m-30) REVERT: E 215 TYR cc_start: 0.6010 (OUTLIER) cc_final: 0.5637 (m-80) REVERT: E 348 ASP cc_start: 0.9067 (m-30) cc_final: 0.8797 (m-30) REVERT: E 362 MET cc_start: 0.8733 (mtp) cc_final: 0.8506 (mtm) REVERT: F 215 TYR cc_start: 0.6230 (OUTLIER) cc_final: 0.5818 (m-80) REVERT: F 348 ASP cc_start: 0.9091 (m-30) cc_final: 0.8794 (m-30) REVERT: G 215 TYR cc_start: 0.6130 (OUTLIER) cc_final: 0.5740 (m-80) REVERT: G 348 ASP cc_start: 0.9061 (m-30) cc_final: 0.8790 (m-30) outliers start: 36 outliers final: 15 residues processed: 170 average time/residue: 0.0965 time to fit residues: 27.4895 Evaluate side-chains 165 residues out of total 1617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 143 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 215 TYR Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain B residue 215 TYR Chi-restraints excluded: chain B residue 284 ASP Chi-restraints excluded: chain C residue 215 TYR Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 215 TYR Chi-restraints excluded: chain D residue 284 ASP Chi-restraints excluded: chain E residue 215 TYR Chi-restraints excluded: chain E residue 284 ASP Chi-restraints excluded: chain E residue 388 VAL Chi-restraints excluded: chain F residue 211 ASP Chi-restraints excluded: chain F residue 215 TYR Chi-restraints excluded: chain F residue 284 ASP Chi-restraints excluded: chain G residue 211 ASP Chi-restraints excluded: chain G residue 215 TYR Chi-restraints excluded: chain G residue 284 ASP Chi-restraints excluded: chain G residue 474 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 72 optimal weight: 6.9990 chunk 131 optimal weight: 10.0000 chunk 106 optimal weight: 0.9980 chunk 99 optimal weight: 0.7980 chunk 168 optimal weight: 5.9990 chunk 26 optimal weight: 6.9990 chunk 123 optimal weight: 7.9990 chunk 182 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 109 optimal weight: 6.9990 chunk 186 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.077086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.056190 restraints weight = 50877.352| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 3.86 r_work: 0.2761 rms_B_bonded: 4.90 restraints_weight: 0.5000 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.3865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15050 Z= 0.121 Angle : 0.500 7.237 20335 Z= 0.239 Chirality : 0.038 0.128 2443 Planarity : 0.003 0.028 2520 Dihedral : 3.056 12.119 2030 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.41 % Allowed : 15.52 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.07 (0.20), residues: 1897 helix: 3.31 (0.15), residues: 1099 sheet: -1.04 (0.28), residues: 322 loop : -1.73 (0.25), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 326 TYR 0.009 0.001 TYR C 467 PHE 0.022 0.001 PHE B 222 TRP 0.004 0.001 TRP B 253 HIS 0.002 0.001 HIS A 484 Details of bonding type rmsd covalent geometry : bond 0.00273 (15050) covalent geometry : angle 0.50044 (20335) hydrogen bonds : bond 0.03052 ( 1071) hydrogen bonds : angle 3.31706 ( 3150) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 142 time to evaluate : 0.595 Fit side-chains REVERT: A 215 TYR cc_start: 0.6226 (OUTLIER) cc_final: 0.5854 (m-80) REVERT: A 348 ASP cc_start: 0.9003 (m-30) cc_final: 0.8754 (m-30) REVERT: B 215 TYR cc_start: 0.6010 (OUTLIER) cc_final: 0.5625 (m-80) REVERT: B 348 ASP cc_start: 0.8995 (m-30) cc_final: 0.8645 (m-30) REVERT: C 215 TYR cc_start: 0.6131 (OUTLIER) cc_final: 0.5704 (m-80) REVERT: D 215 TYR cc_start: 0.6433 (OUTLIER) cc_final: 0.5917 (m-80) REVERT: D 348 ASP cc_start: 0.9051 (m-30) cc_final: 0.8642 (m-30) REVERT: E 215 TYR cc_start: 0.6067 (OUTLIER) cc_final: 0.5672 (m-80) REVERT: E 228 MET cc_start: 0.0232 (ttm) cc_final: 0.0008 (ttt) REVERT: E 348 ASP cc_start: 0.9057 (m-30) cc_final: 0.8766 (m-30) REVERT: E 362 MET cc_start: 0.8753 (mtp) cc_final: 0.8411 (mtm) REVERT: F 215 TYR cc_start: 0.6269 (OUTLIER) cc_final: 0.5835 (m-80) REVERT: F 348 ASP cc_start: 0.9086 (m-30) cc_final: 0.8717 (m-30) REVERT: G 215 TYR cc_start: 0.6163 (OUTLIER) cc_final: 0.5754 (m-80) REVERT: G 348 ASP cc_start: 0.9065 (m-30) cc_final: 0.8810 (m-30) outliers start: 39 outliers final: 18 residues processed: 165 average time/residue: 0.0938 time to fit residues: 26.1140 Evaluate side-chains 162 residues out of total 1617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 137 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 215 TYR Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain B residue 215 TYR Chi-restraints excluded: chain B residue 284 ASP Chi-restraints excluded: chain C residue 215 TYR Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 413 MET Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 215 TYR Chi-restraints excluded: chain D residue 284 ASP Chi-restraints excluded: chain E residue 215 TYR Chi-restraints excluded: chain E residue 284 ASP Chi-restraints excluded: chain E residue 388 VAL Chi-restraints excluded: chain F residue 211 ASP Chi-restraints excluded: chain F residue 215 TYR Chi-restraints excluded: chain F residue 284 ASP Chi-restraints excluded: chain F residue 413 MET Chi-restraints excluded: chain G residue 211 ASP Chi-restraints excluded: chain G residue 215 TYR Chi-restraints excluded: chain G residue 284 ASP Chi-restraints excluded: chain G residue 474 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 70 optimal weight: 0.9980 chunk 94 optimal weight: 5.9990 chunk 89 optimal weight: 6.9990 chunk 165 optimal weight: 9.9990 chunk 147 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 110 optimal weight: 10.0000 chunk 131 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 chunk 172 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.075654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.055047 restraints weight = 51051.338| |-----------------------------------------------------------------------------| r_work (start): 0.2894 rms_B_bonded: 3.84 r_work: 0.2733 rms_B_bonded: 4.90 restraints_weight: 0.5000 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.4117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15050 Z= 0.153 Angle : 0.535 7.659 20335 Z= 0.254 Chirality : 0.039 0.131 2443 Planarity : 0.003 0.027 2520 Dihedral : 3.141 13.917 2030 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.23 % Allowed : 15.58 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.33 (0.20), residues: 1897 helix: 3.47 (0.15), residues: 1092 sheet: -0.71 (0.30), residues: 315 loop : -1.58 (0.25), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 460 TYR 0.010 0.001 TYR C 467 PHE 0.019 0.001 PHE E 222 TRP 0.004 0.001 TRP B 253 HIS 0.003 0.001 HIS B 484 Details of bonding type rmsd covalent geometry : bond 0.00349 (15050) covalent geometry : angle 0.53524 (20335) hydrogen bonds : bond 0.03184 ( 1071) hydrogen bonds : angle 3.36234 ( 3150) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 132 time to evaluate : 0.626 Fit side-chains REVERT: A 215 TYR cc_start: 0.6357 (OUTLIER) cc_final: 0.5971 (m-80) REVERT: A 348 ASP cc_start: 0.9000 (m-30) cc_final: 0.8738 (m-30) REVERT: B 215 TYR cc_start: 0.6162 (OUTLIER) cc_final: 0.5764 (m-80) REVERT: B 348 ASP cc_start: 0.8966 (m-30) cc_final: 0.8603 (m-30) REVERT: C 215 TYR cc_start: 0.6198 (OUTLIER) cc_final: 0.5764 (m-80) REVERT: C 461 MET cc_start: 0.8851 (ttp) cc_final: 0.8584 (ppp) REVERT: D 215 TYR cc_start: 0.6333 (OUTLIER) cc_final: 0.5923 (m-80) REVERT: D 348 ASP cc_start: 0.9013 (m-30) cc_final: 0.8588 (m-30) REVERT: E 215 TYR cc_start: 0.6188 (OUTLIER) cc_final: 0.5743 (m-80) REVERT: E 228 MET cc_start: 0.0315 (ttm) cc_final: 0.0079 (ttt) REVERT: E 348 ASP cc_start: 0.9024 (m-30) cc_final: 0.8687 (m-30) REVERT: E 362 MET cc_start: 0.8794 (mtp) cc_final: 0.8439 (mtm) REVERT: F 215 TYR cc_start: 0.6328 (OUTLIER) cc_final: 0.5870 (m-80) REVERT: F 348 ASP cc_start: 0.9085 (m-30) cc_final: 0.8718 (m-30) REVERT: G 215 TYR cc_start: 0.6121 (OUTLIER) cc_final: 0.5684 (m-80) REVERT: G 348 ASP cc_start: 0.9013 (m-30) cc_final: 0.8692 (m-30) outliers start: 36 outliers final: 19 residues processed: 155 average time/residue: 0.0963 time to fit residues: 24.8146 Evaluate side-chains 155 residues out of total 1617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 129 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 215 TYR Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain B residue 215 TYR Chi-restraints excluded: chain B residue 284 ASP Chi-restraints excluded: chain C residue 215 TYR Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 413 MET Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 215 TYR Chi-restraints excluded: chain D residue 284 ASP Chi-restraints excluded: chain E residue 215 TYR Chi-restraints excluded: chain E residue 284 ASP Chi-restraints excluded: chain E residue 388 VAL Chi-restraints excluded: chain F residue 211 ASP Chi-restraints excluded: chain F residue 215 TYR Chi-restraints excluded: chain F residue 284 ASP Chi-restraints excluded: chain F residue 311 LEU Chi-restraints excluded: chain F residue 340 PHE Chi-restraints excluded: chain G residue 211 ASP Chi-restraints excluded: chain G residue 215 TYR Chi-restraints excluded: chain G residue 284 ASP Chi-restraints excluded: chain G residue 474 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 158 optimal weight: 8.9990 chunk 50 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 chunk 125 optimal weight: 3.9990 chunk 5 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 115 optimal weight: 1.9990 chunk 60 optimal weight: 8.9990 chunk 0 optimal weight: 30.0000 chunk 82 optimal weight: 8.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.075858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.055314 restraints weight = 50998.568| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 3.83 r_work: 0.2742 rms_B_bonded: 4.88 restraints_weight: 0.5000 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.4343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15050 Z= 0.132 Angle : 0.533 9.542 20335 Z= 0.250 Chirality : 0.039 0.254 2443 Planarity : 0.003 0.026 2520 Dihedral : 3.133 20.477 2030 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.98 % Allowed : 16.08 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.44 (0.20), residues: 1897 helix: 3.52 (0.15), residues: 1092 sheet: -0.57 (0.30), residues: 315 loop : -1.50 (0.26), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 460 TYR 0.009 0.001 TYR C 467 PHE 0.022 0.001 PHE E 222 TRP 0.005 0.001 TRP G 397 HIS 0.002 0.001 HIS B 484 Details of bonding type rmsd covalent geometry : bond 0.00298 (15050) covalent geometry : angle 0.53317 (20335) hydrogen bonds : bond 0.03058 ( 1071) hydrogen bonds : angle 3.32079 ( 3150) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 135 time to evaluate : 0.660 Fit side-chains REVERT: A 215 TYR cc_start: 0.6338 (OUTLIER) cc_final: 0.5961 (m-80) REVERT: A 348 ASP cc_start: 0.8997 (m-30) cc_final: 0.8738 (m-30) REVERT: B 215 TYR cc_start: 0.6161 (OUTLIER) cc_final: 0.5740 (m-80) REVERT: B 348 ASP cc_start: 0.8972 (m-30) cc_final: 0.8609 (m-30) REVERT: C 215 TYR cc_start: 0.6281 (OUTLIER) cc_final: 0.5817 (m-80) REVERT: D 215 TYR cc_start: 0.6452 (OUTLIER) cc_final: 0.6056 (m-80) REVERT: D 348 ASP cc_start: 0.9030 (m-30) cc_final: 0.8607 (m-30) REVERT: E 215 TYR cc_start: 0.6216 (OUTLIER) cc_final: 0.5786 (m-80) REVERT: E 228 MET cc_start: 0.0716 (ttm) cc_final: 0.0484 (ttt) REVERT: E 348 ASP cc_start: 0.9026 (m-30) cc_final: 0.8690 (m-30) REVERT: E 362 MET cc_start: 0.8776 (mtp) cc_final: 0.8379 (mtm) REVERT: F 215 TYR cc_start: 0.6337 (OUTLIER) cc_final: 0.5865 (m-80) REVERT: F 348 ASP cc_start: 0.9080 (m-30) cc_final: 0.8700 (m-30) REVERT: F 461 MET cc_start: 0.8619 (ttp) cc_final: 0.8393 (ppp) REVERT: G 215 TYR cc_start: 0.6191 (OUTLIER) cc_final: 0.5770 (m-80) REVERT: G 348 ASP cc_start: 0.9006 (m-30) cc_final: 0.8729 (m-30) outliers start: 32 outliers final: 19 residues processed: 153 average time/residue: 0.0956 time to fit residues: 24.5281 Evaluate side-chains 156 residues out of total 1617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 130 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 215 TYR Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain B residue 215 TYR Chi-restraints excluded: chain B residue 284 ASP Chi-restraints excluded: chain C residue 215 TYR Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 215 TYR Chi-restraints excluded: chain D residue 284 ASP Chi-restraints excluded: chain D residue 346 MET Chi-restraints excluded: chain E residue 215 TYR Chi-restraints excluded: chain E residue 284 ASP Chi-restraints excluded: chain E residue 388 VAL Chi-restraints excluded: chain F residue 211 ASP Chi-restraints excluded: chain F residue 215 TYR Chi-restraints excluded: chain F residue 284 ASP Chi-restraints excluded: chain F residue 388 VAL Chi-restraints excluded: chain G residue 211 ASP Chi-restraints excluded: chain G residue 215 TYR Chi-restraints excluded: chain G residue 284 ASP Chi-restraints excluded: chain G residue 388 VAL Chi-restraints excluded: chain G residue 474 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 30 optimal weight: 9.9990 chunk 44 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 60 optimal weight: 7.9990 chunk 135 optimal weight: 40.0000 chunk 170 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 5 optimal weight: 0.7980 chunk 160 optimal weight: 0.8980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.075442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.054966 restraints weight = 51106.476| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 3.82 r_work: 0.2732 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.4561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15050 Z= 0.141 Angle : 0.539 9.165 20335 Z= 0.254 Chirality : 0.039 0.277 2443 Planarity : 0.003 0.025 2520 Dihedral : 3.150 18.452 2030 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.79 % Allowed : 16.45 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.55 (0.20), residues: 1897 helix: 3.56 (0.15), residues: 1092 sheet: -0.43 (0.31), residues: 315 loop : -1.40 (0.27), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 265 TYR 0.010 0.001 TYR C 467 PHE 0.027 0.001 PHE G 222 TRP 0.005 0.001 TRP A 397 HIS 0.004 0.001 HIS A 484 Details of bonding type rmsd covalent geometry : bond 0.00320 (15050) covalent geometry : angle 0.53914 (20335) hydrogen bonds : bond 0.03128 ( 1071) hydrogen bonds : angle 3.34117 ( 3150) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 136 time to evaluate : 0.643 Fit side-chains revert: symmetry clash REVERT: A 215 TYR cc_start: 0.6429 (OUTLIER) cc_final: 0.6026 (m-80) REVERT: A 348 ASP cc_start: 0.8986 (m-30) cc_final: 0.8716 (m-30) REVERT: B 215 TYR cc_start: 0.6033 (OUTLIER) cc_final: 0.5618 (m-80) REVERT: B 348 ASP cc_start: 0.8983 (m-30) cc_final: 0.8563 (m-30) REVERT: C 215 TYR cc_start: 0.6121 (OUTLIER) cc_final: 0.5718 (m-80) REVERT: D 215 TYR cc_start: 0.6417 (OUTLIER) cc_final: 0.5996 (m-80) REVERT: D 348 ASP cc_start: 0.9021 (m-30) cc_final: 0.8615 (m-30) REVERT: E 215 TYR cc_start: 0.6284 (OUTLIER) cc_final: 0.5816 (m-80) REVERT: E 228 MET cc_start: 0.1014 (ttm) cc_final: 0.0778 (ttt) REVERT: E 348 ASP cc_start: 0.9018 (m-30) cc_final: 0.8671 (m-30) REVERT: E 362 MET cc_start: 0.8758 (mtp) cc_final: 0.8401 (mtm) REVERT: F 215 TYR cc_start: 0.6531 (OUTLIER) cc_final: 0.6059 (m-80) REVERT: F 228 MET cc_start: 0.3646 (ttm) cc_final: 0.3070 (mtt) REVERT: F 348 ASP cc_start: 0.9064 (m-30) cc_final: 0.8690 (m-30) REVERT: G 215 TYR cc_start: 0.6271 (OUTLIER) cc_final: 0.5797 (m-80) REVERT: G 348 ASP cc_start: 0.9013 (m-30) cc_final: 0.8686 (m-30) outliers start: 29 outliers final: 18 residues processed: 153 average time/residue: 0.0884 time to fit residues: 22.7915 Evaluate side-chains 157 residues out of total 1617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 132 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 215 TYR Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain B residue 215 TYR Chi-restraints excluded: chain B residue 284 ASP Chi-restraints excluded: chain C residue 215 TYR Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 215 TYR Chi-restraints excluded: chain D residue 284 ASP Chi-restraints excluded: chain E residue 215 TYR Chi-restraints excluded: chain E residue 284 ASP Chi-restraints excluded: chain F residue 211 ASP Chi-restraints excluded: chain F residue 215 TYR Chi-restraints excluded: chain F residue 284 ASP Chi-restraints excluded: chain F residue 388 VAL Chi-restraints excluded: chain G residue 211 ASP Chi-restraints excluded: chain G residue 215 TYR Chi-restraints excluded: chain G residue 284 ASP Chi-restraints excluded: chain G residue 388 VAL Chi-restraints excluded: chain G residue 474 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 47 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 87 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 chunk 163 optimal weight: 7.9990 chunk 115 optimal weight: 3.9990 chunk 106 optimal weight: 0.8980 chunk 162 optimal weight: 30.0000 chunk 84 optimal weight: 9.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.075825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.055437 restraints weight = 51025.015| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 3.82 r_work: 0.2747 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.4685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15050 Z= 0.121 Angle : 0.538 9.925 20335 Z= 0.251 Chirality : 0.040 0.298 2443 Planarity : 0.003 0.025 2520 Dihedral : 3.125 19.807 2030 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.92 % Allowed : 16.20 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.61 (0.20), residues: 1897 helix: 3.57 (0.15), residues: 1092 sheet: -0.32 (0.31), residues: 315 loop : -1.35 (0.27), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 426 TYR 0.010 0.001 TYR C 467 PHE 0.031 0.001 PHE G 222 TRP 0.006 0.001 TRP G 397 HIS 0.004 0.001 HIS B 484 Details of bonding type rmsd covalent geometry : bond 0.00272 (15050) covalent geometry : angle 0.53814 (20335) hydrogen bonds : bond 0.02994 ( 1071) hydrogen bonds : angle 3.31012 ( 3150) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 133 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 215 TYR cc_start: 0.6455 (OUTLIER) cc_final: 0.6062 (m-80) REVERT: A 348 ASP cc_start: 0.8978 (m-30) cc_final: 0.8714 (m-30) REVERT: B 215 TYR cc_start: 0.5961 (OUTLIER) cc_final: 0.5538 (m-80) REVERT: B 348 ASP cc_start: 0.8984 (m-30) cc_final: 0.8631 (m-30) REVERT: C 215 TYR cc_start: 0.6200 (OUTLIER) cc_final: 0.5778 (m-80) REVERT: D 215 TYR cc_start: 0.6329 (OUTLIER) cc_final: 0.5924 (m-80) REVERT: D 348 ASP cc_start: 0.9035 (m-30) cc_final: 0.8615 (m-30) REVERT: E 215 TYR cc_start: 0.6288 (OUTLIER) cc_final: 0.5837 (m-80) REVERT: E 228 MET cc_start: 0.1247 (ttm) cc_final: 0.1010 (ttt) REVERT: E 348 ASP cc_start: 0.9032 (m-30) cc_final: 0.8699 (m-30) REVERT: E 362 MET cc_start: 0.8736 (mtp) cc_final: 0.8374 (mtm) REVERT: F 215 TYR cc_start: 0.6529 (OUTLIER) cc_final: 0.6055 (m-80) REVERT: F 228 MET cc_start: 0.3656 (ttm) cc_final: 0.3076 (mtt) REVERT: F 348 ASP cc_start: 0.9075 (m-30) cc_final: 0.8697 (m-30) REVERT: G 215 TYR cc_start: 0.6378 (OUTLIER) cc_final: 0.5880 (m-80) REVERT: G 348 ASP cc_start: 0.9037 (m-30) cc_final: 0.8773 (m-30) outliers start: 31 outliers final: 20 residues processed: 151 average time/residue: 0.0969 time to fit residues: 24.4875 Evaluate side-chains 157 residues out of total 1617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 130 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 215 TYR Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain B residue 215 TYR Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 284 ASP Chi-restraints excluded: chain C residue 215 TYR Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 215 TYR Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 284 ASP Chi-restraints excluded: chain E residue 215 TYR Chi-restraints excluded: chain E residue 284 ASP Chi-restraints excluded: chain E residue 388 VAL Chi-restraints excluded: chain F residue 211 ASP Chi-restraints excluded: chain F residue 215 TYR Chi-restraints excluded: chain F residue 284 ASP Chi-restraints excluded: chain F residue 388 VAL Chi-restraints excluded: chain G residue 211 ASP Chi-restraints excluded: chain G residue 215 TYR Chi-restraints excluded: chain G residue 284 ASP Chi-restraints excluded: chain G residue 388 VAL Chi-restraints excluded: chain G residue 474 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 125 optimal weight: 0.0470 chunk 161 optimal weight: 7.9990 chunk 114 optimal weight: 0.2980 chunk 93 optimal weight: 0.5980 chunk 50 optimal weight: 5.9990 chunk 152 optimal weight: 3.9990 chunk 129 optimal weight: 6.9990 chunk 118 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 82 optimal weight: 9.9990 chunk 17 optimal weight: 3.9990 overall best weight: 1.5882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.077458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.058181 restraints weight = 50786.678| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 3.45 r_work: 0.2821 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.4795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15050 Z= 0.125 Angle : 0.563 11.183 20335 Z= 0.261 Chirality : 0.042 0.317 2443 Planarity : 0.003 0.025 2520 Dihedral : 3.174 24.162 2030 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.73 % Allowed : 16.45 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.67 (0.20), residues: 1897 helix: 3.59 (0.15), residues: 1092 sheet: -0.23 (0.32), residues: 315 loop : -1.30 (0.27), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 460 TYR 0.009 0.001 TYR E 467 PHE 0.032 0.001 PHE G 222 TRP 0.006 0.001 TRP A 397 HIS 0.004 0.001 HIS B 484 Details of bonding type rmsd covalent geometry : bond 0.00281 (15050) covalent geometry : angle 0.56328 (20335) hydrogen bonds : bond 0.03018 ( 1071) hydrogen bonds : angle 3.33912 ( 3150) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 133 time to evaluate : 0.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 TYR cc_start: 0.6465 (OUTLIER) cc_final: 0.6003 (m-80) REVERT: B 215 TYR cc_start: 0.6125 (OUTLIER) cc_final: 0.5628 (m-80) REVERT: B 348 ASP cc_start: 0.9041 (m-30) cc_final: 0.8755 (m-30) REVERT: C 215 TYR cc_start: 0.6378 (OUTLIER) cc_final: 0.5907 (m-80) REVERT: D 215 TYR cc_start: 0.6335 (OUTLIER) cc_final: 0.5849 (m-80) REVERT: D 348 ASP cc_start: 0.9000 (m-30) cc_final: 0.8654 (m-30) REVERT: E 215 TYR cc_start: 0.6312 (OUTLIER) cc_final: 0.5831 (m-80) REVERT: E 228 MET cc_start: 0.1291 (ttm) cc_final: 0.1036 (ttt) REVERT: E 348 ASP cc_start: 0.9034 (m-30) cc_final: 0.8775 (m-30) REVERT: E 362 MET cc_start: 0.8639 (mtp) cc_final: 0.8341 (mtm) REVERT: F 215 TYR cc_start: 0.6710 (OUTLIER) cc_final: 0.6129 (m-80) REVERT: F 228 MET cc_start: 0.3720 (ttm) cc_final: 0.3128 (mtt) REVERT: F 348 ASP cc_start: 0.9111 (m-30) cc_final: 0.8783 (m-30) REVERT: G 215 TYR cc_start: 0.6555 (OUTLIER) cc_final: 0.5987 (m-80) REVERT: G 348 ASP cc_start: 0.9019 (m-30) cc_final: 0.8799 (m-30) outliers start: 28 outliers final: 20 residues processed: 149 average time/residue: 0.0982 time to fit residues: 24.2865 Evaluate side-chains 157 residues out of total 1617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 130 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 215 TYR Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain B residue 215 TYR Chi-restraints excluded: chain B residue 284 ASP Chi-restraints excluded: chain C residue 215 TYR Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 215 TYR Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 284 ASP Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain E residue 215 TYR Chi-restraints excluded: chain E residue 284 ASP Chi-restraints excluded: chain E residue 388 VAL Chi-restraints excluded: chain F residue 211 ASP Chi-restraints excluded: chain F residue 215 TYR Chi-restraints excluded: chain F residue 284 ASP Chi-restraints excluded: chain F residue 388 VAL Chi-restraints excluded: chain G residue 211 ASP Chi-restraints excluded: chain G residue 215 TYR Chi-restraints excluded: chain G residue 284 ASP Chi-restraints excluded: chain G residue 474 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 140 optimal weight: 7.9990 chunk 182 optimal weight: 0.8980 chunk 78 optimal weight: 8.9990 chunk 168 optimal weight: 6.9990 chunk 103 optimal weight: 6.9990 chunk 129 optimal weight: 2.9990 chunk 104 optimal weight: 5.9990 chunk 57 optimal weight: 10.0000 chunk 72 optimal weight: 3.9990 chunk 152 optimal weight: 3.9990 chunk 179 optimal weight: 0.8980 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 471 GLN C 471 GLN F 471 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.076451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.057239 restraints weight = 50827.392| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 3.39 r_work: 0.2795 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.4931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 15050 Z= 0.173 Angle : 0.591 10.350 20335 Z= 0.280 Chirality : 0.043 0.332 2443 Planarity : 0.003 0.025 2520 Dihedral : 3.317 23.565 2030 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.98 % Allowed : 16.76 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.72 (0.21), residues: 1897 helix: 3.62 (0.15), residues: 1092 sheet: -0.56 (0.30), residues: 350 loop : -0.98 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 342 TYR 0.011 0.001 TYR E 467 PHE 0.033 0.001 PHE G 222 TRP 0.005 0.001 TRP F 253 HIS 0.008 0.002 HIS A 484 Details of bonding type rmsd covalent geometry : bond 0.00395 (15050) covalent geometry : angle 0.59148 (20335) hydrogen bonds : bond 0.03320 ( 1071) hydrogen bonds : angle 3.45970 ( 3150) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3362.70 seconds wall clock time: 58 minutes 37.03 seconds (3517.03 seconds total)