Starting phenix.real_space_refine on Fri Sep 27 03:13:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxp_21447/09_2024/6vxp_21447.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxp_21447/09_2024/6vxp_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxp_21447/09_2024/6vxp_21447.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxp_21447/09_2024/6vxp_21447.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxp_21447/09_2024/6vxp_21447.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxp_21447/09_2024/6vxp_21447.cif" } resolution = 3.39 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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: 8.71, per 1000 atoms: 0.59 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: 3.61 Conformation dependent library (CDL) restraints added in 2.0 seconds 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: 1.52 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: 4.90 Time building geometry restraints manager: 4.27 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: 0.00 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: 1.060 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: 0.510 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 34.330 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.060 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: 0.010 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.430 ------------------------------------------------------------------------------- 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= 0.511 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.17), 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 TRP 0.005 0.001 TRP G 397 HIS 0.003 0.001 HIS D 439 PHE 0.011 0.002 PHE G 239 TYR 0.010 0.001 TYR G 441 ARG 0.003 0.001 ARG C 444 *********************** 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 fitting. rotamer outliers: 0 poor density : 270 time to evaluate : 1.696 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: 0.2971 time to fit residues: 114.0405 Evaluate side-chains 149 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 149 time to evaluate : 1.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 159 optimal weight: 6.9990 chunk 143 optimal weight: 5.9990 chunk 79 optimal weight: 0.9980 chunk 48 optimal weight: 5.9990 chunk 96 optimal weight: 2.9990 chunk 76 optimal weight: 10.0000 chunk 148 optimal weight: 2.9990 chunk 57 optimal weight: 9.9990 chunk 90 optimal weight: 0.9990 chunk 110 optimal weight: 0.8980 chunk 171 optimal weight: 3.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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 A 428 ASN B 261 ASN B 308 GLN B 331 ASN B 387 GLN B 428 ASN C 261 ASN C 308 GLN C 331 ASN C 387 GLN C 428 ASN D 261 ASN D 308 GLN D 331 ASN D 387 GLN D 428 ASN 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 F 428 ASN G 308 GLN G 331 ASN G 387 GLN G 428 ASN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15050 Z= 0.207 Angle : 0.571 11.183 20335 Z= 0.283 Chirality : 0.039 0.143 2443 Planarity : 0.004 0.038 2520 Dihedral : 3.652 14.850 2030 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.91 % Allowed : 13.73 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.19), residues: 1897 helix: 1.46 (0.16), residues: 1141 sheet: -2.38 (0.23), residues: 308 loop : -3.08 (0.22), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 253 HIS 0.003 0.001 HIS A 484 PHE 0.022 0.001 PHE B 222 TYR 0.015 0.002 TYR D 256 ARG 0.003 0.000 ARG A 342 *********************** 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 216 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 169 time to evaluate : 1.640 Fit side-chains REVERT: E 228 MET cc_start: 0.1398 (ttm) cc_final: 0.0956 (ttt) outliers start: 47 outliers final: 24 residues processed: 187 average time/residue: 0.1881 time to fit residues: 58.1151 Evaluate side-chains 168 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 144 time to evaluate : 1.633 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 95 optimal weight: 7.9990 chunk 53 optimal weight: 0.2980 chunk 142 optimal weight: 8.9990 chunk 116 optimal weight: 0.0870 chunk 47 optimal weight: 3.9990 chunk 171 optimal weight: 6.9990 chunk 185 optimal weight: 4.9990 chunk 153 optimal weight: 3.9990 chunk 170 optimal weight: 2.9990 chunk 58 optimal weight: 9.9990 chunk 137 optimal weight: 0.0370 overall best weight: 1.4840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 261 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.3227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15050 Z= 0.181 Angle : 0.513 12.131 20335 Z= 0.249 Chirality : 0.038 0.134 2443 Planarity : 0.003 0.034 2520 Dihedral : 3.239 10.612 2030 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.20), residues: 1897 helix: 2.42 (0.16), residues: 1134 sheet: -2.23 (0.23), residues: 350 loop : -2.50 (0.24), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 253 HIS 0.001 0.000 HIS A 484 PHE 0.024 0.001 PHE E 222 TYR 0.014 0.002 TYR F 467 ARG 0.003 0.000 ARG F 265 *********************** 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 175 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 146 time to evaluate : 1.771 Fit side-chains REVERT: A 215 TYR cc_start: 0.6825 (OUTLIER) cc_final: 0.6067 (m-80) REVERT: B 215 TYR cc_start: 0.6840 (OUTLIER) cc_final: 0.6056 (m-80) REVERT: C 215 TYR cc_start: 0.6767 (OUTLIER) cc_final: 0.5998 (m-80) REVERT: D 215 TYR cc_start: 0.7015 (OUTLIER) cc_final: 0.6087 (m-80) REVERT: E 215 TYR cc_start: 0.6730 (OUTLIER) cc_final: 0.5834 (m-80) REVERT: F 215 TYR cc_start: 0.6712 (OUTLIER) cc_final: 0.5871 (m-80) REVERT: G 215 TYR cc_start: 0.6807 (OUTLIER) cc_final: 0.5960 (m-80) outliers start: 29 outliers final: 12 residues processed: 156 average time/residue: 0.1938 time to fit residues: 49.8973 Evaluate side-chains 157 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 138 time to evaluate : 1.606 ------------------------------------------------------------------------------- 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 169 optimal weight: 0.9980 chunk 129 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 chunk 115 optimal weight: 7.9990 chunk 172 optimal weight: 0.9980 chunk 182 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 163 optimal weight: 20.0000 chunk 49 optimal weight: 7.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.3634 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= 0.202 Angle : 0.529 9.638 20335 Z= 0.254 Chirality : 0.038 0.131 2443 Planarity : 0.003 0.031 2520 Dihedral : 3.218 12.961 2030 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.54 % Allowed : 16.64 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.20), residues: 1897 helix: 3.12 (0.15), residues: 1092 sheet: -1.56 (0.26), residues: 357 loop : -1.80 (0.25), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 253 HIS 0.003 0.001 HIS A 484 PHE 0.019 0.001 PHE E 222 TYR 0.012 0.001 TYR D 467 ARG 0.001 0.000 ARG A 342 *********************** 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 183 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 142 time to evaluate : 1.702 Fit side-chains REVERT: A 215 TYR cc_start: 0.6852 (OUTLIER) cc_final: 0.6058 (m-80) REVERT: B 215 TYR cc_start: 0.6638 (OUTLIER) cc_final: 0.5905 (m-80) REVERT: C 215 TYR cc_start: 0.6796 (OUTLIER) cc_final: 0.5963 (m-80) REVERT: D 215 TYR cc_start: 0.6927 (OUTLIER) cc_final: 0.5979 (m-80) REVERT: E 215 TYR cc_start: 0.6768 (OUTLIER) cc_final: 0.5879 (m-80) REVERT: F 215 TYR cc_start: 0.6736 (OUTLIER) cc_final: 0.5869 (m-80) REVERT: G 215 TYR cc_start: 0.6804 (OUTLIER) cc_final: 0.5922 (m-80) outliers start: 41 outliers final: 14 residues processed: 163 average time/residue: 0.1978 time to fit residues: 53.2680 Evaluate side-chains 157 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 136 time to evaluate : 1.705 ------------------------------------------------------------------------------- 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 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 152 optimal weight: 4.9990 chunk 103 optimal weight: 5.9990 chunk 2 optimal weight: 4.9990 chunk 136 optimal weight: 9.9990 chunk 75 optimal weight: 0.0050 chunk 155 optimal weight: 2.9990 chunk 126 optimal weight: 6.9990 chunk 0 optimal weight: 50.0000 chunk 93 optimal weight: 0.0470 chunk 163 optimal weight: 10.0000 chunk 46 optimal weight: 0.9990 overall best weight: 1.8098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.3954 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= 0.199 Angle : 0.520 8.774 20335 Z= 0.248 Chirality : 0.038 0.128 2443 Planarity : 0.003 0.029 2520 Dihedral : 3.180 14.863 2030 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.72 % Allowed : 16.02 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.07 (0.20), residues: 1897 helix: 3.30 (0.15), residues: 1099 sheet: -1.03 (0.28), residues: 322 loop : -1.70 (0.25), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 253 HIS 0.003 0.001 HIS A 484 PHE 0.021 0.001 PHE E 222 TYR 0.011 0.001 TYR F 467 ARG 0.001 0.000 ARG A 342 *********************** 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 fitting. rotamer outliers: 44 poor density : 137 time to evaluate : 1.701 Fit side-chains REVERT: A 215 TYR cc_start: 0.6907 (OUTLIER) cc_final: 0.6082 (m-80) REVERT: B 215 TYR cc_start: 0.6673 (OUTLIER) cc_final: 0.5891 (m-80) REVERT: C 215 TYR cc_start: 0.6763 (OUTLIER) cc_final: 0.5906 (m-80) REVERT: D 215 TYR cc_start: 0.6881 (OUTLIER) cc_final: 0.6113 (m-80) REVERT: E 215 TYR cc_start: 0.6787 (OUTLIER) cc_final: 0.5845 (m-80) REVERT: F 215 TYR cc_start: 0.6784 (OUTLIER) cc_final: 0.5875 (m-80) REVERT: G 215 TYR cc_start: 0.6844 (OUTLIER) cc_final: 0.5919 (m-80) outliers start: 44 outliers final: 18 residues processed: 161 average time/residue: 0.1943 time to fit residues: 51.6366 Evaluate side-chains 157 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 132 time to evaluate : 1.803 ------------------------------------------------------------------------------- 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 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 388 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 61 optimal weight: 6.9990 chunk 164 optimal weight: 0.1980 chunk 36 optimal weight: 0.9990 chunk 107 optimal weight: 0.0470 chunk 45 optimal weight: 4.9990 chunk 182 optimal weight: 0.8980 chunk 151 optimal weight: 0.8980 chunk 84 optimal weight: 10.0000 chunk 15 optimal weight: 4.9990 chunk 60 optimal weight: 7.9990 chunk 96 optimal weight: 4.9990 overall best weight: 0.6080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.4184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 15050 Z= 0.120 Angle : 0.505 8.183 20335 Z= 0.235 Chirality : 0.038 0.120 2443 Planarity : 0.003 0.025 2520 Dihedral : 3.024 13.807 2030 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.98 % Allowed : 16.33 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.26 (0.20), residues: 1897 helix: 3.40 (0.15), residues: 1099 sheet: -0.84 (0.29), residues: 322 loop : -1.57 (0.25), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.000 TRP C 397 HIS 0.001 0.000 HIS F 484 PHE 0.022 0.001 PHE E 222 TYR 0.009 0.001 TYR D 256 ARG 0.001 0.000 ARG A 342 *********************** 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 180 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 148 time to evaluate : 1.617 Fit side-chains REVERT: A 215 TYR cc_start: 0.6889 (OUTLIER) cc_final: 0.6115 (m-80) REVERT: B 215 TYR cc_start: 0.6650 (OUTLIER) cc_final: 0.5906 (m-80) REVERT: C 215 TYR cc_start: 0.6765 (OUTLIER) cc_final: 0.5931 (m-80) REVERT: D 215 TYR cc_start: 0.6908 (OUTLIER) cc_final: 0.6114 (m-80) REVERT: E 215 TYR cc_start: 0.6799 (OUTLIER) cc_final: 0.5866 (m-80) REVERT: F 215 TYR cc_start: 0.6779 (OUTLIER) cc_final: 0.5927 (m-80) REVERT: G 215 TYR cc_start: 0.6877 (OUTLIER) cc_final: 0.5939 (m-80) outliers start: 32 outliers final: 14 residues processed: 161 average time/residue: 0.1933 time to fit residues: 51.1213 Evaluate side-chains 158 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 137 time to evaluate : 1.579 ------------------------------------------------------------------------------- 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 D residue 346 MET 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 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 176 optimal weight: 7.9990 chunk 20 optimal weight: 0.5980 chunk 104 optimal weight: 3.9990 chunk 133 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 153 optimal weight: 1.9990 chunk 102 optimal weight: 0.6980 chunk 182 optimal weight: 0.7980 chunk 114 optimal weight: 5.9990 chunk 111 optimal weight: 4.9990 chunk 84 optimal weight: 5.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.4335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 15050 Z= 0.156 Angle : 0.510 9.565 20335 Z= 0.238 Chirality : 0.038 0.195 2443 Planarity : 0.003 0.025 2520 Dihedral : 3.026 17.100 2030 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.48 % Allowed : 17.07 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.47 (0.20), residues: 1897 helix: 3.51 (0.15), residues: 1099 sheet: -0.51 (0.31), residues: 315 loop : -1.52 (0.26), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 397 HIS 0.002 0.001 HIS F 484 PHE 0.022 0.001 PHE E 222 TYR 0.011 0.001 TYR C 467 ARG 0.001 0.000 ARG A 426 *********************** 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 162 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 138 time to evaluate : 1.871 Fit side-chains REVERT: A 215 TYR cc_start: 0.6958 (OUTLIER) cc_final: 0.6146 (m-80) REVERT: B 215 TYR cc_start: 0.6689 (OUTLIER) cc_final: 0.5915 (m-80) REVERT: C 215 TYR cc_start: 0.6748 (OUTLIER) cc_final: 0.5897 (m-80) REVERT: D 215 TYR cc_start: 0.6782 (OUTLIER) cc_final: 0.6041 (m-80) REVERT: E 215 TYR cc_start: 0.6730 (OUTLIER) cc_final: 0.5755 (m-80) REVERT: E 228 MET cc_start: 0.0794 (ttm) cc_final: 0.0504 (ttt) REVERT: E 346 MET cc_start: 0.7797 (tpp) cc_final: 0.7557 (mmt) REVERT: F 215 TYR cc_start: 0.6809 (OUTLIER) cc_final: 0.5947 (m-80) REVERT: G 215 TYR cc_start: 0.6893 (OUTLIER) cc_final: 0.5917 (m-80) outliers start: 24 outliers final: 14 residues processed: 149 average time/residue: 0.1993 time to fit residues: 48.7705 Evaluate side-chains 156 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 135 time to evaluate : 1.826 ------------------------------------------------------------------------------- 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 D residue 346 MET 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 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 112 optimal weight: 10.0000 chunk 72 optimal weight: 0.9980 chunk 108 optimal weight: 40.0000 chunk 54 optimal weight: 40.0000 chunk 35 optimal weight: 5.9990 chunk 115 optimal weight: 4.9990 chunk 124 optimal weight: 0.7980 chunk 90 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 143 optimal weight: 5.9990 chunk 165 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.4464 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= 0.147 Angle : 0.523 9.451 20335 Z= 0.241 Chirality : 0.039 0.306 2443 Planarity : 0.003 0.024 2520 Dihedral : 3.068 17.203 2030 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.55 % Allowed : 16.94 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.55 (0.20), residues: 1897 helix: 3.52 (0.15), residues: 1099 sheet: -0.35 (0.31), residues: 315 loop : -1.44 (0.27), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 397 HIS 0.003 0.001 HIS A 484 PHE 0.023 0.001 PHE E 222 TYR 0.011 0.001 TYR C 467 ARG 0.001 0.000 ARG D 460 *********************** 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 164 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 139 time to evaluate : 1.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 TYR cc_start: 0.6992 (OUTLIER) cc_final: 0.6162 (m-80) REVERT: B 215 TYR cc_start: 0.6689 (OUTLIER) cc_final: 0.5922 (m-80) REVERT: C 215 TYR cc_start: 0.6584 (OUTLIER) cc_final: 0.5828 (m-80) REVERT: D 215 TYR cc_start: 0.6874 (OUTLIER) cc_final: 0.6156 (m-80) REVERT: E 215 TYR cc_start: 0.6754 (OUTLIER) cc_final: 0.5779 (m-80) REVERT: E 228 MET cc_start: 0.0874 (ttm) cc_final: 0.0597 (ttt) REVERT: F 215 TYR cc_start: 0.6797 (OUTLIER) cc_final: 0.5922 (m-80) REVERT: G 215 TYR cc_start: 0.6904 (OUTLIER) cc_final: 0.5932 (m-80) outliers start: 25 outliers final: 16 residues processed: 153 average time/residue: 0.1977 time to fit residues: 49.7654 Evaluate side-chains 157 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 134 time to evaluate : 1.869 ------------------------------------------------------------------------------- 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 249 LEU 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 174 optimal weight: 0.9990 chunk 159 optimal weight: 7.9990 chunk 169 optimal weight: 5.9990 chunk 102 optimal weight: 1.9990 chunk 73 optimal weight: 0.5980 chunk 133 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 153 optimal weight: 3.9990 chunk 160 optimal weight: 0.9990 chunk 111 optimal weight: 2.9990 chunk 179 optimal weight: 6.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.4612 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= 0.139 Angle : 0.526 9.370 20335 Z= 0.242 Chirality : 0.040 0.300 2443 Planarity : 0.003 0.024 2520 Dihedral : 3.037 17.266 2030 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.55 % Allowed : 16.82 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.61 (0.20), residues: 1897 helix: 3.54 (0.15), residues: 1099 sheet: -0.22 (0.32), residues: 315 loop : -1.41 (0.26), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 397 HIS 0.004 0.001 HIS F 484 PHE 0.023 0.001 PHE E 222 TYR 0.010 0.001 TYR C 467 ARG 0.001 0.000 ARG A 342 *********************** 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 162 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 137 time to evaluate : 1.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 TYR cc_start: 0.6994 (OUTLIER) cc_final: 0.6141 (m-80) REVERT: B 215 TYR cc_start: 0.6689 (OUTLIER) cc_final: 0.5898 (m-80) REVERT: C 215 TYR cc_start: 0.6719 (OUTLIER) cc_final: 0.5954 (m-80) REVERT: D 215 TYR cc_start: 0.6800 (OUTLIER) cc_final: 0.6085 (m-80) REVERT: E 215 TYR cc_start: 0.6736 (OUTLIER) cc_final: 0.5739 (m-80) REVERT: E 228 MET cc_start: 0.0966 (ttm) cc_final: 0.0659 (ttt) REVERT: F 215 TYR cc_start: 0.6908 (OUTLIER) cc_final: 0.6065 (m-80) REVERT: G 215 TYR cc_start: 0.6903 (OUTLIER) cc_final: 0.5910 (m-80) outliers start: 25 outliers final: 18 residues processed: 149 average time/residue: 0.1997 time to fit residues: 49.0784 Evaluate side-chains 155 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 130 time to evaluate : 1.735 ------------------------------------------------------------------------------- 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 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 346 MET 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 249 LEU 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 109 optimal weight: 5.9990 chunk 85 optimal weight: 4.9990 chunk 124 optimal weight: 0.9990 chunk 188 optimal weight: 4.9990 chunk 173 optimal weight: 3.9990 chunk 149 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 115 optimal weight: 6.9990 chunk 91 optimal weight: 5.9990 chunk 119 optimal weight: 0.9990 chunk 159 optimal weight: 3.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 471 GLN D 471 GLN E 471 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.4724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15050 Z= 0.185 Angle : 0.559 10.193 20335 Z= 0.258 Chirality : 0.041 0.304 2443 Planarity : 0.003 0.025 2520 Dihedral : 3.141 20.130 2030 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.67 % Allowed : 16.82 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.67 (0.20), residues: 1897 helix: 3.59 (0.15), residues: 1099 sheet: -0.16 (0.32), residues: 315 loop : -1.42 (0.26), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 253 HIS 0.006 0.002 HIS A 484 PHE 0.025 0.001 PHE E 222 TYR 0.012 0.001 TYR C 467 ARG 0.002 0.000 ARG E 460 ********************** 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 156 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 129 time to evaluate : 1.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 TYR cc_start: 0.7005 (OUTLIER) cc_final: 0.6159 (m-80) REVERT: B 215 TYR cc_start: 0.6662 (OUTLIER) cc_final: 0.5851 (m-80) REVERT: C 215 TYR cc_start: 0.6579 (OUTLIER) cc_final: 0.5831 (m-80) REVERT: D 215 TYR cc_start: 0.6814 (OUTLIER) cc_final: 0.6076 (m-80) REVERT: E 215 TYR cc_start: 0.6817 (OUTLIER) cc_final: 0.5815 (m-80) REVERT: E 228 MET cc_start: 0.1043 (ttm) cc_final: 0.0733 (ttt) REVERT: F 215 TYR cc_start: 0.6939 (OUTLIER) cc_final: 0.6052 (m-80) REVERT: G 215 TYR cc_start: 0.6936 (OUTLIER) cc_final: 0.5908 (m-80) outliers start: 27 outliers final: 19 residues processed: 143 average time/residue: 0.2032 time to fit residues: 47.9675 Evaluate side-chains 153 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 127 time to evaluate : 2.652 ------------------------------------------------------------------------------- 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 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 346 MET Chi-restraints excluded: chain D residue 461 MET 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 249 LEU 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 45 optimal weight: 2.9990 chunk 138 optimal weight: 0.9990 chunk 22 optimal weight: 7.9990 chunk 41 optimal weight: 4.9990 chunk 150 optimal weight: 6.9990 chunk 62 optimal weight: 6.9990 chunk 154 optimal weight: 0.9980 chunk 19 optimal weight: 6.9990 chunk 27 optimal weight: 40.0000 chunk 131 optimal weight: 8.9990 chunk 8 optimal weight: 5.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 471 GLN B 471 GLN F 471 GLN G 471 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.076205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.056891 restraints weight = 50516.636| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 3.38 r_work: 0.2797 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.4901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 15050 Z= 0.310 Angle : 0.624 9.815 20335 Z= 0.298 Chirality : 0.043 0.346 2443 Planarity : 0.003 0.026 2520 Dihedral : 3.443 21.658 2030 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.73 % Allowed : 17.01 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.66 (0.20), residues: 1897 helix: 3.62 (0.15), residues: 1092 sheet: -0.27 (0.31), residues: 315 loop : -1.37 (0.27), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 253 HIS 0.010 0.003 HIS A 484 PHE 0.025 0.001 PHE E 222 TYR 0.014 0.001 TYR E 467 ARG 0.002 0.000 ARG E 426 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2580.63 seconds wall clock time: 48 minutes 0.44 seconds (2880.44 seconds total)