Starting phenix.real_space_refine on Wed Jul 30 07:30:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7da7_30624/07_2025/7da7_30624.cif Found real_map, /net/cci-nas-00/data/ceres_data/7da7_30624/07_2025/7da7_30624.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7da7_30624/07_2025/7da7_30624.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7da7_30624/07_2025/7da7_30624.map" model { file = "/net/cci-nas-00/data/ceres_data/7da7_30624/07_2025/7da7_30624.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7da7_30624/07_2025/7da7_30624.cif" } resolution = 3.47 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= 0.003 sd= 0.041 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 90 5.49 5 S 28 5.16 5 C 7309 2.51 5 N 1838 2.21 5 O 2560 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 11825 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 669, 5372 Classifications: {'peptide': 669} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 640} Chain breaks: 1 Chain: "B" Number of atoms: 5372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 669, 5372 Classifications: {'peptide': 669} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 640} Chain breaks: 1 Chain: "C" Number of atoms: 1081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 1081 Classifications: {'RNA': 90} Modifications used: {'rna3p_pur': 42, 'rna3p_pyr': 47} Link IDs: {'rna3p': 89} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 959 Unresolved non-hydrogen angles: 1518 Unresolved non-hydrogen dihedrals: 935 Unresolved non-hydrogen chiralities: 91 Planarities with less than four sites: {' G%rna3p_pur:plan2': 23, ' C%rna3p_pyr:plan': 28, ' A%rna3p_pur:plan2': 19, ' U%rna3p_pyr:plan': 19, ' U:plan': 1, ' C%rna3p_pyr:plan2': 28, ' G%rna3p_pur:plan': 23, ' A%rna3p_pur:plan': 19} Unresolved non-hydrogen planarities: 965 Time building chain proxies: 8.30, per 1000 atoms: 0.70 Number of scatterers: 11825 At special positions: 0 Unit cell: (104.14, 96.76, 166.46, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 28 16.00 P 90 15.00 O 2560 8.00 N 1838 7.00 C 7309 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 29 " - pdb=" SG CYS A 38 " distance=2.03 Simple disulfide: pdb=" SG CYS A 96 " - pdb=" SG CYS A 123 " distance=1.84 Simple disulfide: pdb=" SG CYS A 650 " - pdb=" SG CYS A 678 " distance=2.02 Simple disulfide: pdb=" SG CYS A 652 " - pdb=" SG CYS A 697 " distance=2.03 Simple disulfide: pdb=" SG CYS B 29 " - pdb=" SG CYS B 38 " distance=2.04 Simple disulfide: pdb=" SG CYS B 96 " - pdb=" SG CYS B 123 " distance=1.65 Simple disulfide: pdb=" SG CYS B 650 " - pdb=" SG CYS B 678 " distance=2.00 Simple disulfide: pdb=" SG CYS B 652 " - pdb=" SG CYS B 697 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.75 Conformation dependent library (CDL) restraints added in 1.4 seconds 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2572 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 18 sheets defined 12.6% alpha, 9.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.55 Creating SS restraints... Processing helix chain 'A' and resid 92 through 98 removed outlier: 4.408A pdb=" N CYS A 96 " --> pdb=" O GLU A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 122 removed outlier: 4.483A pdb=" N PHE A 122 " --> pdb=" O GLN A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 246 removed outlier: 4.031A pdb=" N THR A 239 " --> pdb=" O ASN A 235 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N GLU A 240 " --> pdb=" O PRO A 236 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N LYS A 241 " --> pdb=" O HIS A 237 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N TRP A 244 " --> pdb=" O GLU A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 275 removed outlier: 4.483A pdb=" N GLY A 271 " --> pdb=" O THR A 268 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N TRP A 274 " --> pdb=" O GLY A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 320 removed outlier: 4.119A pdb=" N PHE A 319 " --> pdb=" O PRO A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 408 removed outlier: 3.908A pdb=" N VAL A 403 " --> pdb=" O GLU A 400 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N SER A 404 " --> pdb=" O THR A 401 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N HIS A 407 " --> pdb=" O SER A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 454 removed outlier: 3.537A pdb=" N TRP A 453 " --> pdb=" O GLY A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 548 removed outlier: 4.206A pdb=" N TRP A 547 " --> pdb=" O LEU A 543 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS A 548 " --> pdb=" O ALA A 544 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 543 through 548' Processing helix chain 'A' and resid 627 through 636 removed outlier: 3.953A pdb=" N PHE A 631 " --> pdb=" O GLU A 627 " (cutoff:3.500A) Proline residue: A 633 - end of helix Processing helix chain 'A' and resid 651 through 664 removed outlier: 3.674A pdb=" N SER A 656 " --> pdb=" O CYS A 652 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N TRP A 657 " --> pdb=" O GLU A 653 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N PHE A 658 " --> pdb=" O SER A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 692 Processing helix chain 'B' and resid 93 through 98 Processing helix chain 'B' and resid 117 through 122 removed outlier: 4.341A pdb=" N PHE B 122 " --> pdb=" O GLN B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 246 removed outlier: 3.631A pdb=" N TRP B 244 " --> pdb=" O GLU B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 275 removed outlier: 4.525A pdb=" N GLY B 271 " --> pdb=" O THR B 268 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N TRP B 274 " --> pdb=" O GLY B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 408 removed outlier: 3.685A pdb=" N VAL B 403 " --> pdb=" O GLU B 400 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N SER B 404 " --> pdb=" O THR B 401 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N HIS B 407 " --> pdb=" O SER B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 454 removed outlier: 3.549A pdb=" N TRP B 453 " --> pdb=" O GLY B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 548 removed outlier: 4.289A pdb=" N TRP B 547 " --> pdb=" O LEU B 543 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS B 548 " --> pdb=" O ALA B 544 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 543 through 548' Processing helix chain 'B' and resid 627 through 636 removed outlier: 3.647A pdb=" N PHE B 631 " --> pdb=" O GLU B 627 " (cutoff:3.500A) Proline residue: B 633 - end of helix Processing helix chain 'B' and resid 651 through 664 removed outlier: 3.562A pdb=" N SER B 656 " --> pdb=" O CYS B 652 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N TRP B 657 " --> pdb=" O GLU B 653 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N PHE B 658 " --> pdb=" O SER B 654 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 692 removed outlier: 3.514A pdb=" N PHE B 692 " --> pdb=" O LEU B 689 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 37 removed outlier: 7.068A pdb=" N ALA A 36 " --> pdb=" O ASN A 58 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU A 57 " --> pdb=" O ASP A 82 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 186 through 187 Processing sheet with id=AA3, first strand: chain 'A' and resid 199 through 200 Processing sheet with id=AA4, first strand: chain 'A' and resid 253 through 255 removed outlier: 7.084A pdb=" N LEU A 254 " --> pdb=" O ASP A 281 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N LEU A 304 " --> pdb=" O SER A 329 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N LEU A 328 " --> pdb=" O ASN A 362 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N LEU A 361 " --> pdb=" O SER A 386 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N LEU A 385 " --> pdb=" O ASN A 414 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU A 413 " --> pdb=" O ASP A 438 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N MET A 487 " --> pdb=" O ILE A 462 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 263 through 264 Processing sheet with id=AA6, first strand: chain 'A' and resid 313 through 314 removed outlier: 3.611A pdb=" N LEU A 314 " --> pdb=" O ASN A 346 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 396 through 397 Processing sheet with id=AA8, first strand: chain 'A' and resid 445 through 447 removed outlier: 6.649A pdb=" N GLN A 446 " --> pdb=" O GLN A 471 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N LEU A 470 " --> pdb=" O LYS A 494 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 640 through 641 Processing sheet with id=AB1, first strand: chain 'B' and resid 35 through 37 removed outlier: 7.231A pdb=" N ALA B 36 " --> pdb=" O ASN B 58 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LEU B 57 " --> pdb=" O ASP B 82 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N LEU B 129 " --> pdb=" O ASP B 154 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 186 through 187 Processing sheet with id=AB3, first strand: chain 'B' and resid 199 through 200 Processing sheet with id=AB4, first strand: chain 'B' and resid 253 through 255 removed outlier: 7.080A pdb=" N LEU B 254 " --> pdb=" O ASP B 281 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N LEU B 304 " --> pdb=" O SER B 329 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N LEU B 328 " --> pdb=" O ASN B 362 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N LEU B 361 " --> pdb=" O SER B 386 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N LEU B 385 " --> pdb=" O ASN B 414 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N LEU B 413 " --> pdb=" O ASP B 438 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N MET B 487 " --> pdb=" O ILE B 462 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 263 through 264 Processing sheet with id=AB6, first strand: chain 'B' and resid 313 through 314 removed outlier: 3.616A pdb=" N LEU B 314 " --> pdb=" O ASN B 346 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'B' and resid 396 through 397 Processing sheet with id=AB8, first strand: chain 'B' and resid 445 through 447 removed outlier: 6.577A pdb=" N GLN B 446 " --> pdb=" O GLN B 471 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N LEU B 470 " --> pdb=" O LYS B 494 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'B' and resid 640 through 641 112 hydrogen bonds defined for protein. 273 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: 3.21 Time building geometry restraints manager: 3.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 1774 1.31 - 1.44: 3186 1.44 - 1.57: 6962 1.57 - 1.70: 178 1.70 - 1.83: 36 Bond restraints: 12136 Sorted by residual: bond pdb=" C GLU A 653 " pdb=" O GLU A 653 " ideal model delta sigma weight residual 1.235 1.174 0.061 1.33e-02 5.65e+03 2.11e+01 bond pdb=" O3' G C 18 " pdb=" P U C 19 " ideal model delta sigma weight residual 1.607 1.668 -0.061 1.50e-02 4.44e+03 1.66e+01 bond pdb=" O3' U C 29 " pdb=" P A C 30 " ideal model delta sigma weight residual 1.607 1.665 -0.058 1.50e-02 4.44e+03 1.48e+01 bond pdb=" O3' C C 242 " pdb=" P A C 243 " ideal model delta sigma weight residual 1.607 1.664 -0.057 1.50e-02 4.44e+03 1.43e+01 bond pdb=" O3' A C 34 " pdb=" P C C 35 " ideal model delta sigma weight residual 1.607 1.663 -0.056 1.50e-02 4.44e+03 1.41e+01 ... (remaining 12131 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.29: 16038 2.29 - 4.58: 567 4.58 - 6.87: 58 6.87 - 9.17: 14 9.17 - 11.46: 2 Bond angle restraints: 16679 Sorted by residual: angle pdb=" O3' G C 13 " pdb=" C3' G C 13 " pdb=" C2' G C 13 " ideal model delta sigma weight residual 113.70 125.16 -11.46 1.50e+00 4.44e-01 5.83e+01 angle pdb=" N PRO A 236 " pdb=" CA PRO A 236 " pdb=" C PRO A 236 " ideal model delta sigma weight residual 113.86 105.67 8.19 1.25e+00 6.40e-01 4.30e+01 angle pdb=" C4' G C 45 " pdb=" C3' G C 45 " pdb=" O3' G C 45 " ideal model delta sigma weight residual 113.00 122.59 -9.59 1.50e+00 4.44e-01 4.09e+01 angle pdb=" CA HIS A 237 " pdb=" C HIS A 237 " pdb=" O HIS A 237 " ideal model delta sigma weight residual 121.88 115.33 6.55 1.30e+00 5.92e-01 2.54e+01 angle pdb=" C4' A C 258 " pdb=" C3' A C 258 " pdb=" O3' A C 258 " ideal model delta sigma weight residual 113.00 120.48 -7.48 1.50e+00 4.44e-01 2.49e+01 ... (remaining 16674 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.93: 7410 33.93 - 67.86: 333 67.86 - 101.79: 36 101.79 - 135.72: 0 135.72 - 169.64: 2 Dihedral angle restraints: 7781 sinusoidal: 3841 harmonic: 3940 Sorted by residual: dihedral pdb=" C5' U C 259 " pdb=" C4' U C 259 " pdb=" C3' U C 259 " pdb=" O3' U C 259 " ideal model delta sinusoidal sigma weight residual 82.00 166.03 -84.03 1 8.00e+00 1.56e-02 1.34e+02 dihedral pdb=" C4' U C 259 " pdb=" C3' U C 259 " pdb=" C2' U C 259 " pdb=" C1' U C 259 " ideal model delta sinusoidal sigma weight residual 36.00 -40.93 76.93 1 8.00e+00 1.56e-02 1.16e+02 dihedral pdb=" O4' U C 259 " pdb=" C4' U C 259 " pdb=" C3' U C 259 " pdb=" C2' U C 259 " ideal model delta sinusoidal sigma weight residual -35.00 38.01 -73.01 1 8.00e+00 1.56e-02 1.06e+02 ... (remaining 7778 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.177: 2027 0.177 - 0.354: 53 0.354 - 0.531: 2 0.531 - 0.708: 0 0.708 - 0.885: 1 Chirality restraints: 2083 Sorted by residual: chirality pdb=" C3' G C 13 " pdb=" C4' G C 13 " pdb=" O3' G C 13 " pdb=" C2' G C 13 " both_signs ideal model delta sigma weight residual False -2.48 -1.59 -0.88 2.00e-01 2.50e+01 1.96e+01 chirality pdb=" CA PRO B 681 " pdb=" N PRO B 681 " pdb=" C PRO B 681 " pdb=" CB PRO B 681 " both_signs ideal model delta sigma weight residual False 2.72 2.29 0.43 2.00e-01 2.50e+01 4.59e+00 chirality pdb=" C2' G C 13 " pdb=" C3' G C 13 " pdb=" O2' G C 13 " pdb=" C1' G C 13 " both_signs ideal model delta sigma weight residual False -2.75 -2.40 -0.35 2.00e-01 2.50e+01 3.14e+00 ... (remaining 2080 not shown) Planarity restraints: 1908 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO B 681 " -0.017 2.00e-02 2.50e+03 3.72e-02 1.38e+01 pdb=" C PRO B 681 " 0.064 2.00e-02 2.50e+03 pdb=" O PRO B 681 " -0.025 2.00e-02 2.50e+03 pdb=" N HIS B 682 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 593 " 0.018 2.00e-02 2.50e+03 3.53e-02 1.25e+01 pdb=" C ASN B 593 " -0.061 2.00e-02 2.50e+03 pdb=" O ASN B 593 " 0.023 2.00e-02 2.50e+03 pdb=" N LEU B 594 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 626 " 0.011 2.00e-02 2.50e+03 2.23e-02 4.97e+00 pdb=" C VAL B 626 " -0.039 2.00e-02 2.50e+03 pdb=" O VAL B 626 " 0.015 2.00e-02 2.50e+03 pdb=" N GLU B 627 " 0.013 2.00e-02 2.50e+03 ... (remaining 1905 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 202 2.64 - 3.20: 11020 3.20 - 3.77: 16869 3.77 - 4.33: 24683 4.33 - 4.90: 39765 Nonbonded interactions: 92539 Sorted by model distance: nonbonded pdb=" O HIS B 683 " pdb=" ND1 HIS B 683 " model vdw 2.072 3.120 nonbonded pdb=" O ASN A 679 " pdb=" OD1 ASN A 679 " model vdw 2.166 3.040 nonbonded pdb=" O PHE A 85 " pdb=" O2' G C 14 " model vdw 2.197 3.040 nonbonded pdb=" OD1 ASN B 374 " pdb=" OG1 THR B 377 " model vdw 2.198 3.040 nonbonded pdb=" O ASN B 110 " pdb=" ND2 ASN B 134 " model vdw 2.222 3.120 ... (remaining 92534 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' } 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: 6.720 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: 0.530 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 31.220 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.050 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 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 0.379 12144 Z= 0.424 Angle : 1.105 47.090 16695 Z= 0.634 Chirality : 0.071 0.885 2083 Planarity : 0.005 0.049 1908 Dihedral : 17.749 169.644 5185 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.70 % Favored : 90.23 % Rotamer: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -4.59 (0.19), residues: 1330 helix: -4.99 (0.17), residues: 66 sheet: -3.41 (0.32), residues: 208 loop : -3.12 (0.16), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 274 HIS 0.005 0.001 HIS B 683 PHE 0.017 0.001 PHE B 687 TYR 0.015 0.002 TYR B 384 ARG 0.006 0.001 ARG B 490 Details of bonding type rmsd hydrogen bonds : bond 0.28454 ( 112) hydrogen bonds : angle 9.92393 ( 273) SS BOND : bond 0.15131 ( 8) SS BOND : angle 17.19117 ( 16) covalent geometry : bond 0.00731 (12136) covalent geometry : angle 0.96872 (16679) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 1.424 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 132 MET cc_start: 0.7802 (mmm) cc_final: 0.7180 (tpp) REVERT: A 208 ASN cc_start: 0.8118 (m-40) cc_final: 0.7872 (m110) REVERT: A 460 PHE cc_start: 0.7221 (t80) cc_final: 0.6909 (t80) REVERT: A 557 ASN cc_start: 0.8682 (t0) cc_final: 0.8396 (t0) REVERT: B 178 LEU cc_start: 0.8047 (mp) cc_final: 0.7726 (tt) REVERT: B 679 ASN cc_start: 0.7986 (m-40) cc_final: 0.7662 (t0) outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.3001 time to fit residues: 51.1341 Evaluate side-chains 48 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 119 optimal weight: 1.9990 chunk 106 optimal weight: 0.7980 chunk 59 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 72 optimal weight: 30.0000 chunk 57 optimal weight: 0.8980 chunk 110 optimal weight: 2.9990 chunk 42 optimal weight: 6.9990 chunk 67 optimal weight: 20.0000 chunk 82 optimal weight: 0.9990 chunk 128 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 HIS A 62 ASN A 97 GLN ** A 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 118 GLN A 137 HIS A 142 ASN A 157 HIS A 451 GLN A 467 ASN A 471 GLN A 495 ASN A 518 ASN A 585 ASN ** A 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 621 ASN A 637 ASN A 646 ASN B 61 HIS B 62 ASN B 71 ASN B 97 GLN B 118 GLN B 142 ASN B 146 ASN B 158 ASN B 419 HIS B 451 GLN B 467 ASN B 471 GLN B 518 ASN ** B 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 621 ASN B 646 ASN B 660 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.106286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.076699 restraints weight = 27643.008| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 3.01 r_work: 0.3199 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12144 Z= 0.128 Angle : 0.621 10.085 16695 Z= 0.317 Chirality : 0.041 0.213 2083 Planarity : 0.005 0.047 1908 Dihedral : 16.772 171.314 2539 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 1.12 % Allowed : 10.72 % Favored : 88.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -3.19 (0.21), residues: 1330 helix: -2.56 (0.48), residues: 66 sheet: -3.02 (0.32), residues: 240 loop : -2.00 (0.18), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 244 HIS 0.009 0.001 HIS B 45 PHE 0.019 0.001 PHE A 122 TYR 0.010 0.001 TYR B 684 ARG 0.007 0.001 ARG B 32 Details of bonding type rmsd hydrogen bonds : bond 0.05456 ( 112) hydrogen bonds : angle 7.55380 ( 273) SS BOND : bond 0.00780 ( 8) SS BOND : angle 1.50190 ( 16) covalent geometry : bond 0.00296 (12136) covalent geometry : angle 0.62000 (16679) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 1.454 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 PHE cc_start: 0.7961 (m-80) cc_final: 0.7035 (t80) REVERT: A 128 GLU cc_start: 0.8031 (tt0) cc_final: 0.7260 (tm-30) REVERT: A 153 LEU cc_start: 0.8270 (tt) cc_final: 0.8043 (tp) REVERT: A 331 LYS cc_start: 0.8901 (tttt) cc_final: 0.8679 (ttpp) REVERT: A 460 PHE cc_start: 0.7735 (t80) cc_final: 0.7109 (t80) REVERT: A 557 ASN cc_start: 0.8739 (t0) cc_final: 0.8468 (t0) REVERT: B 132 MET cc_start: 0.8316 (mmm) cc_final: 0.8040 (mmm) REVERT: B 152 LYS cc_start: 0.8103 (mppt) cc_final: 0.7869 (mppt) REVERT: B 178 LEU cc_start: 0.8180 (mp) cc_final: 0.7684 (tt) REVERT: B 447 LYS cc_start: 0.8570 (tttp) cc_final: 0.8253 (tttp) REVERT: B 460 PHE cc_start: 0.6614 (t80) cc_final: 0.6238 (m-80) REVERT: B 637 ASN cc_start: 0.8493 (t0) cc_final: 0.8174 (t0) REVERT: B 679 ASN cc_start: 0.8319 (m-40) cc_final: 0.7669 (t0) outliers start: 14 outliers final: 3 residues processed: 79 average time/residue: 0.2168 time to fit residues: 26.9701 Evaluate side-chains 51 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 48 time to evaluate : 1.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain B residue 404 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 107 optimal weight: 6.9990 chunk 73 optimal weight: 6.9990 chunk 83 optimal weight: 9.9990 chunk 88 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 95 optimal weight: 4.9990 chunk 47 optimal weight: 0.8980 chunk 114 optimal weight: 4.9990 chunk 131 optimal weight: 5.9990 chunk 97 optimal weight: 4.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN A 71 ASN A 77 GLN ** A 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 146 ASN A 518 ASN B 63 GLN B 367 ASN B 518 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.100109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.070692 restraints weight = 28847.811| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 3.02 r_work: 0.3072 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.093 12144 Z= 0.364 Angle : 0.786 9.710 16695 Z= 0.396 Chirality : 0.048 0.342 2083 Planarity : 0.006 0.050 1908 Dihedral : 16.621 161.091 2539 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.38 % Favored : 89.62 % Rotamer: Outliers : 2.40 % Allowed : 14.24 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -3.17 (0.22), residues: 1330 helix: -2.09 (0.56), residues: 66 sheet: -3.16 (0.31), residues: 240 loop : -1.97 (0.19), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 244 HIS 0.007 0.002 HIS A 682 PHE 0.021 0.002 PHE A 635 TYR 0.020 0.002 TYR A 327 ARG 0.005 0.001 ARG B 490 Details of bonding type rmsd hydrogen bonds : bond 0.06938 ( 112) hydrogen bonds : angle 7.46818 ( 273) SS BOND : bond 0.00745 ( 8) SS BOND : angle 1.54601 ( 16) covalent geometry : bond 0.00860 (12136) covalent geometry : angle 0.78484 (16679) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 54 time to evaluate : 1.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 GLU cc_start: 0.8219 (tt0) cc_final: 0.7683 (tm-30) REVERT: A 460 PHE cc_start: 0.7739 (t80) cc_final: 0.7085 (t80) REVERT: B 130 ASP cc_start: 0.6897 (OUTLIER) cc_final: 0.6598 (t0) REVERT: B 132 MET cc_start: 0.8364 (mmm) cc_final: 0.8001 (mmm) REVERT: B 152 LYS cc_start: 0.8319 (mppt) cc_final: 0.7833 (mppt) REVERT: B 158 ASN cc_start: 0.8459 (m-40) cc_final: 0.8118 (t0) REVERT: B 178 LEU cc_start: 0.8151 (mp) cc_final: 0.7844 (mp) REVERT: B 460 PHE cc_start: 0.6870 (t80) cc_final: 0.6641 (m-80) REVERT: B 461 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.7875 (pm20) REVERT: B 511 ILE cc_start: 0.8888 (OUTLIER) cc_final: 0.8634 (mt) REVERT: B 637 ASN cc_start: 0.8745 (t0) cc_final: 0.8410 (t0) REVERT: B 679 ASN cc_start: 0.8482 (m-40) cc_final: 0.7927 (t0) outliers start: 30 outliers final: 14 residues processed: 80 average time/residue: 0.2731 time to fit residues: 33.8168 Evaluate side-chains 62 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 45 time to evaluate : 2.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain B residue 33 TYR Chi-restraints excluded: chain B residue 123 CYS Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 461 GLU Chi-restraints excluded: chain B residue 498 ILE Chi-restraints excluded: chain B residue 511 ILE Chi-restraints excluded: chain B residue 640 SER Chi-restraints excluded: chain B residue 650 CYS Chi-restraints excluded: chain B residue 652 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 70 optimal weight: 3.9990 chunk 5 optimal weight: 9.9990 chunk 95 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 112 optimal weight: 0.9990 chunk 123 optimal weight: 0.9990 chunk 134 optimal weight: 9.9990 chunk 32 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 103 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 ASN ** A 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 518 ASN B 71 ASN B 367 ASN ** B 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.103731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.074285 restraints weight = 28113.810| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 3.01 r_work: 0.3153 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.2956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12144 Z= 0.113 Angle : 0.563 8.900 16695 Z= 0.283 Chirality : 0.040 0.267 2083 Planarity : 0.004 0.048 1908 Dihedral : 16.204 163.007 2539 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 1.68 % Allowed : 16.00 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -2.49 (0.23), residues: 1330 helix: 0.06 (0.85), residues: 42 sheet: -2.93 (0.32), residues: 242 loop : -1.50 (0.19), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 244 HIS 0.004 0.001 HIS B 45 PHE 0.023 0.001 PHE A 122 TYR 0.006 0.001 TYR B 684 ARG 0.003 0.000 ARG B 435 Details of bonding type rmsd hydrogen bonds : bond 0.04350 ( 112) hydrogen bonds : angle 6.77747 ( 273) SS BOND : bond 0.00568 ( 8) SS BOND : angle 1.05465 ( 16) covalent geometry : bond 0.00267 (12136) covalent geometry : angle 0.56208 (16679) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 50 time to evaluate : 2.054 Fit side-chains revert: symmetry clash REVERT: A 128 GLU cc_start: 0.8132 (tt0) cc_final: 0.7682 (tm-30) REVERT: A 460 PHE cc_start: 0.7632 (t80) cc_final: 0.6946 (t80) REVERT: A 557 ASN cc_start: 0.8717 (t0) cc_final: 0.8498 (t0) REVERT: B 152 LYS cc_start: 0.8439 (mppt) cc_final: 0.7903 (mppt) REVERT: B 178 LEU cc_start: 0.8156 (mp) cc_final: 0.7942 (mp) REVERT: B 211 LYS cc_start: 0.9326 (tppt) cc_final: 0.8212 (mtmt) REVERT: B 447 LYS cc_start: 0.8781 (tttp) cc_final: 0.8497 (tttp) REVERT: B 460 PHE cc_start: 0.6900 (t80) cc_final: 0.6476 (m-80) REVERT: B 637 ASN cc_start: 0.8723 (t0) cc_final: 0.8345 (t0) REVERT: B 679 ASN cc_start: 0.8471 (m-40) cc_final: 0.7768 (t0) outliers start: 21 outliers final: 9 residues processed: 70 average time/residue: 0.2476 time to fit residues: 27.7432 Evaluate side-chains 54 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 45 time to evaluate : 1.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 588 GLU Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 498 ILE Chi-restraints excluded: chain B residue 640 SER Chi-restraints excluded: chain B residue 652 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 58 optimal weight: 4.9990 chunk 121 optimal weight: 2.9990 chunk 63 optimal weight: 0.0470 chunk 72 optimal weight: 30.0000 chunk 69 optimal weight: 10.0000 chunk 71 optimal weight: 7.9990 chunk 111 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 23 optimal weight: 6.9990 overall best weight: 2.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 518 ASN ** B 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 367 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.100025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.071004 restraints weight = 28459.588| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 3.01 r_work: 0.3080 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 12144 Z= 0.276 Angle : 0.681 11.696 16695 Z= 0.341 Chirality : 0.044 0.308 2083 Planarity : 0.005 0.046 1908 Dihedral : 16.141 160.210 2539 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer: Outliers : 2.16 % Allowed : 16.32 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -2.70 (0.23), residues: 1330 helix: -1.80 (0.65), residues: 56 sheet: -2.91 (0.33), residues: 232 loop : -1.63 (0.20), residues: 1042 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 244 HIS 0.005 0.001 HIS A 109 PHE 0.016 0.002 PHE A 122 TYR 0.016 0.002 TYR A 327 ARG 0.003 0.001 ARG B 457 Details of bonding type rmsd hydrogen bonds : bond 0.05717 ( 112) hydrogen bonds : angle 6.94770 ( 273) SS BOND : bond 0.00607 ( 8) SS BOND : angle 1.22876 ( 16) covalent geometry : bond 0.00660 (12136) covalent geometry : angle 0.68039 (16679) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 47 time to evaluate : 1.375 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 128 GLU cc_start: 0.8218 (tt0) cc_final: 0.7740 (tm-30) REVERT: A 460 PHE cc_start: 0.7701 (t80) cc_final: 0.7004 (t80) REVERT: B 130 ASP cc_start: 0.6793 (t0) cc_final: 0.6575 (t0) REVERT: B 132 MET cc_start: 0.8515 (mmm) cc_final: 0.8270 (mmm) REVERT: B 134 ASN cc_start: 0.5819 (OUTLIER) cc_final: 0.5102 (m110) REVERT: B 178 LEU cc_start: 0.8020 (mp) cc_final: 0.7729 (mp) REVERT: B 460 PHE cc_start: 0.6995 (t80) cc_final: 0.6546 (m-80) REVERT: B 511 ILE cc_start: 0.8884 (OUTLIER) cc_final: 0.8633 (mt) REVERT: B 637 ASN cc_start: 0.8842 (t0) cc_final: 0.8459 (t0) outliers start: 27 outliers final: 20 residues processed: 72 average time/residue: 0.1940 time to fit residues: 22.7814 Evaluate side-chains 66 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 44 time to evaluate : 1.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 518 ASN Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 588 GLU Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain B residue 38 CYS Chi-restraints excluded: chain B residue 123 CYS Chi-restraints excluded: chain B residue 134 ASN Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 461 GLU Chi-restraints excluded: chain B residue 498 ILE Chi-restraints excluded: chain B residue 511 ILE Chi-restraints excluded: chain B residue 525 ASP Chi-restraints excluded: chain B residue 640 SER Chi-restraints excluded: chain B residue 650 CYS Chi-restraints excluded: chain B residue 652 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 62 optimal weight: 0.7980 chunk 116 optimal weight: 3.9990 chunk 7 optimal weight: 8.9990 chunk 40 optimal weight: 3.9990 chunk 69 optimal weight: 8.9990 chunk 23 optimal weight: 0.7980 chunk 3 optimal weight: 10.0000 chunk 133 optimal weight: 20.0000 chunk 5 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 chunk 21 optimal weight: 0.6980 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 518 ASN B 86 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.100653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.071725 restraints weight = 28819.502| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 3.03 r_work: 0.3097 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.3599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 12144 Z= 0.201 Angle : 0.606 10.994 16695 Z= 0.305 Chirality : 0.042 0.287 2083 Planarity : 0.004 0.045 1908 Dihedral : 16.032 161.195 2539 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 2.08 % Allowed : 17.68 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -2.57 (0.23), residues: 1330 helix: -1.57 (0.67), residues: 56 sheet: -2.88 (0.33), residues: 232 loop : -1.52 (0.20), residues: 1042 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 244 HIS 0.003 0.001 HIS B 419 PHE 0.021 0.001 PHE A 122 TYR 0.009 0.001 TYR A 327 ARG 0.003 0.000 ARG A 313 Details of bonding type rmsd hydrogen bonds : bond 0.04924 ( 112) hydrogen bonds : angle 6.74297 ( 273) SS BOND : bond 0.00440 ( 8) SS BOND : angle 1.59656 ( 16) covalent geometry : bond 0.00484 (12136) covalent geometry : angle 0.60417 (16679) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 47 time to evaluate : 1.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 GLU cc_start: 0.8153 (tt0) cc_final: 0.7709 (tm-30) REVERT: A 445 GLU cc_start: 0.8515 (tt0) cc_final: 0.8120 (pp20) REVERT: A 460 PHE cc_start: 0.7736 (t80) cc_final: 0.7012 (t80) REVERT: A 557 ASN cc_start: 0.8805 (t0) cc_final: 0.8544 (t0) REVERT: B 132 MET cc_start: 0.8481 (mmm) cc_final: 0.8223 (mmm) REVERT: B 134 ASN cc_start: 0.5727 (OUTLIER) cc_final: 0.4956 (m110) REVERT: B 176 GLU cc_start: 0.7993 (tt0) cc_final: 0.7721 (mp0) REVERT: B 178 LEU cc_start: 0.7995 (mp) cc_final: 0.7746 (mp) REVERT: B 460 PHE cc_start: 0.6969 (t80) cc_final: 0.6551 (m-80) REVERT: B 511 ILE cc_start: 0.8847 (OUTLIER) cc_final: 0.8616 (mt) REVERT: B 637 ASN cc_start: 0.8856 (t0) cc_final: 0.8455 (t0) outliers start: 26 outliers final: 18 residues processed: 73 average time/residue: 0.2005 time to fit residues: 24.2992 Evaluate side-chains 66 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 46 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 518 ASN Chi-restraints excluded: chain A residue 588 GLU Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain B residue 38 CYS Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain B residue 123 CYS Chi-restraints excluded: chain B residue 134 ASN Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 461 GLU Chi-restraints excluded: chain B residue 498 ILE Chi-restraints excluded: chain B residue 511 ILE Chi-restraints excluded: chain B residue 640 SER Chi-restraints excluded: chain B residue 650 CYS Chi-restraints excluded: chain B residue 652 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 71 optimal weight: 10.0000 chunk 67 optimal weight: 20.0000 chunk 77 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 63 optimal weight: 0.4980 chunk 56 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 136 optimal weight: 40.0000 chunk 34 optimal weight: 0.8980 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 71 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.099952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.071249 restraints weight = 28950.197| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 3.02 r_work: 0.3084 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.3811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 12144 Z= 0.221 Angle : 0.614 10.123 16695 Z= 0.309 Chirality : 0.042 0.279 2083 Planarity : 0.004 0.043 1908 Dihedral : 15.905 160.048 2539 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.62 % Favored : 90.38 % Rotamer: Outliers : 2.32 % Allowed : 17.28 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -2.49 (0.23), residues: 1330 helix: -1.48 (0.68), residues: 56 sheet: -2.65 (0.36), residues: 210 loop : -1.56 (0.20), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 244 HIS 0.004 0.001 HIS B 419 PHE 0.019 0.001 PHE A 122 TYR 0.011 0.001 TYR A 327 ARG 0.003 0.000 ARG A 313 Details of bonding type rmsd hydrogen bonds : bond 0.05058 ( 112) hydrogen bonds : angle 6.76522 ( 273) SS BOND : bond 0.00464 ( 8) SS BOND : angle 1.47512 ( 16) covalent geometry : bond 0.00531 (12136) covalent geometry : angle 0.61234 (16679) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 50 time to evaluate : 1.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 GLU cc_start: 0.8160 (tt0) cc_final: 0.7714 (tm-30) REVERT: A 445 GLU cc_start: 0.8526 (tt0) cc_final: 0.8150 (pp20) REVERT: A 460 PHE cc_start: 0.7742 (t80) cc_final: 0.7011 (t80) REVERT: A 535 ILE cc_start: 0.8881 (OUTLIER) cc_final: 0.8677 (mt) REVERT: A 557 ASN cc_start: 0.8804 (t0) cc_final: 0.8546 (t0) REVERT: B 132 MET cc_start: 0.8456 (mmm) cc_final: 0.8232 (mmm) REVERT: B 134 ASN cc_start: 0.5719 (OUTLIER) cc_final: 0.4930 (m110) REVERT: B 176 GLU cc_start: 0.7970 (tt0) cc_final: 0.7750 (mp0) REVERT: B 178 LEU cc_start: 0.7979 (mp) cc_final: 0.7686 (mp) REVERT: B 460 PHE cc_start: 0.7123 (t80) cc_final: 0.6661 (m-80) REVERT: B 511 ILE cc_start: 0.8857 (OUTLIER) cc_final: 0.8613 (mt) REVERT: B 637 ASN cc_start: 0.8820 (t0) cc_final: 0.8411 (t0) outliers start: 29 outliers final: 20 residues processed: 78 average time/residue: 0.2147 time to fit residues: 27.1691 Evaluate side-chains 71 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 48 time to evaluate : 1.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ARG Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 535 ILE Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 588 GLU Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain B residue 38 CYS Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain B residue 123 CYS Chi-restraints excluded: chain B residue 134 ASN Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 461 GLU Chi-restraints excluded: chain B residue 498 ILE Chi-restraints excluded: chain B residue 511 ILE Chi-restraints excluded: chain B residue 640 SER Chi-restraints excluded: chain B residue 650 CYS Chi-restraints excluded: chain B residue 652 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 21 optimal weight: 0.7980 chunk 81 optimal weight: 10.0000 chunk 45 optimal weight: 0.7980 chunk 7 optimal weight: 7.9990 chunk 124 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 42 optimal weight: 4.9990 chunk 90 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 75 optimal weight: 5.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.099838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.071359 restraints weight = 28816.038| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 3.08 r_work: 0.3090 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.4110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 12144 Z= 0.206 Angle : 0.599 9.586 16695 Z= 0.301 Chirality : 0.042 0.259 2083 Planarity : 0.004 0.043 1908 Dihedral : 15.809 160.442 2539 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 2.32 % Allowed : 17.36 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -2.31 (0.23), residues: 1330 helix: -0.66 (0.83), residues: 42 sheet: -2.64 (0.36), residues: 212 loop : -1.43 (0.20), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 244 HIS 0.004 0.001 HIS B 419 PHE 0.020 0.001 PHE A 122 TYR 0.011 0.001 TYR A 284 ARG 0.003 0.000 ARG A 313 Details of bonding type rmsd hydrogen bonds : bond 0.04818 ( 112) hydrogen bonds : angle 6.62895 ( 273) SS BOND : bond 0.00434 ( 8) SS BOND : angle 1.27759 ( 16) covalent geometry : bond 0.00494 (12136) covalent geometry : angle 0.59767 (16679) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 51 time to evaluate : 1.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 PHE cc_start: 0.7739 (OUTLIER) cc_final: 0.7088 (t80) REVERT: A 128 GLU cc_start: 0.8184 (tt0) cc_final: 0.7720 (tm-30) REVERT: A 445 GLU cc_start: 0.8551 (tt0) cc_final: 0.8154 (pp20) REVERT: A 557 ASN cc_start: 0.8811 (t0) cc_final: 0.8558 (t0) REVERT: B 132 MET cc_start: 0.8424 (mmm) cc_final: 0.8177 (mmm) REVERT: B 134 ASN cc_start: 0.5592 (OUTLIER) cc_final: 0.4750 (m110) REVERT: B 176 GLU cc_start: 0.7947 (tt0) cc_final: 0.7726 (mp0) REVERT: B 178 LEU cc_start: 0.7945 (mp) cc_final: 0.7658 (mp) REVERT: B 211 LYS cc_start: 0.9300 (tppt) cc_final: 0.8192 (mtmt) REVERT: B 460 PHE cc_start: 0.7124 (t80) cc_final: 0.6716 (m-80) REVERT: B 511 ILE cc_start: 0.8805 (OUTLIER) cc_final: 0.8568 (mt) REVERT: B 637 ASN cc_start: 0.8886 (t0) cc_final: 0.8527 (t0) outliers start: 29 outliers final: 21 residues processed: 79 average time/residue: 0.2043 time to fit residues: 26.3104 Evaluate side-chains 73 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 49 time to evaluate : 1.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 538 PHE Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 588 GLU Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain B residue 38 CYS Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain B residue 123 CYS Chi-restraints excluded: chain B residue 134 ASN Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 461 GLU Chi-restraints excluded: chain B residue 498 ILE Chi-restraints excluded: chain B residue 511 ILE Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 640 SER Chi-restraints excluded: chain B residue 650 CYS Chi-restraints excluded: chain B residue 652 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 140 optimal weight: 20.0000 chunk 70 optimal weight: 7.9990 chunk 76 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 81 optimal weight: 9.9990 chunk 40 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 139 optimal weight: 10.0000 chunk 69 optimal weight: 1.9990 chunk 13 optimal weight: 7.9990 chunk 84 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 367 ASN B 682 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.098930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.070822 restraints weight = 28805.641| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 3.01 r_work: 0.3074 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 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 : 0.006 0.065 12144 Z= 0.236 Angle : 0.632 9.236 16695 Z= 0.318 Chirality : 0.043 0.274 2083 Planarity : 0.004 0.043 1908 Dihedral : 16.000 159.565 2539 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.15 % Favored : 89.85 % Rotamer: Outliers : 2.16 % Allowed : 17.44 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -2.35 (0.23), residues: 1330 helix: -0.86 (0.82), residues: 42 sheet: -2.61 (0.36), residues: 210 loop : -1.47 (0.20), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 244 HIS 0.004 0.001 HIS A 682 PHE 0.019 0.001 PHE A 122 TYR 0.012 0.001 TYR A 284 ARG 0.003 0.000 ARG A 313 Details of bonding type rmsd hydrogen bonds : bond 0.05186 ( 112) hydrogen bonds : angle 6.86528 ( 273) SS BOND : bond 0.00488 ( 8) SS BOND : angle 1.37695 ( 16) covalent geometry : bond 0.00565 (12136) covalent geometry : angle 0.63039 (16679) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 48 time to evaluate : 1.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 PHE cc_start: 0.7729 (OUTLIER) cc_final: 0.7175 (t80) REVERT: A 128 GLU cc_start: 0.8193 (tt0) cc_final: 0.7766 (tm-30) REVERT: A 445 GLU cc_start: 0.8522 (tt0) cc_final: 0.8199 (pp20) REVERT: A 460 PHE cc_start: 0.7781 (t80) cc_final: 0.7065 (t80) REVERT: B 132 MET cc_start: 0.8427 (mmm) cc_final: 0.8165 (mmm) REVERT: B 134 ASN cc_start: 0.5612 (OUTLIER) cc_final: 0.4634 (m110) REVERT: B 176 GLU cc_start: 0.8024 (tt0) cc_final: 0.7788 (mp0) REVERT: B 178 LEU cc_start: 0.7974 (mp) cc_final: 0.7695 (mp) REVERT: B 211 LYS cc_start: 0.9345 (tppt) cc_final: 0.8132 (mtmt) REVERT: B 447 LYS cc_start: 0.8566 (tttp) cc_final: 0.8304 (tptt) REVERT: B 460 PHE cc_start: 0.7288 (t80) cc_final: 0.6820 (m-80) REVERT: B 511 ILE cc_start: 0.8889 (OUTLIER) cc_final: 0.8645 (mt) REVERT: B 637 ASN cc_start: 0.8907 (t0) cc_final: 0.8545 (t0) outliers start: 27 outliers final: 23 residues processed: 73 average time/residue: 0.2239 time to fit residues: 26.5889 Evaluate side-chains 73 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 47 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 461 GLU Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 588 GLU Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain B residue 38 CYS Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain B residue 123 CYS Chi-restraints excluded: chain B residue 134 ASN Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 461 GLU Chi-restraints excluded: chain B residue 498 ILE Chi-restraints excluded: chain B residue 511 ILE Chi-restraints excluded: chain B residue 525 ASP Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 640 SER Chi-restraints excluded: chain B residue 650 CYS Chi-restraints excluded: chain B residue 652 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 41 optimal weight: 2.9990 chunk 88 optimal weight: 0.1980 chunk 64 optimal weight: 0.6980 chunk 96 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 118 optimal weight: 0.0470 chunk 90 optimal weight: 2.9990 chunk 136 optimal weight: 30.0000 chunk 8 optimal weight: 0.4980 chunk 69 optimal weight: 9.9990 chunk 73 optimal weight: 6.9990 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 118 GLN ** B 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.102280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.074143 restraints weight = 28664.432| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 3.04 r_work: 0.3152 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.4416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 12144 Z= 0.088 Angle : 0.526 9.056 16695 Z= 0.262 Chirality : 0.039 0.230 2083 Planarity : 0.004 0.043 1908 Dihedral : 15.664 161.462 2539 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 1.36 % Allowed : 18.48 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -2.13 (0.24), residues: 1330 helix: -0.03 (0.85), residues: 42 sheet: -2.60 (0.36), residues: 204 loop : -1.32 (0.20), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 657 HIS 0.003 0.001 HIS B 40 PHE 0.021 0.001 PHE A 122 TYR 0.005 0.001 TYR B 303 ARG 0.003 0.000 ARG B 435 Details of bonding type rmsd hydrogen bonds : bond 0.03458 ( 112) hydrogen bonds : angle 6.20785 ( 273) SS BOND : bond 0.00170 ( 8) SS BOND : angle 1.03371 ( 16) covalent geometry : bond 0.00202 (12136) covalent geometry : angle 0.52516 (16679) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 64 time to evaluate : 1.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 PHE cc_start: 0.7588 (OUTLIER) cc_final: 0.7133 (t80) REVERT: A 128 GLU cc_start: 0.8129 (tt0) cc_final: 0.7707 (tm-30) REVERT: A 208 ASN cc_start: 0.8692 (m-40) cc_final: 0.8429 (m110) REVERT: A 231 ASN cc_start: 0.9079 (t0) cc_final: 0.8766 (m-40) REVERT: A 445 GLU cc_start: 0.8473 (tt0) cc_final: 0.8148 (pp20) REVERT: A 460 PHE cc_start: 0.7624 (t80) cc_final: 0.7278 (t80) REVERT: A 557 ASN cc_start: 0.8728 (t0) cc_final: 0.8511 (t0) REVERT: B 130 ASP cc_start: 0.6832 (t0) cc_final: 0.6283 (t0) REVERT: B 132 MET cc_start: 0.8349 (mmm) cc_final: 0.8054 (mmm) REVERT: B 134 ASN cc_start: 0.5552 (OUTLIER) cc_final: 0.4636 (m110) REVERT: B 176 GLU cc_start: 0.8053 (tt0) cc_final: 0.7761 (mp0) REVERT: B 178 LEU cc_start: 0.8007 (mp) cc_final: 0.7638 (mp) REVERT: B 211 LYS cc_start: 0.9311 (tppt) cc_final: 0.8148 (mtmt) REVERT: B 364 ASP cc_start: 0.8003 (m-30) cc_final: 0.7473 (m-30) REVERT: B 447 LYS cc_start: 0.8462 (tttp) cc_final: 0.8018 (tptp) REVERT: B 460 PHE cc_start: 0.7209 (t80) cc_final: 0.6793 (m-80) REVERT: B 511 ILE cc_start: 0.8806 (OUTLIER) cc_final: 0.8575 (mt) REVERT: B 637 ASN cc_start: 0.8816 (t0) cc_final: 0.8477 (t0) outliers start: 17 outliers final: 11 residues processed: 80 average time/residue: 0.2020 time to fit residues: 26.1110 Evaluate side-chains 71 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 57 time to evaluate : 1.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain B residue 38 CYS Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain B residue 123 CYS Chi-restraints excluded: chain B residue 134 ASN Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 498 ILE Chi-restraints excluded: chain B residue 511 ILE Chi-restraints excluded: chain B residue 640 SER Chi-restraints excluded: chain B residue 652 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 93 optimal weight: 4.9990 chunk 119 optimal weight: 4.9990 chunk 94 optimal weight: 0.5980 chunk 10 optimal weight: 9.9990 chunk 42 optimal weight: 0.0370 chunk 125 optimal weight: 3.9990 chunk 130 optimal weight: 0.5980 chunk 77 optimal weight: 6.9990 chunk 121 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 overall best weight: 1.8462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.099889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.071721 restraints weight = 29065.934| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 3.03 r_work: 0.3101 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.4479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12144 Z= 0.181 Angle : 0.579 8.461 16695 Z= 0.289 Chirality : 0.041 0.144 2083 Planarity : 0.004 0.042 1908 Dihedral : 15.679 159.371 2539 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer: Outliers : 1.52 % Allowed : 18.40 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -2.09 (0.24), residues: 1330 helix: -0.29 (0.85), residues: 42 sheet: -2.53 (0.36), residues: 210 loop : -1.28 (0.20), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 244 HIS 0.003 0.001 HIS A 682 PHE 0.019 0.001 PHE A 122 TYR 0.009 0.001 TYR A 327 ARG 0.003 0.000 ARG B 644 Details of bonding type rmsd hydrogen bonds : bond 0.04598 ( 112) hydrogen bonds : angle 6.51902 ( 273) SS BOND : bond 0.00349 ( 8) SS BOND : angle 1.09617 ( 16) covalent geometry : bond 0.00437 (12136) covalent geometry : angle 0.57811 (16679) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5582.69 seconds wall clock time: 101 minutes 23.52 seconds (6083.52 seconds total)