Starting phenix.real_space_refine on Thu Feb 5 01:35:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9v2q_64737/02_2026/9v2q_64737.cif Found real_map, /net/cci-nas-00/data/ceres_data/9v2q_64737/02_2026/9v2q_64737.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9v2q_64737/02_2026/9v2q_64737.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9v2q_64737/02_2026/9v2q_64737.map" model { file = "/net/cci-nas-00/data/ceres_data/9v2q_64737/02_2026/9v2q_64737.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9v2q_64737/02_2026/9v2q_64737.cif" } resolution = 4.43 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.010 sd= 0.053 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 72 5.16 5 C 8848 2.51 5 N 2342 2.21 5 O 2778 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14040 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 986 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 123} Chain: "B" Number of atoms: 3482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3482 Classifications: {'peptide': 449} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 436} Chain breaks: 1 Chain: "C" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 817 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 103} Chain: "D" Number of atoms: 908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 908 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain: "E" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 827 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 101} Chain: "F" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 986 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 123} Chain: "G" Number of atoms: 3482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3482 Classifications: {'peptide': 449} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 436} Chain breaks: 1 Chain: "H" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 817 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 103} Chain: "I" Number of atoms: 908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 908 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain: "J" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 827 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 101} Time building chain proxies: 3.25, per 1000 atoms: 0.23 Number of scatterers: 14040 At special positions: 0 Unit cell: (163, 117, 159, 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 72 16.00 O 2778 8.00 N 2342 7.00 C 8848 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 37 " - pdb=" SG CYS B 439 " distance=2.03 Simple disulfide: pdb=" SG CYS B 69 " - pdb=" SG CYS B 212 " distance=2.03 Simple disulfide: pdb=" SG CYS B 155 " - pdb=" SG CYS B 290 " distance=2.03 Simple disulfide: pdb=" SG CYS B 313 " - pdb=" SG CYS B 343 " distance=2.08 Simple disulfide: pdb=" SG CYS B 322 " - pdb=" SG CYS B 333 " distance=2.04 Simple disulfide: pdb=" SG CYS B 358 " - pdb=" SG CYS B 367 " distance=2.04 Simple disulfide: pdb=" SG CYS B 382 " - pdb=" SG CYS B 393 " distance=2.03 Simple disulfide: pdb=" SG CYS B 416 " - pdb=" SG CYS B 422 " distance=2.02 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 90 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 90 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 37 " - pdb=" SG CYS G 439 " distance=2.03 Simple disulfide: pdb=" SG CYS G 69 " - pdb=" SG CYS G 212 " distance=2.03 Simple disulfide: pdb=" SG CYS G 155 " - pdb=" SG CYS G 290 " distance=2.03 Simple disulfide: pdb=" SG CYS G 313 " - pdb=" SG CYS G 343 " distance=2.08 Simple disulfide: pdb=" SG CYS G 322 " - pdb=" SG CYS G 333 " distance=2.04 Simple disulfide: pdb=" SG CYS G 358 " - pdb=" SG CYS G 367 " distance=2.04 Simple disulfide: pdb=" SG CYS G 382 " - pdb=" SG CYS G 393 " distance=2.03 Simple disulfide: pdb=" SG CYS G 416 " - pdb=" SG CYS G 422 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 90 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.04 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 90 " 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: 1.01 Conformation dependent library (CDL) restraints added in 723.5 milliseconds 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3348 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 36 sheets defined 18.1% alpha, 25.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'B' and resid 77 through 95 removed outlier: 3.589A pdb=" N GLN B 81 " --> pdb=" O LYS B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 159 Processing helix chain 'B' and resid 163 through 171 removed outlier: 3.794A pdb=" N ILE B 167 " --> pdb=" O GLU B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 203 Processing helix chain 'B' and resid 203 through 208 Processing helix chain 'B' and resid 220 through 226 Processing helix chain 'B' and resid 227 through 238 Processing helix chain 'B' and resid 253 through 262 Processing helix chain 'B' and resid 267 through 277 Processing helix chain 'B' and resid 277 through 285 Processing helix chain 'B' and resid 292 through 296 removed outlier: 3.775A pdb=" N GLU B 295 " --> pdb=" O ILE B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 372 removed outlier: 3.813A pdb=" N ASN B 371 " --> pdb=" O ASP B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 385 Processing helix chain 'B' and resid 445 through 447 No H-bonds generated for 'chain 'B' and resid 445 through 447' Processing helix chain 'B' and resid 473 through 478 removed outlier: 3.720A pdb=" N TYR B 478 " --> pdb=" O ILE B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 491 through 513 Processing helix chain 'C' and resid 81 through 85 removed outlier: 3.634A pdb=" N GLU C 85 " --> pdb=" O PRO C 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 91 removed outlier: 3.903A pdb=" N THR D 91 " --> pdb=" O VAL D 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 95 removed outlier: 3.575A pdb=" N GLN G 81 " --> pdb=" O LYS G 77 " (cutoff:3.500A) Processing helix chain 'G' and resid 149 through 159 Processing helix chain 'G' and resid 163 through 171 removed outlier: 3.794A pdb=" N ILE G 167 " --> pdb=" O GLU G 163 " (cutoff:3.500A) Processing helix chain 'G' and resid 195 through 203 Processing helix chain 'G' and resid 203 through 208 Processing helix chain 'G' and resid 219 through 226 removed outlier: 4.544A pdb=" N PHE G 223 " --> pdb=" O THR G 219 " (cutoff:3.500A) Processing helix chain 'G' and resid 227 through 238 Processing helix chain 'G' and resid 253 through 264 Processing helix chain 'G' and resid 267 through 277 Processing helix chain 'G' and resid 277 through 285 Processing helix chain 'G' and resid 292 through 296 removed outlier: 3.760A pdb=" N GLU G 295 " --> pdb=" O ILE G 292 " (cutoff:3.500A) Processing helix chain 'G' and resid 368 through 372 removed outlier: 3.832A pdb=" N ASN G 371 " --> pdb=" O ASP G 368 " (cutoff:3.500A) Processing helix chain 'G' and resid 379 through 385 Processing helix chain 'G' and resid 445 through 447 No H-bonds generated for 'chain 'G' and resid 445 through 447' Processing helix chain 'G' and resid 473 through 478 removed outlier: 3.712A pdb=" N TYR G 478 " --> pdb=" O ILE G 475 " (cutoff:3.500A) Processing helix chain 'G' and resid 491 through 513 Processing helix chain 'H' and resid 81 through 85 removed outlier: 3.720A pdb=" N GLU H 85 " --> pdb=" O PRO H 82 " (cutoff:3.500A) Processing helix chain 'I' and resid 87 through 91 removed outlier: 3.902A pdb=" N THR I 91 " --> pdb=" O VAL I 88 " (cutoff:3.500A) Processing helix chain 'J' and resid 81 through 85 removed outlier: 3.966A pdb=" N GLU J 85 " --> pdb=" O PRO J 82 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 6 removed outlier: 4.071A pdb=" N LEU A 79 " --> pdb=" O CYS A 22 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR A 78 " --> pdb=" O ASP A 73 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 12 removed outlier: 5.950A pdb=" N GLY A 10 " --> pdb=" O THR A 123 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N ARG A 38 " --> pdb=" O TRP A 47 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N TRP A 47 " --> pdb=" O ARG A 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 10 through 12 removed outlier: 5.950A pdb=" N GLY A 10 " --> pdb=" O THR A 123 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ARG A 98 " --> pdb=" O VAL A 115 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N VAL A 115 " --> pdb=" O ARG A 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 373 through 375 removed outlier: 3.721A pdb=" N VAL B 40 " --> pdb=" O GLU B 31 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU B 31 " --> pdb=" O VAL B 40 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 51 through 52 Processing sheet with id=AA6, first strand: chain 'B' and resid 176 through 177 removed outlier: 3.572A pdb=" N ALA B 177 " --> pdb=" O THR B 189 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N GLU B 60 " --> pdb=" O VAL B 192 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N ASP B 194 " --> pdb=" O GLU B 60 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 333 through 336 Processing sheet with id=AA8, first strand: chain 'B' and resid 359 through 361 Processing sheet with id=AA9, first strand: chain 'B' and resid 404 through 408 removed outlier: 3.841A pdb=" N SER B 404 " --> pdb=" O SER B 415 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLY B 411 " --> pdb=" O THR B 408 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 431 through 434 Processing sheet with id=AB2, first strand: chain 'C' and resid 9 through 11 removed outlier: 3.643A pdb=" N THR C 108 " --> pdb=" O VAL C 10 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N GLN C 39 " --> pdb=" O LEU C 48 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N LEU C 48 " --> pdb=" O GLN C 39 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 9 through 11 removed outlier: 3.643A pdb=" N THR C 108 " --> pdb=" O VAL C 10 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N THR C 98 " --> pdb=" O SER C 94 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 19 through 23 Processing sheet with id=AB5, first strand: chain 'D' and resid 6 through 7 Processing sheet with id=AB6, first strand: chain 'D' and resid 10 through 11 removed outlier: 6.036A pdb=" N GLY D 10 " --> pdb=" O THR D 119 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N SER D 59 " --> pdb=" O SER D 50 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 18 through 23 Processing sheet with id=AB8, first strand: chain 'E' and resid 37 through 39 removed outlier: 5.866A pdb=" N GLN E 39 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N VAL E 48 " --> pdb=" O GLN E 39 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 86 through 88 Processing sheet with id=AC1, first strand: chain 'E' and resid 91 through 92 Processing sheet with id=AC2, first strand: chain 'F' and resid 3 through 6 removed outlier: 4.098A pdb=" N GLN F 3 " --> pdb=" O SER F 25 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N SER F 25 " --> pdb=" O GLN F 3 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LEU F 79 " --> pdb=" O CYS F 22 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.008A pdb=" N GLY F 10 " --> pdb=" O THR F 123 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 373 through 375 removed outlier: 3.774A pdb=" N VAL G 40 " --> pdb=" O GLU G 31 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU G 31 " --> pdb=" O VAL G 40 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 176 through 177 removed outlier: 3.677A pdb=" N ALA G 177 " --> pdb=" O THR G 189 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N GLU G 60 " --> pdb=" O VAL G 192 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N ASP G 194 " --> pdb=" O GLU G 60 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 333 through 336 Processing sheet with id=AC7, first strand: chain 'G' and resid 359 through 361 Processing sheet with id=AC8, first strand: chain 'G' and resid 404 through 408 removed outlier: 3.833A pdb=" N SER G 404 " --> pdb=" O SER G 415 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLY G 411 " --> pdb=" O THR G 408 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 431 through 434 Processing sheet with id=AD1, first strand: chain 'H' and resid 9 through 11 removed outlier: 3.658A pdb=" N THR H 108 " --> pdb=" O VAL H 10 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N GLN H 39 " --> pdb=" O LEU H 48 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N LEU H 48 " --> pdb=" O GLN H 39 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 9 through 11 removed outlier: 3.658A pdb=" N THR H 108 " --> pdb=" O VAL H 10 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N THR H 98 " --> pdb=" O SER H 94 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 19 through 23 Processing sheet with id=AD4, first strand: chain 'I' and resid 6 through 7 Processing sheet with id=AD5, first strand: chain 'I' and resid 10 through 11 removed outlier: 6.040A pdb=" N GLY I 10 " --> pdb=" O THR I 119 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SER I 59 " --> pdb=" O SER I 50 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 18 through 23 Processing sheet with id=AD7, first strand: chain 'J' and resid 37 through 39 removed outlier: 5.868A pdb=" N GLN J 39 " --> pdb=" O VAL J 48 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N VAL J 48 " --> pdb=" O GLN J 39 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 86 through 88 Processing sheet with id=AD9, first strand: chain 'J' and resid 91 through 92 516 hydrogen bonds defined for protein. 1296 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.44 Time building geometry restraints manager: 1.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 4364 1.34 - 1.46: 3467 1.46 - 1.59: 6377 1.59 - 1.71: 2 1.71 - 1.83: 96 Bond restraints: 14306 Sorted by residual: bond pdb=" C LYS C 40 " pdb=" N TYR C 41 " ideal model delta sigma weight residual 1.327 1.212 0.115 2.86e-02 1.22e+03 1.60e+01 bond pdb=" C LYS H 40 " pdb=" N TYR H 41 " ideal model delta sigma weight residual 1.327 1.220 0.107 2.86e-02 1.22e+03 1.39e+01 bond pdb=" N LEU I 86 " pdb=" CA LEU I 86 " ideal model delta sigma weight residual 1.455 1.490 -0.035 1.29e-02 6.01e+03 7.54e+00 bond pdb=" N LEU D 86 " pdb=" CA LEU D 86 " ideal model delta sigma weight residual 1.455 1.490 -0.035 1.29e-02 6.01e+03 7.54e+00 bond pdb=" N SER D 85 " pdb=" CA SER D 85 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.23e-02 6.61e+03 7.46e+00 ... (remaining 14301 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.70: 19326 5.70 - 11.40: 80 11.40 - 17.09: 2 17.09 - 22.79: 2 22.79 - 28.49: 2 Bond angle restraints: 19412 Sorted by residual: angle pdb=" CA CYS G 313 " pdb=" CB CYS G 313 " pdb=" SG CYS G 313 " ideal model delta sigma weight residual 114.40 142.89 -28.49 2.30e+00 1.89e-01 1.53e+02 angle pdb=" CA CYS B 313 " pdb=" CB CYS B 313 " pdb=" SG CYS B 313 " ideal model delta sigma weight residual 114.40 142.57 -28.17 2.30e+00 1.89e-01 1.50e+02 angle pdb=" CA CYS G 343 " pdb=" CB CYS G 343 " pdb=" SG CYS G 343 " ideal model delta sigma weight residual 114.40 134.46 -20.06 2.30e+00 1.89e-01 7.61e+01 angle pdb=" CA CYS B 343 " pdb=" CB CYS B 343 " pdb=" SG CYS B 343 " ideal model delta sigma weight residual 114.40 134.31 -19.91 2.30e+00 1.89e-01 7.49e+01 angle pdb=" N VAL B 482 " pdb=" CA VAL B 482 " pdb=" C VAL B 482 " ideal model delta sigma weight residual 113.71 106.84 6.87 9.50e-01 1.11e+00 5.22e+01 ... (remaining 19407 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.10: 7779 18.10 - 36.19: 652 36.19 - 54.29: 91 54.29 - 72.38: 27 72.38 - 90.48: 15 Dihedral angle restraints: 8564 sinusoidal: 3310 harmonic: 5254 Sorted by residual: dihedral pdb=" CB CYS G 313 " pdb=" SG CYS G 313 " pdb=" SG CYS G 343 " pdb=" CB CYS G 343 " ideal model delta sinusoidal sigma weight residual -86.00 -0.78 -85.22 1 1.00e+01 1.00e-02 8.80e+01 dihedral pdb=" CB CYS B 313 " pdb=" SG CYS B 313 " pdb=" SG CYS B 343 " pdb=" CB CYS B 343 " ideal model delta sinusoidal sigma weight residual -86.00 -0.83 -85.17 1 1.00e+01 1.00e-02 8.79e+01 dihedral pdb=" CB CYS G 382 " pdb=" SG CYS G 382 " pdb=" SG CYS G 393 " pdb=" CB CYS G 393 " ideal model delta sinusoidal sigma weight residual 93.00 162.26 -69.26 1 1.00e+01 1.00e-02 6.20e+01 ... (remaining 8561 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 1906 0.077 - 0.153: 270 0.153 - 0.230: 47 0.230 - 0.306: 3 0.306 - 0.383: 6 Chirality restraints: 2232 Sorted by residual: chirality pdb=" CA CYS B 313 " pdb=" N CYS B 313 " pdb=" C CYS B 313 " pdb=" CB CYS B 313 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.66e+00 chirality pdb=" CA CYS G 313 " pdb=" N CYS G 313 " pdb=" C CYS G 313 " pdb=" CB CYS G 313 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.63e+00 chirality pdb=" CB ILE G 59 " pdb=" CA ILE G 59 " pdb=" CG1 ILE G 59 " pdb=" CG2 ILE G 59 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.38 2.00e-01 2.50e+01 3.59e+00 ... (remaining 2229 not shown) Planarity restraints: 2466 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG I 67 " -0.569 9.50e-02 1.11e+02 2.55e-01 3.98e+01 pdb=" NE ARG I 67 " 0.036 2.00e-02 2.50e+03 pdb=" CZ ARG I 67 " 0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG I 67 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG I 67 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 67 " 0.558 9.50e-02 1.11e+02 2.50e-01 3.83e+01 pdb=" NE ARG D 67 " -0.035 2.00e-02 2.50e+03 pdb=" CZ ARG D 67 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG D 67 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG D 67 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE G 233 " 0.013 2.00e-02 2.50e+03 2.74e-02 7.52e+00 pdb=" C ILE G 233 " -0.047 2.00e-02 2.50e+03 pdb=" O ILE G 233 " 0.018 2.00e-02 2.50e+03 pdb=" N THR G 234 " 0.016 2.00e-02 2.50e+03 ... (remaining 2463 not shown) Histogram of nonbonded interaction distances: 2.47 - 2.96: 6420 2.96 - 3.44: 14965 3.44 - 3.93: 23217 3.93 - 4.41: 26634 4.41 - 4.90: 42377 Nonbonded interactions: 113613 Sorted by model distance: nonbonded pdb=" CB CYS G 313 " pdb=" CB CYS G 343 " model vdw 2.472 3.072 nonbonded pdb=" CB CYS B 313 " pdb=" CB CYS B 343 " model vdw 2.473 3.072 nonbonded pdb=" O TYR A 94 " pdb=" CA GLY A 119 " model vdw 2.531 2.752 nonbonded pdb=" O TYR F 94 " pdb=" CA GLY F 119 " model vdw 2.551 2.752 nonbonded pdb=" N TYR B 44 " pdb=" O TYR B 44 " model vdw 2.564 2.496 ... (remaining 113608 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 'F' } ncs_group { reference = chain 'B' selection = chain 'G' } ncs_group { reference = chain 'C' selection = chain 'H' } ncs_group { reference = chain 'D' selection = chain 'I' } ncs_group { reference = chain 'E' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.330 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: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.270 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 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 : 0.006 0.115 14330 Z= 0.268 Angle : 1.117 28.490 19460 Z= 0.604 Chirality : 0.059 0.383 2232 Planarity : 0.010 0.255 2466 Dihedral : 13.511 90.477 5144 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.40 % Favored : 90.60 % Rotamer: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.32 (0.18), residues: 1808 helix: -1.22 (0.29), residues: 262 sheet: -1.05 (0.22), residues: 516 loop : -1.92 (0.18), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 63 TYR 0.029 0.003 TYR C 41 PHE 0.017 0.002 PHE J 33 TRP 0.030 0.004 TRP A 36 HIS 0.012 0.002 HIS A 35 Details of bonding type rmsd covalent geometry : bond 0.00554 (14306) covalent geometry : angle 1.10784 (19412) SS BOND : bond 0.01563 ( 24) SS BOND : angle 3.04189 ( 48) hydrogen bonds : bond 0.14607 ( 502) hydrogen bonds : angle 8.13634 ( 1296) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.483 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: A 32 TYR cc_start: 0.6779 (m-10) cc_final: 0.6403 (m-10) REVERT: A 34 PHE cc_start: 0.8140 (m-80) cc_final: 0.7413 (m-80) REVERT: A 118 GLN cc_start: 0.8089 (mm-40) cc_final: 0.6824 (tm-30) REVERT: B 261 ILE cc_start: 0.9283 (mm) cc_final: 0.8981 (mm) REVERT: B 266 ILE cc_start: 0.9131 (pt) cc_final: 0.8528 (pt) REVERT: B 297 LEU cc_start: 0.9377 (tt) cc_final: 0.9047 (mp) REVERT: B 396 MET cc_start: -0.0368 (mmm) cc_final: -0.0906 (mmp) REVERT: B 488 PHE cc_start: 0.8364 (p90) cc_final: 0.7851 (p90) REVERT: C 47 LYS cc_start: 0.8905 (tptp) cc_final: 0.8612 (tttt) REVERT: C 83 GLU cc_start: 0.8879 (pp20) cc_final: 0.8326 (pp20) REVERT: E 38 TYR cc_start: 0.8264 (m-80) cc_final: 0.6575 (m-80) REVERT: E 98 ASP cc_start: 0.8099 (m-30) cc_final: 0.7814 (m-30) REVERT: F 32 TYR cc_start: 0.7111 (m-10) cc_final: 0.6772 (m-10) REVERT: F 118 GLN cc_start: 0.8181 (mm-40) cc_final: 0.6833 (tm-30) REVERT: G 297 LEU cc_start: 0.9362 (tt) cc_final: 0.9024 (mp) REVERT: G 396 MET cc_start: -0.0176 (mmm) cc_final: -0.0714 (mmp) REVERT: G 488 PHE cc_start: 0.8390 (p90) cc_final: 0.7876 (p90) REVERT: J 38 TYR cc_start: 0.8337 (m-80) cc_final: 0.6609 (m-80) REVERT: J 98 ASP cc_start: 0.7970 (m-30) cc_final: 0.7736 (m-30) outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 0.1194 time to fit residues: 23.9039 Evaluate side-chains 102 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 30.0000 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 20.0000 chunk 149 optimal weight: 0.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 227 ASN ** B 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.057180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.040909 restraints weight = 117111.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.042541 restraints weight = 67291.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.043641 restraints weight = 45420.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.044399 restraints weight = 34242.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.044901 restraints weight = 27915.001| |-----------------------------------------------------------------------------| r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 14330 Z= 0.214 Angle : 0.711 13.835 19460 Z= 0.372 Chirality : 0.043 0.239 2232 Planarity : 0.005 0.048 2466 Dihedral : 5.846 41.053 1972 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 19.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.96 % Favored : 91.04 % Rotamer: Outliers : 0.19 % Allowed : 7.21 % Favored : 92.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.98 (0.19), residues: 1808 helix: -0.12 (0.33), residues: 266 sheet: -0.98 (0.22), residues: 516 loop : -1.86 (0.18), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 63 TYR 0.021 0.002 TYR A 112 PHE 0.015 0.002 PHE F 29 TRP 0.018 0.003 TRP A 106 HIS 0.007 0.002 HIS E 36 Details of bonding type rmsd covalent geometry : bond 0.00448 (14306) covalent geometry : angle 0.69506 (19412) SS BOND : bond 0.00611 ( 24) SS BOND : angle 3.11059 ( 48) hydrogen bonds : bond 0.03794 ( 502) hydrogen bonds : angle 6.57414 ( 1296) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 119 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 TYR cc_start: 0.6967 (m-10) cc_final: 0.6702 (m-10) REVERT: A 112 TYR cc_start: 0.7888 (OUTLIER) cc_final: 0.7009 (m-10) REVERT: A 118 GLN cc_start: 0.8190 (mm-40) cc_final: 0.6889 (tm-30) REVERT: B 261 ILE cc_start: 0.9422 (mm) cc_final: 0.9151 (mm) REVERT: B 266 ILE cc_start: 0.9262 (pt) cc_final: 0.8114 (pt) REVERT: B 396 MET cc_start: -0.0439 (mmm) cc_final: -0.1013 (mmp) REVERT: B 488 PHE cc_start: 0.8255 (p90) cc_final: 0.7751 (p90) REVERT: D 28 MET cc_start: 0.5594 (tmm) cc_final: 0.5166 (tmm) REVERT: E 98 ASP cc_start: 0.8459 (m-30) cc_final: 0.8226 (m-30) REVERT: F 113 MET cc_start: 0.8852 (mmt) cc_final: 0.8548 (mmt) REVERT: G 264 MET cc_start: 0.8091 (mmm) cc_final: 0.7386 (mmm) REVERT: G 266 ILE cc_start: 0.9393 (pt) cc_final: 0.9140 (pt) REVERT: G 396 MET cc_start: -0.0452 (mmm) cc_final: -0.1027 (mmp) REVERT: G 488 PHE cc_start: 0.8327 (p90) cc_final: 0.7820 (p90) REVERT: I 28 MET cc_start: 0.5709 (tmm) cc_final: 0.5311 (tmm) outliers start: 3 outliers final: 2 residues processed: 121 average time/residue: 0.1238 time to fit residues: 22.4244 Evaluate side-chains 99 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 96 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 4 optimal weight: 2.9990 chunk 159 optimal weight: 3.9990 chunk 68 optimal weight: 8.9990 chunk 19 optimal weight: 20.0000 chunk 144 optimal weight: 20.0000 chunk 35 optimal weight: 0.0870 chunk 72 optimal weight: 20.0000 chunk 41 optimal weight: 20.0000 chunk 9 optimal weight: 3.9990 chunk 97 optimal weight: 9.9990 chunk 62 optimal weight: 10.0000 overall best weight: 4.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 55 HIS ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 55 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.057340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.041818 restraints weight = 113750.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.043432 restraints weight = 63583.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.044510 restraints weight = 42262.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.045244 restraints weight = 31559.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.045773 restraints weight = 25607.456| |-----------------------------------------------------------------------------| r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14330 Z= 0.192 Angle : 0.696 14.781 19460 Z= 0.363 Chirality : 0.043 0.248 2232 Planarity : 0.005 0.050 2466 Dihedral : 5.643 40.433 1972 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 18.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.73 % Favored : 90.27 % Rotamer: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.03 (0.19), residues: 1808 helix: -0.09 (0.32), residues: 278 sheet: -1.14 (0.22), residues: 514 loop : -1.85 (0.18), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 63 TYR 0.014 0.002 TYR B 198 PHE 0.014 0.002 PHE B 190 TRP 0.030 0.002 TRP D 108 HIS 0.007 0.001 HIS E 36 Details of bonding type rmsd covalent geometry : bond 0.00410 (14306) covalent geometry : angle 0.67907 (19412) SS BOND : bond 0.00377 ( 24) SS BOND : angle 3.14934 ( 48) hydrogen bonds : bond 0.03695 ( 502) hydrogen bonds : angle 6.26068 ( 1296) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 TYR cc_start: 0.7271 (m-10) cc_final: 0.7020 (m-10) REVERT: A 112 TYR cc_start: 0.8073 (m-80) cc_final: 0.5921 (m-80) REVERT: A 118 GLN cc_start: 0.8233 (mm-40) cc_final: 0.6814 (tm-30) REVERT: B 220 VAL cc_start: 0.8810 (t) cc_final: 0.8594 (m) REVERT: B 261 ILE cc_start: 0.9402 (mm) cc_final: 0.9144 (mm) REVERT: B 266 ILE cc_start: 0.9213 (pt) cc_final: 0.8105 (pt) REVERT: B 396 MET cc_start: -0.0101 (mmm) cc_final: -0.0837 (mmp) REVERT: B 488 PHE cc_start: 0.8135 (p90) cc_final: 0.7639 (p90) REVERT: C 83 GLU cc_start: 0.9243 (pp20) cc_final: 0.8592 (pp20) REVERT: D 28 MET cc_start: 0.5760 (tmm) cc_final: 0.5124 (tmm) REVERT: F 1 GLN cc_start: 0.6908 (pm20) cc_final: 0.6644 (pm20) REVERT: F 34 PHE cc_start: 0.8345 (m-80) cc_final: 0.7798 (m-80) REVERT: F 113 MET cc_start: 0.8850 (mmt) cc_final: 0.8650 (mmp) REVERT: G 220 VAL cc_start: 0.8721 (t) cc_final: 0.8510 (m) REVERT: G 396 MET cc_start: -0.0088 (mmm) cc_final: -0.0843 (mmp) REVERT: G 488 PHE cc_start: 0.8090 (p90) cc_final: 0.7563 (p90) REVERT: H 83 GLU cc_start: 0.9235 (pp20) cc_final: 0.8558 (pp20) REVERT: I 28 MET cc_start: 0.5886 (tmm) cc_final: 0.5373 (tmm) outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.1291 time to fit residues: 22.5776 Evaluate side-chains 96 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 97 optimal weight: 9.9990 chunk 143 optimal weight: 0.6980 chunk 111 optimal weight: 0.0670 chunk 68 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 170 optimal weight: 10.0000 chunk 174 optimal weight: 6.9990 chunk 72 optimal weight: 7.9990 chunk 38 optimal weight: 5.9990 chunk 151 optimal weight: 0.8980 chunk 23 optimal weight: 5.9990 overall best weight: 1.9322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 1 GLN ** A 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 227 ASN ** G 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.058608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.043245 restraints weight = 113839.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.044909 restraints weight = 63523.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.046029 restraints weight = 42016.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.046791 restraints weight = 31156.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.047306 restraints weight = 25150.345| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 14330 Z= 0.127 Angle : 0.653 15.164 19460 Z= 0.337 Chirality : 0.043 0.226 2232 Planarity : 0.004 0.049 2466 Dihedral : 5.293 38.460 1972 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.18 % Favored : 90.82 % Rotamer: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.75 (0.19), residues: 1808 helix: 0.52 (0.33), residues: 268 sheet: -1.07 (0.21), residues: 548 loop : -1.71 (0.19), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 98 TYR 0.014 0.001 TYR G 198 PHE 0.016 0.001 PHE C 101 TRP 0.032 0.002 TRP I 108 HIS 0.003 0.001 HIS I 35 Details of bonding type rmsd covalent geometry : bond 0.00279 (14306) covalent geometry : angle 0.63644 (19412) SS BOND : bond 0.00275 ( 24) SS BOND : angle 2.99458 ( 48) hydrogen bonds : bond 0.03290 ( 502) hydrogen bonds : angle 5.90349 ( 1296) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 TYR cc_start: 0.7165 (m-10) cc_final: 0.6930 (m-10) REVERT: A 112 TYR cc_start: 0.7827 (m-80) cc_final: 0.6228 (m-80) REVERT: A 118 GLN cc_start: 0.8149 (mm-40) cc_final: 0.6967 (tm-30) REVERT: B 220 VAL cc_start: 0.8820 (t) cc_final: 0.8606 (m) REVERT: B 261 ILE cc_start: 0.9388 (mm) cc_final: 0.9097 (mm) REVERT: B 266 ILE cc_start: 0.9097 (pt) cc_final: 0.7986 (pt) REVERT: B 370 MET cc_start: 0.7444 (tmm) cc_final: 0.7120 (tmm) REVERT: B 396 MET cc_start: 0.0155 (mmm) cc_final: -0.0597 (mmp) REVERT: B 488 PHE cc_start: 0.8131 (p90) cc_final: 0.7636 (p90) REVERT: C 83 GLU cc_start: 0.9154 (pp20) cc_final: 0.8545 (pp20) REVERT: D 28 MET cc_start: 0.5361 (tmm) cc_final: 0.4547 (tmm) REVERT: F 32 TYR cc_start: 0.7414 (m-10) cc_final: 0.7107 (m-10) REVERT: F 34 PHE cc_start: 0.8186 (m-80) cc_final: 0.7847 (m-80) REVERT: F 113 MET cc_start: 0.8874 (mmt) cc_final: 0.8665 (mmt) REVERT: F 118 GLN cc_start: 0.8198 (mm-40) cc_final: 0.6785 (tm-30) REVERT: G 188 LEU cc_start: 0.8354 (tp) cc_final: 0.6967 (tp) REVERT: G 220 VAL cc_start: 0.8714 (t) cc_final: 0.8477 (m) REVERT: G 266 ILE cc_start: 0.9306 (pt) cc_final: 0.9060 (pt) REVERT: G 370 MET cc_start: 0.7419 (tmm) cc_final: 0.7089 (tmm) REVERT: G 396 MET cc_start: 0.0132 (mmm) cc_final: -0.0614 (mmp) REVERT: G 488 PHE cc_start: 0.8123 (p90) cc_final: 0.7624 (p90) REVERT: H 83 GLU cc_start: 0.9167 (pp20) cc_final: 0.8556 (pp20) REVERT: I 28 MET cc_start: 0.5459 (tmm) cc_final: 0.4654 (tmm) REVERT: J 37 TRP cc_start: 0.7899 (m100) cc_final: 0.7522 (m-10) outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.1215 time to fit residues: 24.0803 Evaluate side-chains 102 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 135 optimal weight: 10.0000 chunk 20 optimal weight: 30.0000 chunk 40 optimal weight: 30.0000 chunk 61 optimal weight: 9.9990 chunk 177 optimal weight: 10.0000 chunk 118 optimal weight: 9.9990 chunk 4 optimal weight: 7.9990 chunk 144 optimal weight: 40.0000 chunk 171 optimal weight: 6.9990 chunk 13 optimal weight: 50.0000 chunk 179 optimal weight: 5.9990 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 118 GLN ** B 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 383 ASN C 39 GLN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 118 GLN ** G 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 383 ASN H 39 GLN ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.054198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.038598 restraints weight = 116553.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.040117 restraints weight = 66120.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.041126 restraints weight = 44216.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.041803 restraints weight = 33317.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.042285 restraints weight = 27295.812| |-----------------------------------------------------------------------------| r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.3684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 14330 Z= 0.348 Angle : 0.868 14.924 19460 Z= 0.450 Chirality : 0.046 0.215 2232 Planarity : 0.006 0.052 2466 Dihedral : 6.293 46.095 1972 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 28.01 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.67 % Favored : 88.27 % Rotamer: Outliers : 0.13 % Allowed : 5.76 % Favored : 94.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.21 (0.19), residues: 1808 helix: 0.02 (0.31), residues: 266 sheet: -1.49 (0.21), residues: 534 loop : -1.88 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 19 TYR 0.024 0.003 TYR C 41 PHE 0.033 0.003 PHE H 101 TRP 0.040 0.004 TRP E 37 HIS 0.013 0.003 HIS E 36 Details of bonding type rmsd covalent geometry : bond 0.00726 (14306) covalent geometry : angle 0.85219 (19412) SS BOND : bond 0.00687 ( 24) SS BOND : angle 3.38487 ( 48) hydrogen bonds : bond 0.04261 ( 502) hydrogen bonds : angle 6.75903 ( 1296) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 106 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 261 ILE cc_start: 0.9465 (mm) cc_final: 0.9207 (mm) REVERT: B 396 MET cc_start: 0.1047 (mmm) cc_final: 0.0298 (mmm) REVERT: D 20 LEU cc_start: 0.9231 (mm) cc_final: 0.8909 (mm) REVERT: D 34 MET cc_start: 0.9154 (tpt) cc_final: 0.8812 (tpt) REVERT: D 83 MET cc_start: 0.8351 (mmp) cc_final: 0.8147 (mmp) REVERT: F 113 MET cc_start: 0.9131 (mmt) cc_final: 0.8836 (mmp) REVERT: G 266 ILE cc_start: 0.9493 (pt) cc_final: 0.9195 (pt) REVERT: G 396 MET cc_start: 0.1048 (mmm) cc_final: 0.0310 (mmm) REVERT: G 435 PHE cc_start: 0.9003 (m-80) cc_final: 0.8784 (m-80) REVERT: I 20 LEU cc_start: 0.9182 (mm) cc_final: 0.8869 (mm) REVERT: I 34 MET cc_start: 0.9128 (tpt) cc_final: 0.8827 (tpt) REVERT: I 83 MET cc_start: 0.8298 (mmp) cc_final: 0.8074 (mmp) outliers start: 2 outliers final: 0 residues processed: 108 average time/residue: 0.1213 time to fit residues: 18.9854 Evaluate side-chains 78 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 170 optimal weight: 20.0000 chunk 146 optimal weight: 4.9990 chunk 151 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 chunk 14 optimal weight: 6.9990 chunk 5 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 23 optimal weight: 0.5980 chunk 74 optimal weight: 8.9990 chunk 100 optimal weight: 4.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 383 ASN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 363 ASN G 383 ASN H 39 GLN ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 55 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.056256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.040961 restraints weight = 113359.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.042584 restraints weight = 63409.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.043676 restraints weight = 42088.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.044416 restraints weight = 31304.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.044925 restraints weight = 25347.707| |-----------------------------------------------------------------------------| r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.3601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14330 Z= 0.169 Angle : 0.716 13.474 19460 Z= 0.369 Chirality : 0.044 0.190 2232 Planarity : 0.004 0.053 2466 Dihedral : 5.760 40.064 1972 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 18.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.34 % Favored : 89.66 % Rotamer: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.01 (0.19), residues: 1808 helix: 0.17 (0.32), residues: 268 sheet: -1.33 (0.21), residues: 542 loop : -1.77 (0.19), residues: 998 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 229 TYR 0.029 0.002 TYR B 342 PHE 0.010 0.001 PHE H 101 TRP 0.024 0.003 TRP I 108 HIS 0.006 0.001 HIS E 36 Details of bonding type rmsd covalent geometry : bond 0.00372 (14306) covalent geometry : angle 0.69970 (19412) SS BOND : bond 0.00321 ( 24) SS BOND : angle 3.15356 ( 48) hydrogen bonds : bond 0.03510 ( 502) hydrogen bonds : angle 6.24627 ( 1296) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 261 ILE cc_start: 0.9421 (mm) cc_final: 0.8891 (mt) REVERT: B 266 ILE cc_start: 0.9173 (pt) cc_final: 0.8175 (pt) REVERT: B 396 MET cc_start: 0.1240 (mmm) cc_final: 0.0473 (mmm) REVERT: E 98 ASP cc_start: 0.8067 (m-30) cc_final: 0.7861 (m-30) REVERT: F 1 GLN cc_start: 0.8066 (pm20) cc_final: 0.7839 (pm20) REVERT: F 34 PHE cc_start: 0.8312 (m-80) cc_final: 0.8014 (m-80) REVERT: G 396 MET cc_start: 0.1290 (mmm) cc_final: 0.0482 (mmm) outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.1098 time to fit residues: 17.5838 Evaluate side-chains 82 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 129 optimal weight: 6.9990 chunk 56 optimal weight: 20.0000 chunk 151 optimal weight: 0.9990 chunk 154 optimal weight: 0.8980 chunk 8 optimal weight: 9.9990 chunk 179 optimal weight: 20.0000 chunk 41 optimal weight: 0.0570 chunk 25 optimal weight: 3.9990 chunk 137 optimal weight: 0.0870 chunk 6 optimal weight: 6.9990 chunk 97 optimal weight: 6.9990 overall best weight: 1.2080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 383 ASN H 39 GLN ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 53 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.057744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.042647 restraints weight = 112341.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.044311 restraints weight = 62886.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.045447 restraints weight = 41624.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.046220 restraints weight = 30807.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.046715 restraints weight = 24728.784| |-----------------------------------------------------------------------------| r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.3567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 14330 Z= 0.119 Angle : 0.674 11.730 19460 Z= 0.343 Chirality : 0.043 0.190 2232 Planarity : 0.004 0.053 2466 Dihedral : 5.413 37.039 1972 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.12 % Favored : 89.88 % Rotamer: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.89 (0.19), residues: 1808 helix: 0.45 (0.33), residues: 268 sheet: -1.40 (0.22), residues: 506 loop : -1.66 (0.19), residues: 1034 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 98 TYR 0.022 0.002 TYR G 342 PHE 0.020 0.001 PHE F 27 TRP 0.045 0.003 TRP D 108 HIS 0.006 0.002 HIS E 36 Details of bonding type rmsd covalent geometry : bond 0.00267 (14306) covalent geometry : angle 0.65841 (19412) SS BOND : bond 0.00483 ( 24) SS BOND : angle 2.98887 ( 48) hydrogen bonds : bond 0.03315 ( 502) hydrogen bonds : angle 5.84768 ( 1296) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 PHE cc_start: 0.8367 (m-80) cc_final: 0.8038 (m-80) REVERT: A 113 MET cc_start: 0.8698 (mmp) cc_final: 0.8164 (mmp) REVERT: A 118 GLN cc_start: 0.7936 (mm110) cc_final: 0.7322 (tp40) REVERT: B 251 MET cc_start: 0.8837 (mpp) cc_final: 0.8469 (mpp) REVERT: B 261 ILE cc_start: 0.9403 (mm) cc_final: 0.9142 (mm) REVERT: B 266 ILE cc_start: 0.9080 (pt) cc_final: 0.8104 (pt) REVERT: D 34 MET cc_start: 0.9218 (tpt) cc_final: 0.8976 (tpt) REVERT: E 98 ASP cc_start: 0.7685 (m-30) cc_final: 0.7475 (m-30) REVERT: F 1 GLN cc_start: 0.7342 (pm20) cc_final: 0.7123 (pp30) REVERT: G 264 MET cc_start: 0.8201 (mmp) cc_final: 0.7823 (tpp) REVERT: H 83 GLU cc_start: 0.9051 (pp20) cc_final: 0.8554 (pp20) REVERT: I 34 MET cc_start: 0.9198 (tpt) cc_final: 0.8998 (tpt) REVERT: J 98 ASP cc_start: 0.7743 (m-30) cc_final: 0.7524 (m-30) outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.1154 time to fit residues: 22.1927 Evaluate side-chains 87 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 52 optimal weight: 6.9990 chunk 108 optimal weight: 8.9990 chunk 139 optimal weight: 5.9990 chunk 168 optimal weight: 8.9990 chunk 31 optimal weight: 9.9990 chunk 102 optimal weight: 0.9990 chunk 107 optimal weight: 6.9990 chunk 106 optimal weight: 9.9990 chunk 116 optimal weight: 7.9990 chunk 162 optimal weight: 4.9990 chunk 69 optimal weight: 9.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 363 ASN B 383 ASN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 383 ASN H 39 GLN ** J 6 GLN ** 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 = 0.3601 r_free = 0.3601 target = 0.055363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.040161 restraints weight = 114082.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.041725 restraints weight = 64003.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.042785 restraints weight = 42519.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.043511 restraints weight = 31712.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.043992 restraints weight = 25691.687| |-----------------------------------------------------------------------------| r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.4059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 14330 Z= 0.233 Angle : 0.745 10.795 19460 Z= 0.384 Chirality : 0.044 0.181 2232 Planarity : 0.004 0.052 2466 Dihedral : 5.741 40.548 1972 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 22.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.56 % Favored : 89.44 % Rotamer: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.06 (0.19), residues: 1808 helix: 0.26 (0.33), residues: 266 sheet: -1.52 (0.22), residues: 524 loop : -1.75 (0.19), residues: 1018 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 98 TYR 0.022 0.002 TYR G 53 PHE 0.025 0.002 PHE F 27 TRP 0.031 0.003 TRP D 108 HIS 0.009 0.002 HIS E 36 Details of bonding type rmsd covalent geometry : bond 0.00506 (14306) covalent geometry : angle 0.73069 (19412) SS BOND : bond 0.00441 ( 24) SS BOND : angle 3.04602 ( 48) hydrogen bonds : bond 0.03588 ( 502) hydrogen bonds : angle 6.28933 ( 1296) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.530 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: A 113 MET cc_start: 0.8811 (mmp) cc_final: 0.8399 (mmp) REVERT: B 251 MET cc_start: 0.8984 (mpp) cc_final: 0.8579 (mpp) REVERT: B 261 ILE cc_start: 0.9487 (mm) cc_final: 0.9159 (mm) REVERT: B 266 ILE cc_start: 0.9202 (pt) cc_final: 0.8111 (pt) REVERT: B 488 PHE cc_start: 0.8591 (p90) cc_final: 0.8356 (p90) REVERT: D 20 LEU cc_start: 0.9289 (mm) cc_final: 0.9014 (mt) REVERT: D 83 MET cc_start: 0.8266 (mmp) cc_final: 0.7931 (mmp) REVERT: E 98 ASP cc_start: 0.8193 (m-30) cc_final: 0.7919 (m-30) REVERT: F 1 GLN cc_start: 0.8072 (pm20) cc_final: 0.7699 (pm20) REVERT: G 251 MET cc_start: 0.8950 (mpp) cc_final: 0.8585 (mpp) REVERT: G 264 MET cc_start: 0.8457 (mmp) cc_final: 0.7986 (tpp) REVERT: G 488 PHE cc_start: 0.8590 (p90) cc_final: 0.8354 (p90) REVERT: J 98 ASP cc_start: 0.8037 (m-30) cc_final: 0.7803 (m-30) outliers start: 0 outliers final: 0 residues processed: 107 average time/residue: 0.1192 time to fit residues: 19.1627 Evaluate side-chains 80 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 53 optimal weight: 0.0470 chunk 59 optimal weight: 5.9990 chunk 69 optimal weight: 5.9990 chunk 118 optimal weight: 4.9990 chunk 89 optimal weight: 9.9990 chunk 175 optimal weight: 20.0000 chunk 66 optimal weight: 0.8980 chunk 19 optimal weight: 9.9990 chunk 40 optimal weight: 7.9990 chunk 4 optimal weight: 0.9980 chunk 130 optimal weight: 6.9990 overall best weight: 2.5882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 111 GLN G 383 ASN ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.056748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.040572 restraints weight = 109828.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.042313 restraints weight = 60798.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.043489 restraints weight = 39978.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.044267 restraints weight = 29558.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.044855 restraints weight = 23854.704| |-----------------------------------------------------------------------------| r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.4117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 14330 Z= 0.148 Angle : 0.698 12.345 19460 Z= 0.355 Chirality : 0.044 0.167 2232 Planarity : 0.004 0.051 2466 Dihedral : 5.567 38.081 1972 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 18.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.40 % Favored : 90.60 % Rotamer: Outliers : 0.06 % Allowed : 1.25 % Favored : 98.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.00 (0.19), residues: 1808 helix: 0.34 (0.32), residues: 266 sheet: -1.43 (0.22), residues: 504 loop : -1.75 (0.18), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG I 98 TYR 0.017 0.002 TYR H 38 PHE 0.022 0.001 PHE A 27 TRP 0.032 0.003 TRP D 112 HIS 0.006 0.001 HIS D 35 Details of bonding type rmsd covalent geometry : bond 0.00332 (14306) covalent geometry : angle 0.68411 (19412) SS BOND : bond 0.00395 ( 24) SS BOND : angle 2.82302 ( 48) hydrogen bonds : bond 0.03279 ( 502) hydrogen bonds : angle 6.03371 ( 1296) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 116 time to evaluate : 0.569 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 113 MET cc_start: 0.8669 (mmp) cc_final: 0.8343 (mmp) REVERT: B 251 MET cc_start: 0.8956 (mpp) cc_final: 0.8573 (mpp) REVERT: B 261 ILE cc_start: 0.9492 (mm) cc_final: 0.8969 (mt) REVERT: B 266 ILE cc_start: 0.9100 (pt) cc_final: 0.7997 (pt) REVERT: C 35 VAL cc_start: 0.9190 (t) cc_final: 0.8955 (p) REVERT: C 83 GLU cc_start: 0.9168 (pp20) cc_final: 0.8634 (pp20) REVERT: E 98 ASP cc_start: 0.7830 (m-30) cc_final: 0.7593 (m-30) REVERT: F 2 VAL cc_start: 0.8969 (t) cc_final: 0.8749 (t) REVERT: F 32 TYR cc_start: 0.7115 (m-10) cc_final: 0.6756 (m-10) REVERT: F 111 GLN cc_start: 0.8773 (OUTLIER) cc_final: 0.8460 (pp30) REVERT: G 251 MET cc_start: 0.9007 (mpp) cc_final: 0.8626 (mpp) REVERT: G 264 MET cc_start: 0.8320 (mmp) cc_final: 0.8024 (tpp) REVERT: H 83 GLU cc_start: 0.9038 (pp20) cc_final: 0.8540 (pp20) REVERT: I 34 MET cc_start: 0.9018 (tpt) cc_final: 0.8634 (tpt) REVERT: J 98 ASP cc_start: 0.7908 (m-30) cc_final: 0.7664 (m-30) outliers start: 1 outliers final: 0 residues processed: 117 average time/residue: 0.0980 time to fit residues: 17.3755 Evaluate side-chains 86 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 85 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 112 optimal weight: 9.9990 chunk 119 optimal weight: 5.9990 chunk 52 optimal weight: 20.0000 chunk 144 optimal weight: 8.9990 chunk 80 optimal weight: 6.9990 chunk 9 optimal weight: 6.9990 chunk 33 optimal weight: 0.9990 chunk 105 optimal weight: 4.9990 chunk 163 optimal weight: 4.9990 chunk 140 optimal weight: 50.0000 chunk 129 optimal weight: 9.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 383 ASN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 383 ASN ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.055045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.039827 restraints weight = 114122.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.041428 restraints weight = 63755.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.042519 restraints weight = 42131.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.043271 restraints weight = 31096.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.043802 restraints weight = 24966.085| |-----------------------------------------------------------------------------| r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.4549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 14330 Z= 0.224 Angle : 0.752 12.282 19460 Z= 0.387 Chirality : 0.044 0.174 2232 Planarity : 0.004 0.052 2466 Dihedral : 5.834 40.451 1972 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 22.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.95 % Favored : 89.05 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.16 (0.19), residues: 1808 helix: 0.24 (0.33), residues: 266 sheet: -1.54 (0.22), residues: 510 loop : -1.86 (0.18), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 63 TYR 0.021 0.002 TYR F 71 PHE 0.026 0.002 PHE A 27 TRP 0.027 0.003 TRP D 108 HIS 0.008 0.002 HIS E 36 Details of bonding type rmsd covalent geometry : bond 0.00488 (14306) covalent geometry : angle 0.73886 (19412) SS BOND : bond 0.00354 ( 24) SS BOND : angle 2.86981 ( 48) hydrogen bonds : bond 0.03508 ( 502) hydrogen bonds : angle 6.35654 ( 1296) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.374 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: B 251 MET cc_start: 0.8938 (mpp) cc_final: 0.8584 (mpp) REVERT: B 261 ILE cc_start: 0.9511 (mm) cc_final: 0.8992 (mt) REVERT: B 266 ILE cc_start: 0.9174 (pt) cc_final: 0.8057 (pt) REVERT: C 83 GLU cc_start: 0.9210 (pp20) cc_final: 0.8607 (pp20) REVERT: D 20 LEU cc_start: 0.9519 (mm) cc_final: 0.8776 (mp) REVERT: D 34 MET cc_start: 0.9016 (tpt) cc_final: 0.8685 (tpp) REVERT: D 83 MET cc_start: 0.8109 (mmp) cc_final: 0.7854 (mmp) REVERT: E 98 ASP cc_start: 0.8051 (m-30) cc_final: 0.7782 (m-30) REVERT: G 251 MET cc_start: 0.8896 (mpp) cc_final: 0.8574 (mpp) REVERT: G 266 ILE cc_start: 0.9356 (pt) cc_final: 0.8910 (pt) REVERT: G 370 MET cc_start: 0.7359 (tmm) cc_final: 0.6869 (tmm) REVERT: I 20 LEU cc_start: 0.9242 (mm) cc_final: 0.8963 (mt) REVERT: I 83 MET cc_start: 0.8251 (mmp) cc_final: 0.7994 (mmp) REVERT: J 98 ASP cc_start: 0.8045 (m-30) cc_final: 0.7800 (m-30) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.1143 time to fit residues: 17.8986 Evaluate side-chains 82 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 38 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 74 optimal weight: 10.0000 chunk 132 optimal weight: 10.0000 chunk 153 optimal weight: 6.9990 chunk 94 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 134 optimal weight: 0.5980 chunk 52 optimal weight: 20.0000 chunk 82 optimal weight: 6.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 383 ASN ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.055912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.040885 restraints weight = 110556.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.042530 restraints weight = 61082.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.043657 restraints weight = 39984.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.044396 restraints weight = 29352.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.044958 restraints weight = 23476.028| |-----------------------------------------------------------------------------| r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.4587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 14330 Z= 0.160 Angle : 0.717 12.970 19460 Z= 0.364 Chirality : 0.044 0.212 2232 Planarity : 0.004 0.057 2466 Dihedral : 5.650 38.270 1972 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 18.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.85 % Favored : 90.15 % Rotamer: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.07 (0.19), residues: 1808 helix: 0.30 (0.32), residues: 266 sheet: -1.48 (0.22), residues: 504 loop : -1.80 (0.18), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I 98 TYR 0.021 0.002 TYR C 38 PHE 0.019 0.001 PHE F 27 TRP 0.028 0.003 TRP A 36 HIS 0.006 0.001 HIS E 36 Details of bonding type rmsd covalent geometry : bond 0.00359 (14306) covalent geometry : angle 0.70531 (19412) SS BOND : bond 0.00290 ( 24) SS BOND : angle 2.71434 ( 48) hydrogen bonds : bond 0.03308 ( 502) hydrogen bonds : angle 6.14210 ( 1296) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2497.95 seconds wall clock time: 44 minutes 9.58 seconds (2649.58 seconds total)