Starting phenix.real_space_refine on Wed Feb 4 15:53:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9do6_47072/02_2026/9do6_47072_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9do6_47072/02_2026/9do6_47072.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9do6_47072/02_2026/9do6_47072_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9do6_47072/02_2026/9do6_47072_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9do6_47072/02_2026/9do6_47072.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9do6_47072/02_2026/9do6_47072.map" } resolution = 2.54 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.012 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 22 5.16 5 C 7144 2.51 5 N 1966 2.21 5 O 2250 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 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: 11382 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1042 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 3, 'TRANS': 131} Chain: "B" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1042 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 3, 'TRANS': 131} Chain: "C" Number of atoms: 3573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3573 Classifications: {'peptide': 463} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 433} Chain breaks: 2 Chain: "D" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1042 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 3, 'TRANS': 131} Chain: "E" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1042 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 3, 'TRANS': 131} Chain: "F" Number of atoms: 3641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3641 Classifications: {'peptide': 471} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 439} Time building chain proxies: 2.63, per 1000 atoms: 0.23 Number of scatterers: 11382 At special positions: 0 Unit cell: (112.05, 110.39, 140.27, 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 22 16.00 O 2250 8.00 N 1966 7.00 C 7144 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.86 Conformation dependent library (CDL) restraints added in 525.6 milliseconds 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2690 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 20 sheets defined 14.4% alpha, 35.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'B' and resid 42 through 46 Processing helix chain 'B' and resid 80 through 84 removed outlier: 3.521A pdb=" N ASP B 84 " --> pdb=" O PRO B 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 80 through 84' Processing helix chain 'C' and resid 54 through 60 Processing helix chain 'C' and resid 61 through 72 Processing helix chain 'C' and resid 177 through 181 Processing helix chain 'C' and resid 189 through 201 Processing helix chain 'C' and resid 204 through 220 Processing helix chain 'C' and resid 298 through 302 Processing helix chain 'C' and resid 304 through 309 Processing helix chain 'C' and resid 310 through 318 removed outlier: 4.002A pdb=" N ASN C 313 " --> pdb=" O ALA C 310 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N SER C 315 " --> pdb=" O THR C 312 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N GLU C 316 " --> pdb=" O ASN C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 333 Processing helix chain 'C' and resid 334 through 345 removed outlier: 3.545A pdb=" N GLN C 340 " --> pdb=" O PRO C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 444 through 447 Processing helix chain 'D' and resid 42 through 46 removed outlier: 3.553A pdb=" N ASN D 45 " --> pdb=" O SER D 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 46 Processing helix chain 'F' and resid 54 through 60 Processing helix chain 'F' and resid 61 through 72 Processing helix chain 'F' and resid 177 through 181 Processing helix chain 'F' and resid 189 through 201 Processing helix chain 'F' and resid 204 through 220 Processing helix chain 'F' and resid 298 through 302 Processing helix chain 'F' and resid 304 through 311 Processing helix chain 'F' and resid 312 through 318 removed outlier: 5.812A pdb=" N SER F 315 " --> pdb=" O THR F 312 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N GLU F 316 " --> pdb=" O ASN F 313 " (cutoff:3.500A) Processing helix chain 'F' and resid 330 through 333 Processing helix chain 'F' and resid 334 through 345 removed outlier: 3.623A pdb=" N GLN F 340 " --> pdb=" O PRO F 336 " (cutoff:3.500A) Processing helix chain 'F' and resid 444 through 447 removed outlier: 3.515A pdb=" N THR F 447 " --> pdb=" O PRO F 444 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 444 through 447' Processing helix chain 'F' and resid 467 through 470 Processing sheet with id=AA1, first strand: chain 'A' and resid 30 through 32 removed outlier: 4.719A pdb=" N ASN A 60 " --> pdb=" O HIS A 32 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N TRP A 6 " --> pdb=" O GLY A 127 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N ILE A 129 " --> pdb=" O TRP A 6 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N ILE A 8 " --> pdb=" O ILE A 129 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N VAL A 131 " --> pdb=" O ILE A 8 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ILE A 10 " --> pdb=" O VAL A 131 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N THR A 133 " --> pdb=" O ILE A 10 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N HIS A 12 " --> pdb=" O THR A 133 " (cutoff:3.500A) removed outlier: 8.317A pdb=" N LYS A 135 " --> pdb=" O HIS A 12 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 50 through 51 removed outlier: 4.167A pdb=" N LEU A 24 " --> pdb=" O THR A 74 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N THR A 74 " --> pdb=" O LEU A 24 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N ALA A 26 " --> pdb=" O THR A 72 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N THR A 72 " --> pdb=" O ALA A 26 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ASP A 79 " --> pdb=" O GLN A 86 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N GLN A 86 " --> pdb=" O ASP A 79 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 36 through 40 removed outlier: 6.001A pdb=" N ALA B 39 " --> pdb=" O ALA B 33 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ASN B 60 " --> pdb=" O HIS B 32 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N TRP B 6 " --> pdb=" O GLY B 127 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N ILE B 129 " --> pdb=" O TRP B 6 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ILE B 8 " --> pdb=" O ILE B 129 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N VAL B 131 " --> pdb=" O ILE B 8 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N ILE B 10 " --> pdb=" O VAL B 131 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N THR B 133 " --> pdb=" O ILE B 10 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N HIS B 12 " --> pdb=" O THR B 133 " (cutoff:3.500A) removed outlier: 8.203A pdb=" N LYS B 135 " --> pdb=" O HIS B 12 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 50 through 51 removed outlier: 5.142A pdb=" N ILE B 21 " --> pdb=" O VAL B 78 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N VAL B 78 " --> pdb=" O ILE B 21 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N ASN B 23 " --> pdb=" O ASP B 76 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ASP B 76 " --> pdb=" O ASN B 23 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N THR B 72 " --> pdb=" O SER B 27 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N THR B 71 " --> pdb=" O ASP B 93 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ASP B 93 " --> pdb=" O THR B 71 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N GLY B 73 " --> pdb=" O TYR B 91 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N TYR B 91 " --> pdb=" O GLY B 73 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N PHE B 75 " --> pdb=" O HIS B 89 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N HIS B 89 " --> pdb=" O PHE B 75 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N LEU B 77 " --> pdb=" O VAL B 87 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 78 through 80 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 103 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 100 through 103 current: chain 'C' and resid 139 through 174 removed outlier: 3.580A pdb=" N THR C 140 " --> pdb=" O GLU C 259 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU C 259 " --> pdb=" O THR C 140 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ASN C 142 " --> pdb=" O GLY C 257 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLY C 257 " --> pdb=" O ASN C 142 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ILE C 229 " --> pdb=" O GLN C 170 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ARG C 172 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N VAL C 227 " --> pdb=" O ARG C 172 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ASP C 174 " --> pdb=" O THR C 225 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N THR C 225 " --> pdb=" O ASP C 174 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL C 254 " --> pdb=" O HIS C 273 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N HIS C 273 " --> pdb=" O VAL C 254 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 273 through 295 current: chain 'F' and resid 139 through 174 removed outlier: 6.433A pdb=" N ILE F 229 " --> pdb=" O GLN F 170 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ARG F 172 " --> pdb=" O VAL F 227 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N VAL F 227 " --> pdb=" O ARG F 172 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ASP F 174 " --> pdb=" O THR F 225 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N THR F 225 " --> pdb=" O ASP F 174 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 348 through 357 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 369 through 371 current: chain 'C' and resid 390 through 396 Processing sheet with id=AA8, first strand: chain 'C' and resid 421 through 423 Processing sheet with id=AA9, first strand: chain 'C' and resid 456 through 458 Processing sheet with id=AB1, first strand: chain 'C' and resid 460 through 464 removed outlier: 4.085A pdb=" N SER C 492 " --> pdb=" O THR C 475 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 30 through 32 removed outlier: 4.131A pdb=" N ASN D 60 " --> pdb=" O HIS D 32 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLY D 127 " --> pdb=" O TRP D 6 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ILE D 8 " --> pdb=" O GLY D 127 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 50 through 51 removed outlier: 4.025A pdb=" N LEU D 24 " --> pdb=" O THR D 74 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N THR D 74 " --> pdb=" O LEU D 24 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ALA D 26 " --> pdb=" O THR D 72 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N THR D 72 " --> pdb=" O ALA D 26 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N THR D 71 " --> pdb=" O ASP D 93 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ASP D 93 " --> pdb=" O THR D 71 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N GLY D 73 " --> pdb=" O TYR D 91 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N TYR D 91 " --> pdb=" O GLY D 73 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N PHE D 75 " --> pdb=" O HIS D 89 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N HIS D 89 " --> pdb=" O PHE D 75 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LEU D 77 " --> pdb=" O VAL D 87 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LYS D 85 " --> pdb=" O ASP D 79 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 30 through 32 removed outlier: 3.847A pdb=" N ASN E 60 " --> pdb=" O HIS E 32 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N TRP E 6 " --> pdb=" O GLY E 127 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N ILE E 129 " --> pdb=" O TRP E 6 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ILE E 8 " --> pdb=" O ILE E 129 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N VAL E 131 " --> pdb=" O ILE E 8 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ILE E 10 " --> pdb=" O VAL E 131 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N THR E 133 " --> pdb=" O ILE E 10 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N HIS E 12 " --> pdb=" O THR E 133 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 49 through 51 removed outlier: 4.286A pdb=" N LEU E 24 " --> pdb=" O THR E 74 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N THR E 74 " --> pdb=" O LEU E 24 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ALA E 26 " --> pdb=" O THR E 72 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N THR E 72 " --> pdb=" O ALA E 26 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 76 through 81 removed outlier: 5.093A pdb=" N GLY F 77 " --> pdb=" O SER F 88 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLY F 81 " --> pdb=" O GLY F 84 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 380 through 381 removed outlier: 3.548A pdb=" N LYS F 395 " --> pdb=" O LEU F 349 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N LEU F 348 " --> pdb=" O LEU F 517 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 355 through 357 Processing sheet with id=AB9, first strand: chain 'F' and resid 421 through 423 Processing sheet with id=AC1, first strand: chain 'F' and resid 456 through 458 Processing sheet with id=AC2, first strand: chain 'F' and resid 463 through 464 removed outlier: 3.600A pdb=" N SER F 492 " --> pdb=" O THR F 475 " (cutoff:3.500A) 397 hydrogen bonds defined for protein. 1050 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: 1.49 Time building geometry restraints manager: 1.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2068 1.32 - 1.44: 2985 1.44 - 1.56: 6534 1.56 - 1.68: 0 1.68 - 1.81: 42 Bond restraints: 11629 Sorted by residual: bond pdb=" CA GLY C 220 " pdb=" C GLY C 220 " ideal model delta sigma weight residual 1.518 1.469 0.049 1.02e-02 9.61e+03 2.35e+01 bond pdb=" CA TYR C 127 " pdb=" C TYR C 127 " ideal model delta sigma weight residual 1.521 1.462 0.059 1.28e-02 6.10e+03 2.13e+01 bond pdb=" CA ASN A 120 " pdb=" C ASN A 120 " ideal model delta sigma weight residual 1.526 1.468 0.057 1.28e-02 6.10e+03 2.01e+01 bond pdb=" CA HIS A 32 " pdb=" C HIS A 32 " ideal model delta sigma weight residual 1.523 1.465 0.058 1.34e-02 5.57e+03 1.89e+01 bond pdb=" CA HIS A 89 " pdb=" C HIS A 89 " ideal model delta sigma weight residual 1.520 1.470 0.050 1.17e-02 7.31e+03 1.85e+01 ... (remaining 11624 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 15256 1.65 - 3.29: 417 3.29 - 4.94: 96 4.94 - 6.58: 16 6.58 - 8.23: 6 Bond angle restraints: 15791 Sorted by residual: angle pdb=" N ASP A 122 " pdb=" CA ASP A 122 " pdb=" C ASP A 122 " ideal model delta sigma weight residual 110.97 119.01 -8.04 1.09e+00 8.42e-01 5.44e+01 angle pdb=" N GLY C 220 " pdb=" CA GLY C 220 " pdb=" C GLY C 220 " ideal model delta sigma weight residual 112.08 118.60 -6.52 1.01e+00 9.80e-01 4.17e+01 angle pdb=" N LYS E 135 " pdb=" CA LYS E 135 " pdb=" C LYS E 135 " ideal model delta sigma weight residual 108.52 116.75 -8.23 1.74e+00 3.30e-01 2.24e+01 angle pdb=" O GLY C 81 " pdb=" C GLY C 81 " pdb=" N ARG C 82 " ideal model delta sigma weight residual 122.88 118.81 4.07 9.50e-01 1.11e+00 1.83e+01 angle pdb=" C ILE C 302 " pdb=" CA ILE C 302 " pdb=" CB ILE C 302 " ideal model delta sigma weight residual 112.16 105.63 6.53 1.55e+00 4.16e-01 1.78e+01 ... (remaining 15786 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 6466 17.69 - 35.39: 370 35.39 - 53.08: 62 53.08 - 70.78: 22 70.78 - 88.47: 10 Dihedral angle restraints: 6930 sinusoidal: 2732 harmonic: 4198 Sorted by residual: dihedral pdb=" CA TYR C 430 " pdb=" C TYR C 430 " pdb=" N LEU C 431 " pdb=" CA LEU C 431 " ideal model delta harmonic sigma weight residual -180.00 -158.24 -21.76 0 5.00e+00 4.00e-02 1.89e+01 dihedral pdb=" CA LEU F 425 " pdb=" C LEU F 425 " pdb=" N PRO F 426 " pdb=" CA PRO F 426 " ideal model delta harmonic sigma weight residual 180.00 -159.93 -20.07 0 5.00e+00 4.00e-02 1.61e+01 dihedral pdb=" CA LEU C 425 " pdb=" C LEU C 425 " pdb=" N PRO C 426 " pdb=" CA PRO C 426 " ideal model delta harmonic sigma weight residual -180.00 -160.06 -19.94 0 5.00e+00 4.00e-02 1.59e+01 ... (remaining 6927 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1397 0.049 - 0.099: 235 0.099 - 0.148: 115 0.148 - 0.197: 8 0.197 - 0.246: 1 Chirality restraints: 1756 Sorted by residual: chirality pdb=" CA ASP A 122 " pdb=" N ASP A 122 " pdb=" C ASP A 122 " pdb=" CB ASP A 122 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" CA LYS E 135 " pdb=" N LYS E 135 " pdb=" C LYS E 135 " pdb=" CB LYS E 135 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.39e-01 chirality pdb=" CA VAL C 478 " pdb=" N VAL C 478 " pdb=" C VAL C 478 " pdb=" CB VAL C 478 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.62e-01 ... (remaining 1753 not shown) Planarity restraints: 2047 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 31 " 0.022 2.00e-02 2.50e+03 4.37e-02 1.91e+01 pdb=" C LEU A 31 " -0.076 2.00e-02 2.50e+03 pdb=" O LEU A 31 " 0.029 2.00e-02 2.50e+03 pdb=" N HIS A 32 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY F 502 " 0.015 2.00e-02 2.50e+03 3.04e-02 9.23e+00 pdb=" C GLY F 502 " -0.053 2.00e-02 2.50e+03 pdb=" O GLY F 502 " 0.020 2.00e-02 2.50e+03 pdb=" N ASN F 503 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE D 21 " 0.012 2.00e-02 2.50e+03 2.39e-02 5.70e+00 pdb=" C ILE D 21 " -0.041 2.00e-02 2.50e+03 pdb=" O ILE D 21 " 0.015 2.00e-02 2.50e+03 pdb=" N LYS D 22 " 0.014 2.00e-02 2.50e+03 ... (remaining 2044 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2621 2.79 - 3.32: 10461 3.32 - 3.84: 18837 3.84 - 4.37: 22187 4.37 - 4.90: 39284 Nonbonded interactions: 93390 Sorted by model distance: nonbonded pdb=" OG1 THR C 418 " pdb=" OD1 ASN C 503 " model vdw 2.262 3.040 nonbonded pdb=" OD1 ASP F 331 " pdb=" NZ LYS F 342 " model vdw 2.285 3.120 nonbonded pdb=" OG SER E 16 " pdb=" OE1 GLN E 17 " model vdw 2.309 3.040 nonbonded pdb=" N GLN B 119 " pdb=" OE1 GLN B 119 " model vdw 2.337 3.120 nonbonded pdb=" OG1 THR E 72 " pdb=" OD1 ASP E 93 " model vdw 2.337 3.040 ... (remaining 93385 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'C' selection = (chain 'F' and (resid 52 through 261 or resid 266 through 480 or resid 485 throu \ gh 522)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.160 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: 0.270 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.820 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 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:6.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 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 0.065 11629 Z= 0.383 Angle : 0.690 8.227 15791 Z= 0.424 Chirality : 0.047 0.246 1756 Planarity : 0.004 0.044 2047 Dihedral : 12.419 88.471 4240 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.21), residues: 1458 helix: 0.82 (0.47), residues: 138 sheet: 0.62 (0.21), residues: 549 loop : -0.20 (0.21), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 452 TYR 0.019 0.002 TYR C 127 PHE 0.008 0.001 PHE C 488 TRP 0.012 0.001 TRP B 28 HIS 0.014 0.001 HIS A 12 Details of bonding type rmsd covalent geometry : bond 0.00594 (11629) covalent geometry : angle 0.69006 (15791) hydrogen bonds : bond 0.16895 ( 397) hydrogen bonds : angle 7.78679 ( 1050) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 255 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 207 GLU cc_start: 0.7014 (mt-10) cc_final: 0.6701 (mt-10) REVERT: F 191 GLN cc_start: 0.7790 (mp10) cc_final: 0.7380 (mp10) outliers start: 0 outliers final: 0 residues processed: 255 average time/residue: 0.5534 time to fit residues: 151.7478 Evaluate side-chains 222 residues out of total 1243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 222 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 98 optimal weight: 0.1980 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 6.9990 chunk 55 optimal weight: 0.0570 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 214 ASN C 236 HIS C 277 GLN C 303 GLN C 429 GLN ** E 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 120 ASN F 246 ASN F 252 GLN F 284 GLN F 285 ASN F 340 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.167101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.140122 restraints weight = 15192.547| |-----------------------------------------------------------------------------| r_work (start): 0.3921 rms_B_bonded: 1.73 r_work: 0.3846 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3733 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.1222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 11629 Z= 0.174 Angle : 0.578 11.940 15791 Z= 0.306 Chirality : 0.047 0.191 1756 Planarity : 0.004 0.041 2047 Dihedral : 4.786 20.081 1564 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.85 % Allowed : 7.88 % Favored : 90.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.21), residues: 1458 helix: 0.95 (0.47), residues: 140 sheet: 0.81 (0.21), residues: 553 loop : -0.14 (0.21), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 243 TYR 0.024 0.002 TYR C 161 PHE 0.011 0.002 PHE E 75 TRP 0.015 0.001 TRP E 92 HIS 0.011 0.001 HIS A 12 Details of bonding type rmsd covalent geometry : bond 0.00416 (11629) covalent geometry : angle 0.57798 (15791) hydrogen bonds : bond 0.03776 ( 397) hydrogen bonds : angle 5.74522 ( 1050) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 226 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 91 TYR cc_start: 0.6587 (t80) cc_final: 0.6320 (t80) REVERT: C 207 GLU cc_start: 0.7128 (mt-10) cc_final: 0.6798 (mt-10) REVERT: C 372 LYS cc_start: 0.8636 (ttmm) cc_final: 0.8226 (ttmm) REVERT: C 473 TYR cc_start: 0.7915 (m-80) cc_final: 0.7594 (m-80) REVERT: D 50 ILE cc_start: 0.7868 (pp) cc_final: 0.7612 (mp) REVERT: F 191 GLN cc_start: 0.7871 (mp10) cc_final: 0.7479 (mp10) outliers start: 23 outliers final: 10 residues processed: 233 average time/residue: 0.4883 time to fit residues: 123.1812 Evaluate side-chains 227 residues out of total 1243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 217 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ASN Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 238 MET Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain D residue 11 ILE Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 115 GLU Chi-restraints excluded: chain F residue 361 LEU Chi-restraints excluded: chain F residue 385 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 34 optimal weight: 0.0050 chunk 135 optimal weight: 0.0980 chunk 29 optimal weight: 1.9990 chunk 106 optimal weight: 0.5980 chunk 115 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 121 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 113 optimal weight: 1.9990 chunk 109 optimal weight: 0.2980 overall best weight: 0.3394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 213 GLN C 236 HIS C 285 ASN ** E 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 252 GLN F 285 ASN F 340 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.167350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.140600 restraints weight = 15380.359| |-----------------------------------------------------------------------------| r_work (start): 0.3923 rms_B_bonded: 1.75 r_work: 0.3850 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3739 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11629 Z= 0.140 Angle : 0.530 12.323 15791 Z= 0.278 Chirality : 0.044 0.159 1756 Planarity : 0.004 0.045 2047 Dihedral : 4.502 20.085 1564 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.69 % Allowed : 10.62 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.21), residues: 1458 helix: 1.27 (0.47), residues: 140 sheet: 0.81 (0.21), residues: 555 loop : -0.00 (0.21), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 476 TYR 0.020 0.002 TYR C 161 PHE 0.013 0.001 PHE C 438 TRP 0.013 0.001 TRP D 92 HIS 0.006 0.001 HIS A 89 Details of bonding type rmsd covalent geometry : bond 0.00332 (11629) covalent geometry : angle 0.53010 (15791) hydrogen bonds : bond 0.03338 ( 397) hydrogen bonds : angle 5.32414 ( 1050) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 225 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 207 GLU cc_start: 0.7130 (mt-10) cc_final: 0.6814 (mt-10) REVERT: C 372 LYS cc_start: 0.8585 (ttmm) cc_final: 0.8194 (ttmm) REVERT: C 473 TYR cc_start: 0.7912 (m-80) cc_final: 0.7616 (m-80) REVERT: F 191 GLN cc_start: 0.7775 (mp10) cc_final: 0.7411 (mp10) outliers start: 21 outliers final: 9 residues processed: 234 average time/residue: 0.5405 time to fit residues: 136.4444 Evaluate side-chains 227 residues out of total 1243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 218 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ASN Chi-restraints excluded: chain B residue 9 ILE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain D residue 11 ILE Chi-restraints excluded: chain D residue 115 GLU Chi-restraints excluded: chain F residue 108 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 73 optimal weight: 0.2980 chunk 26 optimal weight: 0.4980 chunk 84 optimal weight: 4.9990 chunk 1 optimal weight: 0.9980 chunk 7 optimal weight: 0.1980 chunk 118 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 120 optimal weight: 0.5980 chunk 141 optimal weight: 0.0470 chunk 67 optimal weight: 0.4980 chunk 33 optimal weight: 0.9980 overall best weight: 0.3078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 236 HIS C 277 GLN C 285 ASN ** E 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 252 GLN F 285 ASN F 303 GLN F 340 GLN F 429 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.167787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.141077 restraints weight = 15318.377| |-----------------------------------------------------------------------------| r_work (start): 0.3927 rms_B_bonded: 1.75 r_work: 0.3856 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3744 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11629 Z= 0.128 Angle : 0.515 12.296 15791 Z= 0.267 Chirality : 0.044 0.160 1756 Planarity : 0.004 0.044 2047 Dihedral : 4.349 19.743 1564 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.21 % Allowed : 13.76 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.21), residues: 1458 helix: 1.37 (0.46), residues: 140 sheet: 0.89 (0.21), residues: 555 loop : 0.00 (0.21), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 286 TYR 0.018 0.001 TYR C 161 PHE 0.012 0.001 PHE C 438 TRP 0.013 0.001 TRP D 92 HIS 0.006 0.001 HIS A 89 Details of bonding type rmsd covalent geometry : bond 0.00303 (11629) covalent geometry : angle 0.51464 (15791) hydrogen bonds : bond 0.03083 ( 397) hydrogen bonds : angle 5.10256 ( 1050) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 216 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 207 GLU cc_start: 0.7109 (mt-10) cc_final: 0.6818 (mt-10) REVERT: F 191 GLN cc_start: 0.7787 (mp10) cc_final: 0.7407 (mp10) outliers start: 15 outliers final: 5 residues processed: 221 average time/residue: 0.5468 time to fit residues: 130.4283 Evaluate side-chains 215 residues out of total 1243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 210 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 120 GLU Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain D residue 11 ILE Chi-restraints excluded: chain F residue 108 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 103 optimal weight: 0.9980 chunk 129 optimal weight: 0.7980 chunk 73 optimal weight: 0.1980 chunk 47 optimal weight: 0.0470 chunk 97 optimal weight: 2.9990 chunk 87 optimal weight: 0.0970 chunk 59 optimal weight: 0.9990 chunk 140 optimal weight: 0.3980 chunk 115 optimal weight: 1.9990 chunk 142 optimal weight: 0.3980 chunk 23 optimal weight: 2.9990 overall best weight: 0.2276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 236 HIS C 285 ASN ** E 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 213 GLN F 217 GLN F 252 GLN F 285 ASN F 303 GLN F 340 GLN F 429 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.168691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.141942 restraints weight = 15324.893| |-----------------------------------------------------------------------------| r_work (start): 0.3938 rms_B_bonded: 1.75 r_work: 0.3866 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3755 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 11629 Z= 0.106 Angle : 0.488 12.325 15791 Z= 0.253 Chirality : 0.044 0.197 1756 Planarity : 0.004 0.043 2047 Dihedral : 4.152 19.427 1564 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 1.77 % Allowed : 13.35 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.21), residues: 1458 helix: 1.49 (0.46), residues: 140 sheet: 1.01 (0.22), residues: 545 loop : 0.11 (0.21), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 243 TYR 0.017 0.001 TYR C 161 PHE 0.010 0.001 PHE E 75 TRP 0.011 0.001 TRP D 92 HIS 0.006 0.001 HIS A 89 Details of bonding type rmsd covalent geometry : bond 0.00247 (11629) covalent geometry : angle 0.48809 (15791) hydrogen bonds : bond 0.02882 ( 397) hydrogen bonds : angle 4.85225 ( 1050) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 215 time to evaluate : 0.411 Fit side-chains revert: symmetry clash REVERT: C 207 GLU cc_start: 0.7107 (mt-10) cc_final: 0.6820 (mt-10) REVERT: C 243 ARG cc_start: 0.8151 (ttt180) cc_final: 0.7934 (ttt90) REVERT: C 291 LYS cc_start: 0.8339 (OUTLIER) cc_final: 0.7961 (tttt) REVERT: F 191 GLN cc_start: 0.7806 (mp10) cc_final: 0.7436 (mp10) outliers start: 22 outliers final: 14 residues processed: 224 average time/residue: 0.5125 time to fit residues: 124.3330 Evaluate side-chains 225 residues out of total 1243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 210 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 ILE Chi-restraints excluded: chain C residue 60 GLN Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 291 LYS Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain D residue 11 ILE Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 115 GLU Chi-restraints excluded: chain F residue 131 SER Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain F residue 361 LEU Chi-restraints excluded: chain F residue 385 THR Chi-restraints excluded: chain F residue 417 MET Chi-restraints excluded: chain F residue 496 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 23 optimal weight: 2.9990 chunk 115 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 89 optimal weight: 0.5980 chunk 40 optimal weight: 0.9990 chunk 86 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 141 optimal weight: 0.9980 chunk 53 optimal weight: 0.0980 chunk 18 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 236 HIS C 277 GLN ** E 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 217 GLN F 252 GLN F 285 ASN F 303 GLN F 340 GLN F 429 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.165322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.138631 restraints weight = 15244.607| |-----------------------------------------------------------------------------| r_work (start): 0.3899 rms_B_bonded: 1.74 r_work: 0.3826 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3713 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 11629 Z= 0.252 Angle : 0.589 13.989 15791 Z= 0.305 Chirality : 0.048 0.194 1756 Planarity : 0.004 0.045 2047 Dihedral : 4.698 21.170 1564 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.57 % Allowed : 13.19 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.21), residues: 1458 helix: 1.19 (0.46), residues: 140 sheet: 0.90 (0.21), residues: 553 loop : -0.12 (0.21), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 90 TYR 0.028 0.002 TYR C 161 PHE 0.017 0.002 PHE C 438 TRP 0.022 0.002 TRP D 92 HIS 0.008 0.002 HIS B 12 Details of bonding type rmsd covalent geometry : bond 0.00607 (11629) covalent geometry : angle 0.58886 (15791) hydrogen bonds : bond 0.03592 ( 397) hydrogen bonds : angle 5.23539 ( 1050) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 226 time to evaluate : 0.443 Fit side-chains revert: symmetry clash REVERT: A 121 LEU cc_start: 0.6097 (mt) cc_final: 0.5896 (mt) REVERT: C 207 GLU cc_start: 0.7111 (mt-10) cc_final: 0.6695 (mt-10) REVERT: C 291 LYS cc_start: 0.8485 (OUTLIER) cc_final: 0.8106 (tttt) REVERT: C 441 ASP cc_start: 0.7564 (m-30) cc_final: 0.7310 (m-30) REVERT: C 452 ARG cc_start: 0.8237 (OUTLIER) cc_final: 0.7453 (ttm170) REVERT: C 473 TYR cc_start: 0.7937 (m-80) cc_final: 0.7641 (m-80) REVERT: F 191 GLN cc_start: 0.7833 (mp10) cc_final: 0.7433 (mp10) REVERT: F 364 LEU cc_start: 0.8370 (mm) cc_final: 0.8142 (mt) outliers start: 32 outliers final: 17 residues processed: 238 average time/residue: 0.5194 time to fit residues: 133.4582 Evaluate side-chains 241 residues out of total 1243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 222 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ASN Chi-restraints excluded: chain B residue 9 ILE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 291 LYS Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 452 ARG Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain F residue 114 MET Chi-restraints excluded: chain F residue 131 SER Chi-restraints excluded: chain F residue 143 SER Chi-restraints excluded: chain F residue 238 MET Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain F residue 361 LEU Chi-restraints excluded: chain F residue 417 MET Chi-restraints excluded: chain F residue 496 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 45 optimal weight: 0.6980 chunk 84 optimal weight: 3.9990 chunk 27 optimal weight: 0.5980 chunk 98 optimal weight: 0.0050 chunk 79 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 41 optimal weight: 0.0870 chunk 57 optimal weight: 0.8980 chunk 116 optimal weight: 0.7980 chunk 118 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 overall best weight: 0.4372 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 109 ASN C 236 HIS C 285 ASN ** E 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 252 GLN F 285 ASN F 303 GLN F 429 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.166560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.139776 restraints weight = 15272.321| |-----------------------------------------------------------------------------| r_work (start): 0.3911 rms_B_bonded: 1.74 r_work: 0.3841 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3727 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11629 Z= 0.162 Angle : 0.535 13.566 15791 Z= 0.277 Chirality : 0.045 0.150 1756 Planarity : 0.004 0.043 2047 Dihedral : 4.492 20.145 1564 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 2.41 % Allowed : 14.56 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.21), residues: 1458 helix: 1.33 (0.46), residues: 140 sheet: 0.87 (0.21), residues: 553 loop : -0.05 (0.21), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 476 TYR 0.021 0.002 TYR F 461 PHE 0.014 0.002 PHE C 438 TRP 0.018 0.001 TRP D 92 HIS 0.006 0.001 HIS C 412 Details of bonding type rmsd covalent geometry : bond 0.00388 (11629) covalent geometry : angle 0.53465 (15791) hydrogen bonds : bond 0.03190 ( 397) hydrogen bonds : angle 5.07616 ( 1050) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 219 time to evaluate : 0.272 Fit side-chains revert: symmetry clash REVERT: B 71 THR cc_start: 0.6487 (OUTLIER) cc_final: 0.6274 (p) REVERT: C 165 ARG cc_start: 0.8235 (OUTLIER) cc_final: 0.8020 (ttt180) REVERT: C 207 GLU cc_start: 0.7035 (mt-10) cc_final: 0.6684 (mt-10) REVERT: C 291 LYS cc_start: 0.8436 (OUTLIER) cc_final: 0.8067 (tttt) REVERT: F 191 GLN cc_start: 0.7834 (mp10) cc_final: 0.7439 (mp10) outliers start: 30 outliers final: 19 residues processed: 231 average time/residue: 0.5193 time to fit residues: 129.8278 Evaluate side-chains 237 residues out of total 1243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 215 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ASN Chi-restraints excluded: chain B residue 9 ILE Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain C residue 60 GLN Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 165 ARG Chi-restraints excluded: chain C residue 291 LYS Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain D residue 11 ILE Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 115 GLU Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain F residue 131 SER Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain F residue 361 LEU Chi-restraints excluded: chain F residue 385 THR Chi-restraints excluded: chain F residue 417 MET Chi-restraints excluded: chain F residue 496 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 104 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 chunk 87 optimal weight: 0.9980 chunk 75 optimal weight: 0.0040 chunk 6 optimal weight: 1.9990 chunk 84 optimal weight: 5.9990 chunk 40 optimal weight: 0.5980 chunk 79 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 236 HIS C 285 ASN ** E 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 217 GLN F 252 GLN F 303 GLN F 429 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.165298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.138567 restraints weight = 15239.813| |-----------------------------------------------------------------------------| r_work (start): 0.3901 rms_B_bonded: 1.74 r_work: 0.3829 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3715 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 11629 Z= 0.228 Angle : 0.586 14.077 15791 Z= 0.303 Chirality : 0.047 0.168 1756 Planarity : 0.004 0.044 2047 Dihedral : 4.708 20.430 1564 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.49 % Allowed : 14.88 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.21), residues: 1458 helix: 1.19 (0.46), residues: 140 sheet: 0.77 (0.21), residues: 553 loop : -0.14 (0.21), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 243 TYR 0.025 0.002 TYR C 161 PHE 0.015 0.002 PHE C 216 TRP 0.020 0.002 TRP D 92 HIS 0.007 0.001 HIS B 12 Details of bonding type rmsd covalent geometry : bond 0.00550 (11629) covalent geometry : angle 0.58561 (15791) hydrogen bonds : bond 0.03489 ( 397) hydrogen bonds : angle 5.21635 ( 1050) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 218 time to evaluate : 0.451 Fit side-chains revert: symmetry clash REVERT: B 71 THR cc_start: 0.6590 (OUTLIER) cc_final: 0.6339 (p) REVERT: C 165 ARG cc_start: 0.8253 (OUTLIER) cc_final: 0.8024 (ttt180) REVERT: C 207 GLU cc_start: 0.7046 (mt-10) cc_final: 0.6677 (mt-10) REVERT: C 291 LYS cc_start: 0.8484 (OUTLIER) cc_final: 0.8102 (tttt) REVERT: C 441 ASP cc_start: 0.7557 (m-30) cc_final: 0.7299 (m-30) REVERT: F 191 GLN cc_start: 0.7834 (mp10) cc_final: 0.7429 (mp10) REVERT: F 364 LEU cc_start: 0.8347 (mm) cc_final: 0.8100 (mt) outliers start: 31 outliers final: 21 residues processed: 231 average time/residue: 0.5638 time to fit residues: 140.9069 Evaluate side-chains 237 residues out of total 1243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 213 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ASN Chi-restraints excluded: chain B residue 9 ILE Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain C residue 60 GLN Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 129 SER Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 165 ARG Chi-restraints excluded: chain C residue 291 LYS Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain F residue 114 MET Chi-restraints excluded: chain F residue 131 SER Chi-restraints excluded: chain F residue 238 MET Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain F residue 355 VAL Chi-restraints excluded: chain F residue 361 LEU Chi-restraints excluded: chain F residue 385 THR Chi-restraints excluded: chain F residue 417 MET Chi-restraints excluded: chain F residue 496 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 107 optimal weight: 0.9990 chunk 73 optimal weight: 0.3980 chunk 56 optimal weight: 0.0470 chunk 138 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 55 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 chunk 15 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 109 ASN C 285 ASN ** E 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 217 GLN F 303 GLN F 429 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.166122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.139467 restraints weight = 15211.975| |-----------------------------------------------------------------------------| r_work (start): 0.3912 rms_B_bonded: 1.74 r_work: 0.3841 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3727 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11629 Z= 0.177 Angle : 0.559 13.691 15791 Z= 0.290 Chirality : 0.046 0.173 1756 Planarity : 0.004 0.043 2047 Dihedral : 4.584 20.223 1564 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.49 % Allowed : 15.21 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.21), residues: 1458 helix: 1.32 (0.46), residues: 140 sheet: 0.77 (0.21), residues: 553 loop : -0.11 (0.21), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 476 TYR 0.024 0.002 TYR F 461 PHE 0.011 0.002 PHE C 216 TRP 0.017 0.002 TRP D 92 HIS 0.005 0.001 HIS B 12 Details of bonding type rmsd covalent geometry : bond 0.00425 (11629) covalent geometry : angle 0.55933 (15791) hydrogen bonds : bond 0.03247 ( 397) hydrogen bonds : angle 5.13467 ( 1050) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 213 time to evaluate : 0.360 Fit side-chains revert: symmetry clash REVERT: B 71 THR cc_start: 0.6606 (OUTLIER) cc_final: 0.6366 (p) REVERT: C 207 GLU cc_start: 0.7051 (mt-10) cc_final: 0.6697 (mt-10) REVERT: C 291 LYS cc_start: 0.8455 (OUTLIER) cc_final: 0.8087 (tttt) REVERT: F 191 GLN cc_start: 0.7855 (mp10) cc_final: 0.7454 (mp10) outliers start: 31 outliers final: 24 residues processed: 226 average time/residue: 0.5735 time to fit residues: 140.3460 Evaluate side-chains 236 residues out of total 1243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 210 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ASN Chi-restraints excluded: chain B residue 9 ILE Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain C residue 60 GLN Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 120 GLU Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 291 LYS Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain D residue 11 ILE Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 115 GLU Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain F residue 143 SER Chi-restraints excluded: chain F residue 144 GLU Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain F residue 355 VAL Chi-restraints excluded: chain F residue 361 LEU Chi-restraints excluded: chain F residue 385 THR Chi-restraints excluded: chain F residue 417 MET Chi-restraints excluded: chain F residue 456 VAL Chi-restraints excluded: chain F residue 496 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 107 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 50 optimal weight: 0.3980 chunk 105 optimal weight: 0.9980 chunk 99 optimal weight: 0.0980 chunk 137 optimal weight: 0.6980 chunk 75 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 133 optimal weight: 0.9980 chunk 73 optimal weight: 0.3980 chunk 134 optimal weight: 0.0770 overall best weight: 0.3338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 109 ASN C 285 ASN C 464 HIS ** E 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 213 GLN F 217 GLN F 303 GLN F 429 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.167231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.140482 restraints weight = 15272.580| |-----------------------------------------------------------------------------| r_work (start): 0.3924 rms_B_bonded: 1.74 r_work: 0.3853 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3738 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11629 Z= 0.136 Angle : 0.540 13.100 15791 Z= 0.280 Chirality : 0.044 0.166 1756 Planarity : 0.004 0.042 2047 Dihedral : 4.407 19.614 1564 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.93 % Allowed : 16.33 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.21), residues: 1458 helix: 1.45 (0.46), residues: 140 sheet: 0.79 (0.21), residues: 558 loop : -0.02 (0.21), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 476 TYR 0.022 0.001 TYR F 461 PHE 0.011 0.001 PHE C 438 TRP 0.014 0.001 TRP D 92 HIS 0.005 0.001 HIS A 89 Details of bonding type rmsd covalent geometry : bond 0.00324 (11629) covalent geometry : angle 0.53961 (15791) hydrogen bonds : bond 0.03038 ( 397) hydrogen bonds : angle 4.99771 ( 1050) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 216 time to evaluate : 0.416 Fit side-chains revert: symmetry clash REVERT: B 71 THR cc_start: 0.6596 (OUTLIER) cc_final: 0.6364 (p) REVERT: C 207 GLU cc_start: 0.7040 (mt-10) cc_final: 0.6693 (mt-10) REVERT: C 291 LYS cc_start: 0.8421 (OUTLIER) cc_final: 0.8051 (tttt) REVERT: F 191 GLN cc_start: 0.7850 (mp10) cc_final: 0.7465 (mp10) REVERT: F 364 LEU cc_start: 0.8303 (mm) cc_final: 0.8054 (mt) outliers start: 24 outliers final: 18 residues processed: 227 average time/residue: 0.5534 time to fit residues: 136.3744 Evaluate side-chains 234 residues out of total 1243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 214 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ASN Chi-restraints excluded: chain B residue 9 ILE Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain C residue 60 GLN Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 291 LYS Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain D residue 11 ILE Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain F residue 238 MET Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain F residue 355 VAL Chi-restraints excluded: chain F residue 361 LEU Chi-restraints excluded: chain F residue 385 THR Chi-restraints excluded: chain F residue 496 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 49 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 122 optimal weight: 0.9990 chunk 103 optimal weight: 0.9980 chunk 134 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 77 optimal weight: 0.0170 chunk 12 optimal weight: 1.9990 overall best weight: 0.8018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 109 ASN C 285 ASN ** E 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 217 GLN F 252 GLN F 303 GLN F 429 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.164675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.138038 restraints weight = 15315.926| |-----------------------------------------------------------------------------| r_work (start): 0.3894 rms_B_bonded: 1.74 r_work: 0.3821 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3706 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 11629 Z= 0.271 Angle : 0.622 14.337 15791 Z= 0.323 Chirality : 0.048 0.180 1756 Planarity : 0.005 0.044 2047 Dihedral : 4.838 21.701 1564 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.17 % Allowed : 15.93 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.21), residues: 1458 helix: 1.12 (0.46), residues: 140 sheet: 0.70 (0.21), residues: 553 loop : -0.19 (0.21), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 243 TYR 0.026 0.002 TYR F 461 PHE 0.016 0.002 PHE C 216 TRP 0.023 0.002 TRP D 92 HIS 0.009 0.002 HIS B 12 Details of bonding type rmsd covalent geometry : bond 0.00653 (11629) covalent geometry : angle 0.62227 (15791) hydrogen bonds : bond 0.03638 ( 397) hydrogen bonds : angle 5.32677 ( 1050) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5276.71 seconds wall clock time: 90 minutes 23.85 seconds (5423.85 seconds total)