Starting phenix.real_space_refine on Fri Jul 19 22:46:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1r_41825/07_2024/8u1r_41825_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1r_41825/07_2024/8u1r_41825.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1r_41825/07_2024/8u1r_41825.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1r_41825/07_2024/8u1r_41825.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1r_41825/07_2024/8u1r_41825_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1r_41825/07_2024/8u1r_41825_neut.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.039 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 60 5.16 5 C 5763 2.51 5 N 1524 2.21 5 O 1779 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 151": "OE1" <-> "OE2" Residue "A GLU 267": "OE1" <-> "OE2" Residue "A GLU 290": "OE1" <-> "OE2" Residue "B GLU 290": "OE1" <-> "OE2" Residue "C GLU 73": "OE1" <-> "OE2" Residue "C GLU 267": "OE1" <-> "OE2" Residue "C GLU 274": "OE1" <-> "OE2" Residue "C GLU 290": "OE1" <-> "OE2" Residue "C GLU 330": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 9126 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3042 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 13, 'TRANS': 385} Chain breaks: 1 Chain: "B" Number of atoms: 3042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3042 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 13, 'TRANS': 385} Chain breaks: 1 Chain: "C" Number of atoms: 3042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3042 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 13, 'TRANS': 385} Chain breaks: 1 Time building chain proxies: 5.44, per 1000 atoms: 0.60 Number of scatterers: 9126 At special positions: 0 Unit cell: (100.58, 102.46, 94, 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 60 16.00 O 1779 8.00 N 1524 7.00 C 5763 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 66 " - pdb=" SG CYS A 187 " distance=2.03 Simple disulfide: pdb=" SG CYS A 99 " - pdb=" SG CYS A 109 " distance=2.02 Simple disulfide: pdb=" SG CYS A 326 " - pdb=" SG CYS A 335 " distance=2.03 Simple disulfide: pdb=" SG CYS A 350 " - pdb=" SG CYS A 358 " distance=2.03 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 387 " distance=2.03 Simple disulfide: pdb=" SG CYS A 389 " - pdb=" SG CYS A 412 " distance=2.01 Simple disulfide: pdb=" SG CYS B 66 " - pdb=" SG CYS B 187 " distance=2.03 Simple disulfide: pdb=" SG CYS B 99 " - pdb=" SG CYS B 109 " distance=2.02 Simple disulfide: pdb=" SG CYS B 326 " - pdb=" SG CYS B 335 " distance=2.03 Simple disulfide: pdb=" SG CYS B 350 " - pdb=" SG CYS B 358 " distance=2.03 Simple disulfide: pdb=" SG CYS B 382 " - pdb=" SG CYS B 387 " distance=2.03 Simple disulfide: pdb=" SG CYS B 389 " - pdb=" SG CYS B 412 " distance=2.03 Simple disulfide: pdb=" SG CYS C 66 " - pdb=" SG CYS C 187 " distance=2.03 Simple disulfide: pdb=" SG CYS C 99 " - pdb=" SG CYS C 109 " distance=2.03 Simple disulfide: pdb=" SG CYS C 326 " - pdb=" SG CYS C 335 " distance=2.03 Simple disulfide: pdb=" SG CYS C 350 " - pdb=" SG CYS C 358 " distance=2.03 Simple disulfide: pdb=" SG CYS C 382 " - pdb=" SG CYS C 387 " distance=2.03 Simple disulfide: pdb=" SG CYS C 389 " - pdb=" SG CYS C 412 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.94 Conformation dependent library (CDL) restraints added in 1.7 seconds 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2250 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 15 sheets defined 41.4% alpha, 29.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.42 Creating SS restraints... Processing helix chain 'A' and resid 24 through 32 Processing helix chain 'A' and resid 67 through 99 removed outlier: 3.559A pdb=" N ASP A 72 " --> pdb=" O GLN A 68 " (cutoff:3.500A) Proline residue: A 84 - end of helix removed outlier: 4.146A pdb=" N CYS A 99 " --> pdb=" O ASN A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 116 removed outlier: 3.552A pdb=" N LEU A 115 " --> pdb=" O ALA A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'A' and resid 132 through 141 Processing helix chain 'A' and resid 142 through 148 Processing helix chain 'A' and resid 168 through 178 Processing helix chain 'A' and resid 179 through 182 Processing helix chain 'A' and resid 186 through 209 Processing helix chain 'A' and resid 209 through 214 removed outlier: 3.699A pdb=" N GLN A 214 " --> pdb=" O GLY A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 228 Processing helix chain 'A' and resid 229 through 231 No H-bonds generated for 'chain 'A' and resid 229 through 231' Processing helix chain 'A' and resid 233 through 241 Processing helix chain 'A' and resid 248 through 253 Processing helix chain 'A' and resid 344 through 353 Processing helix chain 'A' and resid 354 through 358 Processing helix chain 'B' and resid 24 through 32 Processing helix chain 'B' and resid 60 through 64 removed outlier: 3.804A pdb=" N ARG B 64 " --> pdb=" O ASP B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 98 Proline residue: B 84 - end of helix removed outlier: 3.585A pdb=" N VAL B 96 " --> pdb=" O MET B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 116 Processing helix chain 'B' and resid 120 through 142 removed outlier: 4.468A pdb=" N GLU B 134 " --> pdb=" O HIS B 130 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N ASN B 135 " --> pdb=" O ARG B 131 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N MET B 142 " --> pdb=" O ALA B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 148 Processing helix chain 'B' and resid 168 through 178 Processing helix chain 'B' and resid 179 through 182 Processing helix chain 'B' and resid 186 through 209 Processing helix chain 'B' and resid 209 through 214 Processing helix chain 'B' and resid 223 through 228 Processing helix chain 'B' and resid 229 through 231 No H-bonds generated for 'chain 'B' and resid 229 through 231' Processing helix chain 'B' and resid 233 through 241 Processing helix chain 'B' and resid 248 through 254 removed outlier: 4.309A pdb=" N SER B 254 " --> pdb=" O GLU B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 353 Processing helix chain 'B' and resid 354 through 358 Processing helix chain 'C' and resid 24 through 32 Processing helix chain 'C' and resid 60 through 64 removed outlier: 3.794A pdb=" N ARG C 64 " --> pdb=" O ASP C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 99 removed outlier: 3.539A pdb=" N ASP C 72 " --> pdb=" O GLN C 68 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU C 73 " --> pdb=" O LYS C 69 " (cutoff:3.500A) Proline residue: C 84 - end of helix removed outlier: 4.056A pdb=" N ASN C 95 " --> pdb=" O ALA C 91 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL C 96 " --> pdb=" O MET C 92 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N CYS C 99 " --> pdb=" O ASN C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 116 removed outlier: 3.557A pdb=" N GLY C 116 " --> pdb=" O GLY C 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 112 through 116' Processing helix chain 'C' and resid 120 through 142 removed outlier: 4.522A pdb=" N GLU C 134 " --> pdb=" O HIS C 130 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N ASN C 135 " --> pdb=" O ARG C 131 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N MET C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 148 Processing helix chain 'C' and resid 168 through 178 Processing helix chain 'C' and resid 179 through 182 Processing helix chain 'C' and resid 186 through 209 Processing helix chain 'C' and resid 209 through 214 Processing helix chain 'C' and resid 223 through 228 Processing helix chain 'C' and resid 229 through 231 No H-bonds generated for 'chain 'C' and resid 229 through 231' Processing helix chain 'C' and resid 233 through 241 Processing helix chain 'C' and resid 248 through 254 removed outlier: 4.146A pdb=" N SER C 254 " --> pdb=" O GLU C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 344 through 353 Processing helix chain 'C' and resid 354 through 358 Processing sheet with id=AA1, first strand: chain 'A' and resid 153 through 157 removed outlier: 8.055A pdb=" N THR A 163 " --> pdb=" O THR A 49 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N LEU A 51 " --> pdb=" O THR A 163 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N LYS A 35 " --> pdb=" O MET A 292 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N MET A 292 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N LEU A 37 " --> pdb=" O GLU A 290 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 259 through 265 removed outlier: 6.351A pdb=" N GLY A 259 " --> pdb=" O GLU A 276 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N GLU A 276 " --> pdb=" O GLY A 259 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N ILE A 261 " --> pdb=" O GLU A 274 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N GLU A 274 " --> pdb=" O ILE A 261 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASP A 263 " --> pdb=" O ALA A 272 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ASN A 279 " --> pdb=" O SER A 46 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N SER A 46 " --> pdb=" O ASN A 279 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N THR A 281 " --> pdb=" O LYS A 44 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N LYS A 44 " --> pdb=" O THR A 281 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 117 through 119 removed outlier: 3.769A pdb=" N VAL B 378 " --> pdb=" O LEU B 407 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 296 through 298 removed outlier: 4.392A pdb=" N ALA A 359 " --> pdb=" O LEU A 306 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 405 through 407 removed outlier: 3.871A pdb=" N VAL A 378 " --> pdb=" O LEU A 407 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 387 through 388 removed outlier: 3.710A pdb=" N MET C 110 " --> pdb=" O LEU A 421 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 153 through 157 removed outlier: 8.054A pdb=" N THR B 163 " --> pdb=" O THR B 49 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N LEU B 51 " --> pdb=" O THR B 163 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N VAL B 333 " --> pdb=" O THR B 38 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ASN B 40 " --> pdb=" O VAL B 333 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N CYS B 335 " --> pdb=" O ASN B 40 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N LYS B 42 " --> pdb=" O CYS B 335 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 221 through 222 removed outlier: 3.911A pdb=" N ARG B 258 " --> pdb=" O GLU B 276 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ALA B 272 " --> pdb=" O ILE B 262 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N VAL B 264 " --> pdb=" O TYR B 270 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N TYR B 270 " --> pdb=" O VAL B 264 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASN B 279 " --> pdb=" O SER B 46 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N SER B 46 " --> pdb=" O ASN B 279 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N THR B 281 " --> pdb=" O LYS B 44 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N LYS B 44 " --> pdb=" O THR B 281 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N LYS B 35 " --> pdb=" O MET B 292 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N MET B 292 " --> pdb=" O LYS B 35 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N LEU B 37 " --> pdb=" O GLU B 290 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N PHE B 310 " --> pdb=" O ILE B 321 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ILE B 321 " --> pdb=" O PHE B 310 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 110 through 111 removed outlier: 6.800A pdb=" N MET B 110 " --> pdb=" O SER C 423 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 117 through 119 removed outlier: 3.802A pdb=" N VAL C 378 " --> pdb=" O LEU C 407 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU C 407 " --> pdb=" O VAL C 378 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 296 through 298 removed outlier: 4.589A pdb=" N ALA B 359 " --> pdb=" O LEU B 306 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 387 through 389 Processing sheet with id=AB4, first strand: chain 'C' and resid 153 through 157 removed outlier: 8.159A pdb=" N THR C 163 " --> pdb=" O THR C 49 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N LEU C 51 " --> pdb=" O THR C 163 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 221 through 222 removed outlier: 4.108A pdb=" N ARG C 258 " --> pdb=" O GLU C 276 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ALA C 272 " --> pdb=" O ILE C 262 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N VAL C 264 " --> pdb=" O TYR C 270 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N TYR C 270 " --> pdb=" O VAL C 264 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ASN C 279 " --> pdb=" O SER C 46 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N SER C 46 " --> pdb=" O ASN C 279 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N THR C 281 " --> pdb=" O LYS C 44 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N LYS C 44 " --> pdb=" O THR C 281 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N GLU C 290 " --> pdb=" O GLY C 36 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N THR C 38 " --> pdb=" O VAL C 288 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N VAL C 288 " --> pdb=" O THR C 38 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N PHE C 310 " --> pdb=" O ILE C 321 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ILE C 321 " --> pdb=" O PHE C 310 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 296 through 298 removed outlier: 4.486A pdb=" N ALA C 359 " --> pdb=" O LEU C 306 " (cutoff:3.500A) 459 hydrogen bonds defined for protein. 1269 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.67 Time building geometry restraints manager: 4.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2994 1.34 - 1.46: 1468 1.46 - 1.58: 4697 1.58 - 1.70: 0 1.70 - 1.82: 84 Bond restraints: 9243 Sorted by residual: bond pdb=" N ILE C 422 " pdb=" CA ILE C 422 " ideal model delta sigma weight residual 1.456 1.495 -0.039 1.11e-02 8.12e+03 1.23e+01 bond pdb=" N ILE B 422 " pdb=" CA ILE B 422 " ideal model delta sigma weight residual 1.456 1.495 -0.038 1.14e-02 7.69e+03 1.12e+01 bond pdb=" N ILE B 420 " pdb=" CA ILE B 420 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.12e-02 7.97e+03 1.06e+01 bond pdb=" CA SER A 423 " pdb=" CB SER A 423 " ideal model delta sigma weight residual 1.528 1.480 0.048 1.61e-02 3.86e+03 9.07e+00 bond pdb=" N VAL B 96 " pdb=" CA VAL B 96 " ideal model delta sigma weight residual 1.457 1.496 -0.038 1.28e-02 6.10e+03 8.91e+00 ... (remaining 9238 not shown) Histogram of bond angle deviations from ideal: 100.04 - 106.83: 203 106.83 - 113.62: 5423 113.62 - 120.41: 3321 120.41 - 127.20: 3574 127.20 - 133.99: 49 Bond angle restraints: 12570 Sorted by residual: angle pdb=" C CYS A 387 " pdb=" N ARG A 388 " pdb=" CA ARG A 388 " ideal model delta sigma weight residual 122.36 116.09 6.27 1.60e+00 3.91e-01 1.54e+01 angle pdb=" CA SER A 423 " pdb=" C SER A 423 " pdb=" O SER A 423 " ideal model delta sigma weight residual 121.94 117.66 4.28 1.15e+00 7.56e-01 1.39e+01 angle pdb=" N MET A 390 " pdb=" CA MET A 390 " pdb=" C MET A 390 " ideal model delta sigma weight residual 112.38 107.89 4.49 1.22e+00 6.72e-01 1.36e+01 angle pdb=" CA ILE C 422 " pdb=" C ILE C 422 " pdb=" O ILE C 422 " ideal model delta sigma weight residual 121.67 117.85 3.82 1.05e+00 9.07e-01 1.32e+01 angle pdb=" N VAL A 31 " pdb=" CA VAL A 31 " pdb=" C VAL A 31 " ideal model delta sigma weight residual 113.39 108.07 5.32 1.47e+00 4.63e-01 1.31e+01 ... (remaining 12565 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 5101 17.85 - 35.71: 450 35.71 - 53.56: 114 53.56 - 71.41: 19 71.41 - 89.26: 19 Dihedral angle restraints: 5703 sinusoidal: 2214 harmonic: 3489 Sorted by residual: dihedral pdb=" CB CYS C 389 " pdb=" SG CYS C 389 " pdb=" SG CYS C 412 " pdb=" CB CYS C 412 " ideal model delta sinusoidal sigma weight residual -86.00 -170.97 84.97 1 1.00e+01 1.00e-02 8.76e+01 dihedral pdb=" CB CYS A 66 " pdb=" SG CYS A 66 " pdb=" SG CYS A 187 " pdb=" CB CYS A 187 " ideal model delta sinusoidal sigma weight residual -86.00 -124.15 38.15 1 1.00e+01 1.00e-02 2.05e+01 dihedral pdb=" CB CYS C 66 " pdb=" SG CYS C 66 " pdb=" SG CYS C 187 " pdb=" CB CYS C 187 " ideal model delta sinusoidal sigma weight residual -86.00 -123.93 37.93 1 1.00e+01 1.00e-02 2.03e+01 ... (remaining 5700 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1213 0.053 - 0.107: 263 0.107 - 0.160: 67 0.160 - 0.214: 14 0.214 - 0.267: 3 Chirality restraints: 1560 Sorted by residual: chirality pdb=" CA ILE A 422 " pdb=" N ILE A 422 " pdb=" C ILE A 422 " pdb=" CB ILE A 422 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" CA ILE C 422 " pdb=" N ILE C 422 " pdb=" C ILE C 422 " pdb=" CB ILE C 422 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" CA ILE B 422 " pdb=" N ILE B 422 " pdb=" C ILE B 422 " pdb=" CB ILE B 422 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.23 2.00e-01 2.50e+01 1.28e+00 ... (remaining 1557 not shown) Planarity restraints: 1596 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 90 " 0.029 2.00e-02 2.50e+03 5.71e-02 3.26e+01 pdb=" C ASN A 90 " -0.099 2.00e-02 2.50e+03 pdb=" O ASN A 90 " 0.037 2.00e-02 2.50e+03 pdb=" N ALA A 91 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 419 " -0.009 2.00e-02 2.50e+03 1.91e-02 3.65e+00 pdb=" CG ASP A 419 " 0.033 2.00e-02 2.50e+03 pdb=" OD1 ASP A 419 " -0.012 2.00e-02 2.50e+03 pdb=" OD2 ASP A 419 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 57 " -0.030 5.00e-02 4.00e+02 4.49e-02 3.22e+00 pdb=" N PRO A 58 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 58 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 58 " -0.025 5.00e-02 4.00e+02 ... (remaining 1593 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 401 2.73 - 3.27: 9226 3.27 - 3.81: 14383 3.81 - 4.36: 17385 4.36 - 4.90: 29620 Nonbonded interactions: 71015 Sorted by model distance: nonbonded pdb=" OH TYR C 41 " pdb=" O ASP C 338 " model vdw 2.182 2.440 nonbonded pdb=" OH TYR B 41 " pdb=" O ASP B 338 " model vdw 2.228 2.440 nonbonded pdb=" OH TYR A 41 " pdb=" O ASP A 338 " model vdw 2.252 2.440 nonbonded pdb=" OG1 THR C 329 " pdb=" O SER C 332 " model vdw 2.318 2.440 nonbonded pdb=" OD1 ASP A 338 " pdb=" OG SER B 365 " model vdw 2.330 2.440 ... (remaining 71010 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.470 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: 0.000 Extract box with map and model: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 29.030 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 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 : 0.005 0.048 9243 Z= 0.292 Angle : 0.774 10.223 12570 Z= 0.471 Chirality : 0.051 0.267 1560 Planarity : 0.004 0.057 1596 Dihedral : 15.163 89.263 3399 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.05 % Allowed : 13.75 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.23), residues: 1185 helix: 0.62 (0.25), residues: 417 sheet: 0.14 (0.31), residues: 252 loop : -0.97 (0.26), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 303 HIS 0.005 0.001 HIS A 130 PHE 0.012 0.001 PHE B 234 TYR 0.017 0.002 TYR C 415 ARG 0.013 0.001 ARG A 360 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 136 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 390 MET cc_start: 0.8080 (mmp) cc_final: 0.7742 (ttt) REVERT: A 399 SER cc_start: 0.6967 (m) cc_final: 0.6452 (p) REVERT: B 390 MET cc_start: 0.7562 (mmp) cc_final: 0.6877 (ttp) REVERT: C 390 MET cc_start: 0.7399 (mmp) cc_final: 0.6865 (ttp) REVERT: C 399 SER cc_start: 0.6770 (m) cc_final: 0.6222 (p) outliers start: 11 outliers final: 3 residues processed: 141 average time/residue: 0.2195 time to fit residues: 42.8145 Evaluate side-chains 123 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 120 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 110 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 3.9990 chunk 88 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 chunk 91 optimal weight: 0.8980 chunk 35 optimal weight: 6.9990 chunk 55 optimal weight: 0.6980 chunk 68 optimal weight: 0.7980 chunk 106 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.1062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9243 Z= 0.189 Angle : 0.550 11.241 12570 Z= 0.287 Chirality : 0.043 0.162 1560 Planarity : 0.004 0.035 1596 Dihedral : 5.227 57.155 1282 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.01 % Allowed : 13.66 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.24), residues: 1185 helix: 1.26 (0.25), residues: 411 sheet: 0.30 (0.31), residues: 252 loop : -0.79 (0.26), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 303 HIS 0.006 0.001 HIS C 130 PHE 0.014 0.001 PHE B 234 TYR 0.014 0.001 TYR A 415 ARG 0.006 0.001 ARG A 360 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 124 time to evaluate : 0.999 Fit side-chains revert: symmetry clash REVERT: B 390 MET cc_start: 0.7818 (mmp) cc_final: 0.6982 (ttt) REVERT: C 390 MET cc_start: 0.7476 (mmp) cc_final: 0.6718 (ttt) REVERT: C 399 SER cc_start: 0.7019 (m) cc_final: 0.6547 (p) outliers start: 21 outliers final: 12 residues processed: 136 average time/residue: 0.2108 time to fit residues: 40.4367 Evaluate side-chains 118 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 106 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 168 ASP Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 321 ILE Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 408 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 59 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 72 optimal weight: 9.9990 chunk 29 optimal weight: 1.9990 chunk 106 optimal weight: 0.8980 chunk 114 optimal weight: 4.9990 chunk 94 optimal weight: 0.8980 chunk 105 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 381 ASN B 384 ASN C 157 GLN ** C 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 9243 Z= 0.351 Angle : 0.611 7.940 12570 Z= 0.315 Chirality : 0.046 0.156 1560 Planarity : 0.004 0.032 1596 Dihedral : 4.939 31.065 1276 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.77 % Allowed : 14.14 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.24), residues: 1185 helix: 1.02 (0.25), residues: 429 sheet: 0.09 (0.29), residues: 285 loop : -0.86 (0.27), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 303 HIS 0.006 0.002 HIS B 130 PHE 0.018 0.002 PHE B 234 TYR 0.013 0.002 TYR C 249 ARG 0.007 0.000 ARG A 360 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 114 time to evaluate : 1.126 Fit side-chains REVERT: A 367 TYR cc_start: 0.7370 (t80) cc_final: 0.7148 (t80) REVERT: B 390 MET cc_start: 0.8008 (mmp) cc_final: 0.7138 (ttt) REVERT: C 271 ILE cc_start: 0.8760 (OUTLIER) cc_final: 0.8309 (tt) REVERT: C 390 MET cc_start: 0.7655 (mmp) cc_final: 0.6772 (ttt) outliers start: 29 outliers final: 20 residues processed: 136 average time/residue: 0.1764 time to fit residues: 35.7736 Evaluate side-chains 127 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 106 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 168 ASP Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 408 ASP Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 168 ASP Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 321 ILE Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 408 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 105 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 106 optimal weight: 0.9990 chunk 113 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9243 Z= 0.199 Angle : 0.523 6.541 12570 Z= 0.271 Chirality : 0.043 0.150 1560 Planarity : 0.003 0.033 1596 Dihedral : 4.675 31.815 1276 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.96 % Allowed : 14.61 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.24), residues: 1185 helix: 1.13 (0.25), residues: 447 sheet: 0.12 (0.29), residues: 285 loop : -0.58 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 303 HIS 0.004 0.001 HIS B 130 PHE 0.014 0.001 PHE B 234 TYR 0.014 0.001 TYR B 427 ARG 0.005 0.000 ARG A 360 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 121 time to evaluate : 1.099 Fit side-chains REVERT: A 67 THR cc_start: 0.9474 (OUTLIER) cc_final: 0.9208 (t) REVERT: A 110 MET cc_start: 0.8544 (tpp) cc_final: 0.8236 (tpt) REVERT: A 253 HIS cc_start: 0.7893 (t-170) cc_final: 0.7612 (t-170) REVERT: B 390 MET cc_start: 0.8037 (mmp) cc_final: 0.7112 (ttt) REVERT: C 390 MET cc_start: 0.7594 (mmp) cc_final: 0.6640 (ttt) outliers start: 31 outliers final: 19 residues processed: 142 average time/residue: 0.1446 time to fit residues: 32.5277 Evaluate side-chains 128 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 108 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 168 ASP Chi-restraints excluded: chain A residue 187 CYS Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 408 ASP Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 168 ASP Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 408 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 64 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 96 optimal weight: 0.6980 chunk 78 optimal weight: 5.9990 chunk 0 optimal weight: 0.6980 chunk 57 optimal weight: 0.0170 chunk 101 optimal weight: 0.5980 chunk 28 optimal weight: 3.9990 chunk 38 optimal weight: 0.6980 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 253 HIS ** C 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 9243 Z= 0.157 Angle : 0.499 6.182 12570 Z= 0.260 Chirality : 0.042 0.162 1560 Planarity : 0.003 0.034 1596 Dihedral : 4.478 32.158 1276 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.44 % Allowed : 15.38 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.24), residues: 1185 helix: 1.33 (0.25), residues: 447 sheet: 0.15 (0.29), residues: 285 loop : -0.49 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 303 HIS 0.005 0.002 HIS C 253 PHE 0.014 0.001 PHE B 234 TYR 0.022 0.001 TYR A 415 ARG 0.004 0.000 ARG A 360 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 119 time to evaluate : 1.072 Fit side-chains revert: symmetry clash REVERT: A 253 HIS cc_start: 0.7878 (t-170) cc_final: 0.7630 (t-170) REVERT: B 390 MET cc_start: 0.7929 (mmp) cc_final: 0.7112 (ttt) REVERT: C 390 MET cc_start: 0.7586 (mmp) cc_final: 0.6615 (ttt) outliers start: 36 outliers final: 22 residues processed: 143 average time/residue: 0.1422 time to fit residues: 32.3834 Evaluate side-chains 131 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 109 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 168 ASP Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 408 ASP Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 168 ASP Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 348 ILE Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 375 ASP Chi-restraints excluded: chain C residue 408 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 101 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 66 optimal weight: 5.9990 chunk 27 optimal weight: 0.3980 chunk 113 optimal weight: 0.9990 chunk 93 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 109 optimal weight: 5.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 253 HIS ** C 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9243 Z= 0.215 Angle : 0.532 7.922 12570 Z= 0.273 Chirality : 0.043 0.140 1560 Planarity : 0.003 0.036 1596 Dihedral : 4.500 32.353 1276 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 3.15 % Allowed : 16.91 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.24), residues: 1185 helix: 1.49 (0.25), residues: 432 sheet: 0.09 (0.29), residues: 285 loop : -0.55 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 303 HIS 0.005 0.002 HIS B 130 PHE 0.016 0.001 PHE B 234 TYR 0.012 0.001 TYR C 427 ARG 0.004 0.000 ARG A 360 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 115 time to evaluate : 1.030 Fit side-chains revert: symmetry clash REVERT: A 200 GLN cc_start: 0.8550 (OUTLIER) cc_final: 0.8042 (tt0) REVERT: A 253 HIS cc_start: 0.7906 (t-170) cc_final: 0.7638 (t-170) REVERT: B 200 GLN cc_start: 0.8722 (OUTLIER) cc_final: 0.8156 (tt0) REVERT: B 390 MET cc_start: 0.8019 (mmp) cc_final: 0.7226 (ttp) REVERT: C 390 MET cc_start: 0.7547 (mmp) cc_final: 0.6583 (ttt) outliers start: 33 outliers final: 23 residues processed: 140 average time/residue: 0.1451 time to fit residues: 32.0525 Evaluate side-chains 134 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 109 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 168 ASP Chi-restraints excluded: chain A residue 200 GLN Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 200 GLN Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 168 ASP Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 348 ILE Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 375 ASP Chi-restraints excluded: chain C residue 408 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 12 optimal weight: 4.9990 chunk 64 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 112 optimal weight: 4.9990 chunk 70 optimal weight: 0.0770 chunk 68 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 overall best weight: 1.1742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 253 HIS ** C 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9243 Z= 0.234 Angle : 0.538 6.050 12570 Z= 0.279 Chirality : 0.044 0.145 1560 Planarity : 0.003 0.035 1596 Dihedral : 4.524 32.440 1276 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 3.15 % Allowed : 17.19 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.24), residues: 1185 helix: 1.45 (0.25), residues: 429 sheet: -0.04 (0.31), residues: 255 loop : -0.57 (0.27), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 303 HIS 0.005 0.002 HIS B 130 PHE 0.016 0.002 PHE B 234 TYR 0.012 0.001 TYR C 415 ARG 0.004 0.000 ARG A 360 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 116 time to evaluate : 0.978 Fit side-chains revert: symmetry clash REVERT: A 253 HIS cc_start: 0.7906 (t-170) cc_final: 0.7630 (t-170) REVERT: B 200 GLN cc_start: 0.8747 (OUTLIER) cc_final: 0.8141 (tt0) REVERT: B 390 MET cc_start: 0.8041 (mmp) cc_final: 0.7243 (ttp) REVERT: C 390 MET cc_start: 0.7529 (mmp) cc_final: 0.6647 (ttt) outliers start: 33 outliers final: 24 residues processed: 139 average time/residue: 0.1399 time to fit residues: 30.9190 Evaluate side-chains 136 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 111 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 168 ASP Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 200 GLN Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 168 ASP Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain C residue 348 ILE Chi-restraints excluded: chain C residue 355 THR Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 375 ASP Chi-restraints excluded: chain C residue 408 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 67 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 chunk 22 optimal weight: 0.0870 chunk 21 optimal weight: 2.9990 chunk 71 optimal weight: 0.3980 chunk 76 optimal weight: 7.9990 chunk 55 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 102 optimal weight: 1.9990 chunk 108 optimal weight: 0.7980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 253 HIS ** C 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9243 Z= 0.155 Angle : 0.503 6.819 12570 Z= 0.259 Chirality : 0.042 0.143 1560 Planarity : 0.003 0.035 1596 Dihedral : 4.361 32.330 1276 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.06 % Allowed : 17.10 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.24), residues: 1185 helix: 1.55 (0.25), residues: 435 sheet: -0.02 (0.32), residues: 255 loop : -0.50 (0.28), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 303 HIS 0.005 0.002 HIS B 130 PHE 0.014 0.001 PHE B 234 TYR 0.013 0.001 TYR C 415 ARG 0.004 0.000 ARG A 360 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 115 time to evaluate : 0.978 Fit side-chains revert: symmetry clash REVERT: A 200 GLN cc_start: 0.8427 (OUTLIER) cc_final: 0.8071 (tt0) REVERT: A 253 HIS cc_start: 0.7887 (t-170) cc_final: 0.7616 (t-170) REVERT: B 200 GLN cc_start: 0.8664 (OUTLIER) cc_final: 0.8183 (tt0) REVERT: B 390 MET cc_start: 0.7994 (mmp) cc_final: 0.7053 (ttt) REVERT: C 390 MET cc_start: 0.7472 (mmp) cc_final: 0.6612 (ttt) outliers start: 32 outliers final: 21 residues processed: 138 average time/residue: 0.1381 time to fit residues: 30.3017 Evaluate side-chains 131 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 108 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 168 ASP Chi-restraints excluded: chain A residue 200 GLN Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 408 ASP Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 200 GLN Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 168 ASP Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain C residue 345 TYR Chi-restraints excluded: chain C residue 348 ILE Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 375 ASP Chi-restraints excluded: chain C residue 408 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 0.8980 chunk 105 optimal weight: 0.8980 chunk 108 optimal weight: 5.9990 chunk 63 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 99 optimal weight: 6.9990 chunk 104 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 253 HIS ** C 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9243 Z= 0.193 Angle : 0.525 7.187 12570 Z= 0.269 Chirality : 0.043 0.159 1560 Planarity : 0.003 0.035 1596 Dihedral : 4.380 32.463 1276 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.58 % Allowed : 17.67 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.24), residues: 1185 helix: 1.58 (0.25), residues: 435 sheet: -0.01 (0.31), residues: 255 loop : -0.51 (0.27), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 303 HIS 0.005 0.001 HIS B 130 PHE 0.015 0.001 PHE B 234 TYR 0.013 0.001 TYR C 415 ARG 0.003 0.000 ARG A 360 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 112 time to evaluate : 1.109 Fit side-chains revert: symmetry clash REVERT: A 200 GLN cc_start: 0.8500 (OUTLIER) cc_final: 0.8077 (tt0) REVERT: B 67 THR cc_start: 0.9366 (OUTLIER) cc_final: 0.8868 (t) REVERT: B 200 GLN cc_start: 0.8701 (OUTLIER) cc_final: 0.8168 (tt0) REVERT: B 390 MET cc_start: 0.8005 (mmp) cc_final: 0.7062 (ttt) REVERT: C 390 MET cc_start: 0.7505 (mmp) cc_final: 0.6645 (ttt) outliers start: 27 outliers final: 20 residues processed: 131 average time/residue: 0.1425 time to fit residues: 29.6439 Evaluate side-chains 132 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 109 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 168 ASP Chi-restraints excluded: chain A residue 200 GLN Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 408 ASP Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 200 GLN Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 168 ASP Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain C residue 348 ILE Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 408 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 111 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 116 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 92 optimal weight: 0.0970 chunk 9 optimal weight: 3.9990 chunk 71 optimal weight: 0.0980 chunk 56 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 253 HIS ** C 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9243 Z= 0.217 Angle : 0.540 8.518 12570 Z= 0.274 Chirality : 0.043 0.165 1560 Planarity : 0.003 0.033 1596 Dihedral : 4.412 32.555 1276 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.48 % Allowed : 17.86 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.24), residues: 1185 helix: 1.55 (0.25), residues: 435 sheet: -0.04 (0.32), residues: 255 loop : -0.52 (0.27), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 303 HIS 0.005 0.002 HIS B 130 PHE 0.016 0.001 PHE B 234 TYR 0.014 0.001 TYR C 415 ARG 0.004 0.000 ARG A 360 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 112 time to evaluate : 1.035 Fit side-chains revert: symmetry clash REVERT: A 200 GLN cc_start: 0.8556 (OUTLIER) cc_final: 0.8056 (tt0) REVERT: A 253 HIS cc_start: 0.7887 (t-170) cc_final: 0.7597 (t-170) REVERT: B 200 GLN cc_start: 0.8676 (OUTLIER) cc_final: 0.8148 (tt0) REVERT: B 390 MET cc_start: 0.8016 (mmp) cc_final: 0.7076 (ttt) REVERT: C 390 MET cc_start: 0.7518 (mmp) cc_final: 0.6661 (ttt) outliers start: 26 outliers final: 23 residues processed: 130 average time/residue: 0.1405 time to fit residues: 29.1290 Evaluate side-chains 135 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 110 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 168 ASP Chi-restraints excluded: chain A residue 200 GLN Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 408 ASP Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 200 GLN Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 168 ASP Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain C residue 348 ILE Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 408 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 85 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 92 optimal weight: 0.6980 chunk 38 optimal weight: 0.0770 chunk 95 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 81 optimal weight: 0.7980 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 253 HIS ** C 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.124375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.106405 restraints weight = 11433.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.108682 restraints weight = 7821.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.110385 restraints weight = 5878.280| |-----------------------------------------------------------------------------| r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9243 Z= 0.164 Angle : 0.518 8.367 12570 Z= 0.262 Chirality : 0.043 0.160 1560 Planarity : 0.003 0.033 1596 Dihedral : 4.301 32.454 1276 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.58 % Allowed : 18.05 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.25), residues: 1185 helix: 1.60 (0.26), residues: 435 sheet: -0.01 (0.32), residues: 255 loop : -0.44 (0.28), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 303 HIS 0.004 0.002 HIS B 130 PHE 0.015 0.001 PHE B 234 TYR 0.013 0.001 TYR C 415 ARG 0.003 0.000 ARG A 360 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1778.05 seconds wall clock time: 32 minutes 38.98 seconds (1958.98 seconds total)