Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 03:22:40 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xpd_22285/04_2023/6xpd_22285.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xpd_22285/04_2023/6xpd_22285.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xpd_22285/04_2023/6xpd_22285.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xpd_22285/04_2023/6xpd_22285.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xpd_22285/04_2023/6xpd_22285.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xpd_22285/04_2023/6xpd_22285.pdb" } resolution = 3.8 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 ------------------------------------------------------------------------------- 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 144 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 4 6.06 5 S 32 5.16 5 C 3010 2.51 5 N 754 2.21 5 O 822 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 131": "NH1" <-> "NH2" Residue "B TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 170": "OD1" <-> "OD2" Residue "B TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 326": "OD1" <-> "OD2" Residue "B ARG 331": "NH1" <-> "NH2" Residue "B PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 352": "OE1" <-> "OE2" Residue "A PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 131": "NH1" <-> "NH2" Residue "A TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 170": "OD1" <-> "OD2" Residue "A TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 326": "OD1" <-> "OD2" Residue "A ARG 331": "NH1" <-> "NH2" Residue "A PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 352": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 4622 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 2309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2309 Classifications: {'peptide': 303} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 9, 'TRANS': 293} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 2309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2309 Classifications: {'peptide': 303} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 9, 'TRANS': 293} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2325 SG CYS A 53 42.422 21.767 23.908 1.00 88.16 S ATOM 2246 SG CYS B 361 39.757 15.017 23.922 1.00 99.56 S ATOM 2271 SG CYS B 364 39.570 17.025 26.950 1.00 81.28 S ATOM 16 SG CYS B 53 33.976 39.660 23.918 1.00 89.15 S ATOM 4555 SG CYS A 361 36.712 46.426 23.890 1.00100.58 S ATOM 4580 SG CYS A 364 36.887 44.419 26.919 1.00 82.53 S Time building chain proxies: 2.74, per 1000 atoms: 0.59 Number of scatterers: 4622 At special positions: 0 Unit cell: (77.19, 62.25, 102.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 4 29.99 S 32 16.00 O 822 8.00 N 754 7.00 C 3010 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 - 3.50 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: 1.93 Conformation dependent library (CDL) restraints added in 671.2 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 401 " pdb="ZN ZN A 401 " - pdb=" ND1 HIS A 318 " pdb="ZN ZN A 401 " - pdb=" NE2 HIS A 301 " pdb="ZN ZN A 401 " - pdb=" SG CYS B 53 " pdb=" ZN A 402 " pdb="ZN ZN A 402 " - pdb=" SG CYS A 364 " pdb="ZN ZN A 402 " - pdb=" ND1 HIS B 54 " pdb="ZN ZN A 402 " - pdb=" SG CYS A 361 " pdb="ZN ZN A 402 " - pdb=" NE2 HIS B 52 " pdb=" ZN B 401 " pdb="ZN ZN B 401 " - pdb=" NE2 HIS B 301 " pdb="ZN ZN B 401 " - pdb=" ND1 HIS B 318 " pdb="ZN ZN B 401 " - pdb=" SG CYS A 53 " pdb=" ZN B 402 " pdb="ZN ZN B 402 " - pdb=" SG CYS B 364 " pdb="ZN ZN B 402 " - pdb=" ND1 HIS A 54 " pdb="ZN ZN B 402 " - pdb=" SG CYS B 361 " pdb="ZN ZN B 402 " - pdb=" NE2 HIS A 52 " Number of angles added : 4 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1164 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 2 sheets defined 69.0% alpha, 5.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'B' and resid 63 through 94 removed outlier: 3.844A pdb=" N TYR B 67 " --> pdb=" O GLY B 63 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA B 68 " --> pdb=" O ALA B 64 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ALA B 77 " --> pdb=" O LYS B 73 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N GLY B 92 " --> pdb=" O GLU B 88 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N HIS B 93 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE B 94 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 126 removed outlier: 4.078A pdb=" N HIS B 106 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU B 107 " --> pdb=" O ASP B 103 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU B 108 " --> pdb=" O ALA B 104 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LYS B 126 " --> pdb=" O TRP B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 168 Processing helix chain 'B' and resid 176 through 196 removed outlier: 3.637A pdb=" N ILE B 180 " --> pdb=" O THR B 176 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER B 182 " --> pdb=" O MET B 178 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA B 185 " --> pdb=" O VAL B 181 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU B 196 " --> pdb=" O LEU B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 241 removed outlier: 3.688A pdb=" N ASN B 224 " --> pdb=" O HIS B 220 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N VAL B 231 " --> pdb=" O GLN B 227 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU B 232 " --> pdb=" O SER B 228 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N SER B 234 " --> pdb=" O SER B 230 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE B 237 " --> pdb=" O ILE B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 275 removed outlier: 4.478A pdb=" N ILE B 250 " --> pdb=" O ILE B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 293 Processing helix chain 'B' and resid 326 through 342 removed outlier: 3.983A pdb=" N VAL B 330 " --> pdb=" O ASP B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 365 removed outlier: 4.655A pdb=" N LEU B 362 " --> pdb=" O PRO B 359 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N PHE B 363 " --> pdb=" O ASP B 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 94 removed outlier: 3.843A pdb=" N TYR A 67 " --> pdb=" O GLY A 63 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA A 68 " --> pdb=" O ALA A 64 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ALA A 77 " --> pdb=" O LYS A 73 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N GLY A 92 " --> pdb=" O GLU A 88 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N HIS A 93 " --> pdb=" O VAL A 89 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE A 94 " --> pdb=" O VAL A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 126 removed outlier: 4.036A pdb=" N HIS A 106 " --> pdb=" O THR A 102 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU A 107 " --> pdb=" O ASP A 103 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU A 108 " --> pdb=" O ALA A 104 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LYS A 126 " --> pdb=" O TRP A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 168 Processing helix chain 'A' and resid 176 through 196 removed outlier: 3.637A pdb=" N ILE A 180 " --> pdb=" O THR A 176 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER A 182 " --> pdb=" O MET A 178 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA A 185 " --> pdb=" O VAL A 181 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU A 196 " --> pdb=" O LEU A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 241 removed outlier: 3.688A pdb=" N ASN A 224 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N VAL A 231 " --> pdb=" O GLN A 227 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU A 232 " --> pdb=" O SER A 228 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N SER A 234 " --> pdb=" O SER A 230 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE A 237 " --> pdb=" O ILE A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 275 removed outlier: 4.478A pdb=" N ILE A 250 " --> pdb=" O ILE A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 293 Processing helix chain 'A' and resid 326 through 342 removed outlier: 3.983A pdb=" N VAL A 330 " --> pdb=" O ASP A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 365 removed outlier: 4.655A pdb=" N LEU A 362 " --> pdb=" O PRO A 359 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N PHE A 363 " --> pdb=" O ASP A 360 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 297 through 304 removed outlier: 5.680A pdb=" N VAL B 300 " --> pdb=" O ALA B 320 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N ALA B 320 " --> pdb=" O VAL B 300 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N SER B 302 " --> pdb=" O HIS B 318 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N HIS B 318 " --> pdb=" O SER B 302 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N LEU B 315 " --> pdb=" O THR B 348 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 297 through 304 removed outlier: 5.679A pdb=" N VAL A 300 " --> pdb=" O ALA A 320 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N ALA A 320 " --> pdb=" O VAL A 300 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N SER A 302 " --> pdb=" O HIS A 318 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N HIS A 318 " --> pdb=" O SER A 302 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N LEU A 315 " --> pdb=" O THR A 348 " (cutoff:3.500A) 306 hydrogen bonds defined for protein. 894 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: 1.20 Time building geometry restraints manager: 2.09 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: 1432 1.34 - 1.46: 1103 1.46 - 1.58: 2135 1.58 - 1.70: 0 1.70 - 1.82: 44 Bond restraints: 4714 Sorted by residual: bond pdb=" CA THR A 348 " pdb=" CB THR A 348 " ideal model delta sigma weight residual 1.527 1.498 0.029 2.48e-02 1.63e+03 1.38e+00 bond pdb=" C SER B 262 " pdb=" O SER B 262 " ideal model delta sigma weight residual 1.237 1.250 -0.014 1.17e-02 7.31e+03 1.36e+00 bond pdb=" CA THR B 348 " pdb=" CB THR B 348 " ideal model delta sigma weight residual 1.527 1.499 0.029 2.48e-02 1.63e+03 1.33e+00 bond pdb=" CG LEU B 308 " pdb=" CD1 LEU B 308 " ideal model delta sigma weight residual 1.521 1.485 0.036 3.30e-02 9.18e+02 1.20e+00 bond pdb=" CG LEU A 308 " pdb=" CD1 LEU A 308 " ideal model delta sigma weight residual 1.521 1.485 0.036 3.30e-02 9.18e+02 1.16e+00 ... (remaining 4709 not shown) Histogram of bond angle deviations from ideal: 99.06 - 106.04: 81 106.04 - 113.03: 2838 113.03 - 120.02: 1512 120.02 - 127.00: 1929 127.00 - 133.99: 62 Bond angle restraints: 6422 Sorted by residual: angle pdb=" C SER B 353 " pdb=" N PRO B 354 " pdb=" CA PRO B 354 " ideal model delta sigma weight residual 119.05 122.88 -3.83 1.11e+00 8.12e-01 1.19e+01 angle pdb=" C SER A 353 " pdb=" N PRO A 354 " pdb=" CA PRO A 354 " ideal model delta sigma weight residual 119.05 122.56 -3.51 1.11e+00 8.12e-01 9.98e+00 angle pdb=" C ASP B 356 " pdb=" N GLN B 357 " pdb=" CA GLN B 357 " ideal model delta sigma weight residual 122.41 117.98 4.43 1.41e+00 5.03e-01 9.86e+00 angle pdb=" C ASP A 356 " pdb=" N GLN A 357 " pdb=" CA GLN A 357 " ideal model delta sigma weight residual 122.16 118.05 4.11 1.50e+00 4.44e-01 7.51e+00 angle pdb=" N PRO B 354 " pdb=" CA PRO B 354 " pdb=" C PRO B 354 " ideal model delta sigma weight residual 113.53 110.13 3.40 1.39e+00 5.18e-01 6.00e+00 ... (remaining 6417 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.92: 2330 12.92 - 25.83: 325 25.83 - 38.75: 94 38.75 - 51.67: 28 51.67 - 64.58: 11 Dihedral angle restraints: 2788 sinusoidal: 1008 harmonic: 1780 Sorted by residual: dihedral pdb=" CA LEU B 308 " pdb=" C LEU B 308 " pdb=" N THR B 309 " pdb=" CA THR B 309 " ideal model delta harmonic sigma weight residual -180.00 -157.52 -22.48 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" CA LEU A 308 " pdb=" C LEU A 308 " pdb=" N THR A 309 " pdb=" CA THR A 309 " ideal model delta harmonic sigma weight residual -180.00 -157.53 -22.47 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" CA GLU A 88 " pdb=" C GLU A 88 " pdb=" N VAL A 89 " pdb=" CA VAL A 89 " ideal model delta harmonic sigma weight residual 180.00 160.64 19.36 0 5.00e+00 4.00e-02 1.50e+01 ... (remaining 2785 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 520 0.039 - 0.078: 232 0.078 - 0.118: 41 0.118 - 0.157: 5 0.157 - 0.196: 2 Chirality restraints: 800 Sorted by residual: chirality pdb=" CA ASP A 356 " pdb=" N ASP A 356 " pdb=" C ASP A 356 " pdb=" CB ASP A 356 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.61e-01 chirality pdb=" CA ASP B 356 " pdb=" N ASP B 356 " pdb=" C ASP B 356 " pdb=" CB ASP B 356 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.38e-01 chirality pdb=" CB ILE A 305 " pdb=" CA ILE A 305 " pdb=" CG1 ILE A 305 " pdb=" CG2 ILE A 305 " both_signs ideal model delta sigma weight residual False 2.64 2.52 0.13 2.00e-01 2.50e+01 4.21e-01 ... (remaining 797 not shown) Planarity restraints: 776 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS B 220 " -0.010 2.00e-02 2.50e+03 1.21e-02 2.18e+00 pdb=" CG HIS B 220 " 0.026 2.00e-02 2.50e+03 pdb=" ND1 HIS B 220 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 HIS B 220 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 HIS B 220 " 0.002 2.00e-02 2.50e+03 pdb=" NE2 HIS B 220 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 220 " 0.011 2.00e-02 2.50e+03 1.20e-02 2.16e+00 pdb=" CG HIS A 220 " -0.026 2.00e-02 2.50e+03 pdb=" ND1 HIS A 220 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 HIS A 220 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 HIS A 220 " -0.001 2.00e-02 2.50e+03 pdb=" NE2 HIS A 220 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 365 " 0.006 2.00e-02 2.50e+03 1.22e-02 1.49e+00 pdb=" C GLU B 365 " -0.021 2.00e-02 2.50e+03 pdb=" O GLU B 365 " 0.008 2.00e-02 2.50e+03 pdb=" N ASP B 366 " 0.007 2.00e-02 2.50e+03 ... (remaining 773 not shown) Histogram of nonbonded interaction distances: 1.46 - 2.15: 3 2.15 - 2.84: 1695 2.84 - 3.52: 7055 3.52 - 4.21: 10088 4.21 - 4.90: 17725 Nonbonded interactions: 36566 Sorted by model distance: nonbonded pdb=" OE2 GLU A 352 " pdb="ZN ZN A 401 " model vdw 1.461 2.230 nonbonded pdb=" OE2 GLU B 352 " pdb="ZN ZN B 401 " model vdw 1.781 2.230 nonbonded pdb=" OG1 THR B 348 " pdb=" OG1 THR A 348 " model vdw 2.140 2.440 nonbonded pdb=" O GLN B 227 " pdb=" OG SER B 230 " model vdw 2.184 2.440 nonbonded pdb=" O GLN A 227 " pdb=" OG SER A 230 " model vdw 2.185 2.440 ... (remaining 36561 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 1.690 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 16.810 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 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 : 0.007 0.036 4714 Z= 0.456 Angle : 0.770 6.410 6422 Z= 0.430 Chirality : 0.043 0.196 800 Planarity : 0.003 0.022 776 Dihedral : 14.372 64.582 1624 Min Nonbonded Distance : 1.461 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.43 % Favored : 90.57 % Rotamer Outliers : 0.20 % 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: -3.83 (0.30), residues: 594 helix: -1.82 (0.22), residues: 384 sheet: -3.84 (0.69), residues: 46 loop : -3.48 (0.46), residues: 164 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 134 time to evaluate : 0.564 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 134 average time/residue: 0.2114 time to fit residues: 34.2774 Evaluate side-chains 89 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 0.578 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 25 optimal weight: 8.9990 chunk 15 optimal weight: 5.9990 chunk 30 optimal weight: 20.0000 chunk 24 optimal weight: 6.9990 chunk 47 optimal weight: 6.9990 chunk 18 optimal weight: 9.9990 chunk 28 optimal weight: 5.9990 chunk 35 optimal weight: 10.0000 chunk 54 optimal weight: 3.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 GLN B 197 HIS B 211 ASN ** B 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 172 GLN A 211 ASN ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.032 4714 Z= 0.365 Angle : 0.674 5.886 6422 Z= 0.346 Chirality : 0.041 0.117 800 Planarity : 0.004 0.032 776 Dihedral : 5.140 22.253 630 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer Outliers : 3.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.35), residues: 594 helix: 0.42 (0.25), residues: 396 sheet: -3.87 (0.65), residues: 46 loop : -2.36 (0.55), residues: 152 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 95 time to evaluate : 0.593 Fit side-chains outliers start: 17 outliers final: 12 residues processed: 102 average time/residue: 0.1170 time to fit residues: 16.7516 Evaluate side-chains 94 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 82 time to evaluate : 0.576 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0458 time to fit residues: 1.7531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 30 optimal weight: 0.0370 chunk 16 optimal weight: 4.9990 chunk 45 optimal weight: 10.0000 chunk 37 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 chunk 58 optimal weight: 7.9990 chunk 48 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 overall best weight: 1.5864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 HIS A 189 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.020 4714 Z= 0.177 Angle : 0.560 8.308 6422 Z= 0.281 Chirality : 0.037 0.153 800 Planarity : 0.003 0.034 776 Dihedral : 4.374 20.333 630 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer Outliers : 1.95 % 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: 0.54 (0.37), residues: 594 helix: 1.82 (0.26), residues: 382 sheet: -3.79 (0.66), residues: 46 loop : -1.91 (0.53), residues: 166 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 109 time to evaluate : 0.591 Fit side-chains outliers start: 10 outliers final: 6 residues processed: 114 average time/residue: 0.1323 time to fit residues: 20.5025 Evaluate side-chains 98 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 92 time to evaluate : 0.619 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0645 time to fit residues: 1.5090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 41 optimal weight: 10.0000 chunk 28 optimal weight: 6.9990 chunk 6 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 15 optimal weight: 6.9990 chunk 48 optimal weight: 3.9990 chunk 32 optimal weight: 10.0000 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 174 GLN ** B 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 189 ASN ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.029 4714 Z= 0.275 Angle : 0.593 5.439 6422 Z= 0.306 Chirality : 0.039 0.109 800 Planarity : 0.004 0.039 776 Dihedral : 4.534 20.640 630 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer Outliers : 3.52 % 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: 0.59 (0.37), residues: 594 helix: 1.72 (0.26), residues: 390 sheet: -3.75 (0.64), residues: 46 loop : -1.67 (0.55), residues: 158 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 94 time to evaluate : 0.610 Fit side-chains outliers start: 18 outliers final: 14 residues processed: 100 average time/residue: 0.1344 time to fit residues: 18.1030 Evaluate side-chains 97 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 83 time to evaluate : 0.599 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.0488 time to fit residues: 1.9868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 0 optimal weight: 40.0000 chunk 43 optimal weight: 7.9990 chunk 23 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 29 optimal weight: 0.1980 chunk 52 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 34 optimal weight: 10.0000 overall best weight: 1.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 174 GLN ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.020 4714 Z= 0.153 Angle : 0.522 5.527 6422 Z= 0.269 Chirality : 0.037 0.162 800 Planarity : 0.003 0.038 776 Dihedral : 4.066 18.657 630 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer Outliers : 0.20 % 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: 1.03 (0.37), residues: 594 helix: 2.18 (0.26), residues: 382 sheet: -3.45 (0.70), residues: 46 loop : -1.70 (0.54), residues: 166 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 94 time to evaluate : 0.579 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 95 average time/residue: 0.1116 time to fit residues: 15.0831 Evaluate side-chains 84 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 0.558 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 14 optimal weight: 8.9990 chunk 58 optimal weight: 7.9990 chunk 48 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 4 optimal weight: 0.0020 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 30.0000 chunk 55 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 chunk 33 optimal weight: 0.1980 chunk 42 optimal weight: 4.9990 overall best weight: 1.8394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.3516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 4714 Z= 0.192 Angle : 0.593 7.373 6422 Z= 0.290 Chirality : 0.037 0.134 800 Planarity : 0.003 0.039 776 Dihedral : 3.993 18.451 630 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer Outliers : 1.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.37), residues: 594 helix: 2.24 (0.26), residues: 382 sheet: -3.42 (0.67), residues: 46 loop : -1.67 (0.53), residues: 166 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 91 time to evaluate : 0.507 Fit side-chains outliers start: 8 outliers final: 7 residues processed: 94 average time/residue: 0.1070 time to fit residues: 14.3757 Evaluate side-chains 94 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 87 time to evaluate : 0.505 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0460 time to fit residues: 1.3301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 32 optimal weight: 6.9990 chunk 48 optimal weight: 0.4980 chunk 57 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 23 optimal weight: 8.9990 chunk 34 optimal weight: 10.0000 chunk 17 optimal weight: 1.9990 chunk 11 optimal weight: 8.9990 chunk 39 optimal weight: 1.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.3824 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: