Starting phenix.real_space_refine on Sun Nov 17 01:01:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fd8_31536/11_2024/7fd8_31536.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fd8_31536/11_2024/7fd8_31536.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/7fd8_31536/11_2024/7fd8_31536.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fd8_31536/11_2024/7fd8_31536.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fd8_31536/11_2024/7fd8_31536.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fd8_31536/11_2024/7fd8_31536.cif" } resolution = 3.8 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= 0.000 sd= 0.001 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 114 5.16 5 C 7824 2.51 5 N 2004 2.21 5 O 2210 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 12152 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 764, 6014 Classifications: {'peptide': 764} Link IDs: {'PTRANS': 32, 'TRANS': 731} Chain breaks: 2 Chain: "A" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 62 Unusual residues: {'NAG': 1, 'QUS': 1, 'Y01': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: B Time building chain proxies: 13.23, per 1000 atoms: 1.09 Number of scatterers: 12152 At special positions: 0 Unit cell: (77.43, 102.35, 173.55, 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 114 16.00 O 2210 8.00 N 2004 7.00 C 7824 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 57 " - pdb=" SG CYS A 99 " distance=2.03 Simple disulfide: pdb=" SG CYS A 241 " - pdb=" SG CYS A 530 " distance=2.02 Simple disulfide: pdb=" SG CYS A 276 " - pdb=" SG CYS A 278 " distance=2.04 Simple disulfide: pdb=" SG CYS A 365 " - pdb=" SG CYS A 381 " distance=2.03 Simple disulfide: pdb=" SG CYS A 419 " - pdb=" SG CYS A 426 " distance=2.03 Simple disulfide: pdb=" SG CYS A 511 " - pdb=" SG CYS A 531 " distance=2.03 Simple disulfide: pdb=" SG CYS A 515 " - pdb=" SG CYS A 534 " distance=2.03 Simple disulfide: pdb=" SG CYS A 537 " - pdb=" SG CYS A 549 " distance=2.03 Simple disulfide: pdb=" SG CYS A 552 " - pdb=" SG CYS A 565 " distance=2.03 Simple disulfide: pdb=" SG CYS A 644 " - pdb=" SG CYS A 733 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 901 " - " ASN A 210 " " NAG B 901 " - " ASN B 210 " Time building additional restraints: 3.01 Conformation dependent library (CDL) restraints added in 1.7 seconds 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2852 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 12 sheets defined 48.4% alpha, 9.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.17 Creating SS restraints... Processing helix chain 'A' and resid 65 through 81 Processing helix chain 'A' and resid 101 through 113 Processing helix chain 'A' and resid 151 through 163 removed outlier: 3.800A pdb=" N LEU A 161 " --> pdb=" O GLN A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 181 removed outlier: 3.776A pdb=" N ASP A 181 " --> pdb=" O ASP A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 209 Processing helix chain 'A' and resid 221 through 238 Processing helix chain 'A' and resid 253 through 266 Processing helix chain 'A' and resid 279 through 293 Processing helix chain 'A' and resid 317 through 321 removed outlier: 3.521A pdb=" N ALA A 321 " --> pdb=" O GLN A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 342 Processing helix chain 'A' and resid 354 through 364 removed outlier: 3.815A pdb=" N PHE A 363 " --> pdb=" O TRP A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 419 Processing helix chain 'A' and resid 433 through 444 removed outlier: 3.669A pdb=" N LYS A 443 " --> pdb=" O GLU A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 604 removed outlier: 3.517A pdb=" N ALA A 583 " --> pdb=" O GLU A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 612 Processing helix chain 'A' and resid 614 through 636 removed outlier: 3.862A pdb=" N THR A 632 " --> pdb=" O GLY A 628 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N PHE A 633 " --> pdb=" O TYR A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 671 removed outlier: 3.737A pdb=" N ARG A 648 " --> pdb=" O CYS A 644 " (cutoff:3.500A) Proline residue: A 655 - end of helix Processing helix chain 'A' and resid 692 through 715 removed outlier: 3.943A pdb=" N GLN A 704 " --> pdb=" O LEU A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 736 through 760 Proline residue: A 743 - end of helix Processing helix chain 'A' and resid 765 through 788 removed outlier: 5.756A pdb=" N ALA A 771 " --> pdb=" O ASN A 767 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LYS A 772 " --> pdb=" O PHE A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 795 removed outlier: 4.274A pdb=" N PHE A 793 " --> pdb=" O VAL A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 797 through 816 Processing helix chain 'A' and resid 818 through 826 Processing helix chain 'B' and resid 65 through 81 Processing helix chain 'B' and resid 101 through 113 Processing helix chain 'B' and resid 151 through 163 removed outlier: 3.798A pdb=" N LEU B 161 " --> pdb=" O GLN B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 181 removed outlier: 3.776A pdb=" N ASP B 181 " --> pdb=" O ASP B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 209 Processing helix chain 'B' and resid 221 through 238 Processing helix chain 'B' and resid 253 through 266 Processing helix chain 'B' and resid 279 through 293 Processing helix chain 'B' and resid 317 through 321 removed outlier: 3.522A pdb=" N ALA B 321 " --> pdb=" O GLN B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 342 Processing helix chain 'B' and resid 354 through 364 removed outlier: 3.814A pdb=" N PHE B 363 " --> pdb=" O TRP B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 419 Processing helix chain 'B' and resid 433 through 444 removed outlier: 3.669A pdb=" N LYS B 443 " --> pdb=" O GLU B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 604 removed outlier: 3.517A pdb=" N ALA B 583 " --> pdb=" O GLU B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 612 Processing helix chain 'B' and resid 614 through 636 removed outlier: 3.862A pdb=" N THR B 632 " --> pdb=" O GLY B 628 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N PHE B 633 " --> pdb=" O TYR B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 640 through 671 removed outlier: 3.737A pdb=" N ARG B 648 " --> pdb=" O CYS B 644 " (cutoff:3.500A) Proline residue: B 655 - end of helix Processing helix chain 'B' and resid 692 through 715 removed outlier: 3.943A pdb=" N GLN B 704 " --> pdb=" O LEU B 700 " (cutoff:3.500A) Processing helix chain 'B' and resid 736 through 760 Proline residue: B 743 - end of helix Processing helix chain 'B' and resid 765 through 788 removed outlier: 5.757A pdb=" N ALA B 771 " --> pdb=" O ASN B 767 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LYS B 772 " --> pdb=" O PHE B 768 " (cutoff:3.500A) Processing helix chain 'B' and resid 789 through 795 removed outlier: 4.275A pdb=" N PHE B 793 " --> pdb=" O VAL B 789 " (cutoff:3.500A) Processing helix chain 'B' and resid 797 through 816 Processing helix chain 'B' and resid 818 through 826 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 5.827A pdb=" N ILE A 35 " --> pdb=" O GLY A 92 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N GLU A 94 " --> pdb=" O ILE A 35 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ILE A 37 " --> pdb=" O GLU A 94 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N ARG A 96 " --> pdb=" O ILE A 37 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ALA A 39 " --> pdb=" O ARG A 96 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N ILE A 36 " --> pdb=" O VAL A 144 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL A 146 " --> pdb=" O ILE A 36 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N GLY A 38 " --> pdb=" O VAL A 146 " (cutoff:3.500A) removed outlier: 8.610A pdb=" N ILE A 170 " --> pdb=" O VAL A 144 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N VAL A 146 " --> pdb=" O ILE A 170 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 213 through 219 removed outlier: 7.713A pdb=" N VAL A 214 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N SER A 245 " --> pdb=" O VAL A 214 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ALA A 216 " --> pdb=" O SER A 245 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N LYS A 247 " --> pdb=" O ALA A 216 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N HIS A 218 " --> pdb=" O LYS A 247 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 274 through 276 removed outlier: 6.241A pdb=" N VAL A 274 " --> pdb=" O LEU A 302 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE A 325 " --> pdb=" O LEU A 301 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE A 327 " --> pdb=" O GLY A 303 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLY A 324 " --> pdb=" O PHE A 471 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N TYR A 466 " --> pdb=" O SER A 486 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N SER A 486 " --> pdb=" O TYR A 466 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ILE A 468 " --> pdb=" O VAL A 484 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 446 through 447 removed outlier: 3.523A pdb=" N PHE A 446 " --> pdb=" O ILE A 454 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 520 through 523 removed outlier: 3.571A pdb=" N THR A 535 " --> pdb=" O LYS A 521 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 719 through 722 Processing sheet with id=AA7, first strand: chain 'B' and resid 28 through 31 removed outlier: 5.827A pdb=" N ILE B 35 " --> pdb=" O GLY B 92 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N GLU B 94 " --> pdb=" O ILE B 35 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ILE B 37 " --> pdb=" O GLU B 94 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N ARG B 96 " --> pdb=" O ILE B 37 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ALA B 39 " --> pdb=" O ARG B 96 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N ILE B 36 " --> pdb=" O VAL B 144 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL B 146 " --> pdb=" O ILE B 36 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N GLY B 38 " --> pdb=" O VAL B 146 " (cutoff:3.500A) removed outlier: 8.611A pdb=" N ILE B 170 " --> pdb=" O VAL B 144 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N VAL B 146 " --> pdb=" O ILE B 170 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 213 through 219 removed outlier: 7.712A pdb=" N VAL B 214 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N SER B 245 " --> pdb=" O VAL B 214 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ALA B 216 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N LYS B 247 " --> pdb=" O ALA B 216 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N HIS B 218 " --> pdb=" O LYS B 247 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 274 through 276 removed outlier: 6.240A pdb=" N VAL B 274 " --> pdb=" O LEU B 302 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE B 325 " --> pdb=" O LEU B 301 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE B 327 " --> pdb=" O GLY B 303 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLY B 324 " --> pdb=" O PHE B 471 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N TYR B 466 " --> pdb=" O SER B 486 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N SER B 486 " --> pdb=" O TYR B 466 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ILE B 468 " --> pdb=" O VAL B 484 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 446 through 447 removed outlier: 3.523A pdb=" N PHE B 446 " --> pdb=" O ILE B 454 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 520 through 523 removed outlier: 3.570A pdb=" N THR B 535 " --> pdb=" O LYS B 521 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 719 through 722 576 hydrogen bonds defined for protein. 1692 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: 3.73 Time building geometry restraints manager: 3.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1946 1.30 - 1.43: 3302 1.43 - 1.56: 7022 1.56 - 1.69: 0 1.69 - 1.82: 164 Bond restraints: 12434 Sorted by residual: bond pdb=" CAY Y01 B 903 " pdb=" OAG Y01 B 903 " ideal model delta sigma weight residual 1.207 1.422 -0.215 2.00e-02 2.50e+03 1.15e+02 bond pdb=" CAY Y01 A 903 " pdb=" OAG Y01 A 903 " ideal model delta sigma weight residual 1.207 1.422 -0.215 2.00e-02 2.50e+03 1.15e+02 bond pdb=" CAI Y01 B 903 " pdb=" CAZ Y01 B 903 " ideal model delta sigma weight residual 1.332 1.498 -0.166 2.00e-02 2.50e+03 6.93e+01 bond pdb=" CAI Y01 A 903 " pdb=" CAZ Y01 A 903 " ideal model delta sigma weight residual 1.332 1.498 -0.166 2.00e-02 2.50e+03 6.93e+01 bond pdb=" C01 QUS A 902 " pdb=" C02 QUS A 902 " ideal model delta sigma weight residual 1.556 1.458 0.098 2.00e-02 2.50e+03 2.41e+01 ... (remaining 12429 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 14746 2.01 - 4.03: 1950 4.03 - 6.04: 134 6.04 - 8.05: 22 8.05 - 10.06: 10 Bond angle restraints: 16862 Sorted by residual: angle pdb=" C LYS B 379 " pdb=" N THR B 380 " pdb=" CA THR B 380 " ideal model delta sigma weight residual 121.31 127.44 -6.13 1.49e+00 4.50e-01 1.69e+01 angle pdb=" C LYS A 379 " pdb=" N THR A 380 " pdb=" CA THR A 380 " ideal model delta sigma weight residual 121.31 127.36 -6.05 1.49e+00 4.50e-01 1.65e+01 angle pdb=" N LYS B 517 " pdb=" CA LYS B 517 " pdb=" C LYS B 517 " ideal model delta sigma weight residual 112.57 108.07 4.50 1.13e+00 7.83e-01 1.58e+01 angle pdb=" N LYS A 517 " pdb=" CA LYS A 517 " pdb=" C LYS A 517 " ideal model delta sigma weight residual 112.57 108.09 4.48 1.13e+00 7.83e-01 1.57e+01 angle pdb=" C TYR A 317 " pdb=" N GLN A 318 " pdb=" CA GLN A 318 " ideal model delta sigma weight residual 120.28 125.90 -5.62 1.44e+00 4.82e-01 1.52e+01 ... (remaining 16857 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.63: 7259 22.63 - 45.25: 239 45.25 - 67.88: 43 67.88 - 90.50: 17 90.50 - 113.13: 14 Dihedral angle restraints: 7572 sinusoidal: 3124 harmonic: 4448 Sorted by residual: dihedral pdb=" CB CYS A 537 " pdb=" SG CYS A 537 " pdb=" SG CYS A 549 " pdb=" CB CYS A 549 " ideal model delta sinusoidal sigma weight residual 93.00 156.63 -63.63 1 1.00e+01 1.00e-02 5.34e+01 dihedral pdb=" CB CYS A 552 " pdb=" SG CYS A 552 " pdb=" SG CYS A 565 " pdb=" CB CYS A 565 " ideal model delta sinusoidal sigma weight residual -86.00 -129.41 43.41 1 1.00e+01 1.00e-02 2.63e+01 dihedral pdb=" CA GLY B 652 " pdb=" C GLY B 652 " pdb=" N LEU B 653 " pdb=" CA LEU B 653 " ideal model delta harmonic sigma weight residual -180.00 -157.83 -22.17 0 5.00e+00 4.00e-02 1.97e+01 ... (remaining 7569 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.345: 1892 0.345 - 0.689: 4 0.689 - 1.033: 0 1.033 - 1.378: 0 1.378 - 1.722: 2 Chirality restraints: 1898 Sorted by residual: chirality pdb=" C02 QUS B 902 " pdb=" C01 QUS B 902 " pdb=" C03 QUS B 902 " pdb=" NP3 QUS B 902 " both_signs ideal model delta sigma weight residual False 2.50 0.78 1.72 2.00e-01 2.50e+01 7.41e+01 chirality pdb=" C02 QUS A 902 " pdb=" C01 QUS A 902 " pdb=" C03 QUS A 902 " pdb=" NP3 QUS A 902 " both_signs ideal model delta sigma weight residual False 2.50 0.78 1.72 2.00e-01 2.50e+01 7.38e+01 chirality pdb=" C1 NAG B 901 " pdb=" ND2 ASN B 210 " pdb=" C2 NAG B 901 " pdb=" O5 NAG B 901 " both_signs ideal model delta sigma weight residual False -2.40 -1.88 -0.52 2.00e-01 2.50e+01 6.75e+00 ... (remaining 1895 not shown) Planarity restraints: 2116 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CAM Y01 B 903 " -0.025 2.00e-02 2.50e+03 4.43e-02 1.97e+01 pdb=" CAY Y01 B 903 " 0.077 2.00e-02 2.50e+03 pdb=" OAG Y01 B 903 " -0.027 2.00e-02 2.50e+03 pdb=" OAW Y01 B 903 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CAM Y01 A 903 " 0.025 2.00e-02 2.50e+03 4.35e-02 1.89e+01 pdb=" CAY Y01 A 903 " -0.075 2.00e-02 2.50e+03 pdb=" OAG Y01 A 903 " 0.027 2.00e-02 2.50e+03 pdb=" OAW Y01 A 903 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C01 QUS B 902 " -0.046 2.00e-02 2.50e+03 2.64e-02 6.99e+00 pdb=" C02 QUS B 902 " 0.013 2.00e-02 2.50e+03 pdb=" O16 QUS B 902 " 0.016 2.00e-02 2.50e+03 pdb=" O17 QUS B 902 " 0.017 2.00e-02 2.50e+03 ... (remaining 2113 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 124 2.60 - 3.17: 9915 3.17 - 3.75: 19742 3.75 - 4.32: 26015 4.32 - 4.90: 42608 Nonbonded interactions: 98404 Sorted by model distance: nonbonded pdb=" SG CYS B 241 " pdb=" SG CYS B 530 " model vdw 2.025 3.760 nonbonded pdb=" SG CYS B 511 " pdb=" SG CYS B 531 " model vdw 2.028 3.760 nonbonded pdb=" SG CYS B 515 " pdb=" SG CYS B 534 " model vdw 2.030 3.760 nonbonded pdb=" SG CYS B 419 " pdb=" SG CYS B 426 " model vdw 2.031 3.760 nonbonded pdb=" SG CYS B 365 " pdb=" SG CYS B 381 " model vdw 2.031 3.760 ... (remaining 98399 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 34.420 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.215 12434 Z= 0.530 Angle : 1.399 10.063 16862 Z= 0.935 Chirality : 0.108 1.722 1898 Planarity : 0.004 0.044 2114 Dihedral : 13.892 113.126 4690 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.58 % Favored : 91.29 % Rotamer: Outliers : 0.61 % Allowed : 2.88 % Favored : 96.52 % Cbeta Deviations : 0.14 % 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: -2.25 (0.19), residues: 1516 helix: -0.64 (0.16), residues: 706 sheet: -2.08 (0.37), residues: 160 loop : -2.24 (0.23), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP A 575 HIS 0.010 0.002 HIS B 74 PHE 0.020 0.002 PHE B 337 TYR 0.019 0.002 TYR B 223 ARG 0.005 0.001 ARG A 351 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 127 time to evaluate : 2.079 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 414 MET cc_start: 0.8661 (ttt) cc_final: 0.8382 (tmm) REVERT: A 429 MET cc_start: 0.7534 (mpp) cc_final: 0.7218 (mpp) REVERT: A 592 LEU cc_start: 0.8961 (mt) cc_final: 0.8749 (tt) REVERT: A 714 MET cc_start: 0.6864 (mmt) cc_final: 0.5929 (ttp) REVERT: B 414 MET cc_start: 0.8632 (ttt) cc_final: 0.8427 (tmm) REVERT: B 429 MET cc_start: 0.7558 (mpp) cc_final: 0.7267 (mpp) REVERT: B 592 LEU cc_start: 0.8903 (mt) cc_final: 0.8699 (tt) REVERT: B 714 MET cc_start: 0.7060 (mmt) cc_final: 0.6244 (ttp) outliers start: 8 outliers final: 0 residues processed: 135 average time/residue: 0.2661 time to fit residues: 51.7125 Evaluate side-chains 72 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 1.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 5.9990 chunk 115 optimal weight: 3.9990 chunk 63 optimal weight: 6.9990 chunk 39 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 119 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 72 optimal weight: 3.9990 chunk 88 optimal weight: 0.9990 chunk 138 optimal weight: 20.0000 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 GLN A 159 GLN B 159 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12434 Z= 0.235 Angle : 0.650 10.907 16862 Z= 0.321 Chirality : 0.043 0.205 1898 Planarity : 0.003 0.039 2114 Dihedral : 9.722 75.474 1862 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.88 % Favored : 94.99 % Rotamer: Outliers : 0.53 % Allowed : 6.74 % Favored : 92.73 % 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: -1.21 (0.21), residues: 1516 helix: 0.55 (0.19), residues: 732 sheet: -2.33 (0.31), residues: 198 loop : -1.95 (0.26), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 532 HIS 0.005 0.001 HIS A 74 PHE 0.015 0.001 PHE B 337 TYR 0.010 0.001 TYR A 317 ARG 0.004 0.000 ARG A 574 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 80 time to evaluate : 1.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 414 MET cc_start: 0.8695 (ttt) cc_final: 0.8452 (tmm) REVERT: A 429 MET cc_start: 0.7431 (mpp) cc_final: 0.7165 (mpp) REVERT: A 714 MET cc_start: 0.7043 (mmt) cc_final: 0.6108 (ttp) REVERT: B 414 MET cc_start: 0.8666 (ttt) cc_final: 0.8437 (tmm) REVERT: B 592 LEU cc_start: 0.8946 (mt) cc_final: 0.8735 (tt) REVERT: B 714 MET cc_start: 0.7216 (mmt) cc_final: 0.6314 (ttp) outliers start: 7 outliers final: 4 residues processed: 87 average time/residue: 0.2163 time to fit residues: 29.5498 Evaluate side-chains 72 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 68 time to evaluate : 1.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 699 ILE Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 699 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 76 optimal weight: 10.0000 chunk 42 optimal weight: 0.0370 chunk 114 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 138 optimal weight: 20.0000 chunk 149 optimal weight: 10.0000 chunk 123 optimal weight: 10.0000 chunk 137 optimal weight: 6.9990 chunk 47 optimal weight: 3.9990 chunk 110 optimal weight: 7.9990 overall best weight: 2.6064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 222 ASN ** B 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 12434 Z= 0.299 Angle : 0.634 9.122 16862 Z= 0.316 Chirality : 0.043 0.221 1898 Planarity : 0.003 0.037 2114 Dihedral : 8.134 64.237 1862 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.07 % Favored : 93.80 % Rotamer: Outliers : 1.29 % Allowed : 7.73 % Favored : 90.98 % 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: -0.63 (0.22), residues: 1516 helix: 1.04 (0.19), residues: 720 sheet: -2.07 (0.34), residues: 170 loop : -1.67 (0.26), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 532 HIS 0.005 0.001 HIS B 74 PHE 0.014 0.002 PHE A 596 TYR 0.010 0.001 TYR A 341 ARG 0.004 0.001 ARG A 351 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 71 time to evaluate : 1.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 414 MET cc_start: 0.8747 (ttt) cc_final: 0.8535 (tmm) REVERT: A 429 MET cc_start: 0.7371 (mpp) cc_final: 0.7111 (mpp) REVERT: A 714 MET cc_start: 0.7138 (mmt) cc_final: 0.6157 (ttp) REVERT: B 657 MET cc_start: 0.9268 (ptm) cc_final: 0.8887 (ppp) REVERT: B 714 MET cc_start: 0.7288 (mmt) cc_final: 0.6355 (ttp) REVERT: B 783 ILE cc_start: 0.8700 (mt) cc_final: 0.8394 (tt) outliers start: 17 outliers final: 11 residues processed: 86 average time/residue: 0.2398 time to fit residues: 31.3098 Evaluate side-chains 78 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 67 time to evaluate : 1.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 TYR Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 699 ILE Chi-restraints excluded: chain A residue 819 VAL Chi-restraints excluded: chain B residue 405 TYR Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 699 ILE Chi-restraints excluded: chain B residue 819 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 136 optimal weight: 8.9990 chunk 103 optimal weight: 2.9990 chunk 71 optimal weight: 9.9990 chunk 15 optimal weight: 3.9990 chunk 65 optimal weight: 20.0000 chunk 92 optimal weight: 2.9990 chunk 138 optimal weight: 8.9990 chunk 146 optimal weight: 8.9990 chunk 72 optimal weight: 9.9990 chunk 131 optimal weight: 8.9990 chunk 39 optimal weight: 4.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.2991 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: