Starting phenix.real_space_refine on Fri Jan 19 20:04:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eor_28465/01_2024/8eor_28465_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eor_28465/01_2024/8eor_28465.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eor_28465/01_2024/8eor_28465.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eor_28465/01_2024/8eor_28465.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eor_28465/01_2024/8eor_28465_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eor_28465/01_2024/8eor_28465_updated.pdb" } resolution = 2.67 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= 0.061 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 8064 2.51 5 N 2064 2.21 5 O 2334 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 12522 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 4129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4129 Classifications: {'peptide': 532} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 36, 'TRANS': 495} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 4129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4129 Classifications: {'peptide': 532} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 36, 'TRANS': 495} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 4129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4129 Classifications: {'peptide': 532} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 36, 'TRANS': 495} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 6 Unusual residues: {'EEE': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 6 Unusual residues: {'EEE': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 6 Unusual residues: {'EEE': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.95, per 1000 atoms: 0.56 Number of scatterers: 12522 At special positions: 0 Unit cell: (135, 128.52, 65.88, 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 2334 8.00 N 2064 7.00 C 8064 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 87 " - pdb=" SG CYS A 116 " distance=2.03 Simple disulfide: pdb=" SG CYS A 274 " - pdb=" SG CYS A 285 " distance=2.03 Simple disulfide: pdb=" SG CYS B 87 " - pdb=" SG CYS B 116 " distance=2.03 Simple disulfide: pdb=" SG CYS B 274 " - pdb=" SG CYS B 285 " distance=2.03 Simple disulfide: pdb=" SG CYS C 87 " - pdb=" SG CYS C 116 " distance=2.03 Simple disulfide: pdb=" SG CYS C 274 " - pdb=" SG CYS C 285 " 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 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " NAG-ASN " NAG E 1 " - " ASN B 79 " Time building additional restraints: 5.20 Conformation dependent library (CDL) restraints added in 2.3 seconds 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2928 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 58 helices and 6 sheets defined 36.3% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.84 Creating SS restraints... Processing helix chain 'A' and resid 61 through 63 No H-bonds generated for 'chain 'A' and resid 61 through 63' Processing helix chain 'A' and resid 91 through 101 Processing helix chain 'A' and resid 149 through 151 No H-bonds generated for 'chain 'A' and resid 149 through 151' Processing helix chain 'A' and resid 155 through 161 Processing helix chain 'A' and resid 173 through 177 Processing helix chain 'A' and resid 189 through 204 Processing helix chain 'A' and resid 222 through 232 Processing helix chain 'A' and resid 262 through 272 Processing helix chain 'A' and resid 279 through 288 Processing helix chain 'A' and resid 291 through 301 Processing helix chain 'A' and resid 332 through 337 Processing helix chain 'A' and resid 358 through 361 No H-bonds generated for 'chain 'A' and resid 358 through 361' Processing helix chain 'A' and resid 368 through 370 No H-bonds generated for 'chain 'A' and resid 368 through 370' Processing helix chain 'A' and resid 375 through 384 Processing helix chain 'A' and resid 393 through 404 Proline residue: A 397 - end of helix Processing helix chain 'A' and resid 410 through 439 removed outlier: 3.635A pdb=" N ASP A 415 " --> pdb=" O VAL A 411 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N VAL A 428 " --> pdb=" O VAL A 424 " (cutoff:3.500A) Proline residue: A 429 - end of helix Processing helix chain 'A' and resid 470 through 475 Processing helix chain 'A' and resid 478 through 481 No H-bonds generated for 'chain 'A' and resid 478 through 481' Processing helix chain 'A' and resid 487 through 506 Processing helix chain 'A' and resid 541 through 551 Processing helix chain 'B' and resid 61 through 63 No H-bonds generated for 'chain 'B' and resid 61 through 63' Processing helix chain 'B' and resid 91 through 101 Processing helix chain 'B' and resid 155 through 161 Processing helix chain 'B' and resid 173 through 177 Processing helix chain 'B' and resid 189 through 208 removed outlier: 5.711A pdb=" N ALA B 206 " --> pdb=" O GLN B 202 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N SER B 207 " --> pdb=" O ASP B 203 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N PHE B 208 " --> pdb=" O ASN B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 232 Processing helix chain 'B' and resid 262 through 272 Processing helix chain 'B' and resid 279 through 287 Processing helix chain 'B' and resid 291 through 301 Processing helix chain 'B' and resid 332 through 337 Processing helix chain 'B' and resid 358 through 361 No H-bonds generated for 'chain 'B' and resid 358 through 361' Processing helix chain 'B' and resid 368 through 370 No H-bonds generated for 'chain 'B' and resid 368 through 370' Processing helix chain 'B' and resid 375 through 386 removed outlier: 3.810A pdb=" N TYR B 386 " --> pdb=" O LEU B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 404 Proline residue: B 397 - end of helix Processing helix chain 'B' and resid 410 through 439 removed outlier: 3.810A pdb=" N ASP B 415 " --> pdb=" O VAL B 411 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N VAL B 428 " --> pdb=" O VAL B 424 " (cutoff:3.500A) Proline residue: B 429 - end of helix Processing helix chain 'B' and resid 470 through 475 Processing helix chain 'B' and resid 478 through 481 No H-bonds generated for 'chain 'B' and resid 478 through 481' Processing helix chain 'B' and resid 487 through 506 Processing helix chain 'B' and resid 541 through 551 Processing helix chain 'C' and resid 61 through 63 No H-bonds generated for 'chain 'C' and resid 61 through 63' Processing helix chain 'C' and resid 91 through 101 Processing helix chain 'C' and resid 155 through 161 Processing helix chain 'C' and resid 173 through 177 Processing helix chain 'C' and resid 189 through 204 Processing helix chain 'C' and resid 222 through 232 Processing helix chain 'C' and resid 262 through 272 Processing helix chain 'C' and resid 279 through 287 Processing helix chain 'C' and resid 291 through 301 Processing helix chain 'C' and resid 332 through 337 Processing helix chain 'C' and resid 358 through 361 No H-bonds generated for 'chain 'C' and resid 358 through 361' Processing helix chain 'C' and resid 368 through 370 No H-bonds generated for 'chain 'C' and resid 368 through 370' Processing helix chain 'C' and resid 375 through 384 Processing helix chain 'C' and resid 393 through 404 Proline residue: C 397 - end of helix Processing helix chain 'C' and resid 410 through 439 removed outlier: 3.637A pdb=" N ASP C 415 " --> pdb=" O VAL C 411 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N VAL C 428 " --> pdb=" O VAL C 424 " (cutoff:3.500A) Proline residue: C 429 - end of helix Processing helix chain 'C' and resid 470 through 475 removed outlier: 3.585A pdb=" N PHE C 473 " --> pdb=" O ASP C 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 481 No H-bonds generated for 'chain 'C' and resid 478 through 481' Processing helix chain 'C' and resid 487 through 506 Processing helix chain 'C' and resid 541 through 551 Processing sheet with id= A, first strand: chain 'A' and resid 25 through 27 Processing sheet with id= B, first strand: chain 'A' and resid 36 through 38 removed outlier: 5.726A pdb=" N LEU A 119 " --> pdb=" O GLY A 52 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU A 220 " --> pdb=" O ILE A 139 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ARG A 242 " --> pdb=" O ILE A 217 " (cutoff:3.500A) removed outlier: 8.745A pdb=" N GLY A 219 " --> pdb=" O ARG A 242 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ILE A 244 " --> pdb=" O GLY A 219 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N SER A 245 " --> pdb=" O PRO A 345 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N MET A 347 " --> pdb=" O SER A 245 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N GLY A 525 " --> pdb=" O MET A 446 " (cutoff:3.500A) removed outlier: 8.644A pdb=" N GLU A 448 " --> pdb=" O GLY A 525 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LEU A 527 " --> pdb=" O GLU A 448 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N GLN A 450 " --> pdb=" O LEU A 527 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ILE A 529 " --> pdb=" O GLN A 450 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 25 through 27 Processing sheet with id= D, first strand: chain 'B' and resid 36 through 38 removed outlier: 5.741A pdb=" N LEU B 119 " --> pdb=" O GLY B 52 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU B 220 " --> pdb=" O ILE B 139 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ARG B 242 " --> pdb=" O ILE B 217 " (cutoff:3.500A) removed outlier: 8.707A pdb=" N GLY B 219 " --> pdb=" O ARG B 242 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ILE B 244 " --> pdb=" O GLY B 219 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N SER B 245 " --> pdb=" O PRO B 345 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N MET B 347 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR B 447 " --> pdb=" O VAL B 348 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N GLY B 525 " --> pdb=" O MET B 446 " (cutoff:3.500A) removed outlier: 8.733A pdb=" N GLU B 448 " --> pdb=" O GLY B 525 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LEU B 527 " --> pdb=" O GLU B 448 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N GLN B 450 " --> pdb=" O LEU B 527 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ILE B 529 " --> pdb=" O GLN B 450 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 25 through 27 Processing sheet with id= F, first strand: chain 'C' and resid 36 through 38 removed outlier: 5.698A pdb=" N LEU C 119 " --> pdb=" O GLY C 52 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU C 220 " --> pdb=" O ILE C 139 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ARG C 242 " --> pdb=" O ILE C 217 " (cutoff:3.500A) removed outlier: 8.702A pdb=" N GLY C 219 " --> pdb=" O ARG C 242 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ILE C 244 " --> pdb=" O GLY C 219 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N SER C 245 " --> pdb=" O PRO C 345 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N MET C 347 " --> pdb=" O SER C 245 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR C 447 " --> pdb=" O VAL C 348 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N GLY C 525 " --> pdb=" O MET C 446 " (cutoff:3.500A) removed outlier: 8.652A pdb=" N GLU C 448 " --> pdb=" O GLY C 525 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LEU C 527 " --> pdb=" O GLU C 448 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N GLN C 450 " --> pdb=" O LEU C 527 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE C 529 " --> pdb=" O GLN C 450 " (cutoff:3.500A) 423 hydrogen bonds defined for protein. 1218 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: 3.59 Time building geometry restraints manager: 5.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2072 1.31 - 1.43: 3303 1.43 - 1.56: 7357 1.56 - 1.68: 0 1.68 - 1.81: 105 Bond restraints: 12837 Sorted by residual: bond pdb=" C TYR B 403 " pdb=" N LEU B 404 " ideal model delta sigma weight residual 1.333 1.418 -0.084 1.49e-02 4.50e+03 3.21e+01 bond pdb=" C TYR A 403 " pdb=" N LEU A 404 " ideal model delta sigma weight residual 1.333 1.403 -0.070 1.49e-02 4.50e+03 2.19e+01 bond pdb=" C ASN C 103 " pdb=" N ARG C 104 " ideal model delta sigma weight residual 1.330 1.267 0.063 1.37e-02 5.33e+03 2.09e+01 bond pdb=" C ASN A 103 " pdb=" N ARG A 104 " ideal model delta sigma weight residual 1.330 1.267 0.062 1.37e-02 5.33e+03 2.06e+01 bond pdb=" C ASN B 103 " pdb=" N ARG B 104 " ideal model delta sigma weight residual 1.330 1.268 0.061 1.37e-02 5.33e+03 2.01e+01 ... (remaining 12832 not shown) Histogram of bond angle deviations from ideal: 100.50 - 107.21: 602 107.21 - 113.93: 7240 113.93 - 120.65: 5151 120.65 - 127.37: 4237 127.37 - 134.08: 203 Bond angle restraints: 17433 Sorted by residual: angle pdb=" O TYR B 403 " pdb=" C TYR B 403 " pdb=" N LEU B 404 " ideal model delta sigma weight residual 122.30 127.53 -5.23 1.35e+00 5.49e-01 1.50e+01 angle pdb=" O TYR A 403 " pdb=" C TYR A 403 " pdb=" N LEU A 404 " ideal model delta sigma weight residual 122.32 126.77 -4.45 1.15e+00 7.56e-01 1.50e+01 angle pdb=" CA TYR B 403 " pdb=" C TYR B 403 " pdb=" N LEU B 404 " ideal model delta sigma weight residual 117.32 112.20 5.12 1.42e+00 4.96e-01 1.30e+01 angle pdb=" CA TYR A 403 " pdb=" C TYR A 403 " pdb=" N LEU A 404 " ideal model delta sigma weight residual 117.07 113.01 4.06 1.21e+00 6.83e-01 1.12e+01 angle pdb=" C2 EEE C 601 " pdb=" C1 EEE C 601 " pdb=" O2 EEE C 601 " ideal model delta sigma weight residual 111.51 119.77 -8.26 3.00e+00 1.11e-01 7.59e+00 ... (remaining 17428 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.65: 7448 21.65 - 43.29: 282 43.29 - 64.94: 40 64.94 - 86.59: 21 86.59 - 108.24: 12 Dihedral angle restraints: 7803 sinusoidal: 3240 harmonic: 4563 Sorted by residual: dihedral pdb=" O4 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C5 BMA D 3 " pdb=" O5 BMA D 3 " ideal model delta sinusoidal sigma weight residual -71.29 -179.53 108.24 1 3.00e+01 1.11e-03 1.40e+01 dihedral pdb=" O4 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C5 BMA F 3 " pdb=" O5 BMA F 3 " ideal model delta sinusoidal sigma weight residual -71.29 -179.03 107.74 1 3.00e+01 1.11e-03 1.39e+01 dihedral pdb=" O4 BMA E 3 " pdb=" C4 BMA E 3 " pdb=" C5 BMA E 3 " pdb=" O5 BMA E 3 " ideal model delta sinusoidal sigma weight residual -71.29 -178.19 106.90 1 3.00e+01 1.11e-03 1.38e+01 ... (remaining 7800 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1655 0.053 - 0.106: 236 0.106 - 0.158: 63 0.158 - 0.211: 0 0.211 - 0.264: 3 Chirality restraints: 1957 Sorted by residual: chirality pdb=" C5 BMA E 3 " pdb=" C4 BMA E 3 " pdb=" C6 BMA E 3 " pdb=" O5 BMA E 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" C5 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C6 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" C5 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C6 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.53 0.26 2.00e-01 2.50e+01 1.68e+00 ... (remaining 1954 not shown) Planarity restraints: 2230 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 404 " 0.010 2.00e-02 2.50e+03 1.90e-02 3.61e+00 pdb=" C LEU B 404 " -0.033 2.00e-02 2.50e+03 pdb=" O LEU B 404 " 0.012 2.00e-02 2.50e+03 pdb=" N GLY B 405 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 423 " -0.008 2.00e-02 2.50e+03 1.70e-02 2.89e+00 pdb=" C ASP A 423 " 0.029 2.00e-02 2.50e+03 pdb=" O ASP A 423 " -0.011 2.00e-02 2.50e+03 pdb=" N VAL A 424 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 423 " 0.008 2.00e-02 2.50e+03 1.69e-02 2.86e+00 pdb=" C ASP B 423 " -0.029 2.00e-02 2.50e+03 pdb=" O ASP B 423 " 0.011 2.00e-02 2.50e+03 pdb=" N VAL B 424 " 0.010 2.00e-02 2.50e+03 ... (remaining 2227 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 3684 2.82 - 3.34: 11559 3.34 - 3.86: 21455 3.86 - 4.38: 26855 4.38 - 4.90: 43501 Nonbonded interactions: 107054 Sorted by model distance: nonbonded pdb=" N GLU A 471 " pdb=" OE1 GLU A 471 " model vdw 2.303 2.520 nonbonded pdb=" OG SER C 247 " pdb=" OE2 GLU C 354 " model vdw 2.310 2.440 nonbonded pdb=" OG SER B 247 " pdb=" OE2 GLU B 354 " model vdw 2.328 2.440 nonbonded pdb=" N GLU C 471 " pdb=" OE1 GLU C 471 " model vdw 2.329 2.520 nonbonded pdb=" O HIS C 140 " pdb=" OH TYR C 170 " model vdw 2.339 2.440 ... (remaining 107049 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' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.180 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: 6.330 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 36.670 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.080 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:12.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 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 : 0.004 0.084 12837 Z= 0.262 Angle : 0.638 8.263 17433 Z= 0.345 Chirality : 0.042 0.264 1957 Planarity : 0.004 0.030 2229 Dihedral : 13.327 108.235 4857 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.45 % Allowed : 4.40 % Favored : 95.15 % 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: 0.50 (0.21), residues: 1590 helix: 1.42 (0.22), residues: 600 sheet: 0.72 (0.36), residues: 201 loop : -0.62 (0.21), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 74 HIS 0.002 0.001 HIS C 140 PHE 0.010 0.001 PHE A 177 TYR 0.010 0.001 TYR C 152 ARG 0.003 0.000 ARG C 242 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 223 time to evaluate : 1.672 Fit side-chains REVERT: A 57 LYS cc_start: 0.8289 (tttt) cc_final: 0.8089 (tttt) REVERT: A 86 MET cc_start: 0.8385 (ptt) cc_final: 0.8076 (ptt) REVERT: A 106 GLU cc_start: 0.7502 (mm-30) cc_final: 0.6771 (pm20) REVERT: A 111 LYS cc_start: 0.7609 (mtmm) cc_final: 0.7194 (mtmp) REVERT: A 132 ARG cc_start: 0.8240 (mmm160) cc_final: 0.8026 (mtt180) REVERT: A 199 ARG cc_start: 0.7445 (mtt-85) cc_final: 0.6721 (mtp180) REVERT: A 267 GLN cc_start: 0.6646 (tp40) cc_final: 0.6147 (mt0) REVERT: A 296 GLU cc_start: 0.7131 (tt0) cc_final: 0.6756 (tp30) REVERT: A 338 GLU cc_start: 0.7273 (mt-10) cc_final: 0.7048 (mt-10) REVERT: A 376 LYS cc_start: 0.7045 (mttp) cc_final: 0.6774 (tppt) REVERT: A 379 MET cc_start: 0.7133 (mtp) cc_final: 0.6739 (mtt) REVERT: A 494 LYS cc_start: 0.7564 (mttt) cc_final: 0.7335 (mtmt) REVERT: B 95 GLN cc_start: 0.7462 (tt0) cc_final: 0.7125 (tt0) REVERT: B 106 GLU cc_start: 0.7377 (mm-30) cc_final: 0.7134 (pm20) REVERT: B 111 LYS cc_start: 0.7766 (mtmm) cc_final: 0.7229 (mtmm) REVERT: B 132 ARG cc_start: 0.8048 (mmm160) cc_final: 0.7797 (mmt180) REVERT: B 199 ARG cc_start: 0.7111 (mtt-85) cc_final: 0.6507 (mtm110) REVERT: B 267 GLN cc_start: 0.6874 (tp40) cc_final: 0.6337 (mt0) REVERT: B 270 ILE cc_start: 0.7477 (mt) cc_final: 0.7194 (mm) REVERT: B 275 LYS cc_start: 0.7239 (mmtp) cc_final: 0.7009 (mtmt) REVERT: B 282 MET cc_start: 0.8066 (mtm) cc_final: 0.7801 (mtm) REVERT: B 296 GLU cc_start: 0.7070 (tt0) cc_final: 0.6580 (tp30) REVERT: B 338 GLU cc_start: 0.7122 (mt-10) cc_final: 0.6919 (mt-10) REVERT: B 364 MET cc_start: 0.7194 (mtm) cc_final: 0.6759 (mtp) REVERT: B 494 LYS cc_start: 0.7388 (mttt) cc_final: 0.7056 (mtmt) REVERT: C 41 GLU cc_start: 0.7676 (tt0) cc_final: 0.7368 (mp0) REVERT: C 106 GLU cc_start: 0.7546 (mm-30) cc_final: 0.6759 (pm20) REVERT: C 111 LYS cc_start: 0.7632 (mtmm) cc_final: 0.7147 (mtmm) REVERT: C 132 ARG cc_start: 0.8196 (mmm160) cc_final: 0.7925 (mmt180) REVERT: C 199 ARG cc_start: 0.7138 (mtt-85) cc_final: 0.6393 (mtm110) REVERT: C 270 ILE cc_start: 0.7653 (mt) cc_final: 0.7373 (mm) REVERT: C 275 LYS cc_start: 0.7446 (mmtp) cc_final: 0.7197 (mtmt) REVERT: C 296 GLU cc_start: 0.6998 (tt0) cc_final: 0.6282 (tp30) REVERT: C 459 MET cc_start: 0.6999 (mmm) cc_final: 0.6665 (mtm) outliers start: 6 outliers final: 5 residues processed: 229 average time/residue: 1.4397 time to fit residues: 354.6966 Evaluate side-chains 165 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 160 time to evaluate : 1.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain B residue 218 PHE Chi-restraints excluded: chain B residue 444 THR Chi-restraints excluded: chain C residue 218 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 134 optimal weight: 6.9990 chunk 120 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 81 optimal weight: 6.9990 chunk 64 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 144 optimal weight: 7.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 GLN A 372 GLN B 169 GLN B 340 ASN C 169 GLN C 372 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.067 12837 Z= 0.529 Angle : 0.752 9.439 17433 Z= 0.376 Chirality : 0.053 0.158 1957 Planarity : 0.006 0.051 2229 Dihedral : 9.864 73.691 1879 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.68 % Allowed : 11.48 % Favored : 85.83 % 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: -0.08 (0.20), residues: 1590 helix: 0.79 (0.22), residues: 603 sheet: 0.58 (0.36), residues: 198 loop : -0.86 (0.20), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP C 74 HIS 0.006 0.002 HIS C 140 PHE 0.019 0.003 PHE A 218 TYR 0.017 0.003 TYR A 152 ARG 0.008 0.001 ARG C 171 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 144 time to evaluate : 1.434 Fit side-chains REVERT: A 86 MET cc_start: 0.8222 (ptt) cc_final: 0.7996 (ptt) REVERT: A 106 GLU cc_start: 0.7421 (mm-30) cc_final: 0.6716 (pm20) REVERT: A 111 LYS cc_start: 0.7696 (mtmm) cc_final: 0.7118 (mtmp) REVERT: A 132 ARG cc_start: 0.8280 (mmm160) cc_final: 0.8000 (mtt180) REVERT: A 199 ARG cc_start: 0.7507 (mtt-85) cc_final: 0.6737 (mtp180) REVERT: A 267 GLN cc_start: 0.6830 (tp40) cc_final: 0.6361 (mt0) REVERT: A 338 GLU cc_start: 0.7376 (mt-10) cc_final: 0.7172 (mt-10) REVERT: A 376 LYS cc_start: 0.7166 (mttp) cc_final: 0.6836 (tppt) REVERT: A 379 MET cc_start: 0.7158 (mtp) cc_final: 0.6780 (mtt) REVERT: A 494 LYS cc_start: 0.7788 (mttt) cc_final: 0.7445 (mtmt) REVERT: B 95 GLN cc_start: 0.7654 (tt0) cc_final: 0.7279 (tt0) REVERT: B 106 GLU cc_start: 0.7341 (mm-30) cc_final: 0.7025 (pm20) REVERT: B 111 LYS cc_start: 0.7824 (mtmm) cc_final: 0.7281 (mtmm) REVERT: B 132 ARG cc_start: 0.8066 (mmm160) cc_final: 0.7740 (mmt180) REVERT: B 199 ARG cc_start: 0.7204 (mtt-85) cc_final: 0.6507 (mtm110) REVERT: B 267 GLN cc_start: 0.6970 (tp40) cc_final: 0.6561 (mt0) REVERT: B 270 ILE cc_start: 0.7610 (mt) cc_final: 0.7257 (mm) REVERT: B 275 LYS cc_start: 0.7449 (mmtp) cc_final: 0.7127 (mtmt) REVERT: B 296 GLU cc_start: 0.7080 (tt0) cc_final: 0.6548 (tp30) REVERT: B 338 GLU cc_start: 0.7370 (mt-10) cc_final: 0.7125 (mt-10) REVERT: B 364 MET cc_start: 0.7340 (mtm) cc_final: 0.6988 (mtp) REVERT: B 487 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.6706 (mm-30) REVERT: B 521 ASN cc_start: 0.7577 (p0) cc_final: 0.7242 (p0) REVERT: C 41 GLU cc_start: 0.7717 (tt0) cc_final: 0.7379 (mp0) REVERT: C 106 GLU cc_start: 0.7618 (mm-30) cc_final: 0.6890 (pm20) REVERT: C 111 LYS cc_start: 0.7829 (mtmm) cc_final: 0.7361 (mtmm) REVERT: C 199 ARG cc_start: 0.7317 (mtt-85) cc_final: 0.6501 (mtm110) REVERT: C 270 ILE cc_start: 0.7745 (mt) cc_final: 0.7457 (mm) REVERT: C 275 LYS cc_start: 0.7732 (mmtp) cc_final: 0.7509 (mtmt) REVERT: C 296 GLU cc_start: 0.7102 (tt0) cc_final: 0.6323 (tp30) REVERT: C 364 MET cc_start: 0.7255 (mtm) cc_final: 0.7046 (mtt) REVERT: C 379 MET cc_start: 0.7232 (mtm) cc_final: 0.6855 (mtt) REVERT: C 483 GLU cc_start: 0.7306 (OUTLIER) cc_final: 0.6871 (pm20) outliers start: 36 outliers final: 24 residues processed: 168 average time/residue: 1.4765 time to fit residues: 266.9448 Evaluate side-chains 160 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 134 time to evaluate : 1.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 459 MET Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 218 PHE Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 380 SER Chi-restraints excluded: chain B residue 444 THR Chi-restraints excluded: chain B residue 457 SER Chi-restraints excluded: chain B residue 487 GLU Chi-restraints excluded: chain C residue 39 SER Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 104 ARG Chi-restraints excluded: chain C residue 218 PHE Chi-restraints excluded: chain C residue 301 MET Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 363 LEU Chi-restraints excluded: chain C residue 444 THR Chi-restraints excluded: chain C residue 483 GLU Chi-restraints excluded: chain C residue 532 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 80 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 120 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 39 optimal weight: 0.2980 chunk 144 optimal weight: 5.9990 chunk 156 optimal weight: 0.6980 chunk 128 optimal weight: 1.9990 chunk 143 optimal weight: 0.7980 chunk 49 optimal weight: 0.5980 chunk 116 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.1361 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: