Starting phenix.real_space_refine on Tue Jan 21 04:59:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iro_35681/01_2025/8iro_35681_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iro_35681/01_2025/8iro_35681.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8iro_35681/01_2025/8iro_35681.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iro_35681/01_2025/8iro_35681.map" model { file = "/net/cci-nas-00/data/ceres_data/8iro_35681/01_2025/8iro_35681_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iro_35681/01_2025/8iro_35681_trim.cif" } resolution = 2.7 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= 0.007 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: 5 Type Number sf(0) Gaussians S 52 5.16 5 C 5300 2.51 5 N 1316 2.21 5 O 1474 1.98 5 H 8208 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 16350 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 8130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 540, 8130 Classifications: {'peptide': 540} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 516} Chain: "A" Number of atoms: 8130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 540, 8130 Classifications: {'peptide': 540} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 516} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'ZEA': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'ZEA': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 8.20, per 1000 atoms: 0.50 Number of scatterers: 16350 At special positions: 0 Unit cell: (94.461, 108.077, 101.269, 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) S 52 16.00 O 1474 8.00 N 1316 7.00 C 5300 6.00 H 8208 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS B 78 " - pdb=" SG CYS B 123 " distance=2.04 Simple disulfide: pdb=" SG CYS B 83 " - pdb=" SG CYS B 111 " distance=2.03 Simple disulfide: pdb=" SG CYS B 87 " - pdb=" SG CYS B 97 " distance=2.03 Simple disulfide: pdb=" SG CYS B 254 " - pdb=" SG CYS B 287 " distance=2.03 Simple disulfide: pdb=" SG CYS A 78 " - pdb=" SG CYS A 123 " distance=2.04 Simple disulfide: pdb=" SG CYS A 83 " - pdb=" SG CYS A 111 " distance=2.03 Simple disulfide: pdb=" SG CYS A 87 " - pdb=" SG CYS A 97 " distance=2.03 Simple disulfide: pdb=" SG CYS A 254 " - pdb=" SG CYS A 287 " distance=2.03 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 BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG C 1 " - " ASN A 270 " " NAG D 1 " - " ASN B 270 " Time building additional restraints: 4.99 Conformation dependent library (CDL) restraints added in 1.8 seconds 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1940 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 8 sheets defined 68.5% alpha, 4.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.23 Creating SS restraints... Processing helix chain 'B' and resid 19 through 30 Processing helix chain 'B' and resid 31 through 37 Processing helix chain 'B' and resid 39 through 43 Processing helix chain 'B' and resid 46 through 61 Processing helix chain 'B' and resid 62 through 74 removed outlier: 4.779A pdb=" N ALA B 68 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER B 74 " --> pdb=" O ILE B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 83 Processing helix chain 'B' and resid 93 through 97 Processing helix chain 'B' and resid 108 through 113 Processing helix chain 'B' and resid 117 through 150 Processing helix chain 'B' and resid 159 through 169 removed outlier: 3.952A pdb=" N ALA B 164 " --> pdb=" O MET B 160 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TYR B 165 " --> pdb=" O GLY B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 201 Processing helix chain 'B' and resid 203 through 209 removed outlier: 3.574A pdb=" N LEU B 207 " --> pdb=" O PHE B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 232 removed outlier: 4.400A pdb=" N SER B 220 " --> pdb=" O ARG B 216 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ALA B 221 " --> pdb=" O ILE B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 257 No H-bonds generated for 'chain 'B' and resid 255 through 257' Processing helix chain 'B' and resid 294 through 313 Processing helix chain 'B' and resid 317 through 331 Processing helix chain 'B' and resid 343 through 355 removed outlier: 3.906A pdb=" N LYS B 355 " --> pdb=" O ASP B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 375 removed outlier: 4.341A pdb=" N ASN B 375 " --> pdb=" O SER B 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 372 through 375' Processing helix chain 'B' and resid 376 through 405 removed outlier: 3.718A pdb=" N TRP B 380 " --> pdb=" O LYS B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 435 Processing helix chain 'B' and resid 444 through 451 removed outlier: 4.049A pdb=" N GLY B 448 " --> pdb=" O GLU B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 470 Processing helix chain 'B' and resid 472 through 477 Processing helix chain 'B' and resid 480 through 496 Proline residue: B 486 - end of helix Processing helix chain 'B' and resid 497 through 502 removed outlier: 3.659A pdb=" N THR B 500 " --> pdb=" O LYS B 497 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 523 Proline residue: B 512 - end of helix removed outlier: 3.771A pdb=" N MET B 520 " --> pdb=" O THR B 516 " (cutoff:3.500A) Proline residue: B 521 - end of helix Processing helix chain 'B' and resid 525 through 541 Processing helix chain 'B' and resid 541 through 554 Processing helix chain 'A' and resid 19 through 30 Processing helix chain 'A' and resid 31 through 37 Processing helix chain 'A' and resid 39 through 43 Processing helix chain 'A' and resid 46 through 61 Processing helix chain 'A' and resid 62 through 74 removed outlier: 4.779A pdb=" N ALA A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER A 74 " --> pdb=" O ILE A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 83 Processing helix chain 'A' and resid 93 through 97 Processing helix chain 'A' and resid 108 through 113 Processing helix chain 'A' and resid 117 through 150 Processing helix chain 'A' and resid 159 through 169 removed outlier: 3.953A pdb=" N ALA A 164 " --> pdb=" O MET A 160 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TYR A 165 " --> pdb=" O GLY A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 201 Processing helix chain 'A' and resid 203 through 209 removed outlier: 3.574A pdb=" N LEU A 207 " --> pdb=" O PHE A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 232 removed outlier: 4.399A pdb=" N SER A 220 " --> pdb=" O ARG A 216 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ALA A 221 " --> pdb=" O ILE A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 257 No H-bonds generated for 'chain 'A' and resid 255 through 257' Processing helix chain 'A' and resid 294 through 313 Processing helix chain 'A' and resid 317 through 331 Processing helix chain 'A' and resid 343 through 355 removed outlier: 3.907A pdb=" N LYS A 355 " --> pdb=" O ASP A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 375 removed outlier: 4.340A pdb=" N ASN A 375 " --> pdb=" O SER A 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 372 through 375' Processing helix chain 'A' and resid 376 through 405 removed outlier: 3.717A pdb=" N TRP A 380 " --> pdb=" O LYS A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 435 Processing helix chain 'A' and resid 444 through 451 removed outlier: 4.049A pdb=" N GLY A 448 " --> pdb=" O GLU A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 470 Processing helix chain 'A' and resid 472 through 477 Processing helix chain 'A' and resid 480 through 496 Proline residue: A 486 - end of helix Processing helix chain 'A' and resid 497 through 502 removed outlier: 3.659A pdb=" N THR A 500 " --> pdb=" O LYS A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 523 Proline residue: A 512 - end of helix removed outlier: 3.770A pdb=" N MET A 520 " --> pdb=" O THR A 516 " (cutoff:3.500A) Proline residue: A 521 - end of helix Processing helix chain 'A' and resid 525 through 541 Processing helix chain 'A' and resid 541 through 554 Processing sheet with id=AA1, first strand: chain 'B' and resid 86 through 87 Processing sheet with id=AA2, first strand: chain 'B' and resid 156 through 158 Processing sheet with id=AA3, first strand: chain 'B' and resid 241 through 242 Processing sheet with id=AA4, first strand: chain 'B' and resid 274 through 275 removed outlier: 3.692A pdb=" N SER B 274 " --> pdb=" O ILE B 266 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N SER B 261 " --> pdb=" O VAL A 265 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N SER A 261 " --> pdb=" O VAL B 265 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N SER A 274 " --> pdb=" O ILE A 266 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 286 through 287 removed outlier: 3.933A pdb=" N SER B 261 " --> pdb=" O VAL A 265 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N SER A 261 " --> pdb=" O VAL B 265 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 86 through 87 Processing sheet with id=AA7, first strand: chain 'A' and resid 156 through 158 Processing sheet with id=AA8, first strand: chain 'A' and resid 241 through 242 512 hydrogen bonds defined for protein. 1452 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: 6.67 Time building geometry restraints manager: 5.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 8204 1.03 - 1.23: 39 1.23 - 1.42: 3387 1.42 - 1.62: 4822 1.62 - 1.82: 84 Bond restraints: 16536 Sorted by residual: bond pdb=" C6 ZEA B 701 " pdb=" N10 ZEA B 701 " ideal model delta sigma weight residual 1.336 1.464 -0.128 2.00e-02 2.50e+03 4.12e+01 bond pdb=" C6 ZEA A 701 " pdb=" N10 ZEA A 701 " ideal model delta sigma weight residual 1.336 1.464 -0.128 2.00e-02 2.50e+03 4.12e+01 bond pdb=" C13 ZEA A 701 " pdb=" C14 ZEA A 701 " ideal model delta sigma weight residual 1.502 1.589 -0.087 2.00e-02 2.50e+03 1.88e+01 bond pdb=" C13 ZEA B 701 " pdb=" C14 ZEA B 701 " ideal model delta sigma weight residual 1.502 1.588 -0.086 2.00e-02 2.50e+03 1.87e+01 bond pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.406 1.465 -0.059 2.00e-02 2.50e+03 8.73e+00 ... (remaining 16531 not shown) Histogram of bond angle deviations from ideal: 0.00 - 8.22: 29910 8.22 - 16.45: 6 16.45 - 24.67: 0 24.67 - 32.90: 0 32.90 - 41.12: 6 Bond angle restraints: 29922 Sorted by residual: angle pdb=" C12 ZEA B 701 " pdb=" C13 ZEA B 701 " pdb=" C15 ZEA B 701 " ideal model delta sigma weight residual 125.58 166.70 -41.12 3.00e+00 1.11e-01 1.88e+02 angle pdb=" C12 ZEA A 701 " pdb=" C13 ZEA A 701 " pdb=" C15 ZEA A 701 " ideal model delta sigma weight residual 125.58 166.66 -41.08 3.00e+00 1.11e-01 1.88e+02 angle pdb=" C12 ZEA A 701 " pdb=" C13 ZEA A 701 " pdb=" C14 ZEA A 701 " ideal model delta sigma weight residual 121.92 87.45 34.47 3.00e+00 1.11e-01 1.32e+02 angle pdb=" C12 ZEA B 701 " pdb=" C13 ZEA B 701 " pdb=" C14 ZEA B 701 " ideal model delta sigma weight residual 121.92 87.48 34.44 3.00e+00 1.11e-01 1.32e+02 angle pdb=" C14 ZEA A 701 " pdb=" C13 ZEA A 701 " pdb=" C15 ZEA A 701 " ideal model delta sigma weight residual 112.50 79.23 33.27 3.00e+00 1.11e-01 1.23e+02 ... (remaining 29917 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.96: 7423 24.96 - 49.93: 328 49.93 - 74.89: 123 74.89 - 99.86: 6 99.86 - 124.82: 2 Dihedral angle restraints: 7882 sinusoidal: 4248 harmonic: 3634 Sorted by residual: dihedral pdb=" CA VAL A 484 " pdb=" C VAL A 484 " pdb=" N GLY A 485 " pdb=" CA GLY A 485 " ideal model delta harmonic sigma weight residual 180.00 141.09 38.91 0 5.00e+00 4.00e-02 6.05e+01 dihedral pdb=" CA VAL B 484 " pdb=" C VAL B 484 " pdb=" N GLY B 485 " pdb=" CA GLY B 485 " ideal model delta harmonic sigma weight residual 180.00 141.10 38.90 0 5.00e+00 4.00e-02 6.05e+01 dihedral pdb=" CA PHE A 332 " pdb=" C PHE A 332 " pdb=" N ARG A 333 " pdb=" CA ARG A 333 " ideal model delta harmonic sigma weight residual 180.00 -154.19 -25.81 0 5.00e+00 4.00e-02 2.66e+01 ... (remaining 7879 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 1303 0.097 - 0.194: 49 0.194 - 0.291: 3 0.291 - 0.388: 0 0.388 - 0.486: 1 Chirality restraints: 1356 Sorted by residual: chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN A 270 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.89 0.49 2.00e-01 2.50e+01 5.89e+00 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN B 270 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CB THR A 250 " pdb=" CA THR A 250 " pdb=" OG1 THR A 250 " pdb=" CG2 THR A 250 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.21 2.00e-01 2.50e+01 1.09e+00 ... (remaining 1353 not shown) Planarity restraints: 2434 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 270 " -0.091 2.00e-02 2.50e+03 6.88e-02 7.09e+01 pdb=" CG ASN A 270 " 0.018 2.00e-02 2.50e+03 pdb=" OD1 ASN A 270 " 0.053 2.00e-02 2.50e+03 pdb=" ND2 ASN A 270 " 0.073 2.00e-02 2.50e+03 pdb="HD21 ASN A 270 " 0.045 2.00e-02 2.50e+03 pdb=" C1 NAG C 1 " -0.098 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 486 " -0.041 5.00e-02 4.00e+02 6.19e-02 6.14e+00 pdb=" N PRO A 487 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO A 487 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 487 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 486 " -0.041 5.00e-02 4.00e+02 6.19e-02 6.14e+00 pdb=" N PRO B 487 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO B 487 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 487 " -0.035 5.00e-02 4.00e+02 ... (remaining 2431 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.13: 440 2.13 - 2.74: 30686 2.74 - 3.36: 50422 3.36 - 3.98: 64783 3.98 - 4.60: 101898 Nonbonded interactions: 248229 Sorted by model distance: nonbonded pdb="HD22 ASN B 67 " pdb=" OG1 THR B 135 " model vdw 1.507 2.450 nonbonded pdb="HD22 ASN A 67 " pdb=" OG1 THR A 135 " model vdw 1.507 2.450 nonbonded pdb="HH22 ARG B 333 " pdb=" OD1 ASP B 347 " model vdw 1.550 2.450 nonbonded pdb="HH22 ARG A 333 " pdb=" OD1 ASP A 347 " model vdw 1.550 2.450 nonbonded pdb=" O PHE B 419 " pdb=" HG SER B 423 " model vdw 1.553 2.450 ... (remaining 248224 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } 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: 0.910 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: 0.290 Extract box with map and model: 0.700 Check model and map are aligned: 0.130 Set scattering table: 0.180 Process input model: 38.910 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.060 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:14.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.128 8328 Z= 0.369 Angle : 1.088 41.124 11334 Z= 0.454 Chirality : 0.045 0.486 1356 Planarity : 0.005 0.062 1400 Dihedral : 13.581 124.823 2938 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 0.75 (0.26), residues: 1076 helix: 1.28 (0.21), residues: 664 sheet: -4.84 (0.53), residues: 20 loop : -0.47 (0.33), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 380 HIS 0.002 0.001 HIS B 350 PHE 0.012 0.002 PHE A 414 TYR 0.013 0.002 TYR B 524 ARG 0.002 0.000 ARG B 333 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 1.269 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 390 ASP cc_start: 0.7851 (m-30) cc_final: 0.7624 (m-30) REVERT: B 440 THR cc_start: 0.8584 (p) cc_final: 0.8325 (t) REVERT: A 390 ASP cc_start: 0.7851 (m-30) cc_final: 0.7631 (m-30) REVERT: A 440 THR cc_start: 0.8581 (p) cc_final: 0.8315 (t) outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 2.1154 time to fit residues: 208.5984 Evaluate side-chains 75 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.6980 chunk 81 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.126767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.104538 restraints weight = 24813.733| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 1.43 r_work: 0.3022 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 2.47 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.0813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8328 Z= 0.203 Angle : 1.004 37.108 11334 Z= 0.409 Chirality : 0.040 0.156 1356 Planarity : 0.005 0.061 1400 Dihedral : 8.513 108.479 1236 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.58 % Allowed : 5.71 % Favored : 93.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 0.87 (0.26), residues: 1076 helix: 1.45 (0.20), residues: 670 sheet: -4.47 (0.64), residues: 20 loop : -0.64 (0.32), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 482 HIS 0.003 0.001 HIS B 360 PHE 0.011 0.001 PHE B 414 TYR 0.009 0.001 TYR B 399 ARG 0.002 0.000 ARG A 36 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 81 time to evaluate : 1.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 390 ASP cc_start: 0.7816 (m-30) cc_final: 0.7589 (m-30) REVERT: B 440 THR cc_start: 0.8642 (p) cc_final: 0.8109 (t) REVERT: B 494 MET cc_start: 0.8202 (OUTLIER) cc_final: 0.7706 (mtp) REVERT: A 390 ASP cc_start: 0.7810 (m-30) cc_final: 0.7595 (m-30) REVERT: A 440 THR cc_start: 0.8659 (p) cc_final: 0.8089 (t) REVERT: A 494 MET cc_start: 0.8207 (OUTLIER) cc_final: 0.7726 (mtp) outliers start: 5 outliers final: 2 residues processed: 82 average time/residue: 2.3503 time to fit residues: 207.6531 Evaluate side-chains 84 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 80 time to evaluate : 1.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 319 MET Chi-restraints excluded: chain B residue 494 MET Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 494 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 70 optimal weight: 3.9990 chunk 88 optimal weight: 0.3980 chunk 98 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 45 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.124701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.102527 restraints weight = 25708.632| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 1.42 r_work: 0.2977 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.1083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8328 Z= 0.173 Angle : 0.983 36.795 11334 Z= 0.390 Chirality : 0.039 0.166 1356 Planarity : 0.004 0.060 1400 Dihedral : 7.602 96.871 1236 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 0.70 % Allowed : 6.53 % Favored : 92.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 1.10 (0.26), residues: 1076 helix: 1.68 (0.20), residues: 670 sheet: -4.48 (0.63), residues: 20 loop : -0.64 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 482 HIS 0.001 0.001 HIS A 378 PHE 0.010 0.001 PHE B 414 TYR 0.008 0.001 TYR B 418 ARG 0.002 0.000 ARG B 450 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 83 time to evaluate : 1.250 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 390 ASP cc_start: 0.7810 (m-30) cc_final: 0.7569 (m-30) REVERT: B 440 THR cc_start: 0.8625 (p) cc_final: 0.8052 (t) REVERT: A 390 ASP cc_start: 0.7808 (m-30) cc_final: 0.7573 (m-30) REVERT: A 440 THR cc_start: 0.8612 (p) cc_final: 0.8042 (t) outliers start: 6 outliers final: 0 residues processed: 87 average time/residue: 2.2154 time to fit residues: 208.3934 Evaluate side-chains 81 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 103 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.124025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.101563 restraints weight = 25445.568| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 1.46 r_work: 0.2994 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.1083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8328 Z= 0.255 Angle : 1.001 37.208 11334 Z= 0.403 Chirality : 0.040 0.163 1356 Planarity : 0.005 0.060 1400 Dihedral : 7.290 86.928 1236 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.53 % Favored : 96.28 % Rotamer: Outliers : 1.17 % Allowed : 7.69 % Favored : 91.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 0.94 (0.26), residues: 1076 helix: 1.56 (0.20), residues: 670 sheet: -4.36 (0.68), residues: 20 loop : -0.74 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 482 HIS 0.002 0.001 HIS B 350 PHE 0.011 0.002 PHE B 414 TYR 0.009 0.001 TYR B 388 ARG 0.002 0.000 ARG A 36 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 80 time to evaluate : 1.276 Fit side-chains revert: symmetry clash REVERT: B 123 CYS cc_start: 0.6782 (OUTLIER) cc_final: 0.6387 (t) REVERT: B 390 ASP cc_start: 0.7813 (m-30) cc_final: 0.7572 (m-30) REVERT: B 440 THR cc_start: 0.8635 (p) cc_final: 0.8032 (t) REVERT: B 494 MET cc_start: 0.8248 (OUTLIER) cc_final: 0.7643 (mtp) REVERT: A 123 CYS cc_start: 0.6753 (OUTLIER) cc_final: 0.6380 (t) REVERT: A 390 ASP cc_start: 0.7798 (m-30) cc_final: 0.7568 (m-30) REVERT: A 440 THR cc_start: 0.8648 (p) cc_final: 0.8042 (t) REVERT: A 494 MET cc_start: 0.8248 (OUTLIER) cc_final: 0.7668 (mtp) outliers start: 10 outliers final: 3 residues processed: 86 average time/residue: 2.2464 time to fit residues: 208.2991 Evaluate side-chains 87 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 80 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 123 CYS Chi-restraints excluded: chain B residue 319 MET Chi-restraints excluded: chain B residue 494 MET Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 123 CYS Chi-restraints excluded: chain A residue 494 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 81 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 7 optimal weight: 7.9990 chunk 16 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.122637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.100185 restraints weight = 26015.321| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 1.40 r_work: 0.2977 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.1148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8328 Z= 0.254 Angle : 1.002 37.272 11334 Z= 0.403 Chirality : 0.040 0.163 1356 Planarity : 0.005 0.060 1400 Dihedral : 6.509 64.534 1236 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.53 % Favored : 96.28 % Rotamer: Outliers : 1.40 % Allowed : 8.62 % Favored : 89.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 0.91 (0.25), residues: 1076 helix: 1.55 (0.20), residues: 670 sheet: -4.47 (0.62), residues: 20 loop : -0.76 (0.30), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 298 HIS 0.002 0.001 HIS B 350 PHE 0.011 0.001 PHE A 414 TYR 0.009 0.001 TYR B 388 ARG 0.001 0.000 ARG B 333 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 1.362 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 123 CYS cc_start: 0.6862 (OUTLIER) cc_final: 0.6455 (t) REVERT: B 390 ASP cc_start: 0.7814 (m-30) cc_final: 0.7587 (m-30) REVERT: B 440 THR cc_start: 0.8690 (p) cc_final: 0.8055 (t) REVERT: B 494 MET cc_start: 0.8310 (OUTLIER) cc_final: 0.7576 (mtp) REVERT: A 123 CYS cc_start: 0.6841 (OUTLIER) cc_final: 0.6442 (t) REVERT: A 390 ASP cc_start: 0.7822 (m-30) cc_final: 0.7590 (m-30) REVERT: A 440 THR cc_start: 0.8656 (p) cc_final: 0.8024 (t) REVERT: A 494 MET cc_start: 0.8326 (OUTLIER) cc_final: 0.7610 (mtp) outliers start: 12 outliers final: 3 residues processed: 88 average time/residue: 2.1791 time to fit residues: 207.2134 Evaluate side-chains 85 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 78 time to evaluate : 1.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 123 CYS Chi-restraints excluded: chain B residue 494 MET Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 123 CYS Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 494 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 0 optimal weight: 6.9990 chunk 103 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 1 optimal weight: 0.9980 chunk 101 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 59 optimal weight: 0.5980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.121001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.098234 restraints weight = 26002.032| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 1.42 r_work: 0.2978 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.1236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8328 Z= 0.231 Angle : 0.993 37.266 11334 Z= 0.397 Chirality : 0.039 0.162 1356 Planarity : 0.005 0.060 1400 Dihedral : 5.653 40.339 1236 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.90 % Favored : 95.91 % Rotamer: Outliers : 1.05 % Allowed : 9.67 % Favored : 89.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 0.96 (0.26), residues: 1076 helix: 1.60 (0.20), residues: 670 sheet: -4.43 (0.65), residues: 20 loop : -0.76 (0.30), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 298 HIS 0.002 0.001 HIS B 350 PHE 0.011 0.001 PHE A 414 TYR 0.009 0.001 TYR B 388 ARG 0.001 0.000 ARG A 36 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 83 time to evaluate : 1.333 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 123 CYS cc_start: 0.6893 (OUTLIER) cc_final: 0.6506 (t) REVERT: B 390 ASP cc_start: 0.7797 (m-30) cc_final: 0.7559 (m-30) REVERT: B 440 THR cc_start: 0.8656 (p) cc_final: 0.8018 (t) REVERT: B 494 MET cc_start: 0.8315 (OUTLIER) cc_final: 0.7514 (mtp) REVERT: A 123 CYS cc_start: 0.6871 (OUTLIER) cc_final: 0.6499 (t) REVERT: A 390 ASP cc_start: 0.7786 (m-30) cc_final: 0.7559 (m-30) REVERT: A 440 THR cc_start: 0.8634 (p) cc_final: 0.7990 (t) REVERT: A 494 MET cc_start: 0.8348 (OUTLIER) cc_final: 0.7571 (mtp) outliers start: 9 outliers final: 0 residues processed: 86 average time/residue: 2.3037 time to fit residues: 214.2556 Evaluate side-chains 84 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 80 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 123 CYS Chi-restraints excluded: chain B residue 494 MET Chi-restraints excluded: chain A residue 123 CYS Chi-restraints excluded: chain A residue 494 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 19 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 80 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.124641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.102095 restraints weight = 25801.900| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 1.44 r_work: 0.2974 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8328 Z= 0.176 Angle : 0.974 37.036 11334 Z= 0.386 Chirality : 0.039 0.177 1356 Planarity : 0.004 0.059 1400 Dihedral : 5.332 39.167 1236 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.72 % Favored : 96.10 % Rotamer: Outliers : 0.70 % Allowed : 10.14 % Favored : 89.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 1.14 (0.26), residues: 1076 helix: 1.75 (0.20), residues: 670 sheet: -4.43 (0.67), residues: 20 loop : -0.70 (0.30), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 482 HIS 0.001 0.001 HIS A 364 PHE 0.010 0.001 PHE A 414 TYR 0.008 0.001 TYR B 418 ARG 0.001 0.000 ARG A 454 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 85 time to evaluate : 1.265 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 123 CYS cc_start: 0.6867 (OUTLIER) cc_final: 0.6496 (t) REVERT: B 390 ASP cc_start: 0.7795 (m-30) cc_final: 0.7560 (m-30) REVERT: B 440 THR cc_start: 0.8629 (p) cc_final: 0.7975 (t) REVERT: B 494 MET cc_start: 0.8209 (OUTLIER) cc_final: 0.7418 (mtp) REVERT: A 123 CYS cc_start: 0.6846 (OUTLIER) cc_final: 0.6474 (t) REVERT: A 390 ASP cc_start: 0.7828 (m-30) cc_final: 0.7600 (m-30) REVERT: A 440 THR cc_start: 0.8612 (p) cc_final: 0.7962 (t) REVERT: A 494 MET cc_start: 0.8228 (OUTLIER) cc_final: 0.7457 (mtp) outliers start: 6 outliers final: 2 residues processed: 89 average time/residue: 2.1576 time to fit residues: 208.2449 Evaluate side-chains 86 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 80 time to evaluate : 1.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 123 CYS Chi-restraints excluded: chain B residue 494 MET Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 123 CYS Chi-restraints excluded: chain A residue 494 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 57.8065 > 50: distance: 39 - 146: 18.839 distance: 41 - 58: 3.916 distance: 58 - 59: 3.263 distance: 59 - 60: 5.826 distance: 59 - 62: 11.823 distance: 59 - 66: 12.437 distance: 60 - 61: 6.927 distance: 60 - 72: 6.853 distance: 62 - 63: 8.530 distance: 62 - 64: 8.734 distance: 62 - 67: 5.619 distance: 63 - 68: 16.232 distance: 64 - 69: 16.267 distance: 64 - 70: 12.752 distance: 64 - 71: 14.213 distance: 72 - 73: 10.624 distance: 72 - 78: 9.381 distance: 73 - 74: 5.904 distance: 73 - 76: 14.306 distance: 73 - 79: 12.987 distance: 74 - 75: 5.719 distance: 74 - 83: 9.004 distance: 76 - 77: 13.054 distance: 76 - 80: 6.128 distance: 76 - 81: 11.977 distance: 77 - 82: 8.890 distance: 83 - 84: 13.109 distance: 83 - 88: 10.081 distance: 84 - 87: 21.671 distance: 84 - 89: 11.731 distance: 85 - 86: 19.082 distance: 85 - 93: 13.222 distance: 87 - 90: 5.671 distance: 87 - 91: 5.587 distance: 87 - 92: 4.514 distance: 93 - 94: 4.439 distance: 93 - 101: 17.958 distance: 94 - 95: 7.198 distance: 94 - 97: 9.122 distance: 94 - 102: 12.579 distance: 95 - 96: 19.994 distance: 95 - 106: 32.123 distance: 97 - 98: 5.442 distance: 97 - 103: 7.500 distance: 97 - 104: 10.792 distance: 98 - 99: 4.798 distance: 100 - 361: 14.728 distance: 106 - 107: 6.965 distance: 106 - 110: 9.586 distance: 107 - 108: 6.915 distance: 107 - 111: 12.775 distance: 107 - 112: 10.365 distance: 108 - 109: 9.036 distance: 108 - 113: 13.366 distance: 113 - 114: 6.970 distance: 113 - 120: 12.875 distance: 114 - 115: 6.251 distance: 114 - 117: 5.438 distance: 114 - 121: 3.828 distance: 115 - 116: 3.660 distance: 115 - 127: 6.041 distance: 117 - 118: 13.966 distance: 117 - 119: 8.132 distance: 117 - 122: 10.871 distance: 118 - 123: 13.563 distance: 119 - 124: 12.803 distance: 119 - 125: 11.238 distance: 119 - 126: 9.479 distance: 127 - 128: 6.321 distance: 127 - 134: 11.204 distance: 128 - 129: 3.488 distance: 128 - 131: 9.697 distance: 128 - 135: 6.972 distance: 129 - 130: 3.105 distance: 129 - 143: 9.407 distance: 131 - 132: 21.020 distance: 131 - 133: 8.582 distance: 131 - 136: 7.408 distance: 132 - 137: 3.398 distance: 132 - 139: 8.053 distance: 133 - 140: 10.915 distance: 133 - 141: 11.756 distance: 133 - 142: 6.334 distance: 143 - 144: 4.220 distance: 143 - 149: 14.759 distance: 144 - 145: 7.451 distance: 144 - 147: 6.949 distance: 144 - 150: 8.935 distance: 145 - 146: 9.625 distance: 145 - 154: 9.651 distance: 147 - 148: 22.211 distance: 147 - 151: 11.858 distance: 147 - 152: 8.912 distance: 148 - 153: 21.302 distance: 154 - 155: 5.183 distance: 154 - 162: 8.828 distance: 155 - 156: 6.359 distance: 155 - 158: 7.865 distance: 155 - 163: 14.032 distance: 156 - 157: 19.572 distance: 156 - 173: 10.463 distance: 158 - 159: 5.812 distance: 158 - 164: 3.702 distance: 158 - 165: 11.868 distance: 159 - 160: 18.221 distance: 159 - 161: 16.514 distance: 159 - 166: 8.229 distance: 160 - 167: 3.043 distance: 160 - 168: 7.284 distance: 160 - 169: 11.031 distance: 161 - 170: 10.577 distance: 161 - 171: 9.140 distance: 161 - 172: 8.037 distance: 173 - 174: 9.882 distance: 173 - 181: 29.454 distance: 174 - 175: 12.918 distance: 174 - 177: 6.935 distance: 174 - 182: 6.186 distance: 175 - 176: 19.164 distance: 175 - 192: 11.184 distance: 177 - 178: 10.255 distance: 177 - 183: 5.417 distance: 177 - 184: 10.523 distance: 178 - 179: 9.877 distance: 178 - 180: 7.658 distance: 178 - 185: 12.532 distance: 179 - 186: 10.496 distance: 179 - 188: 9.109 distance: 180 - 189: 4.524 distance: 180 - 191: 5.983