Starting phenix.real_space_refine on Thu Jul 2 02:01:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8gp5_34190/07_2026/8gp5_34190.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gp5_34190/07_2026/8gp5_34190.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gp5_34190/07_2026/8gp5_34190.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gp5_34190/07_2026/8gp5_34190.map" model { file = "/net/cci-nas-00/data/ceres_data/8gp5_34190/07_2026/8gp5_34190.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gp5_34190/07_2026/8gp5_34190.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8gp5_34190/07_2026/8gp5_34190.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8gp5_34190/07_2026/8gp5_34190.cif" } resolution = 4.05 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.019 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 33 5.16 5 C 3437 2.51 5 N 901 2.21 5 O 1099 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5470 Number of models: 1 Model: "" Number of chains: 11 Chain: "E" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 993 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "F" Number of atoms: 866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 866 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 106} Chain: "X" Number of atoms: 3265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 410, 3265 Classifications: {'peptide': 410} Link IDs: {'PTRANS': 19, 'TRANS': 390} Chain breaks: 8 Chain: "N" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "A" 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 chiralities: 2 Chain: "B" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 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 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 chiralities: 2 Chain: "G" 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 chiralities: 2 Chain: "H" 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 chiralities: 2 Chain: "X" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 1.43, per 1000 atoms: 0.26 Number of scatterers: 5470 At special positions: 0 Unit cell: (77.38, 78.44, 120.84, 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 33 16.00 O 1099 8.00 N 901 7.00 C 3437 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.04 Simple disulfide: pdb=" SG CYS X 54 " - pdb=" SG CYS X 74 " distance=2.03 Simple disulfide: pdb=" SG CYS X 218 " - pdb=" SG CYS X 247 " distance=2.04 Simple disulfide: pdb=" SG CYS X 228 " - pdb=" SG CYS X 239 " distance=2.03 Simple disulfide: pdb=" SG CYS X 296 " - pdb=" SG CYS X 331 " distance=2.03 Simple disulfide: pdb=" SG CYS X 378 " - pdb=" SG CYS X 445 " distance=2.03 Simple disulfide: pdb=" SG CYS X 385 " - pdb=" SG CYS X 418 " distance=2.03 Simple disulfide: pdb=" SG CYS X 501 " - pdb=" SG CYS X 605 " distance=2.03 Simple disulfide: pdb=" SG CYS X 598 " - pdb=" SG CYS X 604 " 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 ALPHA1-3 " BMA B 3 " - " MAN B 4 " " BMA N 3 " - " MAN N 4 " ALPHA1-6 " BMA B 3 " - " MAN B 5 " " BMA N 3 " - " MAN N 5 " BETA1-4 " NAG A 1 " - " NAG A 2 " " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " NAG-ASN " NAG A 1 " - " ASN X 234 " " NAG B 1 " - " ASN X 262 " " NAG C 1 " - " ASN X 276 " " NAG D 1 " - " ASN X 334 " " NAG G 1 " - " ASN X 386 " " NAG H 1 " - " ASN X 625 " " NAG N 1 " - " ASN X 88 " " NAG X 701 " - " ASN X 241 " " NAG X 702 " - " ASN X 289 " " NAG X 703 " - " ASN X 448 " " NAG X 704 " - " ASN X 339 " " NAG X 705 " - " ASN X 444 " " NAG X 706 " - " ASN X 611 " Time building additional restraints: 0.47 Conformation dependent library (CDL) restraints added in 185.8 milliseconds 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1198 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 13 sheets defined 16.7% alpha, 28.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'X' and resid 96 through 98 No H-bonds generated for 'chain 'X' and resid 96 through 98' Processing helix chain 'X' and resid 99 through 114 removed outlier: 3.773A pdb=" N GLN X 103 " --> pdb=" O ASN X 99 " (cutoff:3.500A) Processing helix chain 'X' and resid 335 through 351 removed outlier: 4.178A pdb=" N GLU X 351 " --> pdb=" O GLU X 347 " (cutoff:3.500A) Processing helix chain 'X' and resid 475 through 479 Processing helix chain 'X' and resid 529 through 536 Processing helix chain 'X' and resid 572 through 596 Processing helix chain 'X' and resid 618 through 625 removed outlier: 3.868A pdb=" N ASN X 625 " --> pdb=" O GLU X 621 " (cutoff:3.500A) Processing helix chain 'X' and resid 627 through 636 Processing helix chain 'X' and resid 638 through 653 Processing sheet with id=AA1, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.551A pdb=" N LEU E 12 " --> pdb=" O THR E 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'E' and resid 34 through 40 removed outlier: 4.171A pdb=" N GLY E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N SER E 40 " --> pdb=" O LEU E 45 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N LEU E 45 " --> pdb=" O SER E 40 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 95 through 99 removed outlier: 4.798A pdb=" N ARG E 96 " --> pdb=" O HIS E 100F" (cutoff:3.500A) removed outlier: 3.594A pdb=" N HIS E 100F" --> pdb=" O ARG E 96 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 5 through 7 removed outlier: 3.671A pdb=" N ASP F 70 " --> pdb=" O SER F 67 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 10 through 12 removed outlier: 4.031A pdb=" N GLU F 105 " --> pdb=" O LEU F 11 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N LEU F 37 " --> pdb=" O LEU F 46 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N LEU F 46 " --> pdb=" O LEU F 37 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'X' and resid 495 through 499 removed outlier: 5.293A pdb=" N VAL X 608 " --> pdb=" O VAL X 36 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N VAL X 38 " --> pdb=" O THR X 606 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N THR X 606 " --> pdb=" O VAL X 38 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'X' and resid 45 through 47 removed outlier: 3.629A pdb=" N ILE X 225 " --> pdb=" O VAL X 245 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'X' and resid 53 through 55 Processing sheet with id=AB1, first strand: chain 'X' and resid 91 through 94 Processing sheet with id=AB2, first strand: chain 'X' and resid 259 through 261 removed outlier: 6.582A pdb=" N LEU X 260 " --> pdb=" O THR X 450 " (cutoff:3.500A) removed outlier: 10.300A pdb=" N THR X 446 " --> pdb=" O VAL X 292 " (cutoff:3.500A) removed outlier: 11.569A pdb=" N VAL X 292 " --> pdb=" O THR X 446 " (cutoff:3.500A) removed outlier: 10.380A pdb=" N ASN X 448 " --> pdb=" O LYS X 290 " (cutoff:3.500A) removed outlier: 11.150A pdb=" N LYS X 290 " --> pdb=" O ASN X 448 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N THR X 450 " --> pdb=" O LEU X 288 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'X' and resid 284 through 296 current: chain 'X' and resid 359 through 361 Processing sheet with id=AB3, first strand: chain 'X' and resid 271 through 273 removed outlier: 6.664A pdb=" N THR X 450 " --> pdb=" O LEU X 288 " (cutoff:3.500A) removed outlier: 11.150A pdb=" N LYS X 290 " --> pdb=" O ASN X 448 " (cutoff:3.500A) removed outlier: 10.380A pdb=" N ASN X 448 " --> pdb=" O LYS X 290 " (cutoff:3.500A) removed outlier: 11.569A pdb=" N VAL X 292 " --> pdb=" O THR X 446 " (cutoff:3.500A) removed outlier: 10.300A pdb=" N THR X 446 " --> pdb=" O VAL X 292 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'X' and resid 445 through 455 current: chain 'X' and resid 413 through 416 Processing sheet with id=AB4, first strand: chain 'X' and resid 374 through 378 173 hydrogen bonds defined for protein. 459 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: 0.74 Time building geometry restraints manager: 0.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1696 1.34 - 1.46: 1383 1.46 - 1.58: 2451 1.58 - 1.70: 0 1.70 - 1.82: 46 Bond restraints: 5576 Sorted by residual: bond pdb=" C1 NAG N 2 " pdb=" O5 NAG N 2 " ideal model delta sigma weight residual 1.406 1.486 -0.080 2.00e-02 2.50e+03 1.59e+01 bond pdb=" C3 BMA B 3 " pdb=" O3 BMA B 3 " ideal model delta sigma weight residual 1.406 1.458 -0.052 2.00e-02 2.50e+03 6.65e+00 bond pdb=" C1 NAG X 704 " pdb=" O5 NAG X 704 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.02e+00 bond pdb=" C1 MAN B 5 " pdb=" C2 MAN B 5 " ideal model delta sigma weight residual 1.526 1.559 -0.033 2.00e-02 2.50e+03 2.69e+00 bond pdb=" C1 NAG H 2 " pdb=" O5 NAG H 2 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.20e+00 ... (remaining 5571 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.51: 7090 1.51 - 3.03: 388 3.03 - 4.54: 61 4.54 - 6.06: 11 6.06 - 7.57: 9 Bond angle restraints: 7559 Sorted by residual: angle pdb=" N ASP F 60 " pdb=" CA ASP F 60 " pdb=" C ASP F 60 " ideal model delta sigma weight residual 113.72 106.79 6.93 1.52e+00 4.33e-01 2.08e+01 angle pdb=" N ASN X 616 " pdb=" CA ASN X 616 " pdb=" C ASN X 616 " ideal model delta sigma weight residual 112.25 108.07 4.18 1.36e+00 5.41e-01 9.45e+00 angle pdb=" N ASP F 60 " pdb=" CA ASP F 60 " pdb=" CB ASP F 60 " ideal model delta sigma weight residual 113.65 109.62 4.03 1.47e+00 4.63e-01 7.51e+00 angle pdb=" N TRP X 479 " pdb=" CA TRP X 479 " pdb=" CB TRP X 479 " ideal model delta sigma weight residual 110.67 106.87 3.80 1.39e+00 5.18e-01 7.46e+00 angle pdb=" CA CYS X 247 " pdb=" CB CYS X 247 " pdb=" SG CYS X 247 " ideal model delta sigma weight residual 114.40 120.68 -6.28 2.30e+00 1.89e-01 7.45e+00 ... (remaining 7554 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.42: 2768 17.42 - 34.83: 289 34.83 - 52.25: 64 52.25 - 69.66: 9 69.66 - 87.08: 5 Dihedral angle restraints: 3135 sinusoidal: 1279 harmonic: 1856 Sorted by residual: dihedral pdb=" CB CYS X 228 " pdb=" SG CYS X 228 " pdb=" SG CYS X 239 " pdb=" CB CYS X 239 " ideal model delta sinusoidal sigma weight residual 93.00 -179.92 -87.08 1 1.00e+01 1.00e-02 9.11e+01 dihedral pdb=" CB CYS F 23 " pdb=" SG CYS F 23 " pdb=" SG CYS F 88 " pdb=" CB CYS F 88 " ideal model delta sinusoidal sigma weight residual 93.00 174.15 -81.15 1 1.00e+01 1.00e-02 8.12e+01 dihedral pdb=" CA CYS X 247 " pdb=" C CYS X 247 " pdb=" N THR X 248 " pdb=" CA THR X 248 " ideal model delta harmonic sigma weight residual -180.00 -152.31 -27.69 0 5.00e+00 4.00e-02 3.07e+01 ... (remaining 3132 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.108: 873 0.108 - 0.215: 45 0.215 - 0.323: 3 0.323 - 0.431: 1 0.431 - 0.539: 1 Chirality restraints: 923 Sorted by residual: chirality pdb=" C1 NAG X 705 " pdb=" ND2 ASN X 444 " pdb=" C2 NAG X 705 " pdb=" O5 NAG X 705 " both_signs ideal model delta sigma weight residual False -2.40 -1.86 -0.54 2.00e-01 2.50e+01 7.25e+00 chirality pdb=" CG LEU E 80 " pdb=" CB LEU E 80 " pdb=" CD1 LEU E 80 " pdb=" CD2 LEU E 80 " both_signs ideal model delta sigma weight residual False -2.59 -2.21 -0.38 2.00e-01 2.50e+01 3.54e+00 chirality pdb=" C5 BMA N 3 " pdb=" C4 BMA N 3 " pdb=" C6 BMA N 3 " pdb=" O5 BMA N 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.29 2.00e-01 2.50e+01 2.09e+00 ... (remaining 920 not shown) Planarity restraints: 928 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP X 479 " 0.024 2.00e-02 2.50e+03 2.45e-02 1.51e+01 pdb=" CG TRP X 479 " -0.066 2.00e-02 2.50e+03 pdb=" CD1 TRP X 479 " 0.032 2.00e-02 2.50e+03 pdb=" CD2 TRP X 479 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP X 479 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP X 479 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP X 479 " 0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP X 479 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP X 479 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP X 479 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS E 13 " 0.037 5.00e-02 4.00e+02 5.73e-02 5.25e+00 pdb=" N PRO E 14 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO E 14 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO E 14 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP F 60 " 0.011 2.00e-02 2.50e+03 2.18e-02 4.77e+00 pdb=" CG ASP F 60 " -0.038 2.00e-02 2.50e+03 pdb=" OD1 ASP F 60 " 0.014 2.00e-02 2.50e+03 pdb=" OD2 ASP F 60 " 0.013 2.00e-02 2.50e+03 ... (remaining 925 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 480 2.74 - 3.28: 5333 3.28 - 3.82: 8470 3.82 - 4.36: 9345 4.36 - 4.90: 16057 Nonbonded interactions: 39685 Sorted by model distance: nonbonded pdb=" OG1 THR E 35 " pdb=" O GLY E 49 " model vdw 2.199 3.040 nonbonded pdb=" NH2 ARG F 61 " pdb=" O ARG F 77 " model vdw 2.246 3.120 nonbonded pdb=" OG SER F 52 " pdb=" O GLY F 64 " model vdw 2.256 3.040 nonbonded pdb=" OE2 GLU F 53 " pdb=" NH2 ARG X 500 " model vdw 2.260 3.120 nonbonded pdb=" O ALA X 525 " pdb=" OG SER X 528 " model vdw 2.282 3.040 ... (remaining 39680 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'D' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'B' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.910 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: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.190 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 5612 Z= 0.231 Angle : 0.849 17.193 7657 Z= 0.398 Chirality : 0.055 0.539 923 Planarity : 0.005 0.057 915 Dihedral : 14.321 77.084 1907 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 0.18 % Allowed : 0.35 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.33), residues: 624 helix: 2.08 (0.51), residues: 103 sheet: -0.49 (0.36), residues: 190 loop : -1.86 (0.32), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 77 TYR 0.024 0.002 TYR X 217 PHE 0.020 0.002 PHE E 78 TRP 0.066 0.003 TRP X 479 HIS 0.004 0.001 HIS X 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00483 / 0.23 ( 5576) covalent geometry : angle 0.79526 / 0.39 ( 7559) SS BOND : bond 0.00369 / 0.18 ( 10) SS BOND : angle 1.35936 / 0.88 ( 20) hydrogen bonds : bond 0.11152 / 7.51 ( 168) hydrogen bonds : angle 5.77161 / 4.01 ( 459) link_ALPHA1-3 : bond 0.00685 / 0.33 ( 2) link_ALPHA1-3 : angle 2.61020 / 1.52 ( 6) link_ALPHA1-6 : bond 0.00308 / 0.15 ( 2) link_ALPHA1-6 : angle 1.56453 / 1.04 ( 6) link_BETA1-4 : bond 0.00523 / 0.25 ( 9) link_BETA1-4 : angle 1.83066 / 1.24 ( 27) link_NAG-ASN : bond 0.00545 / 0.39 ( 13) link_NAG-ASN : angle 3.75502 / 1.64 ( 39) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 163 time to evaluate : 0.130 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 27 GLN cc_start: 0.8616 (tm-30) cc_final: 0.7898 (tm-30) REVERT: F 83 VAL cc_start: 0.8222 (m) cc_final: 0.8014 (p) REVERT: F 90 GLN cc_start: 0.8582 (tm-30) cc_final: 0.8369 (tm-30) REVERT: F 93 GLN cc_start: 0.8324 (pp30) cc_final: 0.8114 (pp30) REVERT: X 457 ASP cc_start: 0.7372 (t70) cc_final: 0.7139 (t0) outliers start: 1 outliers final: 0 residues processed: 163 average time/residue: 0.0637 time to fit residues: 13.5032 Evaluate side-chains 119 residues out of total 571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 49 optimal weight: 6.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 246 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.140493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.112968 restraints weight = 10364.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.116314 restraints weight = 6037.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.118748 restraints weight = 4365.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.120332 restraints weight = 3487.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.121148 restraints weight = 3012.740| |-----------------------------------------------------------------------------| r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.1235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 5612 Z= 0.221 Angle : 0.738 15.365 7657 Z= 0.356 Chirality : 0.050 0.466 923 Planarity : 0.005 0.049 915 Dihedral : 4.982 27.393 690 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.21 (0.33), residues: 624 helix: 2.07 (0.50), residues: 106 sheet: -0.68 (0.36), residues: 175 loop : -1.88 (0.32), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 96 TYR 0.012 0.002 TYR E 32 PHE 0.016 0.002 PHE E 78 TRP 0.017 0.002 TRP X 479 HIS 0.005 0.002 HIS X 375 Details of bonding type rmsd/Z covalent geometry : bond 0.00512 / 0.22 ( 5576) covalent geometry : angle 0.68356 / 0.34 ( 7559) SS BOND : bond 0.00485 / 0.23 ( 10) SS BOND : angle 1.13759 / 0.70 ( 20) hydrogen bonds : bond 0.04409 / 2.88 ( 168) hydrogen bonds : angle 5.30592 / 3.63 ( 459) link_ALPHA1-3 : bond 0.00635 / 0.30 ( 2) link_ALPHA1-3 : angle 2.15559 / 1.34 ( 6) link_ALPHA1-6 : bond 0.00565 / 0.29 ( 2) link_ALPHA1-6 : angle 1.56236 / 1.05 ( 6) link_BETA1-4 : bond 0.00493 / 0.24 ( 9) link_BETA1-4 : angle 1.64678 / 1.15 ( 27) link_NAG-ASN : bond 0.00599 / 0.42 ( 13) link_NAG-ASN : angle 3.56069 / 1.63 ( 39) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 0.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 9 THR cc_start: 0.7906 (p) cc_final: 0.7669 (p) REVERT: F 27 GLN cc_start: 0.8637 (tm-30) cc_final: 0.7967 (tm-30) REVERT: F 92 ARG cc_start: 0.8864 (tmt-80) cc_final: 0.8562 (tpt90) REVERT: F 93 GLN cc_start: 0.8443 (pp30) cc_final: 0.7722 (pp30) REVERT: X 40 TYR cc_start: 0.8587 (t80) cc_final: 0.8369 (t80) REVERT: X 280 ASN cc_start: 0.8288 (t0) cc_final: 0.7960 (t0) REVERT: X 410 PHE cc_start: 0.7275 (p90) cc_final: 0.6967 (p90) outliers start: 0 outliers final: 0 residues processed: 151 average time/residue: 0.0693 time to fit residues: 13.6844 Evaluate side-chains 124 residues out of total 571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 41 optimal weight: 4.9990 chunk 31 optimal weight: 0.5980 chunk 45 optimal weight: 0.7980 chunk 46 optimal weight: 0.0570 chunk 48 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 chunk 50 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 15 optimal weight: 0.3980 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 GLN ** 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 = 0.3766 r_free = 0.3766 target = 0.144034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.117094 restraints weight = 10230.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.120793 restraints weight = 5989.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.123338 restraints weight = 4220.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.125017 restraints weight = 3341.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.126110 restraints weight = 2858.500| |-----------------------------------------------------------------------------| r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 5612 Z= 0.125 Angle : 0.677 14.768 7657 Z= 0.326 Chirality : 0.047 0.438 923 Planarity : 0.004 0.047 915 Dihedral : 4.766 23.184 690 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.33), residues: 624 helix: 2.13 (0.51), residues: 106 sheet: -0.44 (0.36), residues: 177 loop : -1.87 (0.32), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 66 TYR 0.012 0.001 TYR X 217 PHE 0.017 0.001 PHE E 78 TRP 0.032 0.002 TRP X 479 HIS 0.005 0.001 HIS X 375 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 ( 5576) covalent geometry : angle 0.62360 / 0.31 ( 7559) SS BOND : bond 0.00462 / 0.23 ( 10) SS BOND : angle 1.02463 / 0.64 ( 20) hydrogen bonds : bond 0.03636 / 2.32 ( 168) hydrogen bonds : angle 5.02405 / 3.42 ( 459) link_ALPHA1-3 : bond 0.00929 / 0.44 ( 2) link_ALPHA1-3 : angle 2.19313 / 1.31 ( 6) link_ALPHA1-6 : bond 0.00508 / 0.25 ( 2) link_ALPHA1-6 : angle 1.42118 / 0.93 ( 6) link_BETA1-4 : bond 0.00511 / 0.25 ( 9) link_BETA1-4 : angle 1.47866 / 1.00 ( 27) link_NAG-ASN : bond 0.00633 / 0.46 ( 13) link_NAG-ASN : angle 3.38832 / 1.55 ( 39) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 0.207 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 9 THR cc_start: 0.7589 (p) cc_final: 0.7345 (p) REVERT: E 20 LEU cc_start: 0.8220 (mt) cc_final: 0.7947 (mt) REVERT: E 47 TRP cc_start: 0.8777 (t60) cc_final: 0.7679 (t60) REVERT: F 27 GLN cc_start: 0.8616 (tm-30) cc_final: 0.7920 (tm-30) REVERT: F 92 ARG cc_start: 0.8801 (tmt-80) cc_final: 0.8506 (tpt90) REVERT: F 93 GLN cc_start: 0.8343 (pp30) cc_final: 0.7593 (pp30) REVERT: X 215 ILE cc_start: 0.8577 (tt) cc_final: 0.8265 (pt) REVERT: X 280 ASN cc_start: 0.8165 (t0) cc_final: 0.7888 (t0) REVERT: X 410 PHE cc_start: 0.7254 (p90) cc_final: 0.6956 (p90) REVERT: X 457 ASP cc_start: 0.7625 (t70) cc_final: 0.7407 (t0) outliers start: 0 outliers final: 0 residues processed: 166 average time/residue: 0.0728 time to fit residues: 15.6194 Evaluate side-chains 128 residues out of total 571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 7 optimal weight: 0.0370 chunk 4 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 56 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 36 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 chunk 2 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 375 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.144978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.117539 restraints weight = 10328.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.121093 restraints weight = 6037.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.123591 restraints weight = 4329.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.125238 restraints weight = 3471.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.126363 restraints weight = 2994.101| |-----------------------------------------------------------------------------| r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5612 Z= 0.129 Angle : 0.663 14.378 7657 Z= 0.318 Chirality : 0.047 0.431 923 Planarity : 0.004 0.046 915 Dihedral : 4.758 26.849 690 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 0.18 % Allowed : 2.80 % Favored : 97.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.33), residues: 624 helix: 2.20 (0.51), residues: 106 sheet: -0.51 (0.35), residues: 182 loop : -1.80 (0.32), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 96 TYR 0.014 0.001 TYR X 486 PHE 0.015 0.001 PHE E 78 TRP 0.033 0.002 TRP X 479 HIS 0.005 0.001 HIS X 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 ( 5576) covalent geometry : angle 0.61017 / 0.31 ( 7559) SS BOND : bond 0.00596 / 0.29 ( 10) SS BOND : angle 1.01991 / 0.62 ( 20) hydrogen bonds : bond 0.03434 / 2.22 ( 168) hydrogen bonds : angle 4.89401 / 3.34 ( 459) link_ALPHA1-3 : bond 0.00690 / 0.33 ( 2) link_ALPHA1-3 : angle 2.17815 / 1.27 ( 6) link_ALPHA1-6 : bond 0.00472 / 0.23 ( 2) link_ALPHA1-6 : angle 1.46057 / 0.96 ( 6) link_BETA1-4 : bond 0.00475 / 0.23 ( 9) link_BETA1-4 : angle 1.43047 / 0.98 ( 27) link_NAG-ASN : bond 0.00604 / 0.44 ( 13) link_NAG-ASN : angle 3.31799 / 1.54 ( 39) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 156 time to evaluate : 0.228 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 4 LEU cc_start: 0.8583 (mm) cc_final: 0.8375 (mm) REVERT: E 9 THR cc_start: 0.7562 (p) cc_final: 0.7338 (p) REVERT: E 20 LEU cc_start: 0.8264 (mt) cc_final: 0.7965 (mt) REVERT: E 47 TRP cc_start: 0.8774 (t60) cc_final: 0.7640 (t60) REVERT: E 75 LYS cc_start: 0.8967 (mttm) cc_final: 0.8721 (ttmm) REVERT: F 27 GLN cc_start: 0.8308 (tm-30) cc_final: 0.7540 (tm-30) REVERT: X 40 TYR cc_start: 0.8506 (t80) cc_final: 0.8273 (t80) REVERT: X 102 GLU cc_start: 0.7414 (pp20) cc_final: 0.7175 (pp20) REVERT: X 280 ASN cc_start: 0.8185 (t0) cc_final: 0.7933 (t0) REVERT: X 373 MET cc_start: 0.9026 (mmm) cc_final: 0.8585 (tpt) REVERT: X 410 PHE cc_start: 0.7300 (p90) cc_final: 0.6991 (p90) REVERT: X 457 ASP cc_start: 0.7623 (t70) cc_final: 0.7403 (t0) REVERT: X 479 TRP cc_start: 0.7902 (m-10) cc_final: 0.7551 (m-10) outliers start: 1 outliers final: 1 residues processed: 156 average time/residue: 0.0759 time to fit residues: 15.3814 Evaluate side-chains 133 residues out of total 571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 132 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 46 optimal weight: 0.9990 chunk 26 optimal weight: 0.3980 chunk 10 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 16 optimal weight: 0.1980 chunk 9 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 25 optimal weight: 9.9990 chunk 13 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 chunk 53 optimal weight: 0.5980 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 283 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.145333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.117580 restraints weight = 10450.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.121273 restraints weight = 6126.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.123805 restraints weight = 4367.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.125451 restraints weight = 3483.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.126613 restraints weight = 3003.029| |-----------------------------------------------------------------------------| r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5612 Z= 0.120 Angle : 0.657 14.001 7657 Z= 0.316 Chirality : 0.046 0.421 923 Planarity : 0.004 0.045 915 Dihedral : 4.688 26.439 690 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 0.18 % Allowed : 1.93 % Favored : 97.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.33), residues: 624 helix: 2.20 (0.51), residues: 106 sheet: -0.42 (0.37), residues: 174 loop : -1.81 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 24 TYR 0.014 0.002 TYR X 486 PHE 0.013 0.001 PHE E 78 TRP 0.023 0.001 TRP X 479 HIS 0.004 0.001 HIS X 375 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 ( 5576) covalent geometry : angle 0.60753 / 0.31 ( 7559) SS BOND : bond 0.00421 / 0.21 ( 10) SS BOND : angle 1.00024 / 0.62 ( 20) hydrogen bonds : bond 0.03225 / 2.06 ( 168) hydrogen bonds : angle 4.80298 / 3.26 ( 459) link_ALPHA1-3 : bond 0.00650 / 0.31 ( 2) link_ALPHA1-3 : angle 2.15495 / 1.25 ( 6) link_ALPHA1-6 : bond 0.00463 / 0.23 ( 2) link_ALPHA1-6 : angle 1.44386 / 0.96 ( 6) link_BETA1-4 : bond 0.00475 / 0.23 ( 9) link_BETA1-4 : angle 1.41112 / 0.96 ( 27) link_NAG-ASN : bond 0.00593 / 0.44 ( 13) link_NAG-ASN : angle 3.19192 / 1.48 ( 39) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 155 time to evaluate : 0.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 9 THR cc_start: 0.7464 (p) cc_final: 0.7259 (p) REVERT: E 20 LEU cc_start: 0.8291 (mt) cc_final: 0.7950 (mt) REVERT: E 47 TRP cc_start: 0.8711 (t60) cc_final: 0.7532 (t60) REVERT: F 27 GLN cc_start: 0.8373 (tm-30) cc_final: 0.7754 (tm-30) REVERT: F 92 ARG cc_start: 0.8919 (tmt-80) cc_final: 0.8612 (tpt90) REVERT: F 93 GLN cc_start: 0.8328 (pp30) cc_final: 0.7945 (pp30) REVERT: X 47 ASP cc_start: 0.8823 (p0) cc_final: 0.8598 (p0) REVERT: X 102 GLU cc_start: 0.7262 (pp20) cc_final: 0.7018 (pp20) REVERT: X 280 ASN cc_start: 0.8547 (t0) cc_final: 0.8259 (t0) REVERT: X 410 PHE cc_start: 0.7293 (p90) cc_final: 0.6930 (p90) outliers start: 1 outliers final: 0 residues processed: 155 average time/residue: 0.0652 time to fit residues: 13.4195 Evaluate side-chains 128 residues out of total 571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 34 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 1 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 chunk 40 optimal weight: 6.9990 chunk 2 optimal weight: 0.6980 chunk 3 optimal weight: 0.8980 chunk 55 optimal weight: 0.0970 chunk 49 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 283 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.144829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.117040 restraints weight = 10350.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.120715 restraints weight = 6136.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.123203 restraints weight = 4390.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.124848 restraints weight = 3513.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.125932 restraints weight = 3030.521| |-----------------------------------------------------------------------------| r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5612 Z= 0.130 Angle : 0.660 13.669 7657 Z= 0.317 Chirality : 0.046 0.421 923 Planarity : 0.004 0.043 915 Dihedral : 4.688 26.042 690 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 0.18 % Allowed : 2.45 % Favored : 97.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.33), residues: 624 helix: 2.21 (0.51), residues: 106 sheet: -0.36 (0.38), residues: 174 loop : -1.80 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 77 TYR 0.018 0.002 TYR X 486 PHE 0.012 0.001 PHE E 78 TRP 0.049 0.002 TRP X 479 HIS 0.005 0.001 HIS X 375 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 ( 5576) covalent geometry : angle 0.61122 / 0.31 ( 7559) SS BOND : bond 0.00405 / 0.20 ( 10) SS BOND : angle 1.23596 / 0.78 ( 20) hydrogen bonds : bond 0.03298 / 2.11 ( 168) hydrogen bonds : angle 4.74837 / 3.23 ( 459) link_ALPHA1-3 : bond 0.00564 / 0.27 ( 2) link_ALPHA1-3 : angle 2.16830 / 1.26 ( 6) link_ALPHA1-6 : bond 0.00438 / 0.22 ( 2) link_ALPHA1-6 : angle 1.46223 / 0.97 ( 6) link_BETA1-4 : bond 0.00438 / 0.21 ( 9) link_BETA1-4 : angle 1.41788 / 0.98 ( 27) link_NAG-ASN : bond 0.00602 / 0.44 ( 13) link_NAG-ASN : angle 3.12407 / 1.44 ( 39) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 156 time to evaluate : 0.210 Fit side-chains revert: symmetry clash REVERT: E 20 LEU cc_start: 0.8329 (mt) cc_final: 0.7956 (mt) REVERT: E 87 MET cc_start: 0.7597 (tpp) cc_final: 0.7018 (tpp) REVERT: F 27 GLN cc_start: 0.8471 (tm-30) cc_final: 0.7873 (tm-30) REVERT: F 93 GLN cc_start: 0.8221 (pp30) cc_final: 0.8019 (pp30) REVERT: X 280 ASN cc_start: 0.8510 (t0) cc_final: 0.8195 (t0) REVERT: X 373 MET cc_start: 0.9089 (mmm) cc_final: 0.8619 (tpt) REVERT: X 410 PHE cc_start: 0.7325 (p90) cc_final: 0.7009 (p90) outliers start: 1 outliers final: 0 residues processed: 156 average time/residue: 0.0572 time to fit residues: 12.0898 Evaluate side-chains 125 residues out of total 571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 49 optimal weight: 6.9990 chunk 10 optimal weight: 0.1980 chunk 42 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 47 optimal weight: 7.9990 chunk 51 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 25 optimal weight: 0.2980 chunk 44 optimal weight: 2.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 283 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.144417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.116634 restraints weight = 10429.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.120281 restraints weight = 6095.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.122710 restraints weight = 4334.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.124442 restraints weight = 3469.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.125588 restraints weight = 2976.651| |-----------------------------------------------------------------------------| r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5612 Z= 0.142 Angle : 0.680 13.767 7657 Z= 0.328 Chirality : 0.048 0.432 923 Planarity : 0.004 0.042 915 Dihedral : 4.799 30.688 690 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 0.18 % Allowed : 2.10 % Favored : 97.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.33), residues: 624 helix: 2.11 (0.51), residues: 106 sheet: -0.43 (0.38), residues: 174 loop : -1.83 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 42 TYR 0.016 0.002 TYR X 217 PHE 0.018 0.001 PHE E 78 TRP 0.048 0.002 TRP X 479 HIS 0.004 0.001 HIS X 375 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 ( 5576) covalent geometry : angle 0.63299 / 0.32 ( 7559) SS BOND : bond 0.00516 / 0.25 ( 10) SS BOND : angle 1.27161 / 0.80 ( 20) hydrogen bonds : bond 0.03461 / 2.20 ( 168) hydrogen bonds : angle 4.79243 / 3.27 ( 459) link_ALPHA1-3 : bond 0.00592 / 0.28 ( 2) link_ALPHA1-3 : angle 2.15011 / 1.25 ( 6) link_ALPHA1-6 : bond 0.00421 / 0.21 ( 2) link_ALPHA1-6 : angle 1.47978 / 0.98 ( 6) link_BETA1-4 : bond 0.00492 / 0.24 ( 9) link_BETA1-4 : angle 1.43474 / 0.98 ( 27) link_NAG-ASN : bond 0.00573 / 0.42 ( 13) link_NAG-ASN : angle 3.14751 / 1.45 ( 39) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 153 time to evaluate : 0.179 Fit side-chains revert: symmetry clash REVERT: E 20 LEU cc_start: 0.8517 (mt) cc_final: 0.8190 (mt) REVERT: E 87 MET cc_start: 0.7698 (tpp) cc_final: 0.7034 (tpp) REVERT: F 27 GLN cc_start: 0.8534 (tm-30) cc_final: 0.7880 (tm-30) REVERT: F 93 GLN cc_start: 0.8258 (pp30) cc_final: 0.8053 (pp30) REVERT: X 47 ASP cc_start: 0.8874 (p0) cc_final: 0.8608 (p0) REVERT: X 102 GLU cc_start: 0.7252 (pp20) cc_final: 0.7000 (pp20) REVERT: X 280 ASN cc_start: 0.8487 (t0) cc_final: 0.8120 (t0) REVERT: X 410 PHE cc_start: 0.7336 (p90) cc_final: 0.7028 (p90) REVERT: X 457 ASP cc_start: 0.7349 (t70) cc_final: 0.7142 (t0) outliers start: 1 outliers final: 0 residues processed: 153 average time/residue: 0.0669 time to fit residues: 13.4472 Evaluate side-chains 120 residues out of total 571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 38 optimal weight: 6.9990 chunk 39 optimal weight: 5.9990 chunk 17 optimal weight: 0.0970 chunk 62 optimal weight: 0.5980 chunk 4 optimal weight: 0.5980 chunk 2 optimal weight: 4.9990 chunk 46 optimal weight: 0.0470 chunk 30 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 overall best weight: 0.4076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 246 GLN X 283 ASN X 375 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.147189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.119521 restraints weight = 10378.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.123196 restraints weight = 6062.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.125728 restraints weight = 4320.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.127381 restraints weight = 3447.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.128594 restraints weight = 2964.527| |-----------------------------------------------------------------------------| r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5612 Z= 0.115 Angle : 0.685 13.271 7657 Z= 0.329 Chirality : 0.047 0.416 923 Planarity : 0.004 0.046 915 Dihedral : 4.775 32.513 690 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 0.35 % Allowed : 1.23 % Favored : 98.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.33), residues: 624 helix: 2.45 (0.51), residues: 103 sheet: -0.48 (0.37), residues: 179 loop : -1.79 (0.32), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 42 TYR 0.015 0.002 TYR X 638 PHE 0.019 0.001 PHE E 78 TRP 0.033 0.002 TRP E 36 HIS 0.004 0.001 HIS X 375 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 ( 5576) covalent geometry : angle 0.64140 / 0.32 ( 7559) SS BOND : bond 0.00408 / 0.20 ( 10) SS BOND : angle 1.44095 / 0.94 ( 20) hydrogen bonds : bond 0.03088 / 1.94 ( 168) hydrogen bonds : angle 4.72319 / 3.24 ( 459) link_ALPHA1-3 : bond 0.00685 / 0.33 ( 2) link_ALPHA1-3 : angle 2.12214 / 1.25 ( 6) link_ALPHA1-6 : bond 0.00443 / 0.22 ( 2) link_ALPHA1-6 : angle 1.43045 / 0.96 ( 6) link_BETA1-4 : bond 0.00494 / 0.24 ( 9) link_BETA1-4 : angle 1.36571 / 0.93 ( 27) link_NAG-ASN : bond 0.00587 / 0.43 ( 13) link_NAG-ASN : angle 3.01142 / 1.39 ( 39) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 159 time to evaluate : 0.268 Fit side-chains revert: symmetry clash REVERT: E 9 THR cc_start: 0.7418 (p) cc_final: 0.7202 (p) REVERT: E 20 LEU cc_start: 0.8253 (mt) cc_final: 0.7956 (mt) REVERT: F 27 GLN cc_start: 0.8498 (tm-30) cc_final: 0.7892 (tm-30) REVERT: X 47 ASP cc_start: 0.8878 (p0) cc_final: 0.8657 (p0) REVERT: X 280 ASN cc_start: 0.8450 (t0) cc_final: 0.8187 (t0) REVERT: X 373 MET cc_start: 0.9076 (mmm) cc_final: 0.8568 (tpt) REVERT: X 410 PHE cc_start: 0.7313 (p90) cc_final: 0.7007 (p90) REVERT: X 614 TRP cc_start: 0.8744 (m-10) cc_final: 0.8390 (m-90) outliers start: 2 outliers final: 1 residues processed: 159 average time/residue: 0.0698 time to fit residues: 14.7702 Evaluate side-chains 125 residues out of total 571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 124 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 49 optimal weight: 0.5980 chunk 44 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 9 optimal weight: 0.6980 chunk 5 optimal weight: 0.5980 chunk 45 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 chunk 40 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 99 ASN X 283 ASN X 375 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.145816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.118355 restraints weight = 10271.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.122062 restraints weight = 5949.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.124566 restraints weight = 4189.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.126170 restraints weight = 3327.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.127358 restraints weight = 2863.776| |-----------------------------------------------------------------------------| r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5612 Z= 0.132 Angle : 0.715 13.258 7657 Z= 0.344 Chirality : 0.047 0.418 923 Planarity : 0.004 0.048 915 Dihedral : 4.791 31.359 690 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 0.18 % Allowed : 0.35 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.33), residues: 624 helix: 2.25 (0.51), residues: 103 sheet: -0.38 (0.38), residues: 174 loop : -1.86 (0.32), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 42 TYR 0.016 0.002 TYR E 91 PHE 0.016 0.001 PHE E 78 TRP 0.052 0.002 TRP X 479 HIS 0.011 0.002 HIS X 375 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 ( 5576) covalent geometry : angle 0.67421 / 0.34 ( 7559) SS BOND : bond 0.00396 / 0.19 ( 10) SS BOND : angle 1.38329 / 0.90 ( 20) hydrogen bonds : bond 0.03283 / 2.06 ( 168) hydrogen bonds : angle 4.79587 / 3.29 ( 459) link_ALPHA1-3 : bond 0.00640 / 0.31 ( 2) link_ALPHA1-3 : angle 2.11555 / 1.24 ( 6) link_ALPHA1-6 : bond 0.00414 / 0.20 ( 2) link_ALPHA1-6 : angle 1.46050 / 0.98 ( 6) link_BETA1-4 : bond 0.00463 / 0.23 ( 9) link_BETA1-4 : angle 1.37968 / 0.95 ( 27) link_NAG-ASN : bond 0.00561 / 0.41 ( 13) link_NAG-ASN : angle 2.99975 / 1.37 ( 39) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 152 time to evaluate : 0.190 Fit side-chains REVERT: E 20 LEU cc_start: 0.8301 (mt) cc_final: 0.7994 (mt) REVERT: E 87 MET cc_start: 0.8068 (mmm) cc_final: 0.7654 (mmm) REVERT: F 27 GLN cc_start: 0.8540 (tm-30) cc_final: 0.7917 (tm-30) REVERT: X 47 ASP cc_start: 0.8868 (p0) cc_final: 0.8590 (p0) REVERT: X 102 GLU cc_start: 0.7239 (pp20) cc_final: 0.6962 (pp20) REVERT: X 280 ASN cc_start: 0.8453 (t0) cc_final: 0.8190 (t0) REVERT: X 373 MET cc_start: 0.8989 (mmm) cc_final: 0.8509 (tpt) REVERT: X 410 PHE cc_start: 0.7337 (p90) cc_final: 0.7032 (p90) outliers start: 1 outliers final: 0 residues processed: 152 average time/residue: 0.0647 time to fit residues: 13.1803 Evaluate side-chains 124 residues out of total 571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 5 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 8 optimal weight: 9.9990 chunk 23 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 43 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 20 optimal weight: 7.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 99 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.143719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.115647 restraints weight = 10377.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.119125 restraints weight = 6184.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.121573 restraints weight = 4476.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.123129 restraints weight = 3597.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.124132 restraints weight = 3121.884| |-----------------------------------------------------------------------------| r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5612 Z= 0.182 Angle : 0.762 13.389 7657 Z= 0.367 Chirality : 0.048 0.435 923 Planarity : 0.005 0.053 915 Dihedral : 4.885 31.132 690 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.33), residues: 624 helix: 2.09 (0.51), residues: 106 sheet: -0.49 (0.38), residues: 172 loop : -1.84 (0.32), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 77 TYR 0.018 0.002 TYR X 40 PHE 0.017 0.002 PHE E 78 TRP 0.038 0.002 TRP X 479 HIS 0.003 0.001 HIS X 375 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.18 ( 5576) covalent geometry : angle 0.72042 / 0.36 ( 7559) SS BOND : bond 0.00432 / 0.21 ( 10) SS BOND : angle 1.48627 / 0.98 ( 20) hydrogen bonds : bond 0.03714 / 2.36 ( 168) hydrogen bonds : angle 4.86399 / 3.33 ( 459) link_ALPHA1-3 : bond 0.00610 / 0.29 ( 2) link_ALPHA1-3 : angle 2.12476 / 1.24 ( 6) link_ALPHA1-6 : bond 0.00373 / 0.18 ( 2) link_ALPHA1-6 : angle 1.52914 / 1.02 ( 6) link_BETA1-4 : bond 0.00400 / 0.19 ( 9) link_BETA1-4 : angle 1.45059 / 1.00 ( 27) link_NAG-ASN : bond 0.00547 / 0.40 ( 13) link_NAG-ASN : angle 3.11162 / 1.46 ( 39) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 0.148 Fit side-chains REVERT: E 9 THR cc_start: 0.7721 (p) cc_final: 0.7508 (p) REVERT: E 13 LYS cc_start: 0.9158 (tmmt) cc_final: 0.8727 (tmmt) REVERT: E 16 GLU cc_start: 0.8000 (pm20) cc_final: 0.7050 (pm20) REVERT: E 47 TRP cc_start: 0.8714 (t60) cc_final: 0.7588 (t60) REVERT: E 75 LYS cc_start: 0.9009 (mttm) cc_final: 0.8778 (ttmm) REVERT: E 87 MET cc_start: 0.8047 (mmm) cc_final: 0.7675 (mmm) REVERT: E 98 MET cc_start: 0.7804 (tmm) cc_final: 0.7466 (ptt) REVERT: E 99 MET cc_start: 0.6810 (ttt) cc_final: 0.6501 (ttt) REVERT: F 27 GLN cc_start: 0.8565 (tm-30) cc_final: 0.7929 (tm-30) REVERT: X 47 ASP cc_start: 0.8920 (p0) cc_final: 0.8634 (p0) REVERT: X 102 GLU cc_start: 0.7273 (pp20) cc_final: 0.6994 (pp20) REVERT: X 217 TYR cc_start: 0.7722 (m-80) cc_final: 0.7348 (m-80) REVERT: X 280 ASN cc_start: 0.8324 (t0) cc_final: 0.8064 (t0) REVERT: X 373 MET cc_start: 0.9043 (mmm) cc_final: 0.8529 (tpt) REVERT: X 410 PHE cc_start: 0.7238 (p90) cc_final: 0.6970 (p90) REVERT: X 530 MET cc_start: 0.7261 (tpt) cc_final: 0.6926 (tpt) outliers start: 0 outliers final: 0 residues processed: 150 average time/residue: 0.0723 time to fit residues: 13.9933 Evaluate side-chains 120 residues out of total 571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 58 optimal weight: 0.5980 chunk 55 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 62 optimal weight: 0.6980 chunk 37 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 54 optimal weight: 0.4980 chunk 0 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 99 ASN X 246 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.144898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.117104 restraints weight = 10256.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.120830 restraints weight = 6014.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.123329 restraints weight = 4271.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.125002 restraints weight = 3411.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.126002 restraints weight = 2928.735| |-----------------------------------------------------------------------------| r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5612 Z= 0.134 Angle : 0.725 13.296 7657 Z= 0.354 Chirality : 0.047 0.433 923 Planarity : 0.004 0.045 915 Dihedral : 4.909 29.855 690 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.33), residues: 624 helix: 2.34 (0.51), residues: 103 sheet: -0.42 (0.38), residues: 174 loop : -1.87 (0.32), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG X 379 TYR 0.018 0.002 TYR X 40 PHE 0.016 0.001 PHE E 78 TRP 0.055 0.002 TRP X 479 HIS 0.002 0.001 HIS X 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 ( 5576) covalent geometry : angle 0.68480 / 0.35 ( 7559) SS BOND : bond 0.00355 / 0.17 ( 10) SS BOND : angle 1.31879 / 0.86 ( 20) hydrogen bonds : bond 0.03406 / 2.14 ( 168) hydrogen bonds : angle 4.79339 / 3.28 ( 459) link_ALPHA1-3 : bond 0.00634 / 0.30 ( 2) link_ALPHA1-3 : angle 2.11675 / 1.25 ( 6) link_ALPHA1-6 : bond 0.00419 / 0.20 ( 2) link_ALPHA1-6 : angle 1.46451 / 0.98 ( 6) link_BETA1-4 : bond 0.00458 / 0.22 ( 9) link_BETA1-4 : angle 1.39147 / 0.95 ( 27) link_NAG-ASN : bond 0.00553 / 0.40 ( 13) link_NAG-ASN : angle 3.00516 / 1.38 ( 39) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1034.04 seconds wall clock time: 18 minutes 35.97 seconds (1115.97 seconds total)