Starting phenix.real_space_refine on Tue Mar 3 13:07:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7woc_32648/03_2026/7woc_32648.cif Found real_map, /net/cci-nas-00/data/ceres_data/7woc_32648/03_2026/7woc_32648.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7woc_32648/03_2026/7woc_32648.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7woc_32648/03_2026/7woc_32648.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7woc_32648/03_2026/7woc_32648.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7woc_32648/03_2026/7woc_32648.map" } resolution = 3.35 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= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 18 5.16 5 C 3012 2.51 5 N 804 2.21 5 O 912 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4746 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1536 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 11, 'TRANS': 182} Chain: "A" Number of atoms: 1560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1560 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 12, 'TRANS': 191} Chain breaks: 2 Chain: "B" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1636 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 199} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.31, per 1000 atoms: 0.28 Number of scatterers: 4746 At special positions: 0 Unit cell: (91.02, 68.06, 119.72, 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 18 16.00 O 912 8.00 N 804 7.00 C 3012 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS A 147 " - pdb=" SG CYS A 203 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 89 " distance=2.03 Simple disulfide: pdb=" SG CYS B 135 " - pdb=" SG CYS B 195 " 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 NAG-ASN " NAG C 601 " - " ASN C 343 " Time building additional restraints: 0.37 Conformation dependent library (CDL) restraints added in 341.9 milliseconds 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1132 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 14 sheets defined 6.1% alpha, 23.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'C' and resid 365 through 370 removed outlier: 3.904A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 390 removed outlier: 3.612A pdb=" N ASP C 389 " --> pdb=" O LYS C 386 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 386 through 390' Processing helix chain 'C' and resid 405 through 407 No H-bonds generated for 'chain 'C' and resid 405 through 407' Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'A' and resid 87 through 91 removed outlier: 3.836A pdb=" N ASP A 90 " --> pdb=" O LYS A 87 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N THR A 91 " --> pdb=" O SER A 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 87 through 91' Processing helix chain 'B' and resid 122 through 127 removed outlier: 3.749A pdb=" N LYS B 127 " --> pdb=" O ASP B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 190 removed outlier: 3.766A pdb=" N LYS B 189 " --> pdb=" O ALA B 185 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N HIS B 190 " --> pdb=" O ASP B 186 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 185 through 190' Processing sheet with id=AA1, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.543A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYR C 396 " --> pdb=" O SER C 514 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER C 514 " --> pdb=" O TYR C 396 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.663A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.724A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 5 through 6 removed outlier: 3.568A pdb=" N VAL A 20 " --> pdb=" O MET A 81 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 57 through 60 removed outlier: 3.604A pdb=" N ILE A 57 " --> pdb=" O ILE A 52 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N TRP A 47 " --> pdb=" O ARG A 38 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ARG A 38 " --> pdb=" O TRP A 47 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLY A 49 " --> pdb=" O TRP A 36 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA A 92 " --> pdb=" O VAL A 116 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL A 116 " --> pdb=" O ALA A 92 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 127 through 129 removed outlier: 3.835A pdb=" N LEU A 148 " --> pdb=" O PHE A 129 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU A 145 " --> pdb=" O VAL A 189 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU A 185 " --> pdb=" O VAL A 149 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N VAL A 188 " --> pdb=" O HIS A 171 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N HIS A 171 " --> pdb=" O VAL A 188 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 157 through 159 removed outlier: 3.722A pdb=" N LYS A 216 " --> pdb=" O CYS A 203 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 5 through 6 removed outlier: 4.340A pdb=" N THR B 5 " --> pdb=" O ARG B 24 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ARG B 24 " --> pdb=" O THR B 5 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 12 through 13 Processing sheet with id=AB2, first strand: chain 'B' and resid 54 through 55 removed outlier: 6.726A pdb=" N TRP B 36 " --> pdb=" O LEU B 48 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N TYR B 50 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N LEU B 34 " --> pdb=" O TYR B 50 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N THR B 98 " --> pdb=" O GLN B 91 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 86 through 87 Processing sheet with id=AB4, first strand: chain 'B' and resid 117 through 119 removed outlier: 3.742A pdb=" N PHE B 117 " --> pdb=" O LEU B 136 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU B 136 " --> pdb=" O PHE B 117 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL B 134 " --> pdb=" O PHE B 119 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N ASN B 138 " --> pdb=" O LEU B 176 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N LEU B 176 " --> pdb=" O ASN B 138 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 147 through 149 88 hydrogen bonds defined for protein. 228 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: 0.70 Time building geometry restraints manager: 0.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1519 1.34 - 1.46: 1179 1.46 - 1.58: 2147 1.58 - 1.70: 0 1.70 - 1.81: 20 Bond restraints: 4865 Sorted by residual: bond pdb=" C PHE A 153 " pdb=" N PRO A 154 " ideal model delta sigma weight residual 1.331 1.357 -0.026 1.20e-02 6.94e+03 4.78e+00 bond pdb=" C1 NAG C 601 " pdb=" O5 NAG C 601 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.85e+00 bond pdb=" C5 NAG C 601 " pdb=" O5 NAG C 601 " ideal model delta sigma weight residual 1.413 1.435 -0.022 2.00e-02 2.50e+03 1.22e+00 bond pdb=" C GLU A 155 " pdb=" N PRO A 156 " ideal model delta sigma weight residual 1.334 1.358 -0.024 2.34e-02 1.83e+03 1.04e+00 bond pdb=" C3 NAG C 601 " pdb=" O3 NAG C 601 " ideal model delta sigma weight residual 1.403 1.423 -0.020 2.00e-02 2.50e+03 1.02e+00 ... (remaining 4860 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.10: 6425 1.10 - 2.21: 131 2.21 - 3.31: 42 3.31 - 4.42: 10 4.42 - 5.52: 9 Bond angle restraints: 6617 Sorted by residual: angle pdb=" C VAL B 151 " pdb=" N ASP B 152 " pdb=" CA ASP B 152 " ideal model delta sigma weight residual 121.54 126.42 -4.88 1.91e+00 2.74e-01 6.52e+00 angle pdb=" C PRO A 154 " pdb=" N GLU A 155 " pdb=" CA GLU A 155 " ideal model delta sigma weight residual 120.26 123.62 -3.36 1.34e+00 5.57e-01 6.28e+00 angle pdb=" N ASP B 152 " pdb=" CA ASP B 152 " pdb=" C ASP B 152 " ideal model delta sigma weight residual 110.80 115.23 -4.43 2.13e+00 2.20e-01 4.32e+00 angle pdb=" N GLY B 69 " pdb=" CA GLY B 69 " pdb=" C GLY B 69 " ideal model delta sigma weight residual 113.18 117.74 -4.56 2.37e+00 1.78e-01 3.70e+00 angle pdb=" CA LYS A 208 " pdb=" C LYS A 208 " pdb=" N PRO A 209 " ideal model delta sigma weight residual 118.44 121.34 -2.90 1.59e+00 3.96e-01 3.33e+00 ... (remaining 6612 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.48: 2783 17.48 - 34.96: 101 34.96 - 52.44: 15 52.44 - 69.91: 9 69.91 - 87.39: 3 Dihedral angle restraints: 2911 sinusoidal: 1142 harmonic: 1769 Sorted by residual: dihedral pdb=" CA VAL B 151 " pdb=" C VAL B 151 " pdb=" N ASP B 152 " pdb=" CA ASP B 152 " ideal model delta harmonic sigma weight residual 180.00 160.20 19.80 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA CYS C 379 " pdb=" CB CYS C 379 " pdb=" SG CYS C 379 " pdb=" SG CYS C 432 " ideal model delta sinusoidal sigma weight residual 79.00 11.66 67.34 1 2.00e+01 2.50e-03 1.48e+01 dihedral pdb=" SG CYS C 391 " pdb=" CB CYS C 525 " pdb=" SG CYS C 525 " pdb=" CA CYS C 525 " ideal model delta sinusoidal sigma weight residual -73.00 -16.98 -56.02 1 2.00e+01 2.50e-03 1.06e+01 ... (remaining 2908 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 400 0.025 - 0.050: 198 0.050 - 0.076: 58 0.076 - 0.101: 54 0.101 - 0.126: 19 Chirality restraints: 729 Sorted by residual: chirality pdb=" CA ILE B 59 " pdb=" N ILE B 59 " pdb=" C ILE B 59 " pdb=" CB ILE B 59 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.96e-01 chirality pdb=" CA VAL A 157 " pdb=" N VAL A 157 " pdb=" C VAL A 157 " pdb=" CB VAL A 157 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.51e-01 chirality pdb=" CA ILE C 434 " pdb=" N ILE C 434 " pdb=" C ILE C 434 " pdb=" CB ILE C 434 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.36e-01 ... (remaining 726 not shown) Planarity restraints: 856 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA C 520 " 0.031 5.00e-02 4.00e+02 4.73e-02 3.58e+00 pdb=" N PRO C 521 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO C 521 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 521 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 40 " 0.030 5.00e-02 4.00e+02 4.65e-02 3.45e+00 pdb=" N PRO A 41 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 41 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 41 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 14 " 0.019 5.00e-02 4.00e+02 2.94e-02 1.38e+00 pdb=" N PRO B 15 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO B 15 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 15 " 0.016 5.00e-02 4.00e+02 ... (remaining 853 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 1314 2.81 - 3.33: 4052 3.33 - 3.86: 7727 3.86 - 4.38: 8853 4.38 - 4.90: 15570 Nonbonded interactions: 37516 Sorted by model distance: nonbonded pdb=" O GLU B 124 " pdb=" OG SER B 128 " model vdw 2.288 3.040 nonbonded pdb=" OG1 THR A 69 " pdb=" OE1 GLU A 82 " model vdw 2.320 3.040 nonbonded pdb=" OD1 ASN A 206 " pdb=" NZ LYS A 213 " model vdw 2.342 3.120 nonbonded pdb=" OD1 ASN C 448 " pdb=" ND2 ASN C 450 " model vdw 2.348 3.120 nonbonded pdb=" OD2 ASP C 398 " pdb=" OH TYR C 423 " model vdw 2.352 3.040 ... (remaining 37511 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 5.170 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: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.860 Find NCS groups from input model: 0.030 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 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 : 0.002 0.041 4874 Z= 0.101 Angle : 0.478 5.523 6636 Z= 0.256 Chirality : 0.041 0.126 729 Planarity : 0.004 0.047 855 Dihedral : 9.585 87.392 1755 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 4.60 % Allowed : 6.51 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.80 (0.27), residues: 600 helix: -4.88 (0.19), residues: 36 sheet: -2.38 (0.36), residues: 175 loop : -3.63 (0.24), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 50 TYR 0.005 0.001 TYR B 92 PHE 0.005 0.001 PHE B 140 TRP 0.002 0.000 TRP C 353 HIS 0.001 0.000 HIS B 33 Details of bonding type rmsd covalent geometry : bond 0.00204 ( 4865) covalent geometry : angle 0.47711 ( 6617) SS BOND : bond 0.00061 ( 8) SS BOND : angle 0.65785 ( 16) hydrogen bonds : bond 0.31233 ( 88) hydrogen bonds : angle 11.57589 ( 228) link_NAG-ASN : bond 0.00070 ( 1) link_NAG-ASN : angle 0.85623 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 177 time to evaluate : 0.149 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 455 LEU cc_start: 0.7759 (OUTLIER) cc_final: 0.7408 (tt) REVERT: A 122 SER cc_start: 0.8289 (m) cc_final: 0.7910 (p) REVERT: B 119 PHE cc_start: 0.5808 (m-80) cc_final: 0.5006 (m-80) REVERT: B 150 LYS cc_start: 0.5451 (mttp) cc_final: 0.5203 (tptp) REVERT: B 174 TYR cc_start: 0.7070 (m-80) cc_final: 0.6469 (m-80) outliers start: 24 outliers final: 7 residues processed: 189 average time/residue: 0.0985 time to fit residues: 22.2674 Evaluate side-chains 108 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 100 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 166 GLU Chi-restraints excluded: chain B residue 206 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 54 optimal weight: 8.9990 chunk 24 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 439 ASN C 493 GLN A 1 GLN A 178 GLN B 30 ASN B 125 GLN B 148 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.149321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.117973 restraints weight = 7502.192| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 3.02 r_work: 0.3397 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.3812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.121 4874 Z= 0.247 Angle : 0.739 11.745 6636 Z= 0.374 Chirality : 0.049 0.257 729 Planarity : 0.006 0.054 855 Dihedral : 6.589 83.493 696 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.17 % Favored : 89.83 % Rotamer: Outliers : 5.94 % Allowed : 14.37 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.08 (0.30), residues: 600 helix: -4.10 (0.44), residues: 44 sheet: -1.99 (0.35), residues: 203 loop : -3.08 (0.29), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 18 TYR 0.017 0.003 TYR C 421 PHE 0.028 0.003 PHE B 47 TRP 0.009 0.001 TRP C 436 HIS 0.005 0.002 HIS A 171 Details of bonding type rmsd covalent geometry : bond 0.00594 ( 4865) covalent geometry : angle 0.73502 ( 6617) SS BOND : bond 0.00266 ( 8) SS BOND : angle 1.62739 ( 16) hydrogen bonds : bond 0.04007 ( 88) hydrogen bonds : angle 7.55334 ( 228) link_NAG-ASN : bond 0.00433 ( 1) link_NAG-ASN : angle 1.43116 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 93 time to evaluate : 0.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 389 ASP cc_start: 0.7496 (p0) cc_final: 0.7157 (p0) REVERT: C 455 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8102 (tt) REVERT: A 171 HIS cc_start: 0.7630 (m170) cc_final: 0.7021 (m170) REVERT: B 150 LYS cc_start: 0.5946 (mttp) cc_final: 0.5126 (tptp) outliers start: 31 outliers final: 21 residues processed: 118 average time/residue: 0.0895 time to fit residues: 12.7821 Evaluate side-chains 100 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 78 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 166 GLU Chi-restraints excluded: chain B residue 206 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 11 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 3 optimal weight: 0.5980 chunk 29 optimal weight: 0.0270 chunk 33 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 chunk 34 optimal weight: 0.3980 chunk 47 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 354 ASN B 148 GLN B 167 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.151002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.119323 restraints weight = 7507.987| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 3.01 r_work: 0.3397 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.4083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 4874 Z= 0.124 Angle : 0.604 7.747 6636 Z= 0.298 Chirality : 0.044 0.173 729 Planarity : 0.004 0.045 855 Dihedral : 6.323 80.807 696 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 4.60 % Allowed : 16.67 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.67 (0.31), residues: 600 helix: -4.11 (0.65), residues: 32 sheet: -1.69 (0.37), residues: 197 loop : -2.84 (0.29), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 109 TYR 0.011 0.001 TYR A 105 PHE 0.015 0.001 PHE B 47 TRP 0.009 0.001 TRP C 436 HIS 0.003 0.001 HIS A 171 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 4865) covalent geometry : angle 0.60212 ( 6617) SS BOND : bond 0.00415 ( 8) SS BOND : angle 1.10238 ( 16) hydrogen bonds : bond 0.03291 ( 88) hydrogen bonds : angle 6.92955 ( 228) link_NAG-ASN : bond 0.00093 ( 1) link_NAG-ASN : angle 1.07231 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 92 time to evaluate : 0.139 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 389 ASP cc_start: 0.7321 (p0) cc_final: 0.6971 (p0) REVERT: C 455 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.7872 (tt) REVERT: C 456 PHE cc_start: 0.8665 (OUTLIER) cc_final: 0.8047 (p90) REVERT: A 171 HIS cc_start: 0.7590 (m170) cc_final: 0.7071 (m170) REVERT: A 214 VAL cc_start: 0.7704 (OUTLIER) cc_final: 0.7355 (p) REVERT: B 149 TRP cc_start: 0.4600 (m100) cc_final: 0.4043 (m100) REVERT: B 150 LYS cc_start: 0.5699 (mttp) cc_final: 0.5193 (tptp) outliers start: 24 outliers final: 18 residues processed: 109 average time/residue: 0.0898 time to fit residues: 12.0200 Evaluate side-chains 103 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 82 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 166 GLU Chi-restraints excluded: chain B residue 206 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 1 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 3 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 2 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 0 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 36 optimal weight: 6.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 354 ASN B 148 GLN B 167 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.148137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.117306 restraints weight = 7567.575| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 3.12 r_work: 0.3371 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.4523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 4874 Z= 0.148 Angle : 0.601 7.455 6636 Z= 0.300 Chirality : 0.045 0.156 729 Planarity : 0.004 0.041 855 Dihedral : 6.367 79.256 696 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.50 % Favored : 90.50 % Rotamer: Outliers : 6.13 % Allowed : 15.90 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.59 (0.32), residues: 600 helix: -4.09 (0.66), residues: 32 sheet: -1.73 (0.36), residues: 211 loop : -2.72 (0.30), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 457 TYR 0.013 0.002 TYR B 92 PHE 0.017 0.002 PHE B 47 TRP 0.009 0.001 TRP C 436 HIS 0.003 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 4865) covalent geometry : angle 0.59963 ( 6617) SS BOND : bond 0.00458 ( 8) SS BOND : angle 1.03204 ( 16) hydrogen bonds : bond 0.03194 ( 88) hydrogen bonds : angle 6.64518 ( 228) link_NAG-ASN : bond 0.00235 ( 1) link_NAG-ASN : angle 1.15323 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 90 time to evaluate : 0.135 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 389 ASP cc_start: 0.7516 (p0) cc_final: 0.7186 (p0) REVERT: C 455 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.7986 (tt) REVERT: C 456 PHE cc_start: 0.8789 (OUTLIER) cc_final: 0.8080 (p90) REVERT: A 158 THR cc_start: 0.7380 (m) cc_final: 0.6881 (p) REVERT: A 171 HIS cc_start: 0.7739 (m170) cc_final: 0.7206 (m-70) REVERT: B 43 GLN cc_start: 0.8215 (pt0) cc_final: 0.7961 (pt0) REVERT: B 149 TRP cc_start: 0.4825 (m100) cc_final: 0.4322 (m100) REVERT: B 150 LYS cc_start: 0.6033 (mttp) cc_final: 0.5299 (tptp) outliers start: 32 outliers final: 23 residues processed: 113 average time/residue: 0.0864 time to fit residues: 12.1585 Evaluate side-chains 106 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 81 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 484 GLU Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 166 GLU Chi-restraints excluded: chain B residue 206 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 42 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 55 optimal weight: 6.9990 chunk 9 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 chunk 40 optimal weight: 4.9990 chunk 50 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 167 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.143104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.112177 restraints weight = 7634.959| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 3.14 r_work: 0.3306 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.5125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 4874 Z= 0.223 Angle : 0.667 8.704 6636 Z= 0.339 Chirality : 0.048 0.166 729 Planarity : 0.005 0.039 855 Dihedral : 6.717 73.170 695 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.33 % Favored : 87.67 % Rotamer: Outliers : 7.09 % Allowed : 16.28 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.55 (0.32), residues: 600 helix: -3.95 (0.53), residues: 44 sheet: -1.56 (0.38), residues: 197 loop : -2.72 (0.30), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 78 TYR 0.016 0.002 TYR B 92 PHE 0.021 0.002 PHE C 429 TRP 0.011 0.002 TRP C 436 HIS 0.006 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00535 ( 4865) covalent geometry : angle 0.66495 ( 6617) SS BOND : bond 0.00325 ( 8) SS BOND : angle 1.24739 ( 16) hydrogen bonds : bond 0.03425 ( 88) hydrogen bonds : angle 6.68626 ( 228) link_NAG-ASN : bond 0.00402 ( 1) link_NAG-ASN : angle 1.20330 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 79 time to evaluate : 0.116 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 389 ASP cc_start: 0.7663 (p0) cc_final: 0.7315 (p0) REVERT: C 455 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8076 (tt) REVERT: C 456 PHE cc_start: 0.8891 (OUTLIER) cc_final: 0.8267 (p90) REVERT: A 10 GLU cc_start: 0.7215 (mt-10) cc_final: 0.7002 (mt-10) REVERT: B 62 ARG cc_start: 0.7059 (OUTLIER) cc_final: 0.6857 (ptt180) REVERT: B 149 TRP cc_start: 0.4828 (m100) cc_final: 0.4592 (m100) REVERT: B 150 LYS cc_start: 0.6300 (mttp) cc_final: 0.5357 (tptp) outliers start: 37 outliers final: 25 residues processed: 108 average time/residue: 0.0797 time to fit residues: 10.7194 Evaluate side-chains 102 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 74 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 484 GLU Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 62 ARG Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 166 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 53 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 38 optimal weight: 0.0670 chunk 42 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 overall best weight: 0.8920 ------------------------------------------------------------------------------- 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 = 0.3965 r_free = 0.3965 target = 0.144197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.113261 restraints weight = 7809.302| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 3.19 r_work: 0.3316 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.5270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 4874 Z= 0.173 Angle : 0.636 8.133 6636 Z= 0.319 Chirality : 0.046 0.164 729 Planarity : 0.004 0.042 855 Dihedral : 6.520 73.377 694 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.83 % Favored : 89.17 % Rotamer: Outliers : 5.36 % Allowed : 19.73 % Favored : 74.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.52 (0.33), residues: 600 helix: -4.17 (0.52), residues: 38 sheet: -1.69 (0.37), residues: 207 loop : -2.61 (0.31), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 78 TYR 0.014 0.002 TYR A 105 PHE 0.018 0.002 PHE B 47 TRP 0.013 0.001 TRP B 149 HIS 0.006 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00422 ( 4865) covalent geometry : angle 0.63400 ( 6617) SS BOND : bond 0.00403 ( 8) SS BOND : angle 1.14647 ( 16) hydrogen bonds : bond 0.03130 ( 88) hydrogen bonds : angle 6.38552 ( 228) link_NAG-ASN : bond 0.00289 ( 1) link_NAG-ASN : angle 1.19935 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 78 time to evaluate : 0.174 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 389 ASP cc_start: 0.7638 (p0) cc_final: 0.7293 (p0) REVERT: C 455 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8052 (tt) REVERT: C 456 PHE cc_start: 0.8823 (OUTLIER) cc_final: 0.8027 (p90) REVERT: A 10 GLU cc_start: 0.7391 (mt-10) cc_final: 0.7041 (mt-10) REVERT: B 119 PHE cc_start: 0.6460 (m-10) cc_final: 0.6260 (m-80) REVERT: B 149 TRP cc_start: 0.5005 (m100) cc_final: 0.4639 (m100) REVERT: B 150 LYS cc_start: 0.6517 (mttp) cc_final: 0.5632 (tptp) outliers start: 28 outliers final: 24 residues processed: 100 average time/residue: 0.0827 time to fit residues: 10.2264 Evaluate side-chains 99 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 73 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 484 GLU Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 166 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 0.9980 chunk 49 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 chunk 39 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 46 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 23 optimal weight: 0.0670 chunk 42 optimal weight: 0.7980 overall best weight: 0.7520 ------------------------------------------------------------------------------- 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 = 0.3960 r_free = 0.3960 target = 0.143808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.112329 restraints weight = 7710.540| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 2.98 r_work: 0.3331 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.5397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 4874 Z= 0.155 Angle : 0.636 8.414 6636 Z= 0.318 Chirality : 0.046 0.163 729 Planarity : 0.004 0.040 855 Dihedral : 6.366 72.545 694 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.67 % Favored : 89.33 % Rotamer: Outliers : 4.79 % Allowed : 20.50 % Favored : 74.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.43 (0.33), residues: 600 helix: -4.15 (0.52), residues: 38 sheet: -1.64 (0.36), residues: 218 loop : -2.54 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 78 TYR 0.014 0.002 TYR A 105 PHE 0.016 0.002 PHE B 47 TRP 0.010 0.001 TRP C 436 HIS 0.005 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 4865) covalent geometry : angle 0.63428 ( 6617) SS BOND : bond 0.00376 ( 8) SS BOND : angle 1.03806 ( 16) hydrogen bonds : bond 0.03129 ( 88) hydrogen bonds : angle 6.29894 ( 228) link_NAG-ASN : bond 0.00227 ( 1) link_NAG-ASN : angle 1.12516 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 77 time to evaluate : 0.220 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 389 ASP cc_start: 0.7625 (p0) cc_final: 0.7268 (p0) REVERT: C 455 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8023 (tt) REVERT: C 456 PHE cc_start: 0.8781 (OUTLIER) cc_final: 0.8047 (p90) REVERT: A 10 GLU cc_start: 0.7541 (mt-10) cc_final: 0.7190 (mt-10) REVERT: B 62 ARG cc_start: 0.6915 (OUTLIER) cc_final: 0.6635 (mtt180) REVERT: B 149 TRP cc_start: 0.4989 (m100) cc_final: 0.4624 (m100) REVERT: B 150 LYS cc_start: 0.6624 (mttp) cc_final: 0.6005 (tptp) outliers start: 25 outliers final: 22 residues processed: 97 average time/residue: 0.0814 time to fit residues: 9.8908 Evaluate side-chains 98 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 73 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 484 GLU Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 62 ARG Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 166 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 10 optimal weight: 0.7980 chunk 32 optimal weight: 0.3980 chunk 58 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 chunk 26 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 3 optimal weight: 0.4980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.144851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.113261 restraints weight = 7768.737| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 3.24 r_work: 0.3326 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.5466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 4874 Z= 0.146 Angle : 0.620 8.469 6636 Z= 0.311 Chirality : 0.045 0.160 729 Planarity : 0.004 0.044 855 Dihedral : 6.172 71.133 694 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.17 % Favored : 88.83 % Rotamer: Outliers : 5.56 % Allowed : 19.92 % Favored : 74.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -3.34 (0.33), residues: 600 helix: -4.16 (0.51), residues: 38 sheet: -1.59 (0.36), residues: 218 loop : -2.46 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 212 TYR 0.014 0.002 TYR A 105 PHE 0.015 0.001 PHE B 47 TRP 0.010 0.001 TRP C 436 HIS 0.005 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 4865) covalent geometry : angle 0.61837 ( 6617) SS BOND : bond 0.00372 ( 8) SS BOND : angle 0.98859 ( 16) hydrogen bonds : bond 0.03101 ( 88) hydrogen bonds : angle 6.20443 ( 228) link_NAG-ASN : bond 0.00182 ( 1) link_NAG-ASN : angle 1.08954 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 79 time to evaluate : 0.211 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 389 ASP cc_start: 0.7653 (p0) cc_final: 0.7291 (p0) REVERT: C 455 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8024 (tt) REVERT: C 456 PHE cc_start: 0.8749 (OUTLIER) cc_final: 0.8043 (p90) REVERT: A 10 GLU cc_start: 0.7580 (mt-10) cc_final: 0.7284 (mt-10) REVERT: B 62 ARG cc_start: 0.6900 (OUTLIER) cc_final: 0.6688 (mtt180) REVERT: B 149 TRP cc_start: 0.5071 (m100) cc_final: 0.4737 (m100) REVERT: B 150 LYS cc_start: 0.6850 (mttp) cc_final: 0.6066 (tptp) outliers start: 29 outliers final: 24 residues processed: 101 average time/residue: 0.0818 time to fit residues: 10.4339 Evaluate side-chains 106 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 79 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 62 ARG Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 166 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 25 optimal weight: 0.6980 chunk 34 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 498 GLN B 211 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.142711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.111154 restraints weight = 7627.441| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 3.16 r_work: 0.3301 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.5618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 4874 Z= 0.176 Angle : 0.643 8.869 6636 Z= 0.324 Chirality : 0.046 0.158 729 Planarity : 0.004 0.041 855 Dihedral : 6.167 70.077 694 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.50 % Favored : 88.50 % Rotamer: Outliers : 5.75 % Allowed : 19.73 % Favored : 74.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -3.31 (0.33), residues: 600 helix: -4.30 (0.50), residues: 38 sheet: -1.57 (0.36), residues: 218 loop : -2.41 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 212 TYR 0.015 0.002 TYR A 105 PHE 0.017 0.002 PHE B 47 TRP 0.011 0.001 TRP C 436 HIS 0.005 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00429 ( 4865) covalent geometry : angle 0.64114 ( 6617) SS BOND : bond 0.00358 ( 8) SS BOND : angle 1.11201 ( 16) hydrogen bonds : bond 0.03241 ( 88) hydrogen bonds : angle 6.24431 ( 228) link_NAG-ASN : bond 0.00308 ( 1) link_NAG-ASN : angle 1.13433 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 77 time to evaluate : 0.189 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 389 ASP cc_start: 0.7673 (p0) cc_final: 0.7320 (p0) REVERT: C 455 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8062 (tt) REVERT: C 456 PHE cc_start: 0.8824 (OUTLIER) cc_final: 0.8044 (p90) REVERT: A 10 GLU cc_start: 0.7724 (mt-10) cc_final: 0.7434 (mt-10) REVERT: A 204 ASN cc_start: 0.5591 (p0) cc_final: 0.4630 (t0) REVERT: B 62 ARG cc_start: 0.6926 (OUTLIER) cc_final: 0.6724 (mtt180) REVERT: B 149 TRP cc_start: 0.5120 (m100) cc_final: 0.4767 (m100) REVERT: B 150 LYS cc_start: 0.7042 (mttp) cc_final: 0.6318 (tptp) outliers start: 30 outliers final: 25 residues processed: 97 average time/residue: 0.0828 time to fit residues: 10.0707 Evaluate side-chains 101 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 73 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 62 ARG Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 166 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 1 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 14 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 45 optimal weight: 0.3980 chunk 29 optimal weight: 0.7980 chunk 36 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 498 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.143684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.112214 restraints weight = 7792.376| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 3.12 r_work: 0.3312 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.5612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 4874 Z= 0.153 Angle : 0.633 8.871 6636 Z= 0.319 Chirality : 0.046 0.155 729 Planarity : 0.004 0.042 855 Dihedral : 6.063 68.556 693 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.17 % Favored : 88.83 % Rotamer: Outliers : 4.98 % Allowed : 20.50 % Favored : 74.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -3.26 (0.33), residues: 600 helix: -4.28 (0.50), residues: 38 sheet: -1.57 (0.37), residues: 214 loop : -2.35 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 62 TYR 0.015 0.002 TYR A 105 PHE 0.015 0.002 PHE B 47 TRP 0.010 0.001 TRP C 436 HIS 0.005 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 4865) covalent geometry : angle 0.63156 ( 6617) SS BOND : bond 0.00372 ( 8) SS BOND : angle 1.01273 ( 16) hydrogen bonds : bond 0.03248 ( 88) hydrogen bonds : angle 6.14806 ( 228) link_NAG-ASN : bond 0.00230 ( 1) link_NAG-ASN : angle 1.17503 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 78 time to evaluate : 0.180 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 389 ASP cc_start: 0.7611 (p0) cc_final: 0.7239 (p0) REVERT: C 455 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8008 (tt) REVERT: C 456 PHE cc_start: 0.8751 (OUTLIER) cc_final: 0.8010 (p90) REVERT: A 10 GLU cc_start: 0.7723 (mt-10) cc_final: 0.7477 (mt-10) REVERT: A 204 ASN cc_start: 0.5649 (p0) cc_final: 0.4600 (t0) REVERT: B 62 ARG cc_start: 0.6870 (OUTLIER) cc_final: 0.6558 (mtt180) REVERT: B 80 GLU cc_start: 0.7239 (mp0) cc_final: 0.6740 (mp0) REVERT: B 149 TRP cc_start: 0.5118 (m100) cc_final: 0.4771 (m100) REVERT: B 150 LYS cc_start: 0.6967 (mttp) cc_final: 0.6170 (tptp) REVERT: B 157 SER cc_start: 0.7772 (p) cc_final: 0.7419 (t) REVERT: B 212 ARG cc_start: 0.5973 (mmp80) cc_final: 0.5046 (tmm160) outliers start: 26 outliers final: 23 residues processed: 95 average time/residue: 0.0776 time to fit residues: 9.2451 Evaluate side-chains 102 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 76 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 62 ARG Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 166 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 18 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 59 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 47 optimal weight: 0.8980 chunk 9 optimal weight: 0.5980 chunk 50 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 4 optimal weight: 0.0670 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 498 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.144024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.113035 restraints weight = 7784.481| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 3.29 r_work: 0.3315 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.5652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 4874 Z= 0.142 Angle : 0.622 8.741 6636 Z= 0.314 Chirality : 0.046 0.155 729 Planarity : 0.004 0.042 855 Dihedral : 6.002 67.846 693 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.17 % Favored : 89.83 % Rotamer: Outliers : 5.17 % Allowed : 20.50 % Favored : 74.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.20 (0.34), residues: 600 helix: -4.27 (0.50), residues: 38 sheet: -1.57 (0.36), residues: 218 loop : -2.28 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 78 TYR 0.016 0.002 TYR A 105 PHE 0.014 0.001 PHE B 47 TRP 0.010 0.001 TRP C 436 HIS 0.005 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 4865) covalent geometry : angle 0.62041 ( 6617) SS BOND : bond 0.00350 ( 8) SS BOND : angle 0.99391 ( 16) hydrogen bonds : bond 0.03150 ( 88) hydrogen bonds : angle 6.08817 ( 228) link_NAG-ASN : bond 0.00182 ( 1) link_NAG-ASN : angle 1.17713 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1725.68 seconds wall clock time: 30 minutes 10.05 seconds (1810.05 seconds total)