Starting phenix.real_space_refine on Thu Jul 2 00:41:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7woc_32648/07_2026/7woc_32648.cif Found real_map, /net/cci-nas-00/data/ceres_data/7woc_32648/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7woc_32648/07_2026/7woc_32648.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7woc_32648/07_2026/7woc_32648.map" model { file = "/net/cci-nas-00/data/ceres_data/7woc_32648/07_2026/7woc_32648.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7woc_32648/07_2026/7woc_32648.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7woc_32648/07_2026/7woc_32648.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7woc_32648/07_2026/7woc_32648.cif" } 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): 0.01s 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: 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 chiralities: 1 Time building chain proxies: 1.32, 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: 0.39 Conformation dependent library (CDL) restraints added in 177.5 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: 0.16 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: 0.72 Time building geometry restraints manager: 0.53 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: 2764 17.48 - 34.96: 101 34.96 - 52.44: 13 52.44 - 69.91: 9 69.91 - 87.39: 3 Dihedral angle restraints: 2890 sinusoidal: 1121 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 2887 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: 4.580 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: 0.020 Process input model: 6.770 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:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 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 : 9.560 87.392 1734 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/Z covalent geometry : bond 0.00204 / 0.10 ( 4865) covalent geometry : angle 0.47711 / 0.26 ( 6617) SS BOND : bond 0.00061 / 0.03 ( 8) SS BOND : angle 0.65785 / 0.50 ( 16) hydrogen bonds : bond 0.31233 / 20.17 ( 88) hydrogen bonds : angle 11.57589 / 7.85 ( 228) link_NAG-ASN : bond 0.00070 / 0.04 ( 1) link_NAG-ASN : angle 0.85623 / 0.55 ( 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 : 0.219 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: 0.0976 time to fit residues: 22.2935 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 : 0.109 ------------------------------------------------------------------------------- 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... 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 = 0.4029 r_free = 0.4029 target = 0.149471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.118162 restraints weight = 7504.243| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 3.02 r_work: 0.3401 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3263 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.3774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.120 4874 Z= 0.245 Angle : 0.736 11.408 6636 Z= 0.371 Chirality : 0.048 0.244 729 Planarity : 0.006 0.054 855 Dihedral : 6.472 83.184 675 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 9.96 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: -4.12 (0.30), residues: 600 helix: -4.11 (0.44), residues: 44 sheet: -2.07 (0.34), residues: 207 loop : -3.07 (0.29), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 18 TYR 0.016 0.003 TYR B 92 PHE 0.027 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/Z covalent geometry : bond 0.00590 / 0.24 ( 4865) covalent geometry : angle 0.73189 / 0.37 ( 6617) SS BOND : bond 0.00274 / 0.14 ( 8) SS BOND : angle 1.62628 / 1.15 ( 16) hydrogen bonds : bond 0.04193 / 2.65 ( 88) hydrogen bonds : angle 7.60691 / 5.04 ( 228) link_NAG-ASN : bond 0.00447 / 0.24 ( 1) link_NAG-ASN : angle 1.45449 / 1.04 ( 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 123 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 92 time to evaluate : 0.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 389 ASP cc_start: 0.7478 (p0) cc_final: 0.7147 (p0) REVERT: C 455 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8084 (tt) REVERT: A 171 HIS cc_start: 0.7601 (m170) cc_final: 0.6991 (m170) REVERT: A 214 VAL cc_start: 0.7801 (OUTLIER) cc_final: 0.7423 (p) REVERT: B 150 LYS cc_start: 0.5895 (mttp) cc_final: 0.5113 (tptp) outliers start: 31 outliers final: 21 residues processed: 117 average time/residue: 0.0901 time to fit residues: 12.8820 Evaluate side-chains 99 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 76 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 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 115 LEU 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: 3.9990 chunk 3 optimal weight: 0.9980 chunk 29 optimal weight: 0.0870 chunk 33 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 39 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 42 optimal weight: 0.8980 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4022 r_free = 0.4022 target = 0.149229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.118298 restraints weight = 7543.556| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 2.96 r_work: 0.3387 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.4268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 4874 Z= 0.152 Angle : 0.622 7.548 6636 Z= 0.310 Chirality : 0.045 0.173 729 Planarity : 0.005 0.043 855 Dihedral : 6.437 79.929 675 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 5.56 % Allowed : 15.71 % 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: -3.71 (0.31), residues: 600 helix: -4.09 (0.66), residues: 32 sheet: -1.80 (0.35), residues: 208 loop : -2.82 (0.29), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 109 TYR 0.013 0.002 TYR B 92 PHE 0.019 0.002 PHE B 47 TRP 0.010 0.001 TRP C 436 HIS 0.003 0.001 HIS A 171 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.15 ( 4865) covalent geometry : angle 0.61986 / 0.31 ( 6617) SS BOND : bond 0.00469 / 0.21 ( 8) SS BOND : angle 1.20032 / 0.91 ( 16) hydrogen bonds : bond 0.03393 / 2.16 ( 88) hydrogen bonds : angle 6.92474 / 4.55 ( 228) link_NAG-ASN : bond 0.00286 / 0.15 ( 1) link_NAG-ASN : angle 1.06571 / 0.72 ( 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 120 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 91 time to evaluate : 0.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 389 ASP cc_start: 0.7508 (p0) cc_final: 0.7175 (p0) REVERT: C 455 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8008 (tt) REVERT: C 456 PHE cc_start: 0.8798 (OUTLIER) cc_final: 0.8113 (p90) REVERT: A 171 HIS cc_start: 0.7672 (m170) cc_final: 0.7229 (m170) REVERT: A 214 VAL cc_start: 0.7844 (OUTLIER) cc_final: 0.7442 (p) REVERT: B 149 TRP cc_start: 0.4735 (m100) cc_final: 0.4212 (m100) REVERT: B 150 LYS cc_start: 0.5856 (mttp) cc_final: 0.5213 (tptp) outliers start: 29 outliers final: 22 residues processed: 111 average time/residue: 0.0810 time to fit residues: 11.3232 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 : 0.179 ------------------------------------------------------------------------------- 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 484 GLU Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 115 LEU 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 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: 0.5980 chunk 17 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 0 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 31 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 = 0.3987 r_free = 0.3987 target = 0.146567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.116329 restraints weight = 7599.913| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 3.16 r_work: 0.3355 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.4640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 4874 Z= 0.163 Angle : 0.609 7.639 6636 Z= 0.304 Chirality : 0.045 0.149 729 Planarity : 0.005 0.039 855 Dihedral : 6.497 78.335 675 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer: Outliers : 5.94 % Allowed : 16.67 % Favored : 77.39 % 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: -3.61 (0.32), residues: 600 helix: -4.07 (0.58), residues: 38 sheet: -1.76 (0.36), residues: 212 loop : -2.69 (0.31), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 457 TYR 0.017 0.002 TYR A 32 PHE 0.018 0.002 PHE B 47 TRP 0.010 0.001 TRP C 436 HIS 0.004 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.16 ( 4865) covalent geometry : angle 0.60711 / 0.30 ( 6617) SS BOND : bond 0.00491 / 0.21 ( 8) SS BOND : angle 1.08515 / 0.87 ( 16) hydrogen bonds : bond 0.03230 / 2.04 ( 88) hydrogen bonds : angle 6.66133 / 4.40 ( 228) link_NAG-ASN : bond 0.00342 / 0.18 ( 1) link_NAG-ASN : angle 1.02916 / 0.68 ( 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 115 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 84 time to evaluate : 0.203 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 389 ASP cc_start: 0.7532 (p0) cc_final: 0.7200 (p0) REVERT: C 455 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8037 (tt) REVERT: C 456 PHE cc_start: 0.8817 (OUTLIER) cc_final: 0.8085 (p90) REVERT: A 158 THR cc_start: 0.7397 (m) cc_final: 0.6866 (p) REVERT: A 171 HIS cc_start: 0.7783 (m170) cc_final: 0.7247 (m-70) REVERT: B 149 TRP cc_start: 0.4851 (m100) cc_final: 0.4355 (m100) REVERT: B 150 LYS cc_start: 0.6086 (mttp) cc_final: 0.5364 (tptp) outliers start: 31 outliers final: 25 residues processed: 107 average time/residue: 0.0844 time to fit residues: 11.2324 Evaluate side-chains 107 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 80 time to evaluate : 0.189 ------------------------------------------------------------------------------- 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 484 GLU Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 128 VAL 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 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: 1.9990 chunk 52 optimal weight: 0.9990 chunk 54 optimal weight: 5.9990 chunk 55 optimal weight: 0.9990 chunk 9 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 chunk 40 optimal weight: 0.1980 chunk 50 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 167 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.146069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.115073 restraints weight = 7645.815| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 3.14 r_work: 0.3363 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.4872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 4874 Z= 0.142 Angle : 0.594 7.508 6636 Z= 0.298 Chirality : 0.045 0.154 729 Planarity : 0.004 0.039 855 Dihedral : 6.343 73.585 674 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.17 % Favored : 90.83 % Rotamer: Outliers : 6.32 % Allowed : 17.24 % Favored : 76.44 % 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: -3.48 (0.33), residues: 600 helix: -4.08 (0.56), residues: 38 sheet: -1.73 (0.37), residues: 211 loop : -2.54 (0.31), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 457 TYR 0.013 0.002 TYR A 105 PHE 0.016 0.002 PHE B 47 TRP 0.010 0.001 TRP C 436 HIS 0.004 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.14 ( 4865) covalent geometry : angle 0.59246 / 0.30 ( 6617) SS BOND : bond 0.00432 / 0.18 ( 8) SS BOND : angle 0.96827 / 0.80 ( 16) hydrogen bonds : bond 0.03053 / 1.95 ( 88) hydrogen bonds : angle 6.37522 / 4.24 ( 228) link_NAG-ASN : bond 0.00242 / 0.13 ( 1) link_NAG-ASN : angle 0.82219 / 0.56 ( 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 117 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 84 time to evaluate : 0.175 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 389 ASP cc_start: 0.7604 (p0) cc_final: 0.7260 (p0) REVERT: C 455 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8006 (tt) REVERT: C 456 PHE cc_start: 0.8755 (OUTLIER) cc_final: 0.8045 (p90) REVERT: A 158 THR cc_start: 0.7424 (m) cc_final: 0.6924 (p) REVERT: A 171 HIS cc_start: 0.7763 (m170) cc_final: 0.7318 (m-70) REVERT: B 43 GLN cc_start: 0.8258 (pt0) cc_final: 0.8044 (pt0) REVERT: B 83 ASP cc_start: 0.8464 (m-30) cc_final: 0.8261 (m-30) REVERT: B 109 ARG cc_start: 0.7240 (ttp80) cc_final: 0.6974 (ttp80) REVERT: B 149 TRP cc_start: 0.4814 (m100) cc_final: 0.4571 (m100) REVERT: B 150 LYS cc_start: 0.6012 (mttp) cc_final: 0.5320 (tptp) outliers start: 33 outliers final: 21 residues processed: 108 average time/residue: 0.0753 time to fit residues: 10.3838 Evaluate side-chains 104 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 81 time to evaluate : 0.163 ------------------------------------------------------------------------------- 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 469 SER Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain A residue 115 LEU 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 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: 0.4980 chunk 22 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 38 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 167 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 = 0.3980 r_free = 0.3980 target = 0.145398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.114598 restraints weight = 7768.520| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 3.18 r_work: 0.3338 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.5094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 4874 Z= 0.159 Angle : 0.610 7.826 6636 Z= 0.305 Chirality : 0.046 0.159 729 Planarity : 0.004 0.040 855 Dihedral : 6.395 74.225 673 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.33 % Favored : 88.67 % Rotamer: Outliers : 5.36 % Allowed : 19.16 % Favored : 75.48 % 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: -3.46 (0.33), residues: 600 helix: -4.11 (0.54), residues: 38 sheet: -1.65 (0.36), residues: 221 loop : -2.58 (0.32), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 457 TYR 0.013 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/Z covalent geometry : bond 0.00387 / 0.16 ( 4865) covalent geometry : angle 0.60820 / 0.30 ( 6617) SS BOND : bond 0.00406 / 0.17 ( 8) SS BOND : angle 1.02669 / 0.86 ( 16) hydrogen bonds : bond 0.03006 / 1.90 ( 88) hydrogen bonds : angle 6.42390 / 4.26 ( 228) link_NAG-ASN : bond 0.00288 / 0.15 ( 1) link_NAG-ASN : angle 0.77079 / 0.54 ( 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 110 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 82 time to evaluate : 0.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 389 ASP cc_start: 0.7622 (p0) cc_final: 0.7275 (p0) REVERT: C 455 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8028 (tt) REVERT: C 456 PHE cc_start: 0.8797 (OUTLIER) cc_final: 0.8024 (p90) REVERT: A 158 THR cc_start: 0.7447 (m) cc_final: 0.6912 (p) REVERT: B 83 ASP cc_start: 0.8532 (m-30) cc_final: 0.8330 (m-30) REVERT: B 149 TRP cc_start: 0.4807 (m100) cc_final: 0.4529 (m100) REVERT: B 150 LYS cc_start: 0.6155 (mttp) cc_final: 0.5504 (tptp) outliers start: 28 outliers final: 22 residues processed: 101 average time/residue: 0.0722 time to fit residues: 9.2809 Evaluate side-chains 101 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 77 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 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 99 VAL Chi-restraints excluded: chain A residue 115 LEU 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 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: 1.9990 chunk 49 optimal weight: 5.9990 chunk 54 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 46 optimal weight: 6.9990 chunk 16 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 9 optimal weight: 0.2980 chunk 23 optimal weight: 0.2980 chunk 42 optimal weight: 0.5980 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 167 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.145622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.113518 restraints weight = 7665.669| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 2.94 r_work: 0.3354 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.5191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 4874 Z= 0.137 Angle : 0.604 7.912 6636 Z= 0.302 Chirality : 0.045 0.160 729 Planarity : 0.004 0.041 855 Dihedral : 6.402 73.990 673 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.67 % Favored : 90.33 % Rotamer: Outliers : 4.98 % Allowed : 19.92 % Favored : 75.10 % 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: -3.37 (0.33), residues: 600 helix: -4.13 (0.53), residues: 38 sheet: -1.63 (0.36), residues: 222 loop : -2.48 (0.32), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 212 TYR 0.014 0.001 TYR A 105 PHE 0.014 0.001 PHE B 47 TRP 0.010 0.001 TRP C 436 HIS 0.004 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.14 ( 4865) covalent geometry : angle 0.60271 / 0.30 ( 6617) SS BOND : bond 0.00470 / 0.21 ( 8) SS BOND : angle 1.03121 / 0.81 ( 16) hydrogen bonds : bond 0.02847 / 1.79 ( 88) hydrogen bonds : angle 6.27777 / 4.17 ( 228) link_NAG-ASN : bond 0.00202 / 0.11 ( 1) link_NAG-ASN : angle 0.71266 / 0.50 ( 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 105 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 79 time to evaluate : 0.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 389 ASP cc_start: 0.7633 (p0) cc_final: 0.7284 (p0) REVERT: C 455 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8020 (tt) REVERT: C 456 PHE cc_start: 0.8745 (OUTLIER) cc_final: 0.8048 (p90) REVERT: A 158 THR cc_start: 0.7478 (m) cc_final: 0.6943 (p) REVERT: A 171 HIS cc_start: 0.7722 (m90) cc_final: 0.7302 (m-70) REVERT: B 149 TRP cc_start: 0.4907 (m100) cc_final: 0.4591 (m100) REVERT: B 150 LYS cc_start: 0.6352 (mttp) cc_final: 0.5728 (tptp) outliers start: 26 outliers final: 22 residues processed: 96 average time/residue: 0.0839 time to fit residues: 10.1891 Evaluate side-chains 99 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 75 time to evaluate : 0.182 ------------------------------------------------------------------------------- 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 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 69 THR Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 115 LEU 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 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: 0.9980 chunk 32 optimal weight: 4.9990 chunk 58 optimal weight: 7.9990 chunk 5 optimal weight: 0.0060 chunk 34 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 chunk 24 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 498 GLN B 125 GLN ** B 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 167 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.145002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.113600 restraints weight = 7772.015| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 3.22 r_work: 0.3334 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.5296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 4874 Z= 0.142 Angle : 0.604 7.877 6636 Z= 0.303 Chirality : 0.045 0.159 729 Planarity : 0.005 0.042 855 Dihedral : 6.456 73.524 673 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.00 % Favored : 89.00 % Rotamer: Outliers : 5.94 % Allowed : 19.35 % 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: -3.30 (0.33), residues: 600 helix: -4.16 (0.51), residues: 38 sheet: -1.57 (0.36), residues: 221 loop : -2.43 (0.32), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 109 TYR 0.015 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/Z covalent geometry : bond 0.00348 / 0.14 ( 4865) covalent geometry : angle 0.60284 / 0.30 ( 6617) SS BOND : bond 0.00377 / 0.16 ( 8) SS BOND : angle 0.96367 / 0.79 ( 16) hydrogen bonds : bond 0.02921 / 1.86 ( 88) hydrogen bonds : angle 6.20729 / 4.14 ( 228) link_NAG-ASN : bond 0.00216 / 0.11 ( 1) link_NAG-ASN : angle 0.67836 / 0.49 ( 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 109 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 78 time to evaluate : 0.174 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 389 ASP cc_start: 0.7662 (p0) cc_final: 0.7315 (p0) REVERT: C 455 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8027 (tt) REVERT: C 456 PHE cc_start: 0.8742 (OUTLIER) cc_final: 0.8026 (p90) REVERT: A 171 HIS cc_start: 0.7809 (m90) cc_final: 0.7393 (m-70) REVERT: B 149 TRP cc_start: 0.5003 (m100) cc_final: 0.4688 (m100) REVERT: B 150 LYS cc_start: 0.6585 (mttp) cc_final: 0.5916 (tptp) outliers start: 31 outliers final: 24 residues processed: 99 average time/residue: 0.0704 time to fit residues: 8.8634 Evaluate side-chains 101 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 75 time to evaluate : 0.188 ------------------------------------------------------------------------------- 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 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 69 THR Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 115 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 25 optimal weight: 0.8980 chunk 34 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 498 GLN B 159 ASN B 211 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.142590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.110844 restraints weight = 7677.497| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 3.19 r_work: 0.3285 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.5528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 4874 Z= 0.207 Angle : 0.670 8.708 6636 Z= 0.340 Chirality : 0.047 0.157 729 Planarity : 0.005 0.040 855 Dihedral : 6.590 72.417 673 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.33 % Favored : 87.67 % Rotamer: Outliers : 5.36 % Allowed : 20.88 % Favored : 73.75 % 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: -3.37 (0.33), residues: 600 helix: -4.26 (0.48), residues: 38 sheet: -1.65 (0.37), residues: 209 loop : -2.44 (0.31), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 109 TYR 0.016 0.002 TYR A 105 PHE 0.019 0.002 PHE C 429 TRP 0.011 0.001 TRP C 436 HIS 0.006 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00502 / 0.21 ( 4865) covalent geometry : angle 0.66840 / 0.34 ( 6617) SS BOND : bond 0.00394 / 0.18 ( 8) SS BOND : angle 1.17365 / 0.93 ( 16) hydrogen bonds : bond 0.03353 / 2.15 ( 88) hydrogen bonds : angle 6.34801 / 4.26 ( 228) link_NAG-ASN : bond 0.00450 / 0.24 ( 1) link_NAG-ASN : angle 0.69698 / 0.57 ( 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: 28 poor density : 79 time to evaluate : 0.187 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 389 ASP cc_start: 0.7477 (p0) cc_final: 0.7090 (p0) REVERT: C 455 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8035 (tt) REVERT: C 456 PHE cc_start: 0.8852 (OUTLIER) cc_final: 0.8235 (p90) REVERT: A 204 ASN cc_start: 0.5621 (p0) cc_final: 0.4497 (t0) REVERT: B 149 TRP cc_start: 0.5099 (m100) cc_final: 0.4732 (m100) REVERT: B 150 LYS cc_start: 0.6546 (mttp) cc_final: 0.5744 (tptp) REVERT: B 157 SER cc_start: 0.7712 (p) cc_final: 0.7272 (t) outliers start: 28 outliers final: 26 residues processed: 97 average time/residue: 0.0703 time to fit residues: 8.7846 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 ------------------------------------------------------------------------------- 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 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 69 THR Chi-restraints excluded: chain A residue 87 LYS Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 115 LEU 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 159 ASN Chi-restraints excluded: chain B residue 165 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: 0.6980 chunk 14 optimal weight: 6.9990 chunk 39 optimal weight: 0.4980 chunk 32 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.144236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.112611 restraints weight = 7694.831| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 3.14 r_work: 0.3313 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.5549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 4874 Z= 0.154 Angle : 0.640 8.475 6636 Z= 0.322 Chirality : 0.045 0.161 729 Planarity : 0.005 0.062 855 Dihedral : 6.276 71.884 672 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.67 % Favored : 89.33 % Rotamer: Outliers : 5.36 % Allowed : 21.07 % Favored : 73.56 % 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: -4.31 (0.49), residues: 38 sheet: -1.54 (0.37), residues: 215 loop : -2.36 (0.32), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 109 TYR 0.016 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/Z covalent geometry : bond 0.00376 / 0.15 ( 4865) covalent geometry : angle 0.63921 / 0.32 ( 6617) SS BOND : bond 0.00380 / 0.16 ( 8) SS BOND : angle 0.78756 / 0.56 ( 16) hydrogen bonds : bond 0.03112 / 2.01 ( 88) hydrogen bonds : angle 6.27327 / 4.22 ( 228) link_NAG-ASN : bond 0.00230 / 0.12 ( 1) link_NAG-ASN : angle 0.65070 / 0.47 ( 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 105 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 77 time to evaluate : 0.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 389 ASP cc_start: 0.7652 (p0) cc_final: 0.7306 (p0) REVERT: C 455 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8057 (tt) REVERT: C 456 PHE cc_start: 0.8770 (OUTLIER) cc_final: 0.8098 (p90) REVERT: A 46 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7846 (tp30) REVERT: A 204 ASN cc_start: 0.5653 (p0) cc_final: 0.4592 (t0) REVERT: B 149 TRP cc_start: 0.5127 (m100) cc_final: 0.4777 (m100) REVERT: B 150 LYS cc_start: 0.6369 (mttp) cc_final: 0.5650 (tptp) REVERT: B 157 SER cc_start: 0.7899 (p) cc_final: 0.7505 (t) outliers start: 28 outliers final: 25 residues processed: 94 average time/residue: 0.0621 time to fit residues: 7.5805 Evaluate side-chains 103 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 75 time to evaluate : 0.181 ------------------------------------------------------------------------------- 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 399 SER Chi-restraints excluded: chain C residue 430 THR 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 46 GLU Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 115 LEU 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 22 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 18 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 chunk 59 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 chunk 50 optimal weight: 4.9990 chunk 28 optimal weight: 0.6980 chunk 34 optimal weight: 0.9990 chunk 4 optimal weight: 0.3980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 159 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.144914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.112824 restraints weight = 7684.992| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 3.08 r_work: 0.3326 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.5566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 4874 Z= 0.146 Angle : 0.624 8.681 6636 Z= 0.314 Chirality : 0.045 0.160 729 Planarity : 0.005 0.041 855 Dihedral : 6.034 70.647 672 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.50 % Favored : 89.50 % Rotamer: Outliers : 5.36 % Allowed : 21.07 % Favored : 73.56 % 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: -3.16 (0.34), residues: 600 helix: -4.28 (0.49), residues: 38 sheet: -1.43 (0.38), residues: 212 loop : -2.32 (0.32), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 109 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/Z covalent geometry : bond 0.00359 / 0.15 ( 4865) covalent geometry : angle 0.62356 / 0.31 ( 6617) SS BOND : bond 0.00373 / 0.16 ( 8) SS BOND : angle 0.78346 / 0.56 ( 16) hydrogen bonds : bond 0.03101 / 2.00 ( 88) hydrogen bonds : angle 6.17055 / 4.16 ( 228) link_NAG-ASN : bond 0.00216 / 0.11 ( 1) link_NAG-ASN : angle 0.67833 / 0.47 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1639.13 seconds wall clock time: 28 minutes 44.99 seconds (1724.99 seconds total)