Starting phenix.real_space_refine on Tue Feb 3 21:42:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9v2o_64735/02_2026/9v2o_64735.cif Found real_map, /net/cci-nas-00/data/ceres_data/9v2o_64735/02_2026/9v2o_64735.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9v2o_64735/02_2026/9v2o_64735.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9v2o_64735/02_2026/9v2o_64735.map" model { file = "/net/cci-nas-00/data/ceres_data/9v2o_64735/02_2026/9v2o_64735.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9v2o_64735/02_2026/9v2o_64735.cif" } resolution = 4.27 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= 0.007 sd= 0.041 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 36 5.16 5 C 4424 2.51 5 N 1171 2.21 5 O 1389 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7020 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 986 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 123} Chain: "B" Number of atoms: 3482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3482 Classifications: {'peptide': 449} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 436} Chain breaks: 1 Chain: "C" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 817 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 103} Chain: "D" Number of atoms: 908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 908 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain: "E" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 827 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 101} Time building chain proxies: 1.79, per 1000 atoms: 0.25 Number of scatterers: 7020 At special positions: 0 Unit cell: (78, 98, 151, 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 36 16.00 O 1389 8.00 N 1171 7.00 C 4424 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 37 " - pdb=" SG CYS B 439 " distance=2.03 Simple disulfide: pdb=" SG CYS B 69 " - pdb=" SG CYS B 212 " distance=2.03 Simple disulfide: pdb=" SG CYS B 155 " - pdb=" SG CYS B 290 " distance=2.03 Simple disulfide: pdb=" SG CYS B 313 " - pdb=" SG CYS B 343 " distance=2.03 Simple disulfide: pdb=" SG CYS B 322 " - pdb=" SG CYS B 333 " distance=2.04 Simple disulfide: pdb=" SG CYS B 358 " - pdb=" SG CYS B 367 " distance=2.03 Simple disulfide: pdb=" SG CYS B 382 " - pdb=" SG CYS B 393 " distance=2.03 Simple disulfide: pdb=" SG CYS B 416 " - pdb=" SG CYS B 422 " distance=2.02 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 90 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 90 " distance=2.04 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 Time building additional restraints: 0.72 Conformation dependent library (CDL) restraints added in 271.6 milliseconds 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1674 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 19 sheets defined 18.1% alpha, 25.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 87 through 91 removed outlier: 3.902A pdb=" N ASP A 90 " --> pdb=" O ARG A 87 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N THR A 91 " --> pdb=" O ARG A 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 87 through 91' Processing helix chain 'B' and resid 77 through 97 removed outlier: 4.068A pdb=" N MET B 97 " --> pdb=" O LEU B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 142 Processing helix chain 'B' and resid 149 through 159 Processing helix chain 'B' and resid 163 through 171 removed outlier: 3.632A pdb=" N ILE B 167 " --> pdb=" O GLU B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 203 removed outlier: 3.543A pdb=" N LEU B 203 " --> pdb=" O ILE B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 208 Processing helix chain 'B' and resid 217 through 238 removed outlier: 3.889A pdb=" N ILE B 221 " --> pdb=" O ILE B 217 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N GLU B 222 " --> pdb=" O GLU B 218 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N PHE B 223 " --> pdb=" O THR B 219 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N ARG B 229 " --> pdb=" O GLN B 225 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N LEU B 230 " --> pdb=" O LYS B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 262 Processing helix chain 'B' and resid 267 through 277 Processing helix chain 'B' and resid 277 through 285 Processing helix chain 'B' and resid 292 through 296 Processing helix chain 'B' and resid 379 through 385 Processing helix chain 'B' and resid 445 through 447 No H-bonds generated for 'chain 'B' and resid 445 through 447' Processing helix chain 'B' and resid 473 through 477 Processing helix chain 'B' and resid 491 through 513 Processing helix chain 'D' and resid 87 through 91 removed outlier: 3.703A pdb=" N THR D 91 " --> pdb=" O VAL D 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 7 removed outlier: 3.664A pdb=" N GLN A 3 " --> pdb=" O SER A 25 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER A 25 " --> pdb=" O GLN A 3 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER A 21 " --> pdb=" O SER A 7 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 12 removed outlier: 7.511A pdb=" N PHE A 34 " --> pdb=" O LEU A 50 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N LEU A 50 " --> pdb=" O PHE A 34 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N TRP A 36 " --> pdb=" O LEU A 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 31 through 32 removed outlier: 3.638A pdb=" N PHE B 32 " --> pdb=" O LEU B 467 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 38 through 40 Processing sheet with id=AA5, first strand: chain 'B' and resid 176 through 177 removed outlier: 6.365A pdb=" N VAL B 56 " --> pdb=" O PHE B 190 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N VAL B 192 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N THR B 58 " --> pdb=" O VAL B 192 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ASP B 194 " --> pdb=" O THR B 58 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N GLU B 60 " --> pdb=" O ASP B 194 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 333 through 336 Processing sheet with id=AA7, first strand: chain 'B' and resid 359 through 361 Processing sheet with id=AA8, first strand: chain 'B' and resid 405 through 408 removed outlier: 3.767A pdb=" N GLY B 411 " --> pdb=" O THR B 408 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 431 through 434 Processing sheet with id=AB1, first strand: chain 'C' and resid 9 through 12 removed outlier: 6.223A pdb=" N GLN C 39 " --> pdb=" O LEU C 48 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N LEU C 48 " --> pdb=" O GLN C 39 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 9 through 12 removed outlier: 3.820A pdb=" N THR C 98 " --> pdb=" O SER C 94 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 19 through 23 Processing sheet with id=AB4, first strand: chain 'D' and resid 6 through 7 Processing sheet with id=AB5, first strand: chain 'D' and resid 10 through 11 removed outlier: 5.780A pdb=" N GLY D 10 " --> pdb=" O THR D 119 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N MET D 34 " --> pdb=" O SER D 50 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N SER D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER D 59 " --> pdb=" O SER D 50 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 10 through 11 removed outlier: 5.780A pdb=" N GLY D 10 " --> pdb=" O THR D 119 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N CYS D 96 " --> pdb=" O TRP D 112 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N TRP D 112 " --> pdb=" O CYS D 96 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 18 through 23 Processing sheet with id=AB8, first strand: chain 'E' and resid 36 through 39 removed outlier: 5.949A pdb=" N GLN E 39 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N VAL E 48 " --> pdb=" O GLN E 39 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 86 through 88 Processing sheet with id=AC1, first strand: chain 'E' and resid 91 through 92 260 hydrogen bonds defined for protein. 648 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: 1.16 Time building geometry restraints manager: 0.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 2262 1.35 - 1.47: 1741 1.47 - 1.59: 3101 1.59 - 1.71: 1 1.71 - 1.83: 48 Bond restraints: 7153 Sorted by residual: bond pdb=" N ARG D 87 " pdb=" CA ARG D 87 " ideal model delta sigma weight residual 1.455 1.488 -0.034 1.25e-02 6.40e+03 7.30e+00 bond pdb=" N SER D 85 " pdb=" CA SER D 85 " ideal model delta sigma weight residual 1.454 1.487 -0.033 1.23e-02 6.61e+03 7.14e+00 bond pdb=" N LEU D 86 " pdb=" CA LEU D 86 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.19e-02 7.06e+03 6.47e+00 bond pdb=" N ASP D 90 " pdb=" CA ASP D 90 " ideal model delta sigma weight residual 1.459 1.490 -0.032 1.28e-02 6.10e+03 6.10e+00 bond pdb=" N SER D 84 " pdb=" CA SER D 84 " ideal model delta sigma weight residual 1.458 1.489 -0.030 1.23e-02 6.61e+03 5.96e+00 ... (remaining 7148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.71: 9462 2.71 - 5.43: 205 5.43 - 8.14: 28 8.14 - 10.85: 9 10.85 - 13.57: 2 Bond angle restraints: 9706 Sorted by residual: angle pdb=" C GLU E 52 " pdb=" N ASN E 53 " pdb=" CA ASN E 53 " ideal model delta sigma weight residual 121.54 135.11 -13.57 1.91e+00 2.74e-01 5.04e+01 angle pdb=" N VAL B 482 " pdb=" CA VAL B 482 " pdb=" C VAL B 482 " ideal model delta sigma weight residual 113.71 107.09 6.62 9.50e-01 1.11e+00 4.85e+01 angle pdb=" N VAL B 379 " pdb=" CA VAL B 379 " pdb=" C VAL B 379 " ideal model delta sigma weight residual 113.71 107.66 6.05 9.50e-01 1.11e+00 4.05e+01 angle pdb=" C THR B 234 " pdb=" N ARG B 235 " pdb=" CA ARG B 235 " ideal model delta sigma weight residual 122.38 114.31 8.07 1.81e+00 3.05e-01 1.99e+01 angle pdb=" C ARG D 76 " pdb=" N ASN D 77 " pdb=" CA ASN D 77 " ideal model delta sigma weight residual 121.54 129.97 -8.43 1.91e+00 2.74e-01 1.95e+01 ... (remaining 9701 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.61: 3865 17.61 - 35.22: 346 35.22 - 52.83: 56 52.83 - 70.44: 10 70.44 - 88.05: 5 Dihedral angle restraints: 4282 sinusoidal: 1655 harmonic: 2627 Sorted by residual: dihedral pdb=" CB CYS B 382 " pdb=" SG CYS B 382 " pdb=" SG CYS B 393 " pdb=" CB CYS B 393 " ideal model delta sinusoidal sigma weight residual 93.00 164.03 -71.03 1 1.00e+01 1.00e-02 6.48e+01 dihedral pdb=" CB CYS D 22 " pdb=" SG CYS D 22 " pdb=" SG CYS D 96 " pdb=" CB CYS D 96 " ideal model delta sinusoidal sigma weight residual 93.00 152.77 -59.77 1 1.00e+01 1.00e-02 4.77e+01 dihedral pdb=" CB CYS B 416 " pdb=" SG CYS B 416 " pdb=" SG CYS B 422 " pdb=" CB CYS B 422 " ideal model delta sinusoidal sigma weight residual 93.00 151.32 -58.32 1 1.00e+01 1.00e-02 4.56e+01 ... (remaining 4279 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 768 0.049 - 0.099: 268 0.099 - 0.148: 56 0.148 - 0.197: 18 0.197 - 0.247: 6 Chirality restraints: 1116 Sorted by residual: chirality pdb=" CB ILE A 93 " pdb=" CA ILE A 93 " pdb=" CG1 ILE A 93 " pdb=" CG2 ILE A 93 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" CB ILE B 64 " pdb=" CA ILE B 64 " pdb=" CG1 ILE B 64 " pdb=" CG2 ILE B 64 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CA ASN E 53 " pdb=" N ASN E 53 " pdb=" C ASN E 53 " pdb=" CB ASN E 53 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 1113 not shown) Planarity restraints: 1233 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 67 " -0.347 9.50e-02 1.11e+02 1.56e-01 1.48e+01 pdb=" NE ARG D 67 " 0.021 2.00e-02 2.50e+03 pdb=" CZ ARG D 67 " 0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG D 67 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG D 67 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 232 " -0.015 2.00e-02 2.50e+03 3.00e-02 8.98e+00 pdb=" C GLU B 232 " 0.052 2.00e-02 2.50e+03 pdb=" O GLU B 232 " -0.020 2.00e-02 2.50e+03 pdb=" N ILE B 233 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 233 " -0.013 2.00e-02 2.50e+03 2.70e-02 7.31e+00 pdb=" C ILE B 233 " 0.047 2.00e-02 2.50e+03 pdb=" O ILE B 233 " -0.018 2.00e-02 2.50e+03 pdb=" N THR B 234 " -0.016 2.00e-02 2.50e+03 ... (remaining 1230 not shown) Histogram of nonbonded interaction distances: 2.54 - 3.01: 3814 3.01 - 3.48: 7659 3.48 - 3.96: 11474 3.96 - 4.43: 13250 4.43 - 4.90: 20817 Nonbonded interactions: 57014 Sorted by model distance: nonbonded pdb=" O TYR A 94 " pdb=" CA GLY A 119 " model vdw 2.539 2.752 nonbonded pdb=" N ARG D 87 " pdb=" O ARG D 87 " model vdw 2.598 2.496 nonbonded pdb=" N VAL B 482 " pdb=" N PHE B 483 " model vdw 2.599 2.560 nonbonded pdb=" CA ARG E 17 " pdb=" O ILE E 77 " model vdw 2.599 2.776 nonbonded pdb=" N VAL D 2 " pdb=" N GLN D 3 " model vdw 2.600 2.560 ... (remaining 57009 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.560 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: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.650 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:1.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 7165 Z= 0.248 Angle : 0.996 13.565 9730 Z= 0.546 Chirality : 0.055 0.247 1116 Planarity : 0.008 0.156 1233 Dihedral : 13.229 88.053 2572 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.18 % Favored : 89.82 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -2.18 (0.27), residues: 904 helix: -0.70 (0.44), residues: 128 sheet: -1.34 (0.29), residues: 295 loop : -1.69 (0.27), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 235 TYR 0.019 0.002 TYR D 57 PHE 0.018 0.002 PHE E 33 TRP 0.036 0.004 TRP A 36 HIS 0.010 0.003 HIS A 35 Details of bonding type rmsd covalent geometry : bond 0.00496 ( 7153) covalent geometry : angle 0.99384 ( 9706) SS BOND : bond 0.00519 ( 12) SS BOND : angle 1.66272 ( 24) hydrogen bonds : bond 0.13744 ( 249) hydrogen bonds : angle 8.00028 ( 648) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 LEU cc_start: 0.9095 (tp) cc_final: 0.8641 (tp) REVERT: A 79 LEU cc_start: 0.8887 (tp) cc_final: 0.8476 (tp) REVERT: B 289 MET cc_start: 0.8167 (mmp) cc_final: 0.7906 (mmp) REVERT: C 55 GLU cc_start: 0.9581 (mp0) cc_final: 0.9356 (mp0) REVERT: D 34 MET cc_start: 0.9014 (mmp) cc_final: 0.8645 (mmm) REVERT: E 98 ASP cc_start: 0.9381 (m-30) cc_final: 0.8980 (m-30) outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 0.1229 time to fit residues: 10.8121 Evaluate side-chains 54 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 49 optimal weight: 0.0570 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 8.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 8.9990 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 10.0000 chunk 74 optimal weight: 9.9990 overall best weight: 1.8104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 1 GLN B 363 ASN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.037170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.026224 restraints weight = 74842.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.027332 restraints weight = 49009.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.028151 restraints weight = 36018.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.028747 restraints weight = 28483.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.029183 restraints weight = 23864.194| |-----------------------------------------------------------------------------| r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.1111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7165 Z= 0.137 Angle : 0.584 6.931 9730 Z= 0.311 Chirality : 0.041 0.149 1116 Planarity : 0.004 0.047 1233 Dihedral : 5.420 35.169 986 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.85 % Favored : 91.15 % Rotamer: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.64 (0.27), residues: 904 helix: 0.75 (0.49), residues: 122 sheet: -1.19 (0.30), residues: 277 loop : -1.48 (0.27), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 17 TYR 0.016 0.001 TYR D 57 PHE 0.008 0.001 PHE B 190 TRP 0.014 0.002 TRP A 47 HIS 0.003 0.001 HIS E 36 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 7153) covalent geometry : angle 0.58275 ( 9706) SS BOND : bond 0.00267 ( 12) SS BOND : angle 0.86363 ( 24) hydrogen bonds : bond 0.03548 ( 249) hydrogen bonds : angle 5.97443 ( 648) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 LEU cc_start: 0.9257 (tp) cc_final: 0.8748 (tp) REVERT: A 79 LEU cc_start: 0.8825 (tp) cc_final: 0.8624 (tp) REVERT: A 113 MET cc_start: 0.8541 (mmp) cc_final: 0.8124 (mmp) REVERT: D 34 MET cc_start: 0.8747 (mmp) cc_final: 0.8457 (mmm) REVERT: E 98 ASP cc_start: 0.9403 (m-30) cc_final: 0.8989 (m-30) outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.1101 time to fit residues: 9.6835 Evaluate side-chains 54 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 64 optimal weight: 8.9990 chunk 48 optimal weight: 7.9990 chunk 7 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 59 optimal weight: 7.9990 chunk 75 optimal weight: 10.0000 chunk 72 optimal weight: 7.9990 chunk 25 optimal weight: 1.9990 chunk 13 optimal weight: 9.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 1 GLN ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.036365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.025821 restraints weight = 71639.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.026867 restraints weight = 46893.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.027636 restraints weight = 34446.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.028237 restraints weight = 27300.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.028697 restraints weight = 22709.267| |-----------------------------------------------------------------------------| r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7165 Z= 0.128 Angle : 0.570 7.718 9730 Z= 0.300 Chirality : 0.041 0.151 1116 Planarity : 0.004 0.045 1233 Dihedral : 5.110 34.795 986 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.07 % Favored : 89.93 % Rotamer: Outliers : 0.13 % Allowed : 5.51 % Favored : 94.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.49 (0.28), residues: 904 helix: 1.09 (0.50), residues: 129 sheet: -1.29 (0.31), residues: 280 loop : -1.35 (0.27), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 235 TYR 0.014 0.001 TYR D 57 PHE 0.013 0.001 PHE D 29 TRP 0.013 0.002 TRP A 36 HIS 0.004 0.001 HIS A 35 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 7153) covalent geometry : angle 0.56889 ( 9706) SS BOND : bond 0.00267 ( 12) SS BOND : angle 0.96736 ( 24) hydrogen bonds : bond 0.03087 ( 249) hydrogen bonds : angle 5.58304 ( 648) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 65 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 LEU cc_start: 0.8943 (tp) cc_final: 0.8735 (tp) REVERT: A 113 MET cc_start: 0.8742 (mmp) cc_final: 0.8361 (mmp) REVERT: B 264 MET cc_start: 0.9235 (pmm) cc_final: 0.8905 (pmm) REVERT: D 34 MET cc_start: 0.8781 (mmp) cc_final: 0.8473 (mmm) REVERT: D 95 TYR cc_start: 0.9215 (m-10) cc_final: 0.8995 (m-80) REVERT: E 98 ASP cc_start: 0.9371 (m-30) cc_final: 0.8935 (m-30) outliers start: 1 outliers final: 0 residues processed: 66 average time/residue: 0.1067 time to fit residues: 9.3342 Evaluate side-chains 51 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 48 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 49 optimal weight: 20.0000 chunk 56 optimal weight: 0.0040 chunk 2 optimal weight: 7.9990 chunk 3 optimal weight: 0.6980 chunk 33 optimal weight: 10.0000 chunk 27 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 overall best weight: 1.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 1 GLN ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.036433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.025746 restraints weight = 74363.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.026848 restraints weight = 47786.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.027648 restraints weight = 34819.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.028205 restraints weight = 27466.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.028689 restraints weight = 22967.498| |-----------------------------------------------------------------------------| r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7165 Z= 0.120 Angle : 0.569 9.044 9730 Z= 0.298 Chirality : 0.041 0.151 1116 Planarity : 0.004 0.042 1233 Dihedral : 5.010 33.826 986 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.07 % Favored : 90.93 % Rotamer: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.37 (0.28), residues: 904 helix: 1.10 (0.50), residues: 135 sheet: -1.16 (0.32), residues: 269 loop : -1.32 (0.27), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 72 TYR 0.014 0.001 TYR D 57 PHE 0.010 0.001 PHE D 29 TRP 0.012 0.002 TRP A 47 HIS 0.005 0.002 HIS D 35 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 7153) covalent geometry : angle 0.56742 ( 9706) SS BOND : bond 0.00260 ( 12) SS BOND : angle 0.91493 ( 24) hydrogen bonds : bond 0.02908 ( 249) hydrogen bonds : angle 5.41299 ( 648) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 LEU cc_start: 0.9397 (mt) cc_final: 0.9011 (tp) REVERT: A 79 LEU cc_start: 0.9184 (tp) cc_final: 0.8980 (tp) REVERT: B 264 MET cc_start: 0.9260 (pmm) cc_final: 0.8974 (pmm) REVERT: D 34 MET cc_start: 0.8673 (mmp) cc_final: 0.8327 (mmm) REVERT: D 95 TYR cc_start: 0.9165 (m-10) cc_final: 0.8911 (m-80) REVERT: E 55 HIS cc_start: 0.9200 (m90) cc_final: 0.8980 (m170) REVERT: E 98 ASP cc_start: 0.9341 (m-30) cc_final: 0.8869 (m-30) outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.1008 time to fit residues: 8.5949 Evaluate side-chains 52 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 7 optimal weight: 0.9990 chunk 8 optimal weight: 8.9990 chunk 53 optimal weight: 9.9990 chunk 12 optimal weight: 20.0000 chunk 80 optimal weight: 3.9990 chunk 66 optimal weight: 9.9990 chunk 23 optimal weight: 1.9990 chunk 72 optimal weight: 9.9990 chunk 76 optimal weight: 7.9990 chunk 20 optimal weight: 7.9990 chunk 56 optimal weight: 0.3980 overall best weight: 3.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 460 ASN ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.034168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.023853 restraints weight = 76049.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.024847 restraints weight = 50219.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.025568 restraints weight = 36992.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.026129 restraints weight = 29370.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.026565 restraints weight = 24557.762| |-----------------------------------------------------------------------------| r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7165 Z= 0.184 Angle : 0.620 9.258 9730 Z= 0.325 Chirality : 0.041 0.147 1116 Planarity : 0.004 0.040 1233 Dihedral : 5.296 33.911 986 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 19.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.07 % Favored : 89.93 % Rotamer: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.46 (0.28), residues: 904 helix: 1.21 (0.50), residues: 130 sheet: -1.32 (0.30), residues: 298 loop : -1.32 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 235 TYR 0.015 0.002 TYR E 38 PHE 0.013 0.002 PHE B 190 TRP 0.016 0.002 TRP D 47 HIS 0.006 0.002 HIS D 35 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 7153) covalent geometry : angle 0.61760 ( 9706) SS BOND : bond 0.00506 ( 12) SS BOND : angle 1.16719 ( 24) hydrogen bonds : bond 0.03110 ( 249) hydrogen bonds : angle 5.51692 ( 648) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 LEU cc_start: 0.9254 (tp) cc_final: 0.9045 (tp) REVERT: B 264 MET cc_start: 0.9315 (pmm) cc_final: 0.8932 (pmm) REVERT: B 289 MET cc_start: 0.8310 (mmp) cc_final: 0.8066 (mmp) REVERT: D 34 MET cc_start: 0.8697 (mmp) cc_final: 0.8402 (mmm) REVERT: E 55 HIS cc_start: 0.9254 (m90) cc_final: 0.9003 (m90) REVERT: E 98 ASP cc_start: 0.9354 (m-30) cc_final: 0.8877 (m-30) outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 0.0987 time to fit residues: 8.3455 Evaluate side-chains 48 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 3 optimal weight: 0.9990 chunk 23 optimal weight: 0.1980 chunk 43 optimal weight: 6.9990 chunk 49 optimal weight: 7.9990 chunk 7 optimal weight: 10.0000 chunk 58 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 chunk 88 optimal weight: 7.9990 chunk 51 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 overall best weight: 2.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 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 = 0.3120 r_free = 0.3120 target = 0.034239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.023993 restraints weight = 76436.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.025025 restraints weight = 48376.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.025799 restraints weight = 35005.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.026358 restraints weight = 27404.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.026800 restraints weight = 22804.745| |-----------------------------------------------------------------------------| r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7165 Z= 0.145 Angle : 0.597 10.708 9730 Z= 0.312 Chirality : 0.042 0.155 1116 Planarity : 0.004 0.040 1233 Dihedral : 5.153 31.863 986 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 16.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.18 % Favored : 90.82 % Rotamer: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.28), residues: 904 helix: 1.43 (0.51), residues: 128 sheet: -1.16 (0.31), residues: 275 loop : -1.34 (0.28), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 235 TYR 0.015 0.001 TYR D 57 PHE 0.009 0.001 PHE B 190 TRP 0.011 0.002 TRP A 36 HIS 0.005 0.001 HIS D 35 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 7153) covalent geometry : angle 0.59423 ( 9706) SS BOND : bond 0.00256 ( 12) SS BOND : angle 1.30763 ( 24) hydrogen bonds : bond 0.03011 ( 249) hydrogen bonds : angle 5.35466 ( 648) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 TYR cc_start: 0.9366 (p90) cc_final: 0.9149 (p90) REVERT: A 79 LEU cc_start: 0.9318 (tp) cc_final: 0.9097 (tp) REVERT: B 264 MET cc_start: 0.9311 (pmm) cc_final: 0.8919 (pmm) REVERT: D 34 MET cc_start: 0.8593 (mmp) cc_final: 0.8274 (mmm) REVERT: E 55 HIS cc_start: 0.9258 (m90) cc_final: 0.8967 (m90) REVERT: E 98 ASP cc_start: 0.9340 (m-30) cc_final: 0.8817 (m-30) outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.0963 time to fit residues: 8.0051 Evaluate side-chains 49 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 16 optimal weight: 10.0000 chunk 43 optimal weight: 3.9990 chunk 53 optimal weight: 8.9990 chunk 75 optimal weight: 0.3980 chunk 86 optimal weight: 20.0000 chunk 30 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 overall best weight: 1.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 1 GLN C 6 GLN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.034910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.024598 restraints weight = 73640.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.025653 restraints weight = 46636.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.026436 restraints weight = 33646.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.027023 restraints weight = 26338.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.027462 restraints weight = 21843.331| |-----------------------------------------------------------------------------| r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.2888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 7165 Z= 0.109 Angle : 0.589 12.078 9730 Z= 0.303 Chirality : 0.042 0.156 1116 Planarity : 0.004 0.040 1233 Dihedral : 4.949 30.819 986 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.51 % Favored : 90.49 % Rotamer: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.29), residues: 904 helix: 1.47 (0.50), residues: 127 sheet: -1.15 (0.31), residues: 280 loop : -1.23 (0.28), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 235 TYR 0.013 0.001 TYR D 57 PHE 0.009 0.001 PHE C 101 TRP 0.012 0.002 TRP A 47 HIS 0.003 0.001 HIS D 35 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 7153) covalent geometry : angle 0.58709 ( 9706) SS BOND : bond 0.00416 ( 12) SS BOND : angle 1.17242 ( 24) hydrogen bonds : bond 0.02759 ( 249) hydrogen bonds : angle 5.18428 ( 648) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 LEU cc_start: 0.9337 (tp) cc_final: 0.9118 (tp) REVERT: B 264 MET cc_start: 0.9282 (pmm) cc_final: 0.8982 (pmm) REVERT: D 34 MET cc_start: 0.8555 (mmp) cc_final: 0.8229 (mmm) REVERT: D 46 ASP cc_start: 0.9476 (t70) cc_final: 0.9184 (t0) REVERT: D 95 TYR cc_start: 0.9176 (m-80) cc_final: 0.8341 (m-80) REVERT: E 55 HIS cc_start: 0.9191 (m90) cc_final: 0.8895 (m90) REVERT: E 98 ASP cc_start: 0.9287 (m-30) cc_final: 0.8767 (m-30) outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.1089 time to fit residues: 9.3344 Evaluate side-chains 49 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 39 optimal weight: 3.9990 chunk 84 optimal weight: 9.9990 chunk 71 optimal weight: 8.9990 chunk 63 optimal weight: 9.9990 chunk 57 optimal weight: 5.9990 chunk 59 optimal weight: 10.0000 chunk 26 optimal weight: 6.9990 chunk 23 optimal weight: 0.2980 chunk 34 optimal weight: 10.0000 chunk 88 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 overall best weight: 3.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 183 ASN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.033082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.023082 restraints weight = 80883.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.024101 restraints weight = 51070.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.024847 restraints weight = 36905.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.025399 restraints weight = 28904.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.025777 restraints weight = 24044.728| |-----------------------------------------------------------------------------| r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.3526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7165 Z= 0.209 Angle : 0.676 11.870 9730 Z= 0.348 Chirality : 0.042 0.162 1116 Planarity : 0.004 0.039 1233 Dihedral : 5.367 32.709 986 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 20.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.73 % Favored : 89.27 % Rotamer: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.42 (0.29), residues: 904 helix: 1.06 (0.49), residues: 134 sheet: -1.23 (0.31), residues: 289 loop : -1.30 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 235 TYR 0.019 0.002 TYR E 38 PHE 0.015 0.002 PHE B 477 TRP 0.023 0.003 TRP D 112 HIS 0.008 0.002 HIS D 35 Details of bonding type rmsd covalent geometry : bond 0.00432 ( 7153) covalent geometry : angle 0.67379 ( 9706) SS BOND : bond 0.00334 ( 12) SS BOND : angle 1.27015 ( 24) hydrogen bonds : bond 0.03291 ( 249) hydrogen bonds : angle 5.58062 ( 648) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 LEU cc_start: 0.9338 (tp) cc_final: 0.9102 (tp) REVERT: B 264 MET cc_start: 0.9314 (pmm) cc_final: 0.8937 (pmm) REVERT: D 34 MET cc_start: 0.8724 (mmp) cc_final: 0.8409 (mmm) REVERT: E 55 HIS cc_start: 0.9314 (m90) cc_final: 0.9048 (m-70) REVERT: E 98 ASP cc_start: 0.9343 (m-30) cc_final: 0.8861 (m-30) outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.1197 time to fit residues: 9.6296 Evaluate side-chains 44 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 29 optimal weight: 0.9990 chunk 48 optimal weight: 0.0670 chunk 67 optimal weight: 6.9990 chunk 79 optimal weight: 0.0670 chunk 68 optimal weight: 0.0980 chunk 82 optimal weight: 9.9990 chunk 86 optimal weight: 8.9990 chunk 70 optimal weight: 7.9990 chunk 59 optimal weight: 4.9990 chunk 63 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 overall best weight: 1.2460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 1 GLN B 363 ASN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.034238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.024157 restraints weight = 76032.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.025215 restraints weight = 47277.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.025989 restraints weight = 33870.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.026569 restraints weight = 26388.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.027003 restraints weight = 21848.299| |-----------------------------------------------------------------------------| r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.3502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7165 Z= 0.117 Angle : 0.629 13.475 9730 Z= 0.321 Chirality : 0.042 0.154 1116 Planarity : 0.004 0.068 1233 Dihedral : 5.093 30.057 986 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.73 % Favored : 90.27 % Rotamer: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.29), residues: 904 helix: 1.42 (0.50), residues: 127 sheet: -1.19 (0.31), residues: 281 loop : -1.24 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 235 TYR 0.014 0.001 TYR D 57 PHE 0.010 0.001 PHE B 477 TRP 0.022 0.002 TRP D 112 HIS 0.005 0.002 HIS B 159 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 7153) covalent geometry : angle 0.62713 ( 9706) SS BOND : bond 0.00278 ( 12) SS BOND : angle 1.09032 ( 24) hydrogen bonds : bond 0.02835 ( 249) hydrogen bonds : angle 5.27555 ( 648) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 LEU cc_start: 0.9336 (tp) cc_final: 0.9103 (tp) REVERT: B 264 MET cc_start: 0.9306 (pmm) cc_final: 0.8993 (pmm) REVERT: B 289 MET cc_start: 0.8549 (mpp) cc_final: 0.8213 (mpp) REVERT: D 34 MET cc_start: 0.8565 (mmp) cc_final: 0.8238 (mmm) REVERT: D 95 TYR cc_start: 0.9167 (m-80) cc_final: 0.8386 (m-80) REVERT: E 55 HIS cc_start: 0.9248 (m90) cc_final: 0.8963 (m90) REVERT: E 98 ASP cc_start: 0.9317 (m-30) cc_final: 0.8776 (m-30) outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.1102 time to fit residues: 9.7235 Evaluate side-chains 50 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 55 optimal weight: 10.0000 chunk 51 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 41 optimal weight: 0.6980 chunk 65 optimal weight: 0.7980 chunk 56 optimal weight: 20.0000 chunk 11 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 86 optimal weight: 10.0000 chunk 27 optimal weight: 9.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 1 GLN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.034069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.024104 restraints weight = 75772.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.025150 restraints weight = 47418.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.025909 restraints weight = 34057.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.026472 restraints weight = 26607.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.026890 restraints weight = 22069.590| |-----------------------------------------------------------------------------| r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.3655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7165 Z= 0.123 Angle : 0.638 13.992 9730 Z= 0.326 Chirality : 0.042 0.156 1116 Planarity : 0.004 0.041 1233 Dihedral : 5.082 31.159 986 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 15.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.07 % Favored : 89.93 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.21 (0.29), residues: 904 helix: 1.49 (0.50), residues: 127 sheet: -1.10 (0.32), residues: 278 loop : -1.22 (0.28), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 49 TYR 0.028 0.001 TYR C 38 PHE 0.014 0.001 PHE C 101 TRP 0.061 0.003 TRP D 36 HIS 0.005 0.002 HIS D 35 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 7153) covalent geometry : angle 0.63645 ( 9706) SS BOND : bond 0.00293 ( 12) SS BOND : angle 1.08138 ( 24) hydrogen bonds : bond 0.02934 ( 249) hydrogen bonds : angle 5.29746 ( 648) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 LEU cc_start: 0.9338 (tp) cc_final: 0.9105 (tp) REVERT: B 264 MET cc_start: 0.9305 (pmm) cc_final: 0.9033 (pmm) REVERT: B 289 MET cc_start: 0.8449 (mpp) cc_final: 0.8183 (mpp) REVERT: D 34 MET cc_start: 0.8638 (mmp) cc_final: 0.8321 (mmm) REVERT: D 46 ASP cc_start: 0.9488 (t70) cc_final: 0.9234 (t0) REVERT: E 55 HIS cc_start: 0.9229 (m90) cc_final: 0.8938 (m90) REVERT: E 98 ASP cc_start: 0.9300 (m-30) cc_final: 0.8759 (m-30) REVERT: E 101 PHE cc_start: 0.9102 (m-10) cc_final: 0.8864 (m-10) outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.0985 time to fit residues: 8.4307 Evaluate side-chains 50 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 18 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 36 optimal weight: 6.9990 chunk 25 optimal weight: 0.9990 chunk 78 optimal weight: 9.9990 chunk 17 optimal weight: 5.9990 chunk 87 optimal weight: 4.9990 chunk 88 optimal weight: 4.9990 chunk 83 optimal weight: 8.9990 chunk 28 optimal weight: 8.9990 chunk 42 optimal weight: 8.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 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 = 0.3092 r_free = 0.3092 target = 0.033447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.023401 restraints weight = 79060.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.024425 restraints weight = 50082.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.025163 restraints weight = 36266.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.025671 restraints weight = 28548.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.026105 restraints weight = 23938.452| |-----------------------------------------------------------------------------| r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.3903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7165 Z= 0.167 Angle : 0.665 13.752 9730 Z= 0.340 Chirality : 0.042 0.157 1116 Planarity : 0.004 0.040 1233 Dihedral : 5.270 31.117 986 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 18.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.07 % Favored : 89.93 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.29), residues: 904 helix: 1.36 (0.50), residues: 133 sheet: -1.30 (0.31), residues: 284 loop : -1.21 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 339 TYR 0.028 0.002 TYR C 38 PHE 0.017 0.002 PHE B 237 TRP 0.052 0.003 TRP D 36 HIS 0.007 0.002 HIS D 35 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 7153) covalent geometry : angle 0.66352 ( 9706) SS BOND : bond 0.00334 ( 12) SS BOND : angle 1.08990 ( 24) hydrogen bonds : bond 0.03240 ( 249) hydrogen bonds : angle 5.42785 ( 648) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1364.07 seconds wall clock time: 24 minutes 32.21 seconds (1472.21 seconds total)