Starting phenix.real_space_refine on Wed Sep 17 06:21:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b3h_44139/09_2025/9b3h_44139.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b3h_44139/09_2025/9b3h_44139.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9b3h_44139/09_2025/9b3h_44139.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b3h_44139/09_2025/9b3h_44139.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9b3h_44139/09_2025/9b3h_44139.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b3h_44139/09_2025/9b3h_44139.map" } resolution = 4.0 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= -0.002 sd= 0.014 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 51 5.16 5 C 3757 2.51 5 N 1021 2.21 5 O 1150 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5979 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 531, 4129 Classifications: {'peptide': 531} Link IDs: {'PTRANS': 22, 'TRANS': 508} Chain breaks: 2 Chain: "B" Number of atoms: 1780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1780 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 8, 'TRANS': 207} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 1.50, per 1000 atoms: 0.25 Number of scatterers: 5979 At special positions: 0 Unit cell: (70.281, 97.407, 126.999, 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 51 16.00 O 1150 8.00 N 1021 7.00 C 3757 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=19, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 272 " distance=2.03 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 75 " distance=2.03 Simple disulfide: pdb=" SG CYS A 69 " - pdb=" SG CYS A 80 " distance=2.03 Simple disulfide: pdb=" SG CYS A 82 " - pdb=" SG CYS A 114 " distance=2.02 Simple disulfide: pdb=" SG CYS A 88 " - pdb=" SG CYS A 107 " distance=2.03 Simple disulfide: pdb=" SG CYS A 96 " - pdb=" SG CYS A 127 " distance=2.03 Simple disulfide: pdb=" SG CYS A 162 " - pdb=" SG CYS A 199 " distance=2.03 Simple disulfide: pdb=" SG CYS A 175 " - pdb=" SG CYS A 231 " distance=2.03 Simple disulfide: pdb=" SG CYS A 204 " - pdb=" SG CYS A 214 " distance=2.03 Simple disulfide: pdb=" SG CYS A 246 " - pdb=" SG CYS A 264 " distance=2.03 Simple disulfide: pdb=" SG CYS A 258 " - pdb=" SG CYS A 273 " distance=2.03 Simple disulfide: pdb=" SG CYS A 276 " - pdb=" SG CYS A 288 " distance=2.03 Simple disulfide: pdb=" SG CYS A 283 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 295 " - pdb=" SG CYS A 310 " distance=2.03 Simple disulfide: pdb=" SG CYS A 345 " - pdb=" SG CYS A 470 " distance=2.03 Simple disulfide: pdb=" SG CYS A 383 " - pdb=" SG CYS A 399 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 461 " distance=2.03 Simple disulfide: pdb=" SG CYS A 484 " - pdb=" SG CYS A 548 " distance=2.03 Simple disulfide: pdb=" SG CYS A 512 " - pdb=" SG CYS A 527 " 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=1, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " NAG-ASN " NAG A 701 " - " ASN A 511 " " NAG A 702 " - " ASN A 553 " " NAG A 703 " - " ASN A 91 " " NAG C 1 " - " ASN A 439 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.64 Conformation dependent library (CDL) restraints added in 398.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1374 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 13 sheets defined 13.9% alpha, 30.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 51 through 56 removed outlier: 3.835A pdb=" N THR A 56 " --> pdb=" O LYS A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 88 Processing helix chain 'A' and resid 105 through 116 Processing helix chain 'A' and resid 167 through 178 Processing helix chain 'A' and resid 210 through 214 Processing helix chain 'A' and resid 239 through 241 No H-bonds generated for 'chain 'A' and resid 239 through 241' Processing helix chain 'A' and resid 255 through 257 No H-bonds generated for 'chain 'A' and resid 255 through 257' Processing helix chain 'A' and resid 267 through 271 removed outlier: 4.072A pdb=" N LEU A 271 " --> pdb=" O SER A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 294 Processing helix chain 'A' and resid 304 through 308 removed outlier: 3.803A pdb=" N VAL A 308 " --> pdb=" O GLU A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 338 removed outlier: 3.502A pdb=" N SER A 338 " --> pdb=" O LYS A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 400 Processing helix chain 'A' and resid 401 through 406 removed outlier: 5.488A pdb=" N HIS A 406 " --> pdb=" O SER A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 496 Processing helix chain 'A' and resid 582 through 591 Processing helix chain 'A' and resid 591 through 596 removed outlier: 4.121A pdb=" N ILE A 595 " --> pdb=" O GLY A 591 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 73 through 76 Processing sheet with id=AA2, first strand: chain 'A' and resid 102 through 103 removed outlier: 6.974A pdb=" N CYS A 96 " --> pdb=" O LEU A 122 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 134 through 138 Processing sheet with id=AA4, first strand: chain 'A' and resid 134 through 138 removed outlier: 3.512A pdb=" N VAL A 229 " --> pdb=" O GLY A 146 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N ALA A 227 " --> pdb=" O VAL A 148 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL A 230 " --> pdb=" O ASP A 186 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 198 through 203 Processing sheet with id=AA6, first strand: chain 'A' and resid 243 through 245 Processing sheet with id=AA7, first strand: chain 'A' and resid 281 through 282 Processing sheet with id=AA8, first strand: chain 'A' and resid 372 through 377 removed outlier: 3.743A pdb=" N CYS A 383 " --> pdb=" O ILE A 375 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N GLU A 377 " --> pdb=" O ILE A 381 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N ILE A 381 " --> pdb=" O GLU A 377 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N TRP A 392 " --> pdb=" O ILE A 388 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL A 425 " --> pdb=" O THR A 412 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR A 412 " --> pdb=" O VAL A 425 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N VAL A 429 " --> pdb=" O TYR A 408 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N TYR A 408 " --> pdb=" O VAL A 429 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 483 through 488 removed outlier: 6.317A pdb=" N THR A 577 " --> pdb=" O VAL A 561 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N VAL A 561 " --> pdb=" O THR A 577 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N LEU A 546 " --> pdb=" O TRP A 558 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N GLN A 549 " --> pdb=" O LYS A 483 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LYS A 483 " --> pdb=" O GLN A 549 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 109 through 116 removed outlier: 3.523A pdb=" N ILE B 136 " --> pdb=" O VAL B 109 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER B 134 " --> pdb=" O THR B 111 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 141 through 143 removed outlier: 3.929A pdb=" N LEU B 157 " --> pdb=" O VAL B 161 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N VAL B 161 " --> pdb=" O LEU B 157 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 228 through 235 removed outlier: 7.299A pdb=" N THR B 199 " --> pdb=" O LYS B 317 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 243 through 248 removed outlier: 3.703A pdb=" N PHE B 258 " --> pdb=" O GLN B 244 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR B 246 " --> pdb=" O GLU B 256 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N PHE B 248 " --> pdb=" O LYS B 254 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N LYS B 254 " --> pdb=" O PHE B 248 " (cutoff:3.500A) 185 hydrogen bonds defined for protein. 453 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: 0.99 Time building geometry restraints manager: 0.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1951 1.35 - 1.47: 1508 1.47 - 1.59: 2596 1.59 - 1.71: 0 1.71 - 1.83: 62 Bond restraints: 6117 Sorted by residual: bond pdb=" C1 NAG A 702 " pdb=" O5 NAG A 702 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.34e+00 bond pdb=" C1 NAG A 701 " pdb=" O5 NAG A 701 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.61e+00 bond pdb=" C1 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.54e+00 bond pdb=" CB ASP A 242 " pdb=" CG ASP A 242 " ideal model delta sigma weight residual 1.516 1.551 -0.035 2.50e-02 1.60e+03 1.97e+00 bond pdb=" CB ASP A 77 " pdb=" CG ASP A 77 " ideal model delta sigma weight residual 1.516 1.550 -0.034 2.50e-02 1.60e+03 1.83e+00 ... (remaining 6112 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 8058 1.97 - 3.95: 159 3.95 - 5.92: 32 5.92 - 7.89: 10 7.89 - 9.86: 4 Bond angle restraints: 8263 Sorted by residual: angle pdb=" CB MET A 373 " pdb=" CG MET A 373 " pdb=" SD MET A 373 " ideal model delta sigma weight residual 112.70 122.56 -9.86 3.00e+00 1.11e-01 1.08e+01 angle pdb=" CB LYS B 195 " pdb=" CG LYS B 195 " pdb=" CD LYS B 195 " ideal model delta sigma weight residual 111.30 118.75 -7.45 2.30e+00 1.89e-01 1.05e+01 angle pdb=" CA LYS B 137 " pdb=" CB LYS B 137 " pdb=" CG LYS B 137 " ideal model delta sigma weight residual 114.10 120.57 -6.47 2.00e+00 2.50e-01 1.05e+01 angle pdb=" CB LEU A 594 " pdb=" CG LEU A 594 " pdb=" CD2 LEU A 594 " ideal model delta sigma weight residual 110.70 119.55 -8.85 3.00e+00 1.11e-01 8.69e+00 angle pdb=" CA MET A 373 " pdb=" CB MET A 373 " pdb=" CG MET A 373 " ideal model delta sigma weight residual 114.10 119.62 -5.52 2.00e+00 2.50e-01 7.60e+00 ... (remaining 8258 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.38: 3262 16.38 - 32.76: 383 32.76 - 49.15: 90 49.15 - 65.53: 12 65.53 - 81.91: 15 Dihedral angle restraints: 3762 sinusoidal: 1613 harmonic: 2149 Sorted by residual: dihedral pdb=" CB CYS A 88 " pdb=" SG CYS A 88 " pdb=" SG CYS A 107 " pdb=" CB CYS A 107 " ideal model delta sinusoidal sigma weight residual 93.00 172.09 -79.09 1 1.00e+01 1.00e-02 7.78e+01 dihedral pdb=" CB CYS A 64 " pdb=" SG CYS A 64 " pdb=" SG CYS A 75 " pdb=" CB CYS A 75 " ideal model delta sinusoidal sigma weight residual 93.00 47.41 45.59 1 1.00e+01 1.00e-02 2.88e+01 dihedral pdb=" CB CYS A 276 " pdb=" SG CYS A 276 " pdb=" SG CYS A 288 " pdb=" CB CYS A 288 " ideal model delta sinusoidal sigma weight residual -86.00 -126.72 40.72 1 1.00e+01 1.00e-02 2.32e+01 ... (remaining 3759 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 666 0.049 - 0.098: 160 0.098 - 0.147: 51 0.147 - 0.196: 2 0.196 - 0.245: 1 Chirality restraints: 880 Sorted by residual: chirality pdb=" CG LEU A 594 " pdb=" CB LEU A 594 " pdb=" CD1 LEU A 594 " pdb=" CD2 LEU A 594 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" CB VAL A 590 " pdb=" CA VAL A 590 " pdb=" CG1 VAL A 590 " pdb=" CG2 VAL A 590 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.39e-01 chirality pdb=" CA ILE B 257 " pdb=" N ILE B 257 " pdb=" C ILE B 257 " pdb=" CB ILE B 257 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.48e-01 ... (remaining 877 not shown) Planarity restraints: 1075 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 340 " -0.045 5.00e-02 4.00e+02 6.78e-02 7.36e+00 pdb=" N PRO A 341 " 0.117 5.00e-02 4.00e+02 pdb=" CA PRO A 341 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 341 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 77 " -0.013 2.00e-02 2.50e+03 2.52e-02 6.37e+00 pdb=" C ASP A 77 " 0.044 2.00e-02 2.50e+03 pdb=" O ASP A 77 " -0.017 2.00e-02 2.50e+03 pdb=" N GLY A 78 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 242 " 0.010 2.00e-02 2.50e+03 2.05e-02 4.19e+00 pdb=" C ASP A 242 " -0.035 2.00e-02 2.50e+03 pdb=" O ASP A 242 " 0.013 2.00e-02 2.50e+03 pdb=" N SER A 243 " 0.012 2.00e-02 2.50e+03 ... (remaining 1072 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 168 2.69 - 3.24: 6036 3.24 - 3.79: 9878 3.79 - 4.35: 12913 4.35 - 4.90: 20819 Nonbonded interactions: 49814 Sorted by model distance: nonbonded pdb=" OG SER B 290 " pdb=" OD1 ASN B 292 " model vdw 2.133 3.040 nonbonded pdb=" O ARG A 592 " pdb=" OG SER A 596 " model vdw 2.151 3.040 nonbonded pdb=" OG1 THR B 169 " pdb=" O ARG B 174 " model vdw 2.177 3.040 nonbonded pdb=" OH TYR B 179 " pdb=" OG SER B 207 " model vdw 2.195 3.040 nonbonded pdb=" OG1 THR A 303 " pdb=" OE1 GLU A 305 " model vdw 2.202 3.040 ... (remaining 49809 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: 0.550 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: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.370 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 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 : 0.004 0.043 6142 Z= 0.155 Angle : 0.729 9.864 8316 Z= 0.360 Chirality : 0.047 0.245 880 Planarity : 0.005 0.068 1071 Dihedral : 14.644 81.912 2331 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 16.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 0.15 % Allowed : 22.58 % Favored : 77.27 % 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 aren not related in a simple way. whole: 1.02 (0.31), residues: 739 helix: -0.09 (0.71), residues: 45 sheet: 1.13 (0.38), residues: 180 loop : 0.71 (0.28), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 228 TYR 0.010 0.001 TYR B 112 PHE 0.019 0.001 PHE B 287 TRP 0.011 0.001 TRP A 503 HIS 0.003 0.001 HIS A 507 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 6117) covalent geometry : angle 0.72219 ( 8263) SS BOND : bond 0.00387 ( 19) SS BOND : angle 1.17691 ( 38) hydrogen bonds : bond 0.26600 ( 179) hydrogen bonds : angle 10.37375 ( 453) Misc. bond : bond 0.00021 ( 1) link_BETA1-4 : bond 0.00892 ( 1) link_BETA1-4 : angle 1.65823 ( 3) link_NAG-ASN : bond 0.00261 ( 4) link_NAG-ASN : angle 2.03490 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 53 time to evaluate : 0.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 244 GLN cc_start: 0.7886 (mm110) cc_final: 0.7614 (mm110) REVERT: B 283 MET cc_start: 0.7976 (mmm) cc_final: 0.7667 (mmm) outliers start: 1 outliers final: 1 residues processed: 53 average time/residue: 0.0753 time to fit residues: 5.5129 Evaluate side-chains 51 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 50 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 594 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 HIS A 382 HIS B 148 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.058840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2614 r_free = 0.2614 target = 0.043749 restraints weight = 22335.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2675 r_free = 0.2675 target = 0.045857 restraints weight = 11744.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.047380 restraints weight = 7696.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.048440 restraints weight = 5759.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.049189 restraints weight = 4710.491| |-----------------------------------------------------------------------------| r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.1330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 6142 Z= 0.239 Angle : 0.644 7.285 8316 Z= 0.342 Chirality : 0.045 0.143 880 Planarity : 0.005 0.055 1071 Dihedral : 5.261 36.384 909 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.15 % Allowed : 16.59 % Favored : 81.26 % 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 aren not related in a simple way. whole: 0.94 (0.31), residues: 739 helix: -0.31 (0.65), residues: 51 sheet: 1.07 (0.37), residues: 178 loop : 0.70 (0.29), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 190 TYR 0.011 0.001 TYR B 263 PHE 0.018 0.002 PHE B 221 TRP 0.009 0.002 TRP B 238 HIS 0.004 0.001 HIS A 507 Details of bonding type rmsd covalent geometry : bond 0.00531 ( 6117) covalent geometry : angle 0.63668 ( 8263) SS BOND : bond 0.00428 ( 19) SS BOND : angle 1.08556 ( 38) hydrogen bonds : bond 0.04805 ( 179) hydrogen bonds : angle 7.20014 ( 453) Misc. bond : bond 0.00087 ( 1) link_BETA1-4 : bond 0.00372 ( 1) link_BETA1-4 : angle 1.46856 ( 3) link_NAG-ASN : bond 0.00229 ( 4) link_NAG-ASN : angle 2.08771 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 51 time to evaluate : 0.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 MET cc_start: 0.8549 (ppp) cc_final: 0.8281 (ppp) REVERT: B 172 MET cc_start: 0.7664 (OUTLIER) cc_final: 0.7304 (tpt) REVERT: B 222 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8860 (tp) REVERT: B 314 MET cc_start: 0.7714 (tpp) cc_final: 0.7496 (mmm) outliers start: 14 outliers final: 7 residues processed: 63 average time/residue: 0.0652 time to fit residues: 5.8335 Evaluate side-chains 52 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 43 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 430 ASN Chi-restraints excluded: chain A residue 510 ASN Chi-restraints excluded: chain B residue 172 MET Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 222 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 36 optimal weight: 0.8980 chunk 55 optimal weight: 8.9990 chunk 29 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 28 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 chunk 32 optimal weight: 3.9990 chunk 73 optimal weight: 0.7980 chunk 70 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.058420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2599 r_free = 0.2599 target = 0.043283 restraints weight = 22319.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2660 r_free = 0.2660 target = 0.045411 restraints weight = 11696.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2702 r_free = 0.2702 target = 0.046888 restraints weight = 7686.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.047866 restraints weight = 5796.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.048636 restraints weight = 4808.307| |-----------------------------------------------------------------------------| r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 6142 Z= 0.204 Angle : 0.603 8.070 8316 Z= 0.316 Chirality : 0.045 0.144 880 Planarity : 0.004 0.053 1071 Dihedral : 4.803 25.677 907 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.46 % Allowed : 16.74 % Favored : 80.80 % 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 aren not related in a simple way. whole: 0.91 (0.31), residues: 739 helix: -0.30 (0.63), residues: 51 sheet: 0.92 (0.37), residues: 180 loop : 0.72 (0.29), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 270 TYR 0.011 0.001 TYR B 263 PHE 0.014 0.001 PHE B 221 TRP 0.009 0.001 TRP B 238 HIS 0.004 0.001 HIS A 507 Details of bonding type rmsd covalent geometry : bond 0.00456 ( 6117) covalent geometry : angle 0.59569 ( 8263) SS BOND : bond 0.00349 ( 19) SS BOND : angle 1.04104 ( 38) hydrogen bonds : bond 0.04222 ( 179) hydrogen bonds : angle 6.64881 ( 453) Misc. bond : bond 0.00072 ( 1) link_BETA1-4 : bond 0.00651 ( 1) link_BETA1-4 : angle 1.43209 ( 3) link_NAG-ASN : bond 0.00214 ( 4) link_NAG-ASN : angle 1.84162 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 48 time to evaluate : 0.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 ASP cc_start: 0.8530 (t0) cc_final: 0.8225 (t0) REVERT: A 113 GLU cc_start: 0.8507 (tp30) cc_final: 0.8280 (tp30) REVERT: A 159 MET cc_start: 0.8632 (ppp) cc_final: 0.8328 (ppp) REVERT: A 329 MET cc_start: 0.8969 (mmm) cc_final: 0.8588 (mmm) REVERT: A 588 GLN cc_start: 0.9372 (OUTLIER) cc_final: 0.8996 (pp30) REVERT: B 203 GLN cc_start: 0.8461 (mt0) cc_final: 0.8152 (mt0) REVERT: B 222 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8855 (tp) REVERT: B 244 GLN cc_start: 0.8223 (mm110) cc_final: 0.7820 (mm110) REVERT: B 270 ARG cc_start: 0.8823 (ttm-80) cc_final: 0.8567 (tpp80) REVERT: B 307 GLN cc_start: 0.9420 (mm-40) cc_final: 0.9198 (mm-40) outliers start: 16 outliers final: 9 residues processed: 62 average time/residue: 0.0749 time to fit residues: 6.4033 Evaluate side-chains 55 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 44 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 430 ASN Chi-restraints excluded: chain A residue 510 ASN Chi-restraints excluded: chain A residue 588 GLN Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 238 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 5 optimal weight: 4.9990 chunk 26 optimal weight: 8.9990 chunk 37 optimal weight: 0.5980 chunk 35 optimal weight: 0.8980 chunk 9 optimal weight: 4.9990 chunk 73 optimal weight: 8.9990 chunk 57 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 41 optimal weight: 5.9990 chunk 7 optimal weight: 0.7980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.058800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2617 r_free = 0.2617 target = 0.043852 restraints weight = 22006.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2677 r_free = 0.2677 target = 0.045959 restraints weight = 11397.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.047488 restraints weight = 7433.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.048582 restraints weight = 5554.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.049254 restraints weight = 4519.532| |-----------------------------------------------------------------------------| r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6142 Z= 0.145 Angle : 0.571 8.854 8316 Z= 0.297 Chirality : 0.044 0.155 880 Planarity : 0.004 0.045 1071 Dihedral : 4.561 21.409 907 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.61 % Allowed : 17.36 % Favored : 80.03 % 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 aren not related in a simple way. whole: 0.93 (0.31), residues: 739 helix: -0.04 (0.65), residues: 51 sheet: 0.80 (0.37), residues: 184 loop : 0.76 (0.30), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 228 TYR 0.010 0.001 TYR B 200 PHE 0.012 0.001 PHE B 221 TRP 0.008 0.001 TRP A 585 HIS 0.004 0.001 HIS A 507 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 6117) covalent geometry : angle 0.56531 ( 8263) SS BOND : bond 0.00246 ( 19) SS BOND : angle 0.92684 ( 38) hydrogen bonds : bond 0.03753 ( 179) hydrogen bonds : angle 6.50812 ( 453) Misc. bond : bond 0.00053 ( 1) link_BETA1-4 : bond 0.00673 ( 1) link_BETA1-4 : angle 1.36420 ( 3) link_NAG-ASN : bond 0.00230 ( 4) link_NAG-ASN : angle 1.65402 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 48 time to evaluate : 0.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 ASP cc_start: 0.8524 (t0) cc_final: 0.8209 (t0) REVERT: A 159 MET cc_start: 0.8736 (ppp) cc_final: 0.8375 (ppp) REVERT: A 329 MET cc_start: 0.9025 (mmm) cc_final: 0.8638 (mmm) REVERT: A 588 GLN cc_start: 0.9376 (OUTLIER) cc_final: 0.8982 (pp30) REVERT: B 222 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8787 (tp) REVERT: B 244 GLN cc_start: 0.8230 (mm110) cc_final: 0.7884 (mm110) REVERT: B 270 ARG cc_start: 0.8753 (ttm-80) cc_final: 0.8540 (tpp80) outliers start: 17 outliers final: 9 residues processed: 64 average time/residue: 0.0675 time to fit residues: 6.1140 Evaluate side-chains 54 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 43 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 430 ASN Chi-restraints excluded: chain A residue 510 ASN Chi-restraints excluded: chain A residue 588 GLN Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 238 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 25 optimal weight: 5.9990 chunk 26 optimal weight: 6.9990 chunk 53 optimal weight: 5.9990 chunk 42 optimal weight: 7.9990 chunk 19 optimal weight: 10.0000 chunk 4 optimal weight: 3.9990 chunk 1 optimal weight: 6.9990 chunk 70 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 49 optimal weight: 0.8980 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 194 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 = 0.2963 r_free = 0.2963 target = 0.055961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2536 r_free = 0.2536 target = 0.041112 restraints weight = 23079.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2596 r_free = 0.2596 target = 0.043119 restraints weight = 12077.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2638 r_free = 0.2638 target = 0.044556 restraints weight = 7963.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2667 r_free = 0.2667 target = 0.045566 restraints weight = 6028.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2688 r_free = 0.2688 target = 0.046277 restraints weight = 4970.435| |-----------------------------------------------------------------------------| r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 6142 Z= 0.333 Angle : 0.669 8.374 8316 Z= 0.353 Chirality : 0.045 0.148 880 Planarity : 0.004 0.042 1071 Dihedral : 4.918 25.139 907 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.92 % Allowed : 19.51 % Favored : 77.57 % 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 aren not related in a simple way. whole: 0.59 (0.31), residues: 739 helix: -0.43 (0.61), residues: 51 sheet: 0.62 (0.36), residues: 185 loop : 0.52 (0.30), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 277 TYR 0.011 0.002 TYR A 438 PHE 0.015 0.002 PHE B 258 TRP 0.011 0.002 TRP B 238 HIS 0.005 0.001 HIS A 507 Details of bonding type rmsd covalent geometry : bond 0.00727 ( 6117) covalent geometry : angle 0.66119 ( 8263) SS BOND : bond 0.00513 ( 19) SS BOND : angle 1.07622 ( 38) hydrogen bonds : bond 0.04337 ( 179) hydrogen bonds : angle 6.53874 ( 453) Misc. bond : bond 0.00107 ( 1) link_BETA1-4 : bond 0.00739 ( 1) link_BETA1-4 : angle 1.84669 ( 3) link_NAG-ASN : bond 0.00336 ( 4) link_NAG-ASN : angle 2.07906 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 43 time to evaluate : 0.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 ASP cc_start: 0.8574 (t0) cc_final: 0.8290 (t0) REVERT: A 159 MET cc_start: 0.8658 (ppp) cc_final: 0.8288 (ppp) REVERT: A 329 MET cc_start: 0.9052 (mmm) cc_final: 0.8798 (mmm) REVERT: A 417 TRP cc_start: 0.8547 (p-90) cc_final: 0.8330 (p90) REVERT: B 203 GLN cc_start: 0.8949 (mt0) cc_final: 0.8372 (mt0) REVERT: B 244 GLN cc_start: 0.8054 (mm110) cc_final: 0.7800 (mm110) REVERT: B 270 ARG cc_start: 0.8835 (ttm-80) cc_final: 0.8629 (tpp80) REVERT: B 271 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8511 (mm) REVERT: B 307 GLN cc_start: 0.9517 (mm-40) cc_final: 0.9253 (mm-40) REVERT: B 314 MET cc_start: 0.7794 (mmm) cc_final: 0.7400 (tpp) outliers start: 19 outliers final: 15 residues processed: 60 average time/residue: 0.0688 time to fit residues: 5.8260 Evaluate side-chains 58 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 42 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 86 TYR Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 430 ASN Chi-restraints excluded: chain A residue 510 ASN Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 238 TRP Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 271 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 29 optimal weight: 6.9990 chunk 71 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 24 optimal weight: 0.2980 chunk 40 optimal weight: 0.8980 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.057806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2588 r_free = 0.2588 target = 0.042870 restraints weight = 22142.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2648 r_free = 0.2648 target = 0.044956 restraints weight = 11563.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.046454 restraints weight = 7569.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.047471 restraints weight = 5667.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.048135 restraints weight = 4663.312| |-----------------------------------------------------------------------------| r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6142 Z= 0.153 Angle : 0.570 9.926 8316 Z= 0.299 Chirality : 0.044 0.158 880 Planarity : 0.004 0.040 1071 Dihedral : 4.522 22.479 907 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.15 % Allowed : 20.43 % Favored : 77.42 % 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 aren not related in a simple way. whole: 0.78 (0.32), residues: 739 helix: 0.05 (0.62), residues: 51 sheet: 0.61 (0.37), residues: 182 loop : 0.67 (0.30), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 228 TYR 0.008 0.001 TYR B 224 PHE 0.012 0.001 PHE B 258 TRP 0.010 0.001 TRP A 585 HIS 0.004 0.001 HIS A 507 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 6117) covalent geometry : angle 0.56427 ( 8263) SS BOND : bond 0.00253 ( 19) SS BOND : angle 0.92535 ( 38) hydrogen bonds : bond 0.03664 ( 179) hydrogen bonds : angle 6.23541 ( 453) Misc. bond : bond 0.00057 ( 1) link_BETA1-4 : bond 0.00581 ( 1) link_BETA1-4 : angle 1.39752 ( 3) link_NAG-ASN : bond 0.00242 ( 4) link_NAG-ASN : angle 1.66056 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 44 time to evaluate : 0.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 ASP cc_start: 0.8583 (t0) cc_final: 0.8274 (t0) REVERT: A 113 GLU cc_start: 0.8464 (tp30) cc_final: 0.8174 (tp30) REVERT: A 159 MET cc_start: 0.8755 (ppp) cc_final: 0.8344 (ppp) REVERT: A 329 MET cc_start: 0.9050 (mmm) cc_final: 0.8764 (mmm) REVERT: A 588 GLN cc_start: 0.9399 (OUTLIER) cc_final: 0.8946 (pp30) REVERT: B 203 GLN cc_start: 0.8926 (mt0) cc_final: 0.8329 (mt0) REVERT: B 222 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8797 (tp) REVERT: B 244 GLN cc_start: 0.8229 (mm110) cc_final: 0.7915 (mm110) outliers start: 14 outliers final: 9 residues processed: 57 average time/residue: 0.0702 time to fit residues: 5.4597 Evaluate side-chains 54 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 43 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 430 ASN Chi-restraints excluded: chain A residue 588 GLN Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 238 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 4 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 28 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 71 optimal weight: 0.9990 chunk 16 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 17 optimal weight: 0.2980 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.058348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2606 r_free = 0.2606 target = 0.043486 restraints weight = 22059.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2665 r_free = 0.2665 target = 0.045545 restraints weight = 11625.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2707 r_free = 0.2707 target = 0.047031 restraints weight = 7668.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.048060 restraints weight = 5776.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.048688 restraints weight = 4742.010| |-----------------------------------------------------------------------------| r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6142 Z= 0.134 Angle : 0.589 10.608 8316 Z= 0.305 Chirality : 0.044 0.180 880 Planarity : 0.003 0.039 1071 Dihedral : 4.378 20.636 907 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.30 % Allowed : 20.43 % Favored : 77.27 % 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 aren not related in a simple way. whole: 0.91 (0.32), residues: 739 helix: 0.27 (0.64), residues: 51 sheet: 0.71 (0.37), residues: 181 loop : 0.75 (0.30), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 270 TYR 0.007 0.001 TYR B 224 PHE 0.012 0.001 PHE B 258 TRP 0.010 0.001 TRP A 417 HIS 0.004 0.001 HIS A 507 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 6117) covalent geometry : angle 0.58413 ( 8263) SS BOND : bond 0.00229 ( 19) SS BOND : angle 0.97130 ( 38) hydrogen bonds : bond 0.03497 ( 179) hydrogen bonds : angle 6.23422 ( 453) Misc. bond : bond 0.00049 ( 1) link_BETA1-4 : bond 0.00828 ( 1) link_BETA1-4 : angle 1.45684 ( 3) link_NAG-ASN : bond 0.00244 ( 4) link_NAG-ASN : angle 1.53494 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 42 time to evaluate : 0.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 ASP cc_start: 0.8562 (t0) cc_final: 0.8267 (t0) REVERT: A 159 MET cc_start: 0.8800 (ppp) cc_final: 0.8296 (ppp) REVERT: A 329 MET cc_start: 0.9030 (mmm) cc_final: 0.8725 (mmm) REVERT: A 382 HIS cc_start: 0.8117 (t-90) cc_final: 0.7901 (t70) REVERT: A 588 GLN cc_start: 0.9386 (OUTLIER) cc_final: 0.8947 (pp30) REVERT: B 203 GLN cc_start: 0.8814 (mt0) cc_final: 0.8268 (mt0) REVERT: B 222 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8800 (tp) REVERT: B 244 GLN cc_start: 0.8237 (mm110) cc_final: 0.7972 (mm110) outliers start: 15 outliers final: 10 residues processed: 56 average time/residue: 0.0635 time to fit residues: 5.0823 Evaluate side-chains 54 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 42 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 86 TYR Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 588 GLN Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 238 TRP Chi-restraints excluded: chain B residue 305 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 31 optimal weight: 0.9980 chunk 21 optimal weight: 9.9990 chunk 44 optimal weight: 0.9990 chunk 41 optimal weight: 5.9990 chunk 10 optimal weight: 8.9990 chunk 39 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 chunk 59 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.058687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2615 r_free = 0.2615 target = 0.043714 restraints weight = 22145.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2674 r_free = 0.2674 target = 0.045785 restraints weight = 11724.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.047269 restraints weight = 7726.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.048245 restraints weight = 5816.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.049003 restraints weight = 4815.499| |-----------------------------------------------------------------------------| r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.2692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6142 Z= 0.129 Angle : 0.592 10.982 8316 Z= 0.304 Chirality : 0.044 0.190 880 Planarity : 0.003 0.038 1071 Dihedral : 4.271 20.921 907 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.69 % Allowed : 21.51 % Favored : 76.80 % 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 aren not related in a simple way. whole: 0.90 (0.32), residues: 739 helix: 0.28 (0.65), residues: 51 sheet: 0.59 (0.38), residues: 179 loop : 0.78 (0.30), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 228 TYR 0.007 0.001 TYR B 308 PHE 0.012 0.001 PHE B 258 TRP 0.009 0.001 TRP A 166 HIS 0.003 0.001 HIS A 507 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 6117) covalent geometry : angle 0.58708 ( 8263) SS BOND : bond 0.00237 ( 19) SS BOND : angle 0.97962 ( 38) hydrogen bonds : bond 0.03442 ( 179) hydrogen bonds : angle 6.12995 ( 453) Misc. bond : bond 0.00043 ( 1) link_BETA1-4 : bond 0.00649 ( 1) link_BETA1-4 : angle 1.45667 ( 3) link_NAG-ASN : bond 0.00249 ( 4) link_NAG-ASN : angle 1.43285 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 44 time to evaluate : 0.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 ASP cc_start: 0.8577 (t0) cc_final: 0.8280 (t0) REVERT: A 159 MET cc_start: 0.8857 (ppp) cc_final: 0.8308 (ppp) REVERT: A 329 MET cc_start: 0.9052 (mmm) cc_final: 0.8750 (mmm) REVERT: A 588 GLN cc_start: 0.9378 (OUTLIER) cc_final: 0.8948 (pp30) REVERT: B 203 GLN cc_start: 0.8893 (mt0) cc_final: 0.8514 (mt0) REVERT: B 222 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8810 (tp) REVERT: B 244 GLN cc_start: 0.8227 (mm110) cc_final: 0.7952 (mm110) REVERT: B 307 GLN cc_start: 0.9357 (mm-40) cc_final: 0.9150 (mm110) outliers start: 11 outliers final: 9 residues processed: 55 average time/residue: 0.0649 time to fit residues: 5.0008 Evaluate side-chains 53 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 42 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 588 GLN Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 238 TRP Chi-restraints excluded: chain B residue 305 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 45 optimal weight: 7.9990 chunk 48 optimal weight: 0.6980 chunk 41 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 chunk 42 optimal weight: 7.9990 chunk 69 optimal weight: 0.0870 chunk 4 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 26 optimal weight: 9.9990 chunk 28 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 overall best weight: 1.5564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 148 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.058262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2607 r_free = 0.2607 target = 0.043405 restraints weight = 22218.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2666 r_free = 0.2666 target = 0.045467 restraints weight = 11676.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.046940 restraints weight = 7680.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.047968 restraints weight = 5777.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.048630 restraints weight = 4744.826| |-----------------------------------------------------------------------------| r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6142 Z= 0.151 Angle : 0.601 10.872 8316 Z= 0.310 Chirality : 0.044 0.186 880 Planarity : 0.003 0.037 1071 Dihedral : 4.247 21.233 907 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.69 % Allowed : 21.66 % Favored : 76.65 % 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 aren not related in a simple way. whole: 0.89 (0.32), residues: 739 helix: 0.30 (0.65), residues: 51 sheet: 0.59 (0.38), residues: 179 loop : 0.77 (0.30), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 228 TYR 0.009 0.001 TYR B 200 PHE 0.012 0.001 PHE B 258 TRP 0.013 0.001 TRP A 417 HIS 0.003 0.001 HIS A 507 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 6117) covalent geometry : angle 0.59665 ( 8263) SS BOND : bond 0.00251 ( 19) SS BOND : angle 0.92928 ( 38) hydrogen bonds : bond 0.03462 ( 179) hydrogen bonds : angle 6.14937 ( 453) Misc. bond : bond 0.00063 ( 1) link_BETA1-4 : bond 0.00712 ( 1) link_BETA1-4 : angle 1.55653 ( 3) link_NAG-ASN : bond 0.00215 ( 4) link_NAG-ASN : angle 1.44788 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 43 time to evaluate : 0.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 ASP cc_start: 0.8609 (t0) cc_final: 0.8310 (t0) REVERT: A 159 MET cc_start: 0.8840 (ppp) cc_final: 0.8175 (ppp) REVERT: A 329 MET cc_start: 0.9070 (mmm) cc_final: 0.8769 (mmm) REVERT: A 588 GLN cc_start: 0.9387 (OUTLIER) cc_final: 0.8949 (pp30) REVERT: B 203 GLN cc_start: 0.8917 (mt0) cc_final: 0.8352 (mt0) REVERT: B 222 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8810 (tp) outliers start: 11 outliers final: 6 residues processed: 54 average time/residue: 0.0678 time to fit residues: 5.1692 Evaluate side-chains 48 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 40 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 588 GLN Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 238 TRP Chi-restraints excluded: chain B residue 305 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 26 optimal weight: 0.9990 chunk 57 optimal weight: 7.9990 chunk 39 optimal weight: 4.9990 chunk 1 optimal weight: 0.1980 chunk 29 optimal weight: 1.9990 chunk 68 optimal weight: 0.4980 chunk 17 optimal weight: 10.0000 chunk 56 optimal weight: 2.9990 chunk 50 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 13 optimal weight: 8.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 HIS B 148 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.058977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2616 r_free = 0.2616 target = 0.043866 restraints weight = 22258.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2675 r_free = 0.2675 target = 0.045916 restraints weight = 11860.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.047409 restraints weight = 7834.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.048448 restraints weight = 5906.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.049126 restraints weight = 4866.965| |-----------------------------------------------------------------------------| r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6142 Z= 0.127 Angle : 0.596 11.112 8316 Z= 0.305 Chirality : 0.044 0.182 880 Planarity : 0.003 0.038 1071 Dihedral : 4.128 19.965 907 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 1.84 % Allowed : 22.12 % Favored : 76.04 % 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 aren not related in a simple way. whole: 0.96 (0.32), residues: 739 helix: 0.39 (0.66), residues: 51 sheet: 0.65 (0.38), residues: 179 loop : 0.81 (0.30), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 228 TYR 0.009 0.001 TYR B 200 PHE 0.010 0.001 PHE B 258 TRP 0.009 0.001 TRP A 585 HIS 0.008 0.001 HIS A 382 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 6117) covalent geometry : angle 0.59213 ( 8263) SS BOND : bond 0.00198 ( 19) SS BOND : angle 0.92622 ( 38) hydrogen bonds : bond 0.03321 ( 179) hydrogen bonds : angle 6.07750 ( 453) Misc. bond : bond 0.00035 ( 1) link_BETA1-4 : bond 0.00703 ( 1) link_BETA1-4 : angle 1.44523 ( 3) link_NAG-ASN : bond 0.00239 ( 4) link_NAG-ASN : angle 1.32230 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 40 time to evaluate : 0.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 ASP cc_start: 0.8579 (t0) cc_final: 0.8270 (t0) REVERT: A 113 GLU cc_start: 0.8534 (tp30) cc_final: 0.8296 (tp30) REVERT: A 159 MET cc_start: 0.8954 (ppp) cc_final: 0.8426 (ppp) REVERT: A 242 ASP cc_start: 0.8364 (p0) cc_final: 0.7932 (t0) REVERT: A 329 MET cc_start: 0.9010 (mmm) cc_final: 0.8687 (mmm) REVERT: A 588 GLN cc_start: 0.9386 (OUTLIER) cc_final: 0.8964 (pp30) REVERT: B 203 GLN cc_start: 0.8909 (mt0) cc_final: 0.8588 (mt0) REVERT: B 222 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8792 (tp) outliers start: 12 outliers final: 9 residues processed: 52 average time/residue: 0.0602 time to fit residues: 4.5050 Evaluate side-chains 51 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 40 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 588 GLN Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 238 TRP Chi-restraints excluded: chain B residue 305 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 39 optimal weight: 5.9990 chunk 19 optimal weight: 0.9980 chunk 50 optimal weight: 7.9990 chunk 61 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 58 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 148 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.059513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2636 r_free = 0.2636 target = 0.044428 restraints weight = 22073.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.046518 restraints weight = 11596.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.047988 restraints weight = 7614.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.049057 restraints weight = 5719.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.049769 restraints weight = 4692.050| |-----------------------------------------------------------------------------| r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.2915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6142 Z= 0.116 Angle : 0.589 11.314 8316 Z= 0.301 Chirality : 0.044 0.180 880 Planarity : 0.003 0.038 1071 Dihedral : 4.022 19.990 907 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.54 % Allowed : 22.12 % Favored : 76.34 % 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 aren not related in a simple way. whole: 1.00 (0.32), residues: 739 helix: 0.49 (0.67), residues: 51 sheet: 0.69 (0.38), residues: 179 loop : 0.83 (0.30), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 228 TYR 0.008 0.001 TYR B 308 PHE 0.011 0.001 PHE B 258 TRP 0.010 0.001 TRP A 166 HIS 0.003 0.001 HIS A 507 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 6117) covalent geometry : angle 0.58579 ( 8263) SS BOND : bond 0.00177 ( 19) SS BOND : angle 0.87985 ( 38) hydrogen bonds : bond 0.03208 ( 179) hydrogen bonds : angle 6.01521 ( 453) Misc. bond : bond 0.00027 ( 1) link_BETA1-4 : bond 0.00635 ( 1) link_BETA1-4 : angle 1.42552 ( 3) link_NAG-ASN : bond 0.00260 ( 4) link_NAG-ASN : angle 1.24551 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 966.79 seconds wall clock time: 17 minutes 34.37 seconds (1054.37 seconds total)