Starting phenix.real_space_refine on Thu Jul 2 06:49:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7f3x_31442/07_2026/7f3x_31442.cif Found real_map, /net/cci-nas-00/data/ceres_data/7f3x_31442/07_2026/7f3x_31442.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7f3x_31442/07_2026/7f3x_31442.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7f3x_31442/07_2026/7f3x_31442.map" model { file = "/net/cci-nas-00/data/ceres_data/7f3x_31442/07_2026/7f3x_31442.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7f3x_31442/07_2026/7f3x_31442.cif" } resolution = 3.57 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= 0.005 sd= 0.061 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 46 5.16 5 C 4968 2.51 5 N 1148 2.21 5 O 1244 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7408 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3675 Classifications: {'peptide': 449} Link IDs: {'PTRANS': 17, 'TRANS': 431} Chain: "B" Number of atoms: 3675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3675 Classifications: {'peptide': 449} Link IDs: {'PTRANS': 17, 'TRANS': 431} Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'LAP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'LAP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.21, per 1000 atoms: 0.16 Number of scatterers: 7408 At special positions: 0 Unit cell: (111.8, 117.82, 77.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 46 16.00 P 2 15.00 O 1244 8.00 N 1148 7.00 C 4968 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.56 Conformation dependent library (CDL) restraints added in 254.5 milliseconds 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1680 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 2 sheets defined 69.6% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 42 through 50 Processing helix chain 'A' and resid 52 through 64 removed outlier: 3.556A pdb=" N LEU A 56 " --> pdb=" O SER A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 76 removed outlier: 3.879A pdb=" N PHE A 68 " --> pdb=" O MET A 64 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR A 74 " --> pdb=" O LEU A 70 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU A 76 " --> pdb=" O GLN A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 100 Processing helix chain 'A' and resid 103 through 120 removed outlier: 4.250A pdb=" N SER A 107 " --> pdb=" O GLN A 103 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU A 112 " --> pdb=" O LEU A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 147 removed outlier: 4.291A pdb=" N VAL A 128 " --> pdb=" O THR A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 177 removed outlier: 3.904A pdb=" N HIS A 159 " --> pdb=" O TRP A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 190 Processing helix chain 'A' and resid 197 through 206 Processing helix chain 'A' and resid 219 through 227 Processing helix chain 'A' and resid 240 through 262 removed outlier: 3.508A pdb=" N ALA A 244 " --> pdb=" O SER A 240 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LYS A 246 " --> pdb=" O VAL A 242 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG A 247 " --> pdb=" O PRO A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 290 Processing helix chain 'A' and resid 294 through 311 removed outlier: 4.200A pdb=" N TYR A 298 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N THR A 300 " --> pdb=" O TYR A 296 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N CYS A 301 " --> pdb=" O LYS A 297 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TRP A 302 " --> pdb=" O TYR A 298 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL A 308 " --> pdb=" O VAL A 304 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU A 311 " --> pdb=" O GLY A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 348 removed outlier: 3.809A pdb=" N THR A 347 " --> pdb=" O PHE A 344 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE A 348 " --> pdb=" O THR A 345 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 344 through 348' Processing helix chain 'A' and resid 353 through 363 Processing helix chain 'A' and resid 364 through 367 Processing helix chain 'A' and resid 375 through 388 removed outlier: 3.918A pdb=" N LEU A 381 " --> pdb=" O GLN A 377 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N HIS A 388 " --> pdb=" O LEU A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 415 removed outlier: 3.569A pdb=" N VAL A 396 " --> pdb=" O SER A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 427 removed outlier: 4.417A pdb=" N LEU A 424 " --> pdb=" O THR A 420 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N SER A 426 " --> pdb=" O SER A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 455 removed outlier: 3.985A pdb=" N SER A 449 " --> pdb=" O PHE A 445 " (cutoff:3.500A) Proline residue: A 452 - end of helix Processing helix chain 'A' and resid 459 through 467 removed outlier: 4.248A pdb=" N SER A 467 " --> pdb=" O LYS A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 490 Proline residue: A 484 - end of helix Processing helix chain 'B' and resid 43 through 50 Processing helix chain 'B' and resid 52 through 64 removed outlier: 3.563A pdb=" N LEU B 56 " --> pdb=" O SER B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 75 removed outlier: 3.977A pdb=" N PHE B 68 " --> pdb=" O MET B 64 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TYR B 74 " --> pdb=" O LEU B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 100 Processing helix chain 'B' and resid 104 through 120 removed outlier: 3.656A pdb=" N LEU B 108 " --> pdb=" O PHE B 104 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ILE B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLN B 114 " --> pdb=" O CYS B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 147 removed outlier: 4.372A pdb=" N VAL B 128 " --> pdb=" O THR B 124 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE B 129 " --> pdb=" O VAL B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 175 removed outlier: 3.832A pdb=" N HIS B 159 " --> pdb=" O TRP B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 191 Processing helix chain 'B' and resid 197 through 206 Processing helix chain 'B' and resid 219 through 227 removed outlier: 3.701A pdb=" N GLN B 223 " --> pdb=" O MET B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 262 removed outlier: 4.204A pdb=" N LYS B 246 " --> pdb=" O VAL B 242 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ARG B 247 " --> pdb=" O PRO B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 290 Processing helix chain 'B' and resid 294 through 311 removed outlier: 4.197A pdb=" N TYR B 298 " --> pdb=" O ILE B 294 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THR B 300 " --> pdb=" O TYR B 296 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N CYS B 301 " --> pdb=" O LYS B 297 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TRP B 302 " --> pdb=" O TYR B 298 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL B 308 " --> pdb=" O VAL B 304 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU B 311 " --> pdb=" O GLY B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 348 removed outlier: 3.920A pdb=" N THR B 347 " --> pdb=" O PHE B 344 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE B 348 " --> pdb=" O THR B 345 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 344 through 348' Processing helix chain 'B' and resid 354 through 363 removed outlier: 3.631A pdb=" N TRP B 358 " --> pdb=" O ASN B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 388 removed outlier: 4.109A pdb=" N LEU B 381 " --> pdb=" O GLN B 377 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N PHE B 382 " --> pdb=" O ALA B 378 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N HIS B 388 " --> pdb=" O LEU B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 415 removed outlier: 3.552A pdb=" N VAL B 396 " --> pdb=" O SER B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 455 removed outlier: 4.019A pdb=" N SER B 449 " --> pdb=" O PHE B 445 " (cutoff:3.500A) Proline residue: B 452 - end of helix Processing helix chain 'B' and resid 457 through 467 removed outlier: 3.845A pdb=" N MET B 462 " --> pdb=" O TRP B 458 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N SER B 467 " --> pdb=" O LYS B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 490 Proline residue: B 484 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 318 through 319 removed outlier: 4.271A pdb=" N GLY A 318 " --> pdb=" O VAL A 326 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 318 through 319 removed outlier: 4.275A pdb=" N GLY B 318 " --> pdb=" O VAL B 326 " (cutoff:3.500A) 396 hydrogen bonds defined for protein. 1185 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.70 Time building geometry restraints manager: 0.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1068 1.31 - 1.44: 2330 1.44 - 1.56: 4154 1.56 - 1.69: 4 1.69 - 1.81: 76 Bond restraints: 7632 Sorted by residual: bond pdb=" C1 LAP B 601 " pdb=" C2 LAP B 601 " ideal model delta sigma weight residual 1.497 1.545 -0.048 2.00e-02 2.50e+03 5.79e+00 bond pdb=" C1 LAP A 601 " pdb=" C2 LAP A 601 " ideal model delta sigma weight residual 1.497 1.545 -0.048 2.00e-02 2.50e+03 5.75e+00 bond pdb=" C1 LAP A 601 " pdb=" O1 LAP A 601 " ideal model delta sigma weight residual 1.366 1.414 -0.048 2.00e-02 2.50e+03 5.69e+00 bond pdb=" C14 LAP A 601 " pdb=" O3 LAP A 601 " ideal model delta sigma weight residual 1.436 1.389 0.047 2.00e-02 2.50e+03 5.52e+00 bond pdb=" C1 LAP B 601 " pdb=" O1 LAP B 601 " ideal model delta sigma weight residual 1.366 1.413 -0.047 2.00e-02 2.50e+03 5.50e+00 ... (remaining 7627 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.51: 10219 2.51 - 5.01: 131 5.01 - 7.52: 15 7.52 - 10.02: 7 10.02 - 12.53: 4 Bond angle restraints: 10376 Sorted by residual: angle pdb=" O5 LAP A 601 " pdb=" P9 LAP A 601 " pdb=" O7 LAP A 601 " ideal model delta sigma weight residual 121.86 109.33 12.53 3.00e+00 1.11e-01 1.74e+01 angle pdb=" O5 LAP B 601 " pdb=" P9 LAP B 601 " pdb=" O7 LAP B 601 " ideal model delta sigma weight residual 121.86 109.34 12.52 3.00e+00 1.11e-01 1.74e+01 angle pdb=" O4 LAP B 601 " pdb=" P9 LAP B 601 " pdb=" O6 LAP B 601 " ideal model delta sigma weight residual 98.02 109.52 -11.50 3.00e+00 1.11e-01 1.47e+01 angle pdb=" O4 LAP A 601 " pdb=" P9 LAP A 601 " pdb=" O6 LAP A 601 " ideal model delta sigma weight residual 98.02 109.44 -11.42 3.00e+00 1.11e-01 1.45e+01 angle pdb=" C SER B 272 " pdb=" N ASP B 273 " pdb=" CA ASP B 273 " ideal model delta sigma weight residual 121.54 128.14 -6.60 1.91e+00 2.74e-01 1.19e+01 ... (remaining 10371 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 3864 17.90 - 35.80: 403 35.80 - 53.69: 105 53.69 - 71.59: 16 71.59 - 89.49: 4 Dihedral angle restraints: 4392 sinusoidal: 1756 harmonic: 2636 Sorted by residual: dihedral pdb=" CA TRP B 155 " pdb=" C TRP B 155 " pdb=" N THR B 156 " pdb=" CA THR B 156 " ideal model delta harmonic sigma weight residual 180.00 -162.04 -17.96 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA GLN B 431 " pdb=" C GLN B 431 " pdb=" N PRO B 432 " pdb=" CA PRO B 432 " ideal model delta harmonic sigma weight residual 180.00 162.10 17.90 0 5.00e+00 4.00e-02 1.28e+01 dihedral pdb=" CA TRP A 155 " pdb=" C TRP A 155 " pdb=" N THR A 156 " pdb=" CA THR A 156 " ideal model delta harmonic sigma weight residual -180.00 -162.61 -17.39 0 5.00e+00 4.00e-02 1.21e+01 ... (remaining 4389 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 823 0.040 - 0.079: 263 0.079 - 0.119: 58 0.119 - 0.159: 6 0.159 - 0.199: 4 Chirality restraints: 1154 Sorted by residual: chirality pdb=" CB THR A 341 " pdb=" CA THR A 341 " pdb=" OG1 THR A 341 " pdb=" CG2 THR A 341 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 9.86e-01 chirality pdb=" CB THR B 341 " pdb=" CA THR B 341 " pdb=" OG1 THR B 341 " pdb=" CG2 THR B 341 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 8.53e-01 chirality pdb=" CA MET B 157 " pdb=" N MET B 157 " pdb=" C MET B 157 " pdb=" CB MET B 157 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.61e-01 ... (remaining 1151 not shown) Planarity restraints: 1250 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 233 " 0.029 5.00e-02 4.00e+02 4.47e-02 3.19e+00 pdb=" N PRO A 234 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 234 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 234 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TRP B 302 " 0.008 2.00e-02 2.50e+03 1.61e-02 2.60e+00 pdb=" C TRP B 302 " -0.028 2.00e-02 2.50e+03 pdb=" O TRP B 302 " 0.010 2.00e-02 2.50e+03 pdb=" N LEU B 303 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP A 302 " 0.008 2.00e-02 2.50e+03 1.58e-02 2.50e+00 pdb=" C TRP A 302 " -0.027 2.00e-02 2.50e+03 pdb=" O TRP A 302 " 0.010 2.00e-02 2.50e+03 pdb=" N LEU A 303 " 0.009 2.00e-02 2.50e+03 ... (remaining 1247 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 74 2.67 - 3.23: 7375 3.23 - 3.79: 10736 3.79 - 4.34: 13692 4.34 - 4.90: 22252 Nonbonded interactions: 54129 Sorted by model distance: nonbonded pdb=" OG1 THR B 197 " pdb=" OE1 GLU B 200 " model vdw 2.117 3.040 nonbonded pdb=" OG1 THR A 197 " pdb=" OE1 GLU A 200 " model vdw 2.188 3.040 nonbonded pdb=" OH TYR B 448 " pdb=" OH TYR B 465 " model vdw 2.202 3.040 nonbonded pdb=" OH TYR A 448 " pdb=" OH TYR A 465 " model vdw 2.202 3.040 nonbonded pdb=" OE1 GLN A 135 " pdb=" OG1 THR A 163 " model vdw 2.252 3.040 ... (remaining 54124 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 1.130 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: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.770 Find NCS groups from input model: 0.080 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: 0.010 Load rotamer database and sin/cos tables:1.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 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 : 0.003 0.048 7632 Z= 0.170 Angle : 0.738 12.525 10376 Z= 0.370 Chirality : 0.040 0.199 1154 Planarity : 0.004 0.045 1250 Dihedral : 15.720 89.491 2712 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.16 % Favored : 92.62 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.30), residues: 894 helix: 0.66 (0.22), residues: 596 sheet: None (None), residues: 0 loop : -2.67 (0.36), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 409 TYR 0.013 0.001 TYR B 82 PHE 0.012 0.001 PHE A 105 TRP 0.022 0.001 TRP B 461 HIS 0.005 0.001 HIS A 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.17 ( 7632) covalent geometry : angle 0.73838 / 0.37 (10376) hydrogen bonds : bond 0.17153 / 10.79 ( 396) hydrogen bonds : angle 6.29942 / 4.61 ( 1185) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 0.186 Fit side-chains REVERT: A 124 THR cc_start: 0.8776 (t) cc_final: 0.8510 (p) REVERT: A 338 TYR cc_start: 0.8316 (t80) cc_final: 0.7976 (t80) REVERT: B 102 MET cc_start: 0.6755 (tpt) cc_final: 0.6301 (tpp) REVERT: B 338 TYR cc_start: 0.8313 (t80) cc_final: 0.8040 (t80) outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 0.0563 time to fit residues: 13.0262 Evaluate side-chains 127 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 49 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.0570 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 0.0870 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 overall best weight: 1.0080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 439 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.135023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.101372 restraints weight = 12159.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.106335 restraints weight = 7212.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.107921 restraints weight = 4735.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.108031 restraints weight = 3793.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.108591 restraints weight = 3981.375| |-----------------------------------------------------------------------------| r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.1287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7632 Z= 0.143 Angle : 0.653 9.174 10376 Z= 0.329 Chirality : 0.042 0.185 1154 Planarity : 0.004 0.042 1250 Dihedral : 9.040 60.720 1048 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.72 % Favored : 92.17 % Rotamer: Outliers : 0.63 % Allowed : 10.48 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.30), residues: 894 helix: 1.07 (0.22), residues: 620 sheet: None (None), residues: 0 loop : -2.65 (0.39), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 193 TYR 0.017 0.001 TYR A 174 PHE 0.016 0.001 PHE A 369 TRP 0.011 0.001 TRP B 461 HIS 0.005 0.001 HIS A 388 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 ( 7632) covalent geometry : angle 0.65266 / 0.33 (10376) hydrogen bonds : bond 0.04894 / 3.12 ( 396) hydrogen bonds : angle 4.02786 / 3.00 ( 1185) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 143 time to evaluate : 0.249 Fit side-chains REVERT: B 102 MET cc_start: 0.7136 (tpt) cc_final: 0.6591 (tpp) REVERT: B 173 TYR cc_start: 0.7748 (t80) cc_final: 0.7531 (t80) outliers start: 5 outliers final: 3 residues processed: 145 average time/residue: 0.0452 time to fit residues: 9.8489 Evaluate side-chains 125 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 122 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain B residue 248 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 54 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 87 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 39 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 99 ASN A 388 HIS B 388 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.131281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.097441 restraints weight = 11727.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.101579 restraints weight = 7923.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.103679 restraints weight = 5132.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.103317 restraints weight = 4058.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.103933 restraints weight = 4385.995| |-----------------------------------------------------------------------------| r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 7632 Z= 0.216 Angle : 0.691 6.655 10376 Z= 0.353 Chirality : 0.045 0.281 1154 Planarity : 0.004 0.039 1250 Dihedral : 8.839 54.845 1048 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.95 % Favored : 90.94 % Rotamer: Outliers : 1.52 % Allowed : 14.02 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.30), residues: 894 helix: 0.96 (0.22), residues: 626 sheet: None (None), residues: 0 loop : -2.85 (0.38), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 237 TYR 0.018 0.002 TYR A 269 PHE 0.017 0.002 PHE A 364 TRP 0.012 0.001 TRP B 155 HIS 0.006 0.001 HIS A 442 Details of bonding type rmsd/Z covalent geometry : bond 0.00509 / 0.22 ( 7632) covalent geometry : angle 0.69103 / 0.35 (10376) hydrogen bonds : bond 0.05807 / 3.68 ( 396) hydrogen bonds : angle 4.00589 / 3.00 ( 1185) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 130 time to evaluate : 0.217 Fit side-chains REVERT: B 102 MET cc_start: 0.7326 (tpt) cc_final: 0.6905 (tpp) REVERT: B 173 TYR cc_start: 0.7969 (t80) cc_final: 0.7751 (t80) REVERT: B 175 ASP cc_start: 0.7140 (t0) cc_final: 0.6881 (t0) outliers start: 12 outliers final: 9 residues processed: 141 average time/residue: 0.0471 time to fit residues: 9.9590 Evaluate side-chains 134 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 125 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 289 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 22 optimal weight: 0.0040 chunk 10 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 27 optimal weight: 5.9990 chunk 63 optimal weight: 6.9990 chunk 69 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 56 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 216 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 = 0.3706 r_free = 0.3706 target = 0.135886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.102970 restraints weight = 11897.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.106598 restraints weight = 6966.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.108852 restraints weight = 5082.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.110416 restraints weight = 4237.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.111259 restraints weight = 3760.474| |-----------------------------------------------------------------------------| r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7632 Z= 0.120 Angle : 0.609 7.043 10376 Z= 0.310 Chirality : 0.041 0.269 1154 Planarity : 0.004 0.038 1250 Dihedral : 8.538 54.689 1048 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.72 % Favored : 92.17 % Rotamer: Outliers : 0.88 % Allowed : 17.55 % Favored : 81.57 % 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 are not related in a simple way. whole: 0.22 (0.30), residues: 894 helix: 1.30 (0.22), residues: 616 sheet: None (None), residues: 0 loop : -2.59 (0.38), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 237 TYR 0.013 0.001 TYR B 66 PHE 0.012 0.001 PHE A 445 TRP 0.011 0.001 TRP B 461 HIS 0.002 0.001 HIS B 442 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.12 ( 7632) covalent geometry : angle 0.60858 / 0.31 (10376) hydrogen bonds : bond 0.04300 / 2.75 ( 396) hydrogen bonds : angle 3.62754 / 2.72 ( 1185) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 134 time to evaluate : 0.250 Fit side-chains REVERT: B 102 MET cc_start: 0.7173 (tpt) cc_final: 0.6705 (tpp) REVERT: B 173 TYR cc_start: 0.7738 (t80) cc_final: 0.7415 (t80) outliers start: 7 outliers final: 6 residues processed: 137 average time/residue: 0.0476 time to fit residues: 9.8698 Evaluate side-chains 138 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 132 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 461 TRP Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 266 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 36 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 75 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 74 optimal weight: 0.7980 chunk 76 optimal weight: 0.3980 chunk 83 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.137877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.105154 restraints weight = 11720.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.108845 restraints weight = 6692.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.111213 restraints weight = 4808.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.112482 restraints weight = 3959.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.113775 restraints weight = 3544.312| |-----------------------------------------------------------------------------| r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7632 Z= 0.122 Angle : 0.605 7.461 10376 Z= 0.306 Chirality : 0.041 0.207 1154 Planarity : 0.004 0.037 1250 Dihedral : 8.254 54.340 1048 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.17 % Favored : 91.72 % Rotamer: Outliers : 1.52 % Allowed : 18.56 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.30), residues: 894 helix: 1.42 (0.22), residues: 616 sheet: None (None), residues: 0 loop : -2.57 (0.38), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 237 TYR 0.011 0.001 TYR B 82 PHE 0.019 0.001 PHE B 344 TRP 0.008 0.001 TRP A 458 HIS 0.002 0.001 HIS A 442 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 ( 7632) covalent geometry : angle 0.60542 / 0.31 (10376) hydrogen bonds : bond 0.04018 / 2.57 ( 396) hydrogen bonds : angle 3.55113 / 2.66 ( 1185) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 142 time to evaluate : 0.201 Fit side-chains REVERT: A 344 PHE cc_start: 0.7979 (m-80) cc_final: 0.7737 (t80) REVERT: B 102 MET cc_start: 0.7139 (tpt) cc_final: 0.6725 (tpp) REVERT: B 173 TYR cc_start: 0.7725 (t80) cc_final: 0.7440 (t80) REVERT: B 466 LYS cc_start: 0.8893 (ttpp) cc_final: 0.8678 (tttt) outliers start: 12 outliers final: 11 residues processed: 146 average time/residue: 0.0432 time to fit residues: 9.3463 Evaluate side-chains 139 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 128 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 461 TRP Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 461 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 25 optimal weight: 2.9990 chunk 47 optimal weight: 0.0980 chunk 33 optimal weight: 0.0980 chunk 7 optimal weight: 3.9990 chunk 59 optimal weight: 0.0970 chunk 83 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 29 optimal weight: 4.9990 chunk 56 optimal weight: 0.6980 chunk 23 optimal weight: 0.2980 chunk 41 optimal weight: 1.9990 overall best weight: 0.2578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 99 ASN B 187 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.135928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.102094 restraints weight = 12220.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.106055 restraints weight = 7025.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.108704 restraints weight = 5070.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.110385 restraints weight = 4163.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.111346 restraints weight = 3689.562| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 7632 Z= 0.113 Angle : 0.586 7.626 10376 Z= 0.296 Chirality : 0.040 0.180 1154 Planarity : 0.004 0.037 1250 Dihedral : 8.081 58.895 1048 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.27 % Favored : 92.62 % Rotamer: Outliers : 1.77 % Allowed : 19.57 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.30), residues: 894 helix: 1.53 (0.22), residues: 622 sheet: None (None), residues: 0 loop : -2.71 (0.38), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 237 TYR 0.012 0.001 TYR A 82 PHE 0.012 0.001 PHE A 445 TRP 0.009 0.001 TRP A 458 HIS 0.001 0.000 HIS A 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 ( 7632) covalent geometry : angle 0.58634 / 0.30 (10376) hydrogen bonds : bond 0.03281 / 2.12 ( 396) hydrogen bonds : angle 3.44903 / 2.57 ( 1185) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 140 time to evaluate : 0.341 Fit side-chains REVERT: A 344 PHE cc_start: 0.7836 (m-80) cc_final: 0.7572 (t80) REVERT: A 434 PHE cc_start: 0.6994 (OUTLIER) cc_final: 0.6244 (m-80) REVERT: A 465 TYR cc_start: 0.8632 (OUTLIER) cc_final: 0.8303 (t80) REVERT: A 466 LYS cc_start: 0.8892 (ttpp) cc_final: 0.8543 (tttt) REVERT: B 102 MET cc_start: 0.7232 (tpt) cc_final: 0.6744 (tpp) REVERT: B 173 TYR cc_start: 0.7507 (t80) cc_final: 0.7218 (t80) REVERT: B 200 GLU cc_start: 0.6172 (mp0) cc_final: 0.5970 (mp0) REVERT: B 277 GLU cc_start: 0.8485 (tp30) cc_final: 0.8250 (tp30) REVERT: B 466 LYS cc_start: 0.8847 (ttpp) cc_final: 0.8611 (tppt) outliers start: 14 outliers final: 7 residues processed: 149 average time/residue: 0.0506 time to fit residues: 10.9752 Evaluate side-chains 144 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 135 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 434 PHE Chi-restraints excluded: chain A residue 465 TYR Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 370 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 59 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 6 optimal weight: 0.1980 chunk 44 optimal weight: 10.0000 chunk 1 optimal weight: 4.9990 chunk 17 optimal weight: 0.6980 chunk 14 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 61 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 63 optimal weight: 6.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.135330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.100638 restraints weight = 12576.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.104732 restraints weight = 6848.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.107434 restraints weight = 4826.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.109207 restraints weight = 3918.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.110105 restraints weight = 3447.911| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7632 Z= 0.121 Angle : 0.615 8.119 10376 Z= 0.306 Chirality : 0.041 0.202 1154 Planarity : 0.004 0.036 1250 Dihedral : 8.017 59.466 1048 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.83 % Favored : 92.06 % Rotamer: Outliers : 1.64 % Allowed : 20.96 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.30), residues: 894 helix: 1.60 (0.22), residues: 620 sheet: None (None), residues: 0 loop : -2.68 (0.38), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 123 TYR 0.010 0.001 TYR A 82 PHE 0.012 0.001 PHE A 445 TRP 0.014 0.001 TRP B 461 HIS 0.002 0.001 HIS B 442 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 ( 7632) covalent geometry : angle 0.61529 / 0.31 (10376) hydrogen bonds : bond 0.03711 / 2.37 ( 396) hydrogen bonds : angle 3.43234 / 2.57 ( 1185) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 139 time to evaluate : 0.214 Fit side-chains REVERT: A 344 PHE cc_start: 0.7844 (m-80) cc_final: 0.7595 (t80) REVERT: A 434 PHE cc_start: 0.7001 (OUTLIER) cc_final: 0.6252 (m-80) REVERT: A 465 TYR cc_start: 0.8651 (OUTLIER) cc_final: 0.8370 (t80) REVERT: A 466 LYS cc_start: 0.8892 (ttpp) cc_final: 0.8551 (tttt) REVERT: B 102 MET cc_start: 0.7264 (tpt) cc_final: 0.6782 (tpp) REVERT: B 173 TYR cc_start: 0.7630 (t80) cc_final: 0.7318 (t80) REVERT: B 200 GLU cc_start: 0.6191 (mp0) cc_final: 0.5976 (mp0) REVERT: B 277 GLU cc_start: 0.8507 (tp30) cc_final: 0.8257 (tp30) REVERT: B 466 LYS cc_start: 0.8853 (ttpp) cc_final: 0.8609 (tppt) outliers start: 13 outliers final: 8 residues processed: 146 average time/residue: 0.0458 time to fit residues: 9.9597 Evaluate side-chains 147 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 137 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 434 PHE Chi-restraints excluded: chain A residue 461 TRP Chi-restraints excluded: chain A residue 465 TYR Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 370 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 77 optimal weight: 0.0270 chunk 61 optimal weight: 3.9990 chunk 71 optimal weight: 8.9990 chunk 87 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 23 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 82 optimal weight: 0.1980 chunk 2 optimal weight: 3.9990 overall best weight: 0.7642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 106 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.135000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.100303 restraints weight = 12787.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.104420 restraints weight = 6903.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.107151 restraints weight = 4844.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.108802 restraints weight = 3926.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.110004 restraints weight = 3478.051| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7632 Z= 0.121 Angle : 0.614 7.928 10376 Z= 0.308 Chirality : 0.042 0.295 1154 Planarity : 0.004 0.037 1250 Dihedral : 8.010 59.865 1048 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.49 % Favored : 92.39 % Rotamer: Outliers : 1.64 % Allowed : 21.59 % Favored : 76.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.30), residues: 894 helix: 1.57 (0.21), residues: 630 sheet: None (None), residues: 0 loop : -2.66 (0.39), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 123 TYR 0.011 0.001 TYR B 82 PHE 0.011 0.001 PHE A 445 TRP 0.011 0.001 TRP B 461 HIS 0.002 0.001 HIS A 442 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 ( 7632) covalent geometry : angle 0.61420 / 0.31 (10376) hydrogen bonds : bond 0.03720 / 2.38 ( 396) hydrogen bonds : angle 3.42270 / 2.56 ( 1185) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 146 time to evaluate : 0.156 Fit side-chains REVERT: A 344 PHE cc_start: 0.7842 (m-80) cc_final: 0.7579 (t80) REVERT: A 434 PHE cc_start: 0.7010 (OUTLIER) cc_final: 0.6259 (m-80) REVERT: A 465 TYR cc_start: 0.8672 (OUTLIER) cc_final: 0.8361 (t80) REVERT: A 466 LYS cc_start: 0.8875 (ttpp) cc_final: 0.8546 (tttt) REVERT: B 102 MET cc_start: 0.7294 (tpt) cc_final: 0.6807 (tpp) REVERT: B 173 TYR cc_start: 0.7629 (t80) cc_final: 0.7347 (t80) REVERT: B 200 GLU cc_start: 0.6233 (mp0) cc_final: 0.5992 (mp0) REVERT: B 277 GLU cc_start: 0.8477 (tp30) cc_final: 0.8244 (tp30) REVERT: B 466 LYS cc_start: 0.8858 (ttpp) cc_final: 0.8629 (tppt) outliers start: 13 outliers final: 7 residues processed: 152 average time/residue: 0.0457 time to fit residues: 10.3532 Evaluate side-chains 147 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 138 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 155 TRP Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 434 PHE Chi-restraints excluded: chain A residue 461 TRP Chi-restraints excluded: chain A residue 465 TYR Chi-restraints excluded: chain B residue 242 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 15 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 1 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 44 optimal weight: 10.0000 chunk 52 optimal weight: 1.9990 chunk 6 optimal weight: 6.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.130293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.095437 restraints weight = 12592.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.099325 restraints weight = 6966.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.101945 restraints weight = 4964.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.103441 restraints weight = 4060.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.104611 restraints weight = 3612.721| |-----------------------------------------------------------------------------| r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7632 Z= 0.174 Angle : 0.666 7.815 10376 Z= 0.338 Chirality : 0.044 0.257 1154 Planarity : 0.004 0.036 1250 Dihedral : 8.157 56.796 1048 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.39 % Favored : 91.50 % Rotamer: Outliers : 1.39 % Allowed : 21.59 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.30), residues: 894 helix: 1.45 (0.21), residues: 634 sheet: None (None), residues: 0 loop : -2.71 (0.40), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 123 TYR 0.014 0.001 TYR B 269 PHE 0.012 0.001 PHE A 445 TRP 0.011 0.001 TRP A 387 HIS 0.004 0.001 HIS A 442 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.17 ( 7632) covalent geometry : angle 0.66626 / 0.34 (10376) hydrogen bonds : bond 0.04923 / 3.12 ( 396) hydrogen bonds : angle 3.61249 / 2.71 ( 1185) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 141 time to evaluate : 0.179 Fit side-chains REVERT: A 465 TYR cc_start: 0.8786 (OUTLIER) cc_final: 0.8513 (t80) REVERT: A 466 LYS cc_start: 0.8888 (ttpp) cc_final: 0.8560 (tttt) REVERT: B 102 MET cc_start: 0.7454 (tpt) cc_final: 0.7043 (tpp) REVERT: B 173 TYR cc_start: 0.7794 (t80) cc_final: 0.7448 (t80) REVERT: B 200 GLU cc_start: 0.6331 (mp0) cc_final: 0.6039 (mp0) REVERT: B 277 GLU cc_start: 0.8499 (tp30) cc_final: 0.8250 (tp30) REVERT: B 466 LYS cc_start: 0.8862 (ttpp) cc_final: 0.8626 (tppt) outliers start: 11 outliers final: 9 residues processed: 146 average time/residue: 0.0491 time to fit residues: 10.6319 Evaluate side-chains 145 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 135 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 155 TRP Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 461 TRP Chi-restraints excluded: chain A residue 465 TYR Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 461 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 62 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 68 optimal weight: 0.4980 chunk 20 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 73 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.133207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.098524 restraints weight = 12668.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.102570 restraints weight = 6903.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.105258 restraints weight = 4872.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.106994 restraints weight = 3960.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.107887 restraints weight = 3485.774| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7632 Z= 0.131 Angle : 0.657 8.097 10376 Z= 0.331 Chirality : 0.042 0.249 1154 Planarity : 0.004 0.046 1250 Dihedral : 8.173 59.544 1048 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.49 % Favored : 92.39 % Rotamer: Outliers : 1.14 % Allowed : 22.73 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.30), residues: 894 helix: 1.49 (0.21), residues: 634 sheet: None (None), residues: 0 loop : -2.71 (0.40), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 123 TYR 0.011 0.001 TYR B 82 PHE 0.019 0.001 PHE A 344 TRP 0.009 0.001 TRP B 443 HIS 0.002 0.001 HIS A 442 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 ( 7632) covalent geometry : angle 0.65734 / 0.33 (10376) hydrogen bonds : bond 0.04132 / 2.64 ( 396) hydrogen bonds : angle 3.50328 / 2.62 ( 1185) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 147 time to evaluate : 0.328 Fit side-chains REVERT: A 121 MET cc_start: 0.8397 (ptp) cc_final: 0.8168 (pmm) REVERT: A 465 TYR cc_start: 0.8731 (OUTLIER) cc_final: 0.8463 (t80) REVERT: A 466 LYS cc_start: 0.8857 (ttpp) cc_final: 0.8538 (tttt) REVERT: B 102 MET cc_start: 0.7392 (tpt) cc_final: 0.6968 (tpp) REVERT: B 172 ASP cc_start: 0.7770 (t70) cc_final: 0.7450 (t0) REVERT: B 173 TYR cc_start: 0.7766 (t80) cc_final: 0.7429 (t80) REVERT: B 277 GLU cc_start: 0.8475 (tp30) cc_final: 0.8248 (tp30) REVERT: B 466 LYS cc_start: 0.8862 (ttpp) cc_final: 0.8632 (tppt) outliers start: 9 outliers final: 8 residues processed: 149 average time/residue: 0.0675 time to fit residues: 15.0085 Evaluate side-chains 152 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 143 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 155 TRP Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 461 TRP Chi-restraints excluded: chain A residue 465 TYR Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 461 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 69 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 77 optimal weight: 7.9990 chunk 74 optimal weight: 3.9990 chunk 76 optimal weight: 0.2980 chunk 0 optimal weight: 10.0000 chunk 13 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.132769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.097882 restraints weight = 12634.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.101849 restraints weight = 6951.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.104547 restraints weight = 4921.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.106080 restraints weight = 4010.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.107219 restraints weight = 3556.459| |-----------------------------------------------------------------------------| r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7632 Z= 0.136 Angle : 0.654 8.016 10376 Z= 0.329 Chirality : 0.042 0.239 1154 Planarity : 0.004 0.051 1250 Dihedral : 8.148 59.575 1048 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.05 % Favored : 91.83 % Rotamer: Outliers : 1.26 % Allowed : 22.98 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.30), residues: 894 helix: 1.50 (0.21), residues: 634 sheet: None (None), residues: 0 loop : -2.69 (0.40), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 123 TYR 0.011 0.001 TYR B 82 PHE 0.013 0.001 PHE A 344 TRP 0.008 0.001 TRP B 461 HIS 0.002 0.001 HIS B 442 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 ( 7632) covalent geometry : angle 0.65380 / 0.33 (10376) hydrogen bonds : bond 0.04153 / 2.65 ( 396) hydrogen bonds : angle 3.50396 / 2.63 ( 1185) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1096.18 seconds wall clock time: 19 minutes 38.53 seconds (1178.53 seconds total)