Starting phenix.real_space_refine on Thu Jul 2 15:40:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qro_18621/07_2026/8qro_18621.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qro_18621/07_2026/8qro_18621.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8qro_18621/07_2026/8qro_18621.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qro_18621/07_2026/8qro_18621.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8qro_18621/07_2026/8qro_18621.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qro_18621/07_2026/8qro_18621.map" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 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 S 45 5.16 5 Na 9 4.78 5 C 6093 2.51 5 N 1509 2.21 5 O 1617 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 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: 9273 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3078 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 16, 'TRANS': 397} Chain breaks: 2 Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 10 Ad-hoc single atom residues: {' NA': 3} Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain breaks: 3 Restraints were copied for chains: B, C Time building chain proxies: 2.06, per 1000 atoms: 0.22 Number of scatterers: 9273 At special positions: 0 Unit cell: (102.828, 101.992, 71.06, 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 45 16.00 Na 9 11.00 O 1617 8.00 N 1509 7.00 C 6093 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: 0.75 Conformation dependent library (CDL) restraints added in 223.3 milliseconds 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2250 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 3 sheets defined 86.6% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 49 through 75 Processing helix chain 'A' and resid 77 through 82 Processing helix chain 'A' and resid 82 through 90 Processing helix chain 'A' and resid 90 through 118 removed outlier: 3.521A pdb=" N GLU A 94 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE A 103 " --> pdb=" O LEU A 99 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N LEU A 105 " --> pdb=" O ARG A 101 " (cutoff:3.500A) Proline residue: A 106 - end of helix Processing helix chain 'A' and resid 120 through 154 Processing helix chain 'A' and resid 179 through 192 Processing helix chain 'A' and resid 195 through 200 Processing helix chain 'A' and resid 230 through 249 Processing helix chain 'A' and resid 252 through 291 removed outlier: 3.889A pdb=" N TRP A 275 " --> pdb=" O SER A 271 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N TYR A 276 " --> pdb=" O TRP A 272 " (cutoff:3.500A) Proline residue: A 278 - end of helix Processing helix chain 'A' and resid 294 through 319 removed outlier: 3.669A pdb=" N LEU A 298 " --> pdb=" O ASP A 294 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ARG A 301 " --> pdb=" O LEU A 297 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N LYS A 304 " --> pdb=" O ALA A 300 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N TYR A 305 " --> pdb=" O ARG A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 329 Processing helix chain 'A' and resid 332 through 339 removed outlier: 3.660A pdb=" N PHE A 336 " --> pdb=" O ASN A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 351 Processing helix chain 'A' and resid 352 through 367 Proline residue: A 358 - end of helix Processing helix chain 'A' and resid 371 through 386 Proline residue: A 380 - end of helix removed outlier: 3.802A pdb=" N THR A 384 " --> pdb=" O PRO A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 405 Processing helix chain 'A' and resid 410 through 428 removed outlier: 3.921A pdb=" N VAL A 426 " --> pdb=" O THR A 422 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLY A 427 " --> pdb=" O ALA A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 446 removed outlier: 3.853A pdb=" N ALA A 440 " --> pdb=" O VAL A 436 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ILE A 441 " --> pdb=" O LEU A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 457 removed outlier: 3.883A pdb=" N ILE A 456 " --> pdb=" O HIS A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 487 removed outlier: 4.137A pdb=" N ARG A 465 " --> pdb=" O TRP A 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 75 Processing helix chain 'B' and resid 77 through 82 Processing helix chain 'B' and resid 82 through 90 Processing helix chain 'B' and resid 90 through 118 removed outlier: 3.520A pdb=" N GLU B 94 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE B 103 " --> pdb=" O LEU B 99 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N LEU B 105 " --> pdb=" O ARG B 101 " (cutoff:3.500A) Proline residue: B 106 - end of helix Processing helix chain 'B' and resid 120 through 154 Processing helix chain 'B' and resid 179 through 192 Processing helix chain 'B' and resid 195 through 200 Processing helix chain 'B' and resid 230 through 249 Processing helix chain 'B' and resid 252 through 291 removed outlier: 3.889A pdb=" N TRP B 275 " --> pdb=" O SER B 271 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N TYR B 276 " --> pdb=" O TRP B 272 " (cutoff:3.500A) Proline residue: B 278 - end of helix Processing helix chain 'B' and resid 294 through 319 removed outlier: 3.669A pdb=" N LEU B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ARG B 301 " --> pdb=" O LEU B 297 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N LYS B 304 " --> pdb=" O ALA B 300 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N TYR B 305 " --> pdb=" O ARG B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 329 Processing helix chain 'B' and resid 332 through 339 removed outlier: 3.660A pdb=" N PHE B 336 " --> pdb=" O ASN B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 351 Processing helix chain 'B' and resid 352 through 367 Proline residue: B 358 - end of helix Processing helix chain 'B' and resid 371 through 386 Proline residue: B 380 - end of helix removed outlier: 3.803A pdb=" N THR B 384 " --> pdb=" O PRO B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 405 Processing helix chain 'B' and resid 410 through 428 removed outlier: 3.921A pdb=" N VAL B 426 " --> pdb=" O THR B 422 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLY B 427 " --> pdb=" O ALA B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 446 removed outlier: 3.854A pdb=" N ALA B 440 " --> pdb=" O VAL B 436 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ILE B 441 " --> pdb=" O LEU B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 457 removed outlier: 3.884A pdb=" N ILE B 456 " --> pdb=" O HIS B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 487 removed outlier: 4.137A pdb=" N ARG B 465 " --> pdb=" O TRP B 461 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 75 Processing helix chain 'C' and resid 77 through 82 Processing helix chain 'C' and resid 82 through 90 Processing helix chain 'C' and resid 90 through 118 removed outlier: 3.520A pdb=" N GLU C 94 " --> pdb=" O VAL C 90 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE C 103 " --> pdb=" O LEU C 99 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N LEU C 105 " --> pdb=" O ARG C 101 " (cutoff:3.500A) Proline residue: C 106 - end of helix Processing helix chain 'C' and resid 120 through 154 Processing helix chain 'C' and resid 179 through 192 Processing helix chain 'C' and resid 195 through 200 Processing helix chain 'C' and resid 230 through 249 Processing helix chain 'C' and resid 252 through 291 removed outlier: 3.889A pdb=" N TRP C 275 " --> pdb=" O SER C 271 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N TYR C 276 " --> pdb=" O TRP C 272 " (cutoff:3.500A) Proline residue: C 278 - end of helix Processing helix chain 'C' and resid 294 through 319 removed outlier: 3.669A pdb=" N LEU C 298 " --> pdb=" O ASP C 294 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ARG C 301 " --> pdb=" O LEU C 297 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N LYS C 304 " --> pdb=" O ALA C 300 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N TYR C 305 " --> pdb=" O ARG C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 329 Processing helix chain 'C' and resid 332 through 339 removed outlier: 3.660A pdb=" N PHE C 336 " --> pdb=" O ASN C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 351 Processing helix chain 'C' and resid 352 through 367 Proline residue: C 358 - end of helix Processing helix chain 'C' and resid 371 through 386 Proline residue: C 380 - end of helix removed outlier: 3.803A pdb=" N THR C 384 " --> pdb=" O PRO C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 405 Processing helix chain 'C' and resid 410 through 428 removed outlier: 3.921A pdb=" N VAL C 426 " --> pdb=" O THR C 422 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLY C 427 " --> pdb=" O ALA C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 446 removed outlier: 3.853A pdb=" N ALA C 440 " --> pdb=" O VAL C 436 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ILE C 441 " --> pdb=" O LEU C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 457 removed outlier: 3.884A pdb=" N ILE C 456 " --> pdb=" O HIS C 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 459 through 487 removed outlier: 4.137A pdb=" N ARG C 465 " --> pdb=" O TRP C 461 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 202 through 209 Processing sheet with id=AA2, first strand: chain 'B' and resid 202 through 209 Processing sheet with id=AA3, first strand: chain 'C' and resid 202 through 209 775 hydrogen bonds defined for protein. 2316 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.36 Time building geometry restraints manager: 0.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2928 1.34 - 1.46: 1858 1.46 - 1.58: 4571 1.58 - 1.69: 0 1.69 - 1.81: 72 Bond restraints: 9429 Sorted by residual: bond pdb=" N LEU B 49 " pdb=" CA LEU B 49 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.07e+00 bond pdb=" N LEU A 49 " pdb=" CA LEU A 49 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.98e+00 bond pdb=" N LEU C 49 " pdb=" CA LEU C 49 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.95e+00 bond pdb=" N GLN A 604 " pdb=" CA GLN A 604 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.91e+00 bond pdb=" N GLN B 604 " pdb=" CA GLN B 604 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.87e+00 ... (remaining 9424 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.89: 12055 0.89 - 1.78: 604 1.78 - 2.67: 104 2.67 - 3.56: 47 3.56 - 4.44: 33 Bond angle restraints: 12843 Sorted by residual: angle pdb=" CA PHE A 299 " pdb=" C PHE A 299 " pdb=" O PHE A 299 " ideal model delta sigma weight residual 120.70 118.49 2.21 1.03e+00 9.43e-01 4.59e+00 angle pdb=" CA PHE B 299 " pdb=" C PHE B 299 " pdb=" O PHE B 299 " ideal model delta sigma weight residual 120.70 118.52 2.18 1.03e+00 9.43e-01 4.46e+00 angle pdb=" CA PHE C 299 " pdb=" C PHE C 299 " pdb=" O PHE C 299 " ideal model delta sigma weight residual 120.70 118.54 2.16 1.03e+00 9.43e-01 4.41e+00 angle pdb=" N VAL C 90 " pdb=" CA VAL C 90 " pdb=" C VAL C 90 " ideal model delta sigma weight residual 109.34 113.24 -3.90 2.08e+00 2.31e-01 3.52e+00 angle pdb=" N PHE B 299 " pdb=" CA PHE B 299 " pdb=" C PHE B 299 " ideal model delta sigma weight residual 111.14 113.16 -2.02 1.08e+00 8.57e-01 3.50e+00 ... (remaining 12838 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.48: 4821 12.48 - 24.97: 525 24.97 - 37.45: 126 37.45 - 49.94: 39 49.94 - 62.42: 15 Dihedral angle restraints: 5526 sinusoidal: 2022 harmonic: 3504 Sorted by residual: dihedral pdb=" CA LEU C 455 " pdb=" CB LEU C 455 " pdb=" CG LEU C 455 " pdb=" CD1 LEU C 455 " ideal model delta sinusoidal sigma weight residual 60.00 114.43 -54.43 3 1.50e+01 4.44e-03 9.28e+00 dihedral pdb=" CA LEU A 455 " pdb=" CB LEU A 455 " pdb=" CG LEU A 455 " pdb=" CD1 LEU A 455 " ideal model delta sinusoidal sigma weight residual 60.00 114.42 -54.42 3 1.50e+01 4.44e-03 9.28e+00 dihedral pdb=" CA LEU B 455 " pdb=" CB LEU B 455 " pdb=" CG LEU B 455 " pdb=" CD1 LEU B 455 " ideal model delta sinusoidal sigma weight residual 60.00 114.40 -54.40 3 1.50e+01 4.44e-03 9.28e+00 ... (remaining 5523 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1092 0.026 - 0.053: 232 0.053 - 0.079: 189 0.079 - 0.105: 69 0.105 - 0.131: 29 Chirality restraints: 1611 Sorted by residual: chirality pdb=" CB ILE B 289 " pdb=" CA ILE B 289 " pdb=" CG1 ILE B 289 " pdb=" CG2 ILE B 289 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.13 2.00e-01 2.50e+01 4.31e-01 chirality pdb=" CA VAL B 220 " pdb=" N VAL B 220 " pdb=" C VAL B 220 " pdb=" CB VAL B 220 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.28e-01 chirality pdb=" CB ILE C 289 " pdb=" CA ILE C 289 " pdb=" CG1 ILE C 289 " pdb=" CG2 ILE C 289 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.13 2.00e-01 2.50e+01 4.28e-01 ... (remaining 1608 not shown) Planarity restraints: 1587 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 357 " 0.027 5.00e-02 4.00e+02 4.03e-02 2.60e+00 pdb=" N PRO A 358 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 358 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 358 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 357 " -0.027 5.00e-02 4.00e+02 4.02e-02 2.59e+00 pdb=" N PRO C 358 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO C 358 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 358 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 357 " -0.026 5.00e-02 4.00e+02 4.01e-02 2.58e+00 pdb=" N PRO B 358 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO B 358 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 358 " -0.022 5.00e-02 4.00e+02 ... (remaining 1584 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1734 2.76 - 3.30: 9812 3.30 - 3.83: 16750 3.83 - 4.37: 19125 4.37 - 4.90: 33800 Nonbonded interactions: 81221 Sorted by model distance: nonbonded pdb=" CD1 PHE A 393 " pdb=" CG1 VAL A 463 " model vdw 2.231 3.760 nonbonded pdb=" CD1 PHE B 393 " pdb=" CG1 VAL B 463 " model vdw 2.231 3.760 nonbonded pdb=" CD1 PHE C 393 " pdb=" CG1 VAL C 463 " model vdw 2.231 3.760 nonbonded pdb=" OG1 THR B 138 " pdb="NA NA B 603 " model vdw 2.241 3.210 nonbonded pdb=" OG1 THR A 138 " pdb="NA NA A 603 " model vdw 2.241 3.210 ... (remaining 81216 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.850 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 8.400 Find NCS groups from input model: 0.070 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:5.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9429 Z= 0.126 Angle : 0.519 4.445 12843 Z= 0.291 Chirality : 0.037 0.131 1611 Planarity : 0.004 0.040 1587 Dihedral : 11.990 62.424 3276 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 0.31 % Allowed : 7.34 % Favored : 92.35 % 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: 0.95 (0.24), residues: 1224 helix: 1.19 (0.16), residues: 981 sheet: -1.43 (0.65), residues: 60 loop : -1.37 (0.38), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 330 TYR 0.007 0.001 TYR A 208 PHE 0.009 0.001 PHE A 299 TRP 0.006 0.001 TRP A 275 HIS 0.001 0.001 HIS C 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.13 ( 9429) covalent geometry : angle 0.51869 / 0.29 (12843) hydrogen bonds : bond 0.11097 / 7.65 ( 775) hydrogen bonds : angle 5.38920 / 3.75 ( 2316) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 125 time to evaluate : 0.242 Fit side-chains REVERT: A 224 GLN cc_start: 0.8159 (pm20) cc_final: 0.7761 (pm20) REVERT: A 400 PHE cc_start: 0.7795 (t80) cc_final: 0.7498 (t80) REVERT: B 400 PHE cc_start: 0.7759 (t80) cc_final: 0.7497 (t80) REVERT: C 224 GLN cc_start: 0.8192 (pm20) cc_final: 0.7897 (pm20) REVERT: C 274 MET cc_start: 0.8267 (mtm) cc_final: 0.7965 (mtt) REVERT: C 387 MET cc_start: 0.8842 (mtt) cc_final: 0.8622 (mtt) REVERT: C 400 PHE cc_start: 0.7650 (t80) cc_final: 0.7422 (t80) REVERT: C 475 ASP cc_start: 0.7561 (m-30) cc_final: 0.7205 (m-30) outliers start: 3 outliers final: 0 residues processed: 128 average time/residue: 0.3909 time to fit residues: 54.1461 Evaluate side-chains 105 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 5.9990 chunk 113 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 117 optimal weight: 0.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 367 ASN B 367 ASN B 484 ASN C 367 ASN C 452 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.147958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.094981 restraints weight = 10607.489| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 2.01 r_work: 0.2937 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2787 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.1329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9429 Z= 0.152 Angle : 0.546 5.581 12843 Z= 0.276 Chirality : 0.040 0.141 1611 Planarity : 0.005 0.041 1587 Dihedral : 3.532 12.396 1302 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 1.53 % Allowed : 10.50 % Favored : 87.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.10 (0.24), residues: 1224 helix: 1.85 (0.16), residues: 1023 sheet: -1.56 (0.62), residues: 60 loop : -0.38 (0.48), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 376 TYR 0.010 0.001 TYR B 208 PHE 0.013 0.002 PHE C 237 TRP 0.005 0.001 TRP B 275 HIS 0.002 0.001 HIS A 316 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 ( 9429) covalent geometry : angle 0.54633 / 0.28 (12843) hydrogen bonds : bond 0.04477 / 3.04 ( 775) hydrogen bonds : angle 4.70929 / 3.30 ( 2316) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 115 time to evaluate : 0.315 Fit side-chains REVERT: A 85 ARG cc_start: 0.6375 (OUTLIER) cc_final: 0.5874 (mtp85) REVERT: A 179 GLU cc_start: 0.7518 (mm-30) cc_final: 0.7179 (mm-30) REVERT: A 327 LEU cc_start: 0.7686 (OUTLIER) cc_final: 0.7367 (mp) REVERT: A 475 ASP cc_start: 0.6361 (m-30) cc_final: 0.6129 (m-30) REVERT: B 85 ARG cc_start: 0.6355 (OUTLIER) cc_final: 0.5514 (mtp85) REVERT: B 291 GLU cc_start: 0.7603 (mt-10) cc_final: 0.7393 (mt-10) REVERT: C 85 ARG cc_start: 0.6434 (OUTLIER) cc_final: 0.5788 (mtp85) REVERT: C 274 MET cc_start: 0.8372 (mtm) cc_final: 0.8060 (mtt) REVERT: C 328 PHE cc_start: 0.8636 (m-80) cc_final: 0.8408 (m-80) outliers start: 15 outliers final: 2 residues processed: 125 average time/residue: 0.4536 time to fit residues: 60.6894 Evaluate side-chains 106 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 100 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ARG Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain B residue 85 ARG Chi-restraints excluded: chain B residue 308 CYS Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 85 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 120 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 2 optimal weight: 6.9990 chunk 94 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 85 optimal weight: 0.3980 chunk 29 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 54 optimal weight: 0.0170 chunk 90 optimal weight: 0.8980 chunk 98 optimal weight: 0.9980 overall best weight: 0.8620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 224 GLN A 316 HIS A 367 ASN B 484 ASN C 316 HIS C 367 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.148631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.095746 restraints weight = 10671.086| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 2.02 r_work: 0.2955 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9429 Z= 0.125 Angle : 0.499 5.483 12843 Z= 0.251 Chirality : 0.038 0.137 1611 Planarity : 0.005 0.045 1587 Dihedral : 3.402 12.913 1302 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 2.65 % Allowed : 10.50 % Favored : 86.85 % 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: 2.50 (0.24), residues: 1224 helix: 2.12 (0.16), residues: 1020 sheet: None (None), residues: 0 loop : -0.75 (0.39), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 376 TYR 0.010 0.001 TYR B 208 PHE 0.011 0.001 PHE C 237 TRP 0.006 0.001 TRP A 275 HIS 0.001 0.000 HIS B 316 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 ( 9429) covalent geometry : angle 0.49909 / 0.25 (12843) hydrogen bonds : bond 0.03984 / 2.70 ( 775) hydrogen bonds : angle 4.49286 / 3.16 ( 2316) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 110 time to evaluate : 0.249 Fit side-chains REVERT: A 85 ARG cc_start: 0.6288 (OUTLIER) cc_final: 0.5855 (mtp85) REVERT: A 179 GLU cc_start: 0.7372 (mm-30) cc_final: 0.7051 (mm-30) REVERT: A 330 ARG cc_start: 0.6827 (OUTLIER) cc_final: 0.6601 (mpt180) REVERT: A 388 ASP cc_start: 0.8243 (OUTLIER) cc_final: 0.7924 (m-30) REVERT: B 85 ARG cc_start: 0.6209 (OUTLIER) cc_final: 0.5348 (mtp85) REVERT: B 291 GLU cc_start: 0.7565 (mt-10) cc_final: 0.7343 (mt-10) REVERT: B 330 ARG cc_start: 0.6982 (OUTLIER) cc_final: 0.6760 (mpt180) REVERT: C 85 ARG cc_start: 0.6393 (OUTLIER) cc_final: 0.5763 (mtp85) REVERT: C 179 GLU cc_start: 0.7476 (mm-30) cc_final: 0.7229 (mm-30) REVERT: C 274 MET cc_start: 0.8278 (mtm) cc_final: 0.7938 (mtt) REVERT: C 330 ARG cc_start: 0.6816 (OUTLIER) cc_final: 0.6598 (mpt180) REVERT: C 367 ASN cc_start: 0.8468 (m-40) cc_final: 0.8177 (m110) outliers start: 26 outliers final: 7 residues processed: 131 average time/residue: 0.4324 time to fit residues: 60.8334 Evaluate side-chains 117 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 103 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ARG Chi-restraints excluded: chain A residue 224 GLN Chi-restraints excluded: chain A residue 330 ARG Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain B residue 85 ARG Chi-restraints excluded: chain B residue 308 CYS Chi-restraints excluded: chain B residue 330 ARG Chi-restraints excluded: chain B residue 466 SER Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 85 ARG Chi-restraints excluded: chain C residue 330 ARG Chi-restraints excluded: chain C residue 466 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 57 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 44 optimal weight: 8.9990 chunk 11 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 79 optimal weight: 8.9990 chunk 19 optimal weight: 0.6980 chunk 106 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 367 ASN B 316 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.144979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.091296 restraints weight = 10737.858| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 2.00 r_work: 0.2886 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2737 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 9429 Z= 0.201 Angle : 0.556 7.493 12843 Z= 0.277 Chirality : 0.041 0.147 1611 Planarity : 0.005 0.043 1587 Dihedral : 3.583 14.625 1302 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 2.45 % Allowed : 11.72 % Favored : 85.83 % 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: 2.30 (0.24), residues: 1224 helix: 1.90 (0.16), residues: 1023 sheet: None (None), residues: 0 loop : -0.29 (0.44), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 376 TYR 0.015 0.002 TYR C 334 PHE 0.015 0.002 PHE A 237 TRP 0.006 0.001 TRP B 275 HIS 0.002 0.000 HIS B 316 Details of bonding type rmsd/Z covalent geometry : bond 0.00490 / 0.20 ( 9429) covalent geometry : angle 0.55553 / 0.28 (12843) hydrogen bonds : bond 0.04652 / 3.15 ( 775) hydrogen bonds : angle 4.66012 / 3.30 ( 2316) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 107 time to evaluate : 0.227 Fit side-chains REVERT: A 85 ARG cc_start: 0.6370 (OUTLIER) cc_final: 0.5995 (mtp85) REVERT: A 179 GLU cc_start: 0.7543 (mm-30) cc_final: 0.7141 (mm-30) REVERT: A 247 LYS cc_start: 0.8345 (mmtt) cc_final: 0.7871 (mtpt) REVERT: B 85 ARG cc_start: 0.6276 (OUTLIER) cc_final: 0.5446 (mtp85) REVERT: B 291 GLU cc_start: 0.7642 (mt-10) cc_final: 0.7435 (mt-10) REVERT: B 330 ARG cc_start: 0.7084 (OUTLIER) cc_final: 0.6857 (mpt180) REVERT: C 85 ARG cc_start: 0.6455 (OUTLIER) cc_final: 0.5833 (mtp85) REVERT: C 179 GLU cc_start: 0.7546 (mm-30) cc_final: 0.7273 (mm-30) REVERT: C 367 ASN cc_start: 0.8489 (m-40) cc_final: 0.8224 (m110) outliers start: 24 outliers final: 8 residues processed: 126 average time/residue: 0.5381 time to fit residues: 72.4308 Evaluate side-chains 114 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 102 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ARG Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain B residue 85 ARG Chi-restraints excluded: chain B residue 274 MET Chi-restraints excluded: chain B residue 308 CYS Chi-restraints excluded: chain B residue 330 ARG Chi-restraints excluded: chain B residue 466 SER Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 85 ARG Chi-restraints excluded: chain C residue 393 PHE Chi-restraints excluded: chain C residue 466 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 32 optimal weight: 8.9990 chunk 120 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 70 optimal weight: 0.8980 chunk 57 optimal weight: 0.6980 chunk 67 optimal weight: 0.1980 chunk 46 optimal weight: 0.9980 chunk 88 optimal weight: 0.6980 chunk 38 optimal weight: 6.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 224 GLN A 367 ASN B 484 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.148440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.095494 restraints weight = 10600.101| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 2.03 r_work: 0.2954 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9429 Z= 0.119 Angle : 0.484 6.669 12843 Z= 0.243 Chirality : 0.037 0.136 1611 Planarity : 0.005 0.047 1587 Dihedral : 3.450 13.816 1302 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 2.55 % Allowed : 11.93 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.68 (0.24), residues: 1224 helix: 2.20 (0.16), residues: 1017 sheet: None (None), residues: 0 loop : -0.35 (0.43), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 330 TYR 0.007 0.001 TYR B 208 PHE 0.010 0.001 PHE A 400 TRP 0.007 0.001 TRP A 130 HIS 0.001 0.000 HIS C 316 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 ( 9429) covalent geometry : angle 0.48448 / 0.24 (12843) hydrogen bonds : bond 0.03863 / 2.61 ( 775) hydrogen bonds : angle 4.46804 / 3.15 ( 2316) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 113 time to evaluate : 0.402 Fit side-chains REVERT: A 85 ARG cc_start: 0.6191 (OUTLIER) cc_final: 0.5810 (mtp85) REVERT: A 179 GLU cc_start: 0.7378 (mm-30) cc_final: 0.7009 (mm-30) REVERT: B 85 ARG cc_start: 0.6160 (OUTLIER) cc_final: 0.5319 (mtp85) REVERT: B 291 GLU cc_start: 0.7581 (mt-10) cc_final: 0.7374 (mt-10) REVERT: B 388 ASP cc_start: 0.8262 (OUTLIER) cc_final: 0.7655 (m-30) REVERT: C 85 ARG cc_start: 0.6354 (OUTLIER) cc_final: 0.5692 (mtp85) REVERT: C 179 GLU cc_start: 0.7455 (mm-30) cc_final: 0.7186 (mm-30) REVERT: C 274 MET cc_start: 0.8316 (mtm) cc_final: 0.8005 (mtt) REVERT: C 367 ASN cc_start: 0.8404 (m-40) cc_final: 0.8152 (m110) outliers start: 25 outliers final: 6 residues processed: 132 average time/residue: 0.4454 time to fit residues: 63.5977 Evaluate side-chains 121 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 111 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 85 ARG Chi-restraints excluded: chain A residue 224 GLN Chi-restraints excluded: chain A residue 288 LYS Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain B residue 85 ARG Chi-restraints excluded: chain B residue 308 CYS Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 85 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 62 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 96 optimal weight: 0.2980 chunk 48 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 367 ASN B 484 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.148817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.096262 restraints weight = 10645.669| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 1.96 r_work: 0.2965 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9429 Z= 0.118 Angle : 0.484 6.529 12843 Z= 0.241 Chirality : 0.037 0.135 1611 Planarity : 0.005 0.048 1587 Dihedral : 3.413 15.296 1302 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 2.24 % Allowed : 13.25 % Favored : 84.51 % 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: 2.81 (0.24), residues: 1224 helix: 2.23 (0.16), residues: 1035 sheet: None (None), residues: 0 loop : -0.21 (0.44), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 202 TYR 0.006 0.001 TYR B 208 PHE 0.010 0.001 PHE A 237 TRP 0.008 0.001 TRP A 130 HIS 0.001 0.000 HIS C 316 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 ( 9429) covalent geometry : angle 0.48420 / 0.24 (12843) hydrogen bonds : bond 0.03815 / 2.57 ( 775) hydrogen bonds : angle 4.40697 / 3.11 ( 2316) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 115 time to evaluate : 0.245 Fit side-chains REVERT: A 85 ARG cc_start: 0.6222 (OUTLIER) cc_final: 0.5833 (mtp85) REVERT: A 179 GLU cc_start: 0.7424 (mm-30) cc_final: 0.7004 (mm-30) REVERT: A 388 ASP cc_start: 0.8195 (OUTLIER) cc_final: 0.7358 (m-30) REVERT: B 85 ARG cc_start: 0.6192 (OUTLIER) cc_final: 0.5352 (mtp85) REVERT: B 291 GLU cc_start: 0.7597 (mt-10) cc_final: 0.7375 (mt-10) REVERT: C 85 ARG cc_start: 0.6397 (OUTLIER) cc_final: 0.5702 (mtp85) REVERT: C 179 GLU cc_start: 0.7514 (mm-30) cc_final: 0.7259 (mm-30) REVERT: C 274 MET cc_start: 0.8320 (mtm) cc_final: 0.8012 (mtt) REVERT: C 367 ASN cc_start: 0.8382 (m-40) cc_final: 0.8127 (m110) outliers start: 22 outliers final: 4 residues processed: 132 average time/residue: 0.4213 time to fit residues: 60.1937 Evaluate side-chains 120 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 112 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ARG Chi-restraints excluded: chain A residue 288 LYS Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain B residue 85 ARG Chi-restraints excluded: chain B residue 308 CYS Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 85 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 48 optimal weight: 0.7980 chunk 120 optimal weight: 5.9990 chunk 116 optimal weight: 5.9990 chunk 13 optimal weight: 0.8980 chunk 39 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 122 optimal weight: 1.9990 chunk 108 optimal weight: 6.9990 chunk 46 optimal weight: 0.4980 chunk 109 optimal weight: 6.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 224 GLN A 367 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.148933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.096298 restraints weight = 10690.274| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 1.95 r_work: 0.2967 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9429 Z= 0.120 Angle : 0.485 6.281 12843 Z= 0.240 Chirality : 0.037 0.136 1611 Planarity : 0.005 0.049 1587 Dihedral : 3.390 16.790 1302 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 1.53 % Allowed : 14.48 % Favored : 84.00 % 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: 2.90 (0.24), residues: 1224 helix: 2.27 (0.16), residues: 1035 sheet: -1.48 (0.67), residues: 60 loop : 0.88 (0.57), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 376 TYR 0.006 0.001 TYR B 208 PHE 0.012 0.001 PHE C 393 TRP 0.009 0.001 TRP A 130 HIS 0.001 0.000 HIS B 316 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 ( 9429) covalent geometry : angle 0.48472 / 0.24 (12843) hydrogen bonds : bond 0.03816 / 2.57 ( 775) hydrogen bonds : angle 4.37390 / 3.09 ( 2316) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 117 time to evaluate : 0.280 Fit side-chains REVERT: A 85 ARG cc_start: 0.6211 (OUTLIER) cc_final: 0.5829 (mtp85) REVERT: A 179 GLU cc_start: 0.7517 (mm-30) cc_final: 0.7133 (mm-30) REVERT: A 388 ASP cc_start: 0.8266 (OUTLIER) cc_final: 0.7432 (m-30) REVERT: A 482 LEU cc_start: 0.8068 (OUTLIER) cc_final: 0.7811 (mm) REVERT: B 85 ARG cc_start: 0.6248 (OUTLIER) cc_final: 0.5394 (mtp85) REVERT: B 291 GLU cc_start: 0.7616 (mt-10) cc_final: 0.7402 (mt-10) REVERT: C 85 ARG cc_start: 0.6429 (OUTLIER) cc_final: 0.5769 (mtp85) REVERT: C 179 GLU cc_start: 0.7580 (mm-30) cc_final: 0.7347 (mm-30) REVERT: C 367 ASN cc_start: 0.8413 (m-40) cc_final: 0.8165 (m110) outliers start: 15 outliers final: 5 residues processed: 126 average time/residue: 0.4729 time to fit residues: 64.5100 Evaluate side-chains 122 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 112 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ARG Chi-restraints excluded: chain A residue 224 GLN Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain B residue 85 ARG Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 308 CYS Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 85 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 35 optimal weight: 6.9990 chunk 9 optimal weight: 6.9990 chunk 93 optimal weight: 0.9980 chunk 96 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 49 optimal weight: 8.9990 chunk 77 optimal weight: 10.0000 chunk 50 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 224 GLN A 367 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.146717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.093523 restraints weight = 10573.543| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 1.98 r_work: 0.2925 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9429 Z= 0.164 Angle : 0.522 6.562 12843 Z= 0.258 Chirality : 0.039 0.140 1611 Planarity : 0.005 0.049 1587 Dihedral : 3.454 16.229 1302 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 1.33 % Allowed : 14.88 % Favored : 83.79 % 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: 2.68 (0.24), residues: 1224 helix: 2.18 (0.16), residues: 1020 sheet: None (None), residues: 0 loop : -0.30 (0.44), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 376 TYR 0.009 0.001 TYR C 334 PHE 0.014 0.002 PHE C 237 TRP 0.009 0.001 TRP A 130 HIS 0.001 0.000 HIS C 316 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.16 ( 9429) covalent geometry : angle 0.52197 / 0.26 (12843) hydrogen bonds : bond 0.04192 / 2.83 ( 775) hydrogen bonds : angle 4.45962 / 3.16 ( 2316) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 112 time to evaluate : 0.263 Fit side-chains REVERT: A 85 ARG cc_start: 0.6260 (OUTLIER) cc_final: 0.5922 (mtp85) REVERT: A 179 GLU cc_start: 0.7514 (mm-30) cc_final: 0.7187 (mm-30) REVERT: A 388 ASP cc_start: 0.8280 (OUTLIER) cc_final: 0.7500 (m-30) REVERT: A 482 LEU cc_start: 0.7998 (OUTLIER) cc_final: 0.7738 (mm) REVERT: B 85 ARG cc_start: 0.6204 (OUTLIER) cc_final: 0.5383 (mtp85) REVERT: B 291 GLU cc_start: 0.7627 (mt-10) cc_final: 0.7416 (mt-10) REVERT: C 85 ARG cc_start: 0.6406 (OUTLIER) cc_final: 0.5755 (mtp85) REVERT: C 179 GLU cc_start: 0.7568 (mm-30) cc_final: 0.7312 (mm-30) REVERT: C 367 ASN cc_start: 0.8374 (m-40) cc_final: 0.8120 (m110) outliers start: 13 outliers final: 3 residues processed: 119 average time/residue: 0.4741 time to fit residues: 60.8705 Evaluate side-chains 119 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 111 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ARG Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain B residue 85 ARG Chi-restraints excluded: chain B residue 308 CYS Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 85 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 78 optimal weight: 10.0000 chunk 22 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 39 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 chunk 69 optimal weight: 8.9990 chunk 102 optimal weight: 0.8980 chunk 101 optimal weight: 0.6980 chunk 100 optimal weight: 0.9980 chunk 9 optimal weight: 6.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 224 GLN A 367 ASN C 484 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.148624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.096147 restraints weight = 10560.831| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 1.94 r_work: 0.2961 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9429 Z= 0.123 Angle : 0.494 6.251 12843 Z= 0.243 Chirality : 0.037 0.135 1611 Planarity : 0.005 0.049 1587 Dihedral : 3.421 17.231 1302 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 1.43 % Allowed : 14.98 % Favored : 83.59 % 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: 2.90 (0.24), residues: 1224 helix: 2.28 (0.16), residues: 1035 sheet: -1.50 (0.66), residues: 60 loop : 0.86 (0.57), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 376 TYR 0.007 0.001 TYR A 334 PHE 0.011 0.001 PHE B 237 TRP 0.010 0.001 TRP A 130 HIS 0.001 0.000 HIS C 316 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 ( 9429) covalent geometry : angle 0.49419 / 0.24 (12843) hydrogen bonds : bond 0.03853 / 2.60 ( 775) hydrogen bonds : angle 4.37450 / 3.10 ( 2316) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 113 time to evaluate : 0.348 Fit side-chains REVERT: A 85 ARG cc_start: 0.6232 (OUTLIER) cc_final: 0.5933 (mtp85) REVERT: A 179 GLU cc_start: 0.7476 (mm-30) cc_final: 0.7085 (mm-30) REVERT: A 366 GLU cc_start: 0.7407 (mt-10) cc_final: 0.7105 (mm-30) REVERT: A 388 ASP cc_start: 0.8238 (OUTLIER) cc_final: 0.7475 (m-30) REVERT: A 482 LEU cc_start: 0.8014 (OUTLIER) cc_final: 0.7753 (mm) REVERT: B 85 ARG cc_start: 0.6217 (OUTLIER) cc_final: 0.5367 (mtp85) REVERT: B 291 GLU cc_start: 0.7593 (mt-10) cc_final: 0.7370 (mt-10) REVERT: C 85 ARG cc_start: 0.6413 (OUTLIER) cc_final: 0.5770 (mtp85) REVERT: C 179 GLU cc_start: 0.7574 (mm-30) cc_final: 0.7357 (mm-30) REVERT: C 367 ASN cc_start: 0.8401 (m-40) cc_final: 0.8135 (m110) outliers start: 14 outliers final: 5 residues processed: 122 average time/residue: 0.4673 time to fit residues: 61.5831 Evaluate side-chains 124 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 114 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ARG Chi-restraints excluded: chain A residue 224 GLN Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain B residue 85 ARG Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 308 CYS Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 85 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 95 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 19 optimal weight: 0.5980 chunk 36 optimal weight: 9.9990 chunk 32 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 58 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 367 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.148586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.095884 restraints weight = 10534.925| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 1.99 r_work: 0.2963 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9429 Z= 0.120 Angle : 0.501 7.417 12843 Z= 0.245 Chirality : 0.037 0.134 1611 Planarity : 0.005 0.050 1587 Dihedral : 3.417 17.497 1302 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 1.02 % Allowed : 15.19 % Favored : 83.79 % 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: 2.92 (0.24), residues: 1224 helix: 2.30 (0.16), residues: 1035 sheet: -1.51 (0.67), residues: 60 loop : 0.76 (0.56), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 376 TYR 0.007 0.001 TYR A 334 PHE 0.010 0.001 PHE B 237 TRP 0.010 0.001 TRP A 130 HIS 0.001 0.000 HIS C 316 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 ( 9429) covalent geometry : angle 0.50123 / 0.25 (12843) hydrogen bonds : bond 0.03829 / 2.58 ( 775) hydrogen bonds : angle 4.36032 / 3.09 ( 2316) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 118 time to evaluate : 0.332 Fit side-chains REVERT: A 85 ARG cc_start: 0.6201 (OUTLIER) cc_final: 0.5903 (mtp85) REVERT: A 179 GLU cc_start: 0.7459 (mm-30) cc_final: 0.7081 (mm-30) REVERT: A 327 LEU cc_start: 0.7617 (mt) cc_final: 0.7401 (mt) REVERT: A 366 GLU cc_start: 0.7446 (mt-10) cc_final: 0.7148 (mm-30) REVERT: A 388 ASP cc_start: 0.8211 (OUTLIER) cc_final: 0.7468 (m-30) REVERT: A 482 LEU cc_start: 0.7996 (OUTLIER) cc_final: 0.7742 (mm) REVERT: B 85 ARG cc_start: 0.6167 (OUTLIER) cc_final: 0.5327 (mtp85) REVERT: B 291 GLU cc_start: 0.7601 (mt-10) cc_final: 0.7389 (mt-10) REVERT: C 179 GLU cc_start: 0.7543 (mm-30) cc_final: 0.7328 (mm-30) REVERT: C 367 ASN cc_start: 0.8375 (m-40) cc_final: 0.8141 (m110) outliers start: 10 outliers final: 4 residues processed: 125 average time/residue: 0.4620 time to fit residues: 62.1977 Evaluate side-chains 123 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 115 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ARG Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain B residue 85 ARG Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 308 CYS Chi-restraints excluded: chain C residue 56 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 34 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 44 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 11 optimal weight: 1.9990 chunk 65 optimal weight: 7.9990 chunk 106 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 224 GLN A 367 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.148066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.095422 restraints weight = 10489.746| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 1.94 r_work: 0.2953 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9429 Z= 0.129 Angle : 0.510 8.405 12843 Z= 0.249 Chirality : 0.038 0.136 1611 Planarity : 0.005 0.050 1587 Dihedral : 3.422 17.140 1302 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 1.02 % Allowed : 15.70 % Favored : 83.28 % 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: 2.86 (0.24), residues: 1224 helix: 2.26 (0.16), residues: 1035 sheet: -1.57 (0.66), residues: 60 loop : 0.70 (0.55), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 376 TYR 0.008 0.001 TYR B 208 PHE 0.011 0.001 PHE B 237 TRP 0.009 0.001 TRP A 130 HIS 0.001 0.000 HIS C 316 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 ( 9429) covalent geometry : angle 0.50999 / 0.25 (12843) hydrogen bonds : bond 0.03934 / 2.65 ( 775) hydrogen bonds : angle 4.38065 / 3.11 ( 2316) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3141.61 seconds wall clock time: 54 minutes 12.70 seconds (3252.70 seconds total)