Starting phenix.real_space_refine on Thu Sep 18 00:39:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ze0_60019/09_2025/8ze0_60019.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ze0_60019/09_2025/8ze0_60019.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ze0_60019/09_2025/8ze0_60019.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ze0_60019/09_2025/8ze0_60019.map" model { file = "/net/cci-nas-00/data/ceres_data/8ze0_60019/09_2025/8ze0_60019.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ze0_60019/09_2025/8ze0_60019.cif" } resolution = 2.54 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 sd= 0.050 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 92 5.16 5 C 8528 2.51 5 N 2124 2.21 5 O 2136 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12880 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3220 Classifications: {'peptide': 392} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 377} Restraints were copied for chains: B, C, D Time building chain proxies: 2.91, per 1000 atoms: 0.23 Number of scatterers: 12880 At special positions: 0 Unit cell: (116.5, 116.5, 98.792, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 92 16.00 O 2136 8.00 N 2124 7.00 C 8528 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: 1.16 Conformation dependent library (CDL) restraints added in 609.8 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3024 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 0 sheets defined 78.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 58 through 73 Proline residue: A 65 - end of helix removed outlier: 3.594A pdb=" N LEU A 69 " --> pdb=" O PRO A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 123 Processing helix chain 'A' and resid 128 through 164 removed outlier: 4.364A pdb=" N LEU A 132 " --> pdb=" O ASN A 128 " (cutoff:3.500A) Proline residue: A 153 - end of helix Processing helix chain 'A' and resid 165 through 168 Processing helix chain 'A' and resid 177 through 214 removed outlier: 3.591A pdb=" N MET A 214 " --> pdb=" O ARG A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 231 Processing helix chain 'A' and resid 242 through 287 removed outlier: 4.096A pdb=" N ASP A 264 " --> pdb=" O TRP A 260 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ARG A 277 " --> pdb=" O GLY A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 341 removed outlier: 3.559A pdb=" N PHE A 298 " --> pdb=" O CYS A 294 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N SER A 321 " --> pdb=" O SER A 317 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N LEU A 322 " --> pdb=" O ALA A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 387 removed outlier: 3.978A pdb=" N ILE A 375 " --> pdb=" O THR A 371 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ASN A 376 " --> pdb=" O ALA A 372 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLY A 382 " --> pdb=" O GLU A 378 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N LEU A 383 " --> pdb=" O SER A 379 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLY A 384 " --> pdb=" O LYS A 380 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N VAL A 385 " --> pdb=" O ARG A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 408 Processing helix chain 'A' and resid 421 through 444 removed outlier: 4.127A pdb=" N GLN A 441 " --> pdb=" O LEU A 437 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N PHE A 442 " --> pdb=" O VAL A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 447 No H-bonds generated for 'chain 'A' and resid 445 through 447' Processing helix chain 'B' and resid 58 through 73 Proline residue: B 65 - end of helix removed outlier: 3.595A pdb=" N LEU B 69 " --> pdb=" O PRO B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 123 Processing helix chain 'B' and resid 128 through 164 removed outlier: 4.363A pdb=" N LEU B 132 " --> pdb=" O ASN B 128 " (cutoff:3.500A) Proline residue: B 153 - end of helix Processing helix chain 'B' and resid 165 through 168 Processing helix chain 'B' and resid 177 through 214 removed outlier: 3.592A pdb=" N MET B 214 " --> pdb=" O ARG B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 231 Processing helix chain 'B' and resid 242 through 287 removed outlier: 4.097A pdb=" N ASP B 264 " --> pdb=" O TRP B 260 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ARG B 277 " --> pdb=" O GLY B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 341 removed outlier: 3.559A pdb=" N PHE B 298 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N SER B 321 " --> pdb=" O SER B 317 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N LEU B 322 " --> pdb=" O ALA B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 387 removed outlier: 3.977A pdb=" N ILE B 375 " --> pdb=" O THR B 371 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ASN B 376 " --> pdb=" O ALA B 372 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLY B 382 " --> pdb=" O GLU B 378 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N LEU B 383 " --> pdb=" O SER B 379 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLY B 384 " --> pdb=" O LYS B 380 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N VAL B 385 " --> pdb=" O ARG B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 408 Processing helix chain 'B' and resid 421 through 444 removed outlier: 4.126A pdb=" N GLN B 441 " --> pdb=" O LEU B 437 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N PHE B 442 " --> pdb=" O VAL B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 447 No H-bonds generated for 'chain 'B' and resid 445 through 447' Processing helix chain 'C' and resid 58 through 73 Proline residue: C 65 - end of helix removed outlier: 3.595A pdb=" N LEU C 69 " --> pdb=" O PRO C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 123 Processing helix chain 'C' and resid 128 through 164 removed outlier: 4.364A pdb=" N LEU C 132 " --> pdb=" O ASN C 128 " (cutoff:3.500A) Proline residue: C 153 - end of helix Processing helix chain 'C' and resid 165 through 168 Processing helix chain 'C' and resid 177 through 214 removed outlier: 3.591A pdb=" N MET C 214 " --> pdb=" O ARG C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 231 Processing helix chain 'C' and resid 242 through 287 removed outlier: 4.097A pdb=" N ASP C 264 " --> pdb=" O TRP C 260 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ARG C 277 " --> pdb=" O GLY C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 341 removed outlier: 3.559A pdb=" N PHE C 298 " --> pdb=" O CYS C 294 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N SER C 321 " --> pdb=" O SER C 317 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N LEU C 322 " --> pdb=" O ALA C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 387 removed outlier: 3.978A pdb=" N ILE C 375 " --> pdb=" O THR C 371 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ASN C 376 " --> pdb=" O ALA C 372 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLY C 382 " --> pdb=" O GLU C 378 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N LEU C 383 " --> pdb=" O SER C 379 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLY C 384 " --> pdb=" O LYS C 380 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N VAL C 385 " --> pdb=" O ARG C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 395 through 408 Processing helix chain 'C' and resid 421 through 444 removed outlier: 4.126A pdb=" N GLN C 441 " --> pdb=" O LEU C 437 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N PHE C 442 " --> pdb=" O VAL C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 445 through 447 No H-bonds generated for 'chain 'C' and resid 445 through 447' Processing helix chain 'D' and resid 58 through 73 Proline residue: D 65 - end of helix removed outlier: 3.594A pdb=" N LEU D 69 " --> pdb=" O PRO D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 123 Processing helix chain 'D' and resid 128 through 164 removed outlier: 4.364A pdb=" N LEU D 132 " --> pdb=" O ASN D 128 " (cutoff:3.500A) Proline residue: D 153 - end of helix Processing helix chain 'D' and resid 165 through 168 Processing helix chain 'D' and resid 177 through 214 removed outlier: 3.590A pdb=" N MET D 214 " --> pdb=" O ARG D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 231 Processing helix chain 'D' and resid 242 through 287 removed outlier: 4.097A pdb=" N ASP D 264 " --> pdb=" O TRP D 260 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ARG D 277 " --> pdb=" O GLY D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 341 removed outlier: 3.559A pdb=" N PHE D 298 " --> pdb=" O CYS D 294 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N SER D 321 " --> pdb=" O SER D 317 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N LEU D 322 " --> pdb=" O ALA D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 347 through 387 removed outlier: 3.978A pdb=" N ILE D 375 " --> pdb=" O THR D 371 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ASN D 376 " --> pdb=" O ALA D 372 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLY D 382 " --> pdb=" O GLU D 378 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N LEU D 383 " --> pdb=" O SER D 379 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLY D 384 " --> pdb=" O LYS D 380 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N VAL D 385 " --> pdb=" O ARG D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 408 Processing helix chain 'D' and resid 421 through 444 removed outlier: 4.127A pdb=" N GLN D 441 " --> pdb=" O LEU D 437 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N PHE D 442 " --> pdb=" O VAL D 438 " (cutoff:3.500A) Processing helix chain 'D' and resid 445 through 447 No H-bonds generated for 'chain 'D' and resid 445 through 447' 964 hydrogen bonds defined for protein. 2880 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: 2.07 Time building geometry restraints manager: 1.51 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: 3912 1.34 - 1.46: 3209 1.46 - 1.58: 5935 1.58 - 1.70: 0 1.70 - 1.81: 148 Bond restraints: 13204 Sorted by residual: bond pdb=" CA TYR B 234 " pdb=" CB TYR B 234 " ideal model delta sigma weight residual 1.530 1.548 -0.017 1.69e-02 3.50e+03 1.07e+00 bond pdb=" CA TYR A 234 " pdb=" CB TYR A 234 " ideal model delta sigma weight residual 1.530 1.547 -0.017 1.69e-02 3.50e+03 9.89e-01 bond pdb=" CA TYR C 234 " pdb=" CB TYR C 234 " ideal model delta sigma weight residual 1.530 1.547 -0.017 1.69e-02 3.50e+03 9.83e-01 bond pdb=" CA TYR D 234 " pdb=" CB TYR D 234 " ideal model delta sigma weight residual 1.530 1.546 -0.016 1.69e-02 3.50e+03 9.27e-01 bond pdb=" CA VAL D 410 " pdb=" CB VAL D 410 " ideal model delta sigma weight residual 1.531 1.541 -0.010 1.11e-02 8.12e+03 7.82e-01 ... (remaining 13199 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 17553 1.60 - 3.20: 274 3.20 - 4.80: 54 4.80 - 6.40: 11 6.40 - 8.00: 16 Bond angle restraints: 17908 Sorted by residual: angle pdb=" C ASP B 233 " pdb=" N TYR B 234 " pdb=" CA TYR B 234 " ideal model delta sigma weight residual 121.54 128.06 -6.52 1.91e+00 2.74e-01 1.16e+01 angle pdb=" C ASP D 233 " pdb=" N TYR D 234 " pdb=" CA TYR D 234 " ideal model delta sigma weight residual 121.54 128.00 -6.46 1.91e+00 2.74e-01 1.14e+01 angle pdb=" C ASP C 233 " pdb=" N TYR C 234 " pdb=" CA TYR C 234 " ideal model delta sigma weight residual 121.54 127.98 -6.44 1.91e+00 2.74e-01 1.14e+01 angle pdb=" C ASP A 233 " pdb=" N TYR A 234 " pdb=" CA TYR A 234 " ideal model delta sigma weight residual 121.54 127.95 -6.41 1.91e+00 2.74e-01 1.12e+01 angle pdb=" N TRP B 152 " pdb=" CA TRP B 152 " pdb=" C TRP B 152 " ideal model delta sigma weight residual 109.81 115.22 -5.41 2.21e+00 2.05e-01 6.00e+00 ... (remaining 17903 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.88: 6581 16.88 - 33.76: 895 33.76 - 50.63: 284 50.63 - 67.51: 48 67.51 - 84.39: 16 Dihedral angle restraints: 7824 sinusoidal: 3156 harmonic: 4668 Sorted by residual: dihedral pdb=" CG ARG A 364 " pdb=" CD ARG A 364 " pdb=" NE ARG A 364 " pdb=" CZ ARG A 364 " ideal model delta sinusoidal sigma weight residual -180.00 -137.14 -42.86 2 1.50e+01 4.44e-03 9.87e+00 dihedral pdb=" CG ARG D 364 " pdb=" CD ARG D 364 " pdb=" NE ARG D 364 " pdb=" CZ ARG D 364 " ideal model delta sinusoidal sigma weight residual -180.00 -137.15 -42.85 2 1.50e+01 4.44e-03 9.87e+00 dihedral pdb=" CG ARG B 364 " pdb=" CD ARG B 364 " pdb=" NE ARG B 364 " pdb=" CZ ARG B 364 " ideal model delta sinusoidal sigma weight residual -180.00 -137.15 -42.85 2 1.50e+01 4.44e-03 9.87e+00 ... (remaining 7821 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1288 0.028 - 0.056: 501 0.056 - 0.084: 195 0.084 - 0.113: 68 0.113 - 0.141: 16 Chirality restraints: 2068 Sorted by residual: chirality pdb=" CA TYR A 234 " pdb=" N TYR A 234 " pdb=" C TYR A 234 " pdb=" CB TYR A 234 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.95e-01 chirality pdb=" CA TYR D 234 " pdb=" N TYR D 234 " pdb=" C TYR D 234 " pdb=" CB TYR D 234 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.85e-01 chirality pdb=" CA TYR C 234 " pdb=" N TYR C 234 " pdb=" C TYR C 234 " pdb=" CB TYR C 234 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.72e-01 ... (remaining 2065 not shown) Planarity restraints: 2184 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP D 152 " 0.035 5.00e-02 4.00e+02 5.37e-02 4.62e+00 pdb=" N PRO D 153 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO D 153 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO D 153 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP A 152 " 0.035 5.00e-02 4.00e+02 5.36e-02 4.59e+00 pdb=" N PRO A 153 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO A 153 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 153 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP B 152 " -0.035 5.00e-02 4.00e+02 5.34e-02 4.57e+00 pdb=" N PRO B 153 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO B 153 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 153 " -0.030 5.00e-02 4.00e+02 ... (remaining 2181 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2976 2.78 - 3.31: 12547 3.31 - 3.84: 22524 3.84 - 4.37: 25245 4.37 - 4.90: 43694 Nonbonded interactions: 106986 Sorted by model distance: nonbonded pdb=" OD2 ASP A 316 " pdb=" OG SER A 413 " model vdw 2.254 3.040 nonbonded pdb=" OD2 ASP D 316 " pdb=" OG SER D 413 " model vdw 2.254 3.040 nonbonded pdb=" OD2 ASP C 316 " pdb=" OG SER C 413 " model vdw 2.254 3.040 nonbonded pdb=" OD2 ASP B 316 " pdb=" OG SER B 413 " model vdw 2.254 3.040 nonbonded pdb=" OD1 ASN B 225 " pdb=" OH TYR B 241 " model vdw 2.317 3.040 ... (remaining 106981 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 0.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.630 Find NCS groups from input model: 0.110 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:6.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7051 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 0.027 13204 Z= 0.123 Angle : 0.553 8.005 17908 Z= 0.292 Chirality : 0.037 0.141 2068 Planarity : 0.004 0.054 2184 Dihedral : 17.024 84.391 4800 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.31 % Favored : 97.44 % Rotamer: Outliers : 0.28 % Allowed : 22.82 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.35 (0.20), residues: 1560 helix: 2.41 (0.14), residues: 1168 sheet: None (None), residues: 0 loop : -1.18 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 210 TYR 0.013 0.001 TYR B 227 PHE 0.020 0.001 PHE D 354 TRP 0.006 0.001 TRP B 394 HIS 0.001 0.000 HIS B 290 Details of bonding type rmsd covalent geometry : bond 0.00231 (13204) covalent geometry : angle 0.55307 (17908) hydrogen bonds : bond 0.07913 ( 964) hydrogen bonds : angle 4.10668 ( 2880) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 394 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 394 average time/residue: 0.4184 time to fit residues: 185.9815 Evaluate side-chains 260 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 259 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 8.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 GLN A 231 ASN A 329 ASN B 71 GLN B 231 ASN B 329 ASN C 71 GLN C 231 ASN C 329 ASN D 71 GLN ** D 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 329 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.082621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.064916 restraints weight = 31958.336| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 2.73 r_work: 0.2893 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13204 Z= 0.163 Angle : 0.634 9.318 17908 Z= 0.318 Chirality : 0.041 0.157 2068 Planarity : 0.005 0.052 2184 Dihedral : 3.613 11.994 1754 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.26 % Allowed : 1.99 % Favored : 97.76 % Rotamer: Outliers : 3.73 % Allowed : 25.49 % Favored : 70.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.35 (0.20), residues: 1560 helix: 2.31 (0.14), residues: 1176 sheet: None (None), residues: 0 loop : -0.91 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 392 TYR 0.016 0.002 TYR B 262 PHE 0.023 0.001 PHE D 224 TRP 0.038 0.002 TRP A 347 HIS 0.005 0.001 HIS D 118 Details of bonding type rmsd covalent geometry : bond 0.00356 (13204) covalent geometry : angle 0.63368 (17908) hydrogen bonds : bond 0.04258 ( 964) hydrogen bonds : angle 3.97670 ( 2880) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 276 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 187 LEU cc_start: 0.9426 (tp) cc_final: 0.9202 (tm) REVERT: A 196 GLU cc_start: 0.9242 (tm-30) cc_final: 0.8951 (tp30) REVERT: B 106 ILE cc_start: 0.9601 (OUTLIER) cc_final: 0.9372 (mp) REVERT: B 109 SER cc_start: 0.9104 (p) cc_final: 0.8756 (p) REVERT: C 253 ASN cc_start: 0.8853 (OUTLIER) cc_final: 0.8524 (t0) outliers start: 53 outliers final: 17 residues processed: 313 average time/residue: 0.3762 time to fit residues: 135.1074 Evaluate side-chains 271 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 252 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 317 SER Chi-restraints excluded: chain B residue 431 THR Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 253 ASN Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain C residue 431 THR Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 317 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 75 optimal weight: 0.9990 chunk 140 optimal weight: 9.9990 chunk 101 optimal weight: 10.0000 chunk 107 optimal weight: 5.9990 chunk 90 optimal weight: 9.9990 chunk 31 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 32 optimal weight: 0.9980 chunk 88 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 GLN B 71 GLN B 253 ASN C 71 GLN D 71 GLN D 253 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.081928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.064006 restraints weight = 32120.189| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 2.71 r_work: 0.2876 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.3014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 13204 Z= 0.154 Angle : 0.606 10.242 17908 Z= 0.303 Chirality : 0.040 0.301 2068 Planarity : 0.004 0.045 2184 Dihedral : 3.550 14.637 1752 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.26 % Allowed : 1.92 % Favored : 97.82 % Rotamer: Outliers : 4.23 % Allowed : 24.51 % Favored : 71.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.50 (0.20), residues: 1560 helix: 2.42 (0.14), residues: 1176 sheet: None (None), residues: 0 loop : -0.83 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 210 TYR 0.016 0.002 TYR D 234 PHE 0.019 0.001 PHE A 224 TRP 0.012 0.001 TRP A 347 HIS 0.003 0.001 HIS D 118 Details of bonding type rmsd covalent geometry : bond 0.00344 (13204) covalent geometry : angle 0.60580 (17908) hydrogen bonds : bond 0.04200 ( 964) hydrogen bonds : angle 3.90618 ( 2880) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 257 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 ILE cc_start: 0.9585 (mp) cc_final: 0.9365 (mp) REVERT: A 428 MET cc_start: 0.9489 (ttt) cc_final: 0.9002 (ttt) REVERT: B 71 GLN cc_start: 0.8856 (OUTLIER) cc_final: 0.8540 (tp40) REVERT: D 98 MET cc_start: 0.9402 (tpt) cc_final: 0.9168 (tpt) REVERT: D 440 LEU cc_start: 0.9390 (OUTLIER) cc_final: 0.9115 (mm) outliers start: 60 outliers final: 20 residues processed: 301 average time/residue: 0.3552 time to fit residues: 123.6007 Evaluate side-chains 256 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 234 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain B residue 71 GLN Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 431 THR Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 431 THR Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 398 VAL Chi-restraints excluded: chain D residue 440 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 105 optimal weight: 4.9990 chunk 132 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 118 optimal weight: 8.9990 chunk 55 optimal weight: 3.9990 chunk 148 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 70 optimal weight: 5.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 GLN B 71 GLN C 71 GLN D 71 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.081600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 19)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.063540 restraints weight = 31785.045| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 2.76 r_work: 0.2863 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.3455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 13204 Z= 0.147 Angle : 0.596 11.119 17908 Z= 0.298 Chirality : 0.041 0.287 2068 Planarity : 0.004 0.043 2184 Dihedral : 3.482 12.538 1752 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.18 % Favored : 97.56 % Rotamer: Outliers : 3.52 % Allowed : 24.65 % Favored : 71.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.56 (0.20), residues: 1560 helix: 2.47 (0.14), residues: 1176 sheet: None (None), residues: 0 loop : -0.86 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 423 TYR 0.016 0.001 TYR A 227 PHE 0.015 0.001 PHE D 64 TRP 0.010 0.001 TRP C 355 HIS 0.003 0.001 HIS A 118 Details of bonding type rmsd covalent geometry : bond 0.00321 (13204) covalent geometry : angle 0.59586 (17908) hydrogen bonds : bond 0.04149 ( 964) hydrogen bonds : angle 3.86767 ( 2880) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 248 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 MET cc_start: 0.8429 (mtp) cc_final: 0.8208 (ttt) REVERT: A 106 ILE cc_start: 0.9571 (mp) cc_final: 0.9353 (mp) REVERT: A 113 LEU cc_start: 0.9558 (tm) cc_final: 0.9356 (mm) REVERT: A 381 ARG cc_start: 0.9117 (OUTLIER) cc_final: 0.8154 (mtt90) REVERT: A 428 MET cc_start: 0.9571 (ttt) cc_final: 0.9119 (ttt) REVERT: B 184 LEU cc_start: 0.9465 (OUTLIER) cc_final: 0.9262 (mm) REVERT: D 440 LEU cc_start: 0.9353 (OUTLIER) cc_final: 0.9057 (mm) REVERT: D 441 GLN cc_start: 0.8705 (mm-40) cc_final: 0.8495 (mm-40) outliers start: 50 outliers final: 27 residues processed: 283 average time/residue: 0.3975 time to fit residues: 128.2774 Evaluate side-chains 257 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 227 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 GLN Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 381 ARG Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 431 THR Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain C residue 71 GLN Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 214 MET Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 431 THR Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 398 VAL Chi-restraints excluded: chain D residue 440 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 44 optimal weight: 2.9990 chunk 74 optimal weight: 7.9990 chunk 119 optimal weight: 5.9990 chunk 21 optimal weight: 4.9990 chunk 36 optimal weight: 7.9990 chunk 145 optimal weight: 10.0000 chunk 48 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 81 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 71 GLN C 253 ASN D 71 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.080414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.062688 restraints weight = 32156.304| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 2.73 r_work: 0.2841 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.3926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 13204 Z= 0.179 Angle : 0.610 12.093 17908 Z= 0.307 Chirality : 0.041 0.281 2068 Planarity : 0.004 0.042 2184 Dihedral : 3.483 12.898 1752 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.05 % Favored : 97.69 % Rotamer: Outliers : 3.87 % Allowed : 25.14 % Favored : 70.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.69 (0.20), residues: 1560 helix: 2.57 (0.14), residues: 1176 sheet: None (None), residues: 0 loop : -0.83 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 210 TYR 0.020 0.001 TYR D 208 PHE 0.016 0.001 PHE D 64 TRP 0.009 0.001 TRP A 347 HIS 0.003 0.001 HIS A 118 Details of bonding type rmsd covalent geometry : bond 0.00397 (13204) covalent geometry : angle 0.61048 (17908) hydrogen bonds : bond 0.04223 ( 964) hydrogen bonds : angle 3.88633 ( 2880) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 240 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 MET cc_start: 0.8532 (mtp) cc_final: 0.8268 (ttt) REVERT: A 231 ASN cc_start: 0.8599 (t0) cc_final: 0.8357 (t0) REVERT: A 381 ARG cc_start: 0.9104 (OUTLIER) cc_final: 0.8197 (mtt90) REVERT: B 184 LEU cc_start: 0.9518 (OUTLIER) cc_final: 0.9316 (mm) REVERT: C 442 PHE cc_start: 0.8171 (m-80) cc_final: 0.7567 (m-80) REVERT: D 76 MET cc_start: 0.8571 (mtp) cc_final: 0.8274 (ttt) REVERT: D 432 ILE cc_start: 0.9603 (mt) cc_final: 0.9341 (mp) REVERT: D 440 LEU cc_start: 0.9337 (OUTLIER) cc_final: 0.9024 (mm) REVERT: D 441 GLN cc_start: 0.8745 (mm-40) cc_final: 0.8360 (mm-40) outliers start: 55 outliers final: 27 residues processed: 280 average time/residue: 0.3883 time to fit residues: 124.0905 Evaluate side-chains 253 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 223 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 381 ARG Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain B residue 317 SER Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 431 THR Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 214 MET Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 431 THR Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 398 VAL Chi-restraints excluded: chain D residue 440 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 119 optimal weight: 8.9990 chunk 46 optimal weight: 4.9990 chunk 129 optimal weight: 0.5980 chunk 154 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 27 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 96 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 chunk 121 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 GLN B 71 GLN D 71 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.081101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.063166 restraints weight = 31417.291| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 2.74 r_work: 0.2861 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.4137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 13204 Z= 0.130 Angle : 0.620 13.548 17908 Z= 0.306 Chirality : 0.041 0.339 2068 Planarity : 0.004 0.040 2184 Dihedral : 3.494 12.880 1752 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.12 % Favored : 97.63 % Rotamer: Outliers : 3.31 % Allowed : 26.48 % Favored : 70.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.71 (0.21), residues: 1560 helix: 2.58 (0.14), residues: 1176 sheet: None (None), residues: 0 loop : -0.81 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 381 TYR 0.023 0.001 TYR A 232 PHE 0.015 0.001 PHE D 64 TRP 0.007 0.001 TRP A 347 HIS 0.004 0.001 HIS A 118 Details of bonding type rmsd covalent geometry : bond 0.00278 (13204) covalent geometry : angle 0.62025 (17908) hydrogen bonds : bond 0.04071 ( 964) hydrogen bonds : angle 3.82318 ( 2880) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 244 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 MET cc_start: 0.8493 (mtp) cc_final: 0.8166 (ttt) REVERT: A 115 MET cc_start: 0.9510 (tpt) cc_final: 0.9245 (tpp) REVERT: A 231 ASN cc_start: 0.8647 (t0) cc_final: 0.8425 (t0) REVERT: A 338 LEU cc_start: 0.9117 (mt) cc_final: 0.8899 (mt) REVERT: C 76 MET cc_start: 0.8551 (mtp) cc_final: 0.8309 (ttt) REVERT: C 442 PHE cc_start: 0.8104 (m-80) cc_final: 0.7244 (m-80) REVERT: D 76 MET cc_start: 0.8523 (mtp) cc_final: 0.8208 (ttt) REVERT: D 432 ILE cc_start: 0.9599 (mt) cc_final: 0.9334 (mp) REVERT: D 440 LEU cc_start: 0.9316 (OUTLIER) cc_final: 0.9035 (mm) REVERT: D 441 GLN cc_start: 0.8684 (mm-40) cc_final: 0.8156 (mm110) outliers start: 47 outliers final: 26 residues processed: 276 average time/residue: 0.3838 time to fit residues: 121.2545 Evaluate side-chains 253 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 226 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain B residue 317 SER Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 105 MET Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 214 MET Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 431 THR Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 398 VAL Chi-restraints excluded: chain D residue 440 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 150 optimal weight: 1.9990 chunk 140 optimal weight: 8.9990 chunk 146 optimal weight: 6.9990 chunk 122 optimal weight: 2.9990 chunk 125 optimal weight: 0.9980 chunk 152 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 4 optimal weight: 0.5980 chunk 48 optimal weight: 6.9990 chunk 40 optimal weight: 5.9990 chunk 29 optimal weight: 7.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 GLN B 71 GLN C 71 GLN D 71 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.079111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.061943 restraints weight = 33297.220| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 2.70 r_work: 0.2834 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.4570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 13204 Z= 0.173 Angle : 0.671 13.704 17908 Z= 0.327 Chirality : 0.042 0.308 2068 Planarity : 0.004 0.041 2184 Dihedral : 3.512 13.271 1752 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.18 % Favored : 97.56 % Rotamer: Outliers : 3.94 % Allowed : 25.77 % Favored : 70.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.70 (0.21), residues: 1560 helix: 2.58 (0.14), residues: 1172 sheet: None (None), residues: 0 loop : -0.77 (0.30), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 423 TYR 0.020 0.001 TYR D 208 PHE 0.016 0.001 PHE D 64 TRP 0.010 0.001 TRP A 355 HIS 0.004 0.001 HIS A 118 Details of bonding type rmsd covalent geometry : bond 0.00389 (13204) covalent geometry : angle 0.67053 (17908) hydrogen bonds : bond 0.04227 ( 964) hydrogen bonds : angle 3.88383 ( 2880) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 238 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 MET cc_start: 0.8628 (mtp) cc_final: 0.8369 (ttt) REVERT: A 231 ASN cc_start: 0.8934 (t0) cc_final: 0.8609 (t0) REVERT: A 252 ILE cc_start: 0.8827 (tt) cc_final: 0.8568 (tp) REVERT: A 342 PHE cc_start: 0.9175 (m-80) cc_final: 0.8929 (m-80) REVERT: C 76 MET cc_start: 0.8717 (mtp) cc_final: 0.8471 (ttt) REVERT: C 115 MET cc_start: 0.9441 (tpt) cc_final: 0.9191 (tpp) REVERT: D 76 MET cc_start: 0.8687 (mtp) cc_final: 0.8377 (ttt) REVERT: D 428 MET cc_start: 0.9663 (ttt) cc_final: 0.9334 (ttt) outliers start: 56 outliers final: 24 residues processed: 276 average time/residue: 0.4002 time to fit residues: 125.8231 Evaluate side-chains 245 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 221 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 263 MET Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain B residue 317 SER Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 431 THR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 214 MET Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 431 THR Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 398 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 127 optimal weight: 0.7980 chunk 111 optimal weight: 4.9990 chunk 41 optimal weight: 0.9990 chunk 131 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 4 optimal weight: 8.9990 chunk 151 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 93 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 GLN B 71 GLN C 71 GLN D 71 GLN D 231 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.078211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.060960 restraints weight = 33131.176| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 2.70 r_work: 0.2815 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.5043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13204 Z= 0.188 Angle : 0.696 14.189 17908 Z= 0.339 Chirality : 0.044 0.383 2068 Planarity : 0.004 0.042 2184 Dihedral : 3.578 13.900 1752 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.37 % Favored : 97.37 % Rotamer: Outliers : 3.45 % Allowed : 26.69 % Favored : 69.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.69 (0.20), residues: 1560 helix: 2.56 (0.14), residues: 1176 sheet: None (None), residues: 0 loop : -0.78 (0.30), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 392 TYR 0.022 0.002 TYR D 227 PHE 0.016 0.001 PHE D 64 TRP 0.012 0.001 TRP B 152 HIS 0.004 0.001 HIS A 118 Details of bonding type rmsd covalent geometry : bond 0.00422 (13204) covalent geometry : angle 0.69644 (17908) hydrogen bonds : bond 0.04316 ( 964) hydrogen bonds : angle 3.93131 ( 2880) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 224 time to evaluate : 0.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 LEU cc_start: 0.9564 (OUTLIER) cc_final: 0.9303 (mm) REVERT: A 231 ASN cc_start: 0.8948 (t0) cc_final: 0.8662 (t0) REVERT: A 428 MET cc_start: 0.9652 (ttt) cc_final: 0.9274 (ttt) REVERT: B 428 MET cc_start: 0.9670 (ttt) cc_final: 0.9393 (ttt) REVERT: C 442 PHE cc_start: 0.8496 (m-80) cc_final: 0.8173 (m-10) REVERT: D 76 MET cc_start: 0.8732 (mtp) cc_final: 0.8508 (ttt) REVERT: D 231 ASN cc_start: 0.8906 (t0) cc_final: 0.8704 (t0) REVERT: D 428 MET cc_start: 0.9632 (ttt) cc_final: 0.9224 (ttt) REVERT: D 432 ILE cc_start: 0.9627 (mt) cc_final: 0.9350 (mp) REVERT: D 441 GLN cc_start: 0.8781 (mt0) cc_final: 0.8279 (mp10) outliers start: 49 outliers final: 24 residues processed: 256 average time/residue: 0.4305 time to fit residues: 124.6416 Evaluate side-chains 237 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 212 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain B residue 317 SER Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 431 THR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 214 MET Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 431 THR Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 398 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 132 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 129 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 143 optimal weight: 4.9990 chunk 25 optimal weight: 0.7980 chunk 110 optimal weight: 7.9990 chunk 17 optimal weight: 5.9990 chunk 133 optimal weight: 8.9990 chunk 61 optimal weight: 5.9990 chunk 103 optimal weight: 0.9980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 GLN B 71 GLN C 71 GLN D 71 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.078876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.061725 restraints weight = 33207.124| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 2.71 r_work: 0.2828 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.5190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 13204 Z= 0.158 Angle : 0.725 15.064 17908 Z= 0.345 Chirality : 0.044 0.442 2068 Planarity : 0.004 0.041 2184 Dihedral : 3.597 13.464 1752 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.24 % Favored : 97.50 % Rotamer: Outliers : 2.82 % Allowed : 27.89 % Favored : 69.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.66 (0.21), residues: 1560 helix: 2.53 (0.14), residues: 1176 sheet: None (None), residues: 0 loop : -0.76 (0.30), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 381 TYR 0.024 0.002 TYR D 227 PHE 0.015 0.001 PHE D 64 TRP 0.010 0.001 TRP C 152 HIS 0.004 0.001 HIS A 118 Details of bonding type rmsd covalent geometry : bond 0.00356 (13204) covalent geometry : angle 0.72538 (17908) hydrogen bonds : bond 0.04304 ( 964) hydrogen bonds : angle 3.93732 ( 2880) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 220 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 LEU cc_start: 0.9575 (OUTLIER) cc_final: 0.9307 (mm) REVERT: A 231 ASN cc_start: 0.9038 (t0) cc_final: 0.8771 (t0) REVERT: A 428 MET cc_start: 0.9660 (ttt) cc_final: 0.9301 (ttt) REVERT: B 428 MET cc_start: 0.9677 (ttt) cc_final: 0.9398 (ttt) REVERT: B 442 PHE cc_start: 0.8525 (m-80) cc_final: 0.8313 (m-80) REVERT: C 392 ARG cc_start: 0.8375 (OUTLIER) cc_final: 0.8167 (ppt170) REVERT: C 441 GLN cc_start: 0.8846 (mm110) cc_final: 0.8618 (mm-40) REVERT: C 442 PHE cc_start: 0.8471 (m-80) cc_final: 0.8045 (m-10) REVERT: D 76 MET cc_start: 0.8769 (mtp) cc_final: 0.8526 (ttt) REVERT: D 428 MET cc_start: 0.9629 (ttt) cc_final: 0.9234 (ttt) REVERT: D 432 ILE cc_start: 0.9618 (mt) cc_final: 0.9336 (mp) REVERT: D 441 GLN cc_start: 0.8574 (mt0) cc_final: 0.8212 (mp10) outliers start: 40 outliers final: 22 residues processed: 248 average time/residue: 0.4250 time to fit residues: 119.3278 Evaluate side-chains 240 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 216 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain B residue 317 SER Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 431 THR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 214 MET Chi-restraints excluded: chain C residue 392 ARG Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 431 THR Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 398 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 135 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 66 optimal weight: 4.9990 chunk 61 optimal weight: 5.9990 chunk 79 optimal weight: 3.9990 chunk 128 optimal weight: 0.5980 chunk 81 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 56 optimal weight: 8.9990 chunk 123 optimal weight: 0.0980 chunk 68 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 GLN B 71 GLN B 231 ASN C 71 GLN D 71 GLN D 231 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.078887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.061768 restraints weight = 33050.587| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 2.71 r_work: 0.2833 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.5318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 13204 Z= 0.150 Angle : 0.725 15.605 17908 Z= 0.345 Chirality : 0.044 0.408 2068 Planarity : 0.004 0.041 2184 Dihedral : 3.601 13.374 1752 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.31 % Favored : 97.44 % Rotamer: Outliers : 2.68 % Allowed : 28.24 % Favored : 69.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.64 (0.20), residues: 1560 helix: 2.51 (0.14), residues: 1176 sheet: None (None), residues: 0 loop : -0.76 (0.30), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 381 TYR 0.020 0.001 TYR D 227 PHE 0.015 0.001 PHE D 64 TRP 0.008 0.001 TRP A 347 HIS 0.003 0.001 HIS A 118 Details of bonding type rmsd covalent geometry : bond 0.00334 (13204) covalent geometry : angle 0.72467 (17908) hydrogen bonds : bond 0.04293 ( 964) hydrogen bonds : angle 3.90556 ( 2880) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 219 time to evaluate : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 ILE cc_start: 0.9478 (pp) cc_final: 0.9276 (mp) REVERT: A 184 LEU cc_start: 0.9576 (OUTLIER) cc_final: 0.9305 (mm) REVERT: A 231 ASN cc_start: 0.9063 (t0) cc_final: 0.8756 (t0) REVERT: A 347 TRP cc_start: 0.9019 (m100) cc_final: 0.8376 (m100) REVERT: A 428 MET cc_start: 0.9659 (ttt) cc_final: 0.9344 (ttt) REVERT: B 428 MET cc_start: 0.9668 (ttt) cc_final: 0.9398 (ttt) REVERT: B 442 PHE cc_start: 0.8546 (m-80) cc_final: 0.8333 (m-80) REVERT: C 251 LEU cc_start: 0.9574 (mt) cc_final: 0.9346 (mp) REVERT: C 441 GLN cc_start: 0.8854 (mm110) cc_final: 0.8624 (mm-40) REVERT: C 442 PHE cc_start: 0.8463 (m-80) cc_final: 0.8045 (m-10) REVERT: D 76 MET cc_start: 0.8770 (mtp) cc_final: 0.8551 (ttt) REVERT: D 428 MET cc_start: 0.9631 (ttt) cc_final: 0.9363 (ttt) REVERT: D 441 GLN cc_start: 0.8627 (mt0) cc_final: 0.8219 (mp10) outliers start: 38 outliers final: 20 residues processed: 245 average time/residue: 0.4082 time to fit residues: 113.7854 Evaluate side-chains 231 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 210 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain B residue 317 SER Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 431 THR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 214 MET Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 431 THR Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 398 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 72 optimal weight: 0.9990 chunk 133 optimal weight: 6.9990 chunk 89 optimal weight: 0.4980 chunk 146 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 153 optimal weight: 5.9990 chunk 82 optimal weight: 0.0670 chunk 107 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 55 optimal weight: 6.9990 chunk 140 optimal weight: 10.0000 overall best weight: 0.9122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 GLN B 71 GLN B 231 ASN C 71 GLN C 231 ASN D 71 GLN D 231 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.079594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.062542 restraints weight = 32898.727| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 2.72 r_work: 0.2852 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.5385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13204 Z= 0.134 Angle : 0.737 15.669 17908 Z= 0.345 Chirality : 0.045 0.401 2068 Planarity : 0.004 0.040 2184 Dihedral : 3.588 13.328 1752 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.24 % Favored : 97.50 % Rotamer: Outliers : 2.32 % Allowed : 28.87 % Favored : 68.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.62 (0.20), residues: 1560 helix: 2.50 (0.14), residues: 1176 sheet: None (None), residues: 0 loop : -0.78 (0.30), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 423 TYR 0.024 0.002 TYR B 227 PHE 0.015 0.001 PHE D 64 TRP 0.008 0.001 TRP A 347 HIS 0.004 0.001 HIS A 118 Details of bonding type rmsd covalent geometry : bond 0.00289 (13204) covalent geometry : angle 0.73699 (17908) hydrogen bonds : bond 0.04191 ( 964) hydrogen bonds : angle 3.87796 ( 2880) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5200.91 seconds wall clock time: 89 minutes 36.84 seconds (5376.84 seconds total)