Starting phenix.real_space_refine on Fri Aug 22 20:59:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y5y_38959/08_2025/8y5y_38959.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y5y_38959/08_2025/8y5y_38959.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8y5y_38959/08_2025/8y5y_38959.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y5y_38959/08_2025/8y5y_38959.map" model { file = "/net/cci-nas-00/data/ceres_data/8y5y_38959/08_2025/8y5y_38959.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y5y_38959/08_2025/8y5y_38959.cif" } resolution = 3.3 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= 0.001 sd= 0.048 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 54 5.16 5 C 5320 2.51 5 N 1202 2.21 5 O 1342 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7918 Number of models: 1 Model: "" Number of chains: 2 Chain: "C" Number of atoms: 3954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 3954 Classifications: {'peptide': 506} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 29, 'TRANS': 476} Chain breaks: 3 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'SO4': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B Time building chain proxies: 2.88, per 1000 atoms: 0.36 Number of scatterers: 7918 At special positions: 0 Unit cell: (89.6018, 111.374, 86.2522, 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 54 16.00 O 1342 8.00 N 1202 7.00 C 5320 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: 0.65 Conformation dependent library (CDL) restraints added in 349.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1916 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 0 sheets defined 79.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'C' and resid 2 through 10 removed outlier: 3.597A pdb=" N TYR C 10 " --> pdb=" O TYR C 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 23 Processing helix chain 'C' and resid 24 through 29 removed outlier: 4.003A pdb=" N ILE C 28 " --> pdb=" O LEU C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 33 removed outlier: 3.711A pdb=" N LYS C 33 " --> pdb=" O LEU C 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 30 through 33' Processing helix chain 'C' and resid 34 through 50 Processing helix chain 'C' and resid 54 through 60 Processing helix chain 'C' and resid 61 through 70 Proline residue: C 67 - end of helix Processing helix chain 'C' and resid 73 through 80 Processing helix chain 'C' and resid 83 through 102 removed outlier: 3.586A pdb=" N LEU C 87 " --> pdb=" O LYS C 83 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU C 95 " --> pdb=" O GLY C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 116 removed outlier: 3.568A pdb=" N ARG C 107 " --> pdb=" O ASN C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 138 removed outlier: 3.586A pdb=" N THR C 124 " --> pdb=" O PRO C 120 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N TRP C 137 " --> pdb=" O PHE C 133 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU C 138 " --> pdb=" O LEU C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 162 removed outlier: 3.667A pdb=" N ALA C 145 " --> pdb=" O THR C 141 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N MET C 148 " --> pdb=" O ALA C 144 " (cutoff:3.500A) Proline residue: C 149 - end of helix removed outlier: 3.536A pdb=" N VAL C 155 " --> pdb=" O ALA C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 247 removed outlier: 3.590A pdb=" N ILE C 244 " --> pdb=" O THR C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 273 Processing helix chain 'C' and resid 284 through 307 Proline residue: C 290 - end of helix removed outlier: 3.687A pdb=" N ILE C 294 " --> pdb=" O PRO C 290 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE C 295 " --> pdb=" O ALA C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 316 removed outlier: 4.334A pdb=" N MET C 315 " --> pdb=" O ASN C 311 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N PHE C 316 " --> pdb=" O PHE C 312 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 311 through 316' Processing helix chain 'C' and resid 324 through 341 removed outlier: 3.674A pdb=" N GLY C 341 " --> pdb=" O TYR C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 344 through 363 Processing helix chain 'C' and resid 371 through 375 Processing helix chain 'C' and resid 384 through 394 removed outlier: 3.865A pdb=" N VAL C 388 " --> pdb=" O THR C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 395 through 398 Processing helix chain 'C' and resid 423 through 429 Processing helix chain 'C' and resid 432 through 452 Processing helix chain 'C' and resid 454 through 463 Processing helix chain 'C' and resid 470 through 485 removed outlier: 4.035A pdb=" N ILE C 474 " --> pdb=" O ALA C 470 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N ILE C 476 " --> pdb=" O LEU C 472 " (cutoff:3.500A) Processing helix chain 'C' and resid 489 through 508 Proline residue: C 499 - end of helix Proline residue: C 503 - end of helix Processing helix chain 'C' and resid 511 through 524 removed outlier: 4.021A pdb=" N ILE C 515 " --> pdb=" O ASN C 511 " (cutoff:3.500A) Proline residue: C 518 - end of helix removed outlier: 4.342A pdb=" N SER C 524 " --> pdb=" O THR C 520 " (cutoff:3.500A) Processing helix chain 'C' and resid 533 through 541 removed outlier: 3.588A pdb=" N VAL C 539 " --> pdb=" O PRO C 535 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 572 removed outlier: 3.827A pdb=" N MET C 550 " --> pdb=" O LYS C 546 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLY C 556 " --> pdb=" O LYS C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 578 removed outlier: 4.084A pdb=" N PHE C 577 " --> pdb=" O ILE C 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 10 removed outlier: 3.597A pdb=" N TYR B 10 " --> pdb=" O TYR B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 23 Processing helix chain 'B' and resid 24 through 29 removed outlier: 4.004A pdb=" N ILE B 28 " --> pdb=" O LEU B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 33 removed outlier: 3.711A pdb=" N LYS B 33 " --> pdb=" O LEU B 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'B' and resid 34 through 50 Processing helix chain 'B' and resid 54 through 60 Processing helix chain 'B' and resid 61 through 70 Proline residue: B 67 - end of helix Processing helix chain 'B' and resid 73 through 80 Processing helix chain 'B' and resid 83 through 102 removed outlier: 3.586A pdb=" N LEU B 87 " --> pdb=" O LYS B 83 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU B 95 " --> pdb=" O GLY B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 116 removed outlier: 3.568A pdb=" N ARG B 107 " --> pdb=" O ASN B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 138 removed outlier: 3.586A pdb=" N THR B 124 " --> pdb=" O PRO B 120 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N TRP B 137 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU B 138 " --> pdb=" O LEU B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 162 removed outlier: 3.666A pdb=" N ALA B 145 " --> pdb=" O THR B 141 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N MET B 148 " --> pdb=" O ALA B 144 " (cutoff:3.500A) Proline residue: B 149 - end of helix removed outlier: 3.535A pdb=" N VAL B 155 " --> pdb=" O ALA B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 247 removed outlier: 3.590A pdb=" N ILE B 244 " --> pdb=" O THR B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 273 Processing helix chain 'B' and resid 284 through 307 Proline residue: B 290 - end of helix removed outlier: 3.687A pdb=" N ILE B 294 " --> pdb=" O PRO B 290 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE B 295 " --> pdb=" O ALA B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 316 removed outlier: 4.334A pdb=" N MET B 315 " --> pdb=" O ASN B 311 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N PHE B 316 " --> pdb=" O PHE B 312 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 311 through 316' Processing helix chain 'B' and resid 324 through 341 removed outlier: 3.674A pdb=" N GLY B 341 " --> pdb=" O TYR B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 363 Processing helix chain 'B' and resid 371 through 375 Processing helix chain 'B' and resid 384 through 394 removed outlier: 3.866A pdb=" N VAL B 388 " --> pdb=" O THR B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 398 Processing helix chain 'B' and resid 423 through 429 Processing helix chain 'B' and resid 432 through 452 Processing helix chain 'B' and resid 454 through 463 Processing helix chain 'B' and resid 470 through 485 removed outlier: 4.035A pdb=" N ILE B 474 " --> pdb=" O ALA B 470 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N ILE B 476 " --> pdb=" O LEU B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 489 through 508 Proline residue: B 499 - end of helix Proline residue: B 503 - end of helix Processing helix chain 'B' and resid 511 through 524 removed outlier: 4.021A pdb=" N ILE B 515 " --> pdb=" O ASN B 511 " (cutoff:3.500A) Proline residue: B 518 - end of helix removed outlier: 4.341A pdb=" N SER B 524 " --> pdb=" O THR B 520 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 541 removed outlier: 3.588A pdb=" N VAL B 539 " --> pdb=" O PRO B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 572 removed outlier: 3.827A pdb=" N MET B 550 " --> pdb=" O LYS B 546 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLY B 556 " --> pdb=" O LYS B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 578 removed outlier: 4.084A pdb=" N PHE B 577 " --> pdb=" O ILE B 573 " (cutoff:3.500A) 481 hydrogen bonds defined for protein. 1425 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: 1.18 Time building geometry restraints manager: 0.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1231 1.32 - 1.45: 2223 1.45 - 1.57: 4604 1.57 - 1.69: 0 1.69 - 1.81: 86 Bond restraints: 8144 Sorted by residual: bond pdb=" CA LEU B 496 " pdb=" C LEU B 496 " ideal model delta sigma weight residual 1.524 1.474 0.050 1.24e-02 6.50e+03 1.63e+01 bond pdb=" CA LEU C 496 " pdb=" C LEU C 496 " ideal model delta sigma weight residual 1.524 1.474 0.050 1.24e-02 6.50e+03 1.60e+01 bond pdb=" N LEU B 496 " pdb=" CA LEU B 496 " ideal model delta sigma weight residual 1.459 1.425 0.035 1.18e-02 7.18e+03 8.58e+00 bond pdb=" CA PRO B 512 " pdb=" C PRO B 512 " ideal model delta sigma weight residual 1.516 1.469 0.047 1.61e-02 3.86e+03 8.48e+00 bond pdb=" N LEU C 496 " pdb=" CA LEU C 496 " ideal model delta sigma weight residual 1.459 1.425 0.034 1.18e-02 7.18e+03 8.40e+00 ... (remaining 8139 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 10836 1.81 - 3.63: 219 3.63 - 5.44: 47 5.44 - 7.26: 18 7.26 - 9.07: 8 Bond angle restraints: 11128 Sorted by residual: angle pdb=" N LEU C 501 " pdb=" CA LEU C 501 " pdb=" C LEU C 501 " ideal model delta sigma weight residual 111.36 120.43 -9.07 1.09e+00 8.42e-01 6.93e+01 angle pdb=" N LEU B 501 " pdb=" CA LEU B 501 " pdb=" C LEU B 501 " ideal model delta sigma weight residual 111.36 120.42 -9.06 1.09e+00 8.42e-01 6.91e+01 angle pdb=" N ILE B 508 " pdb=" CA ILE B 508 " pdb=" C ILE B 508 " ideal model delta sigma weight residual 110.05 103.55 6.50 1.09e+00 8.42e-01 3.56e+01 angle pdb=" N ILE C 508 " pdb=" CA ILE C 508 " pdb=" C ILE C 508 " ideal model delta sigma weight residual 110.05 103.60 6.45 1.09e+00 8.42e-01 3.50e+01 angle pdb=" N ASN B 511 " pdb=" CA ASN B 511 " pdb=" C ASN B 511 " ideal model delta sigma weight residual 109.50 101.59 7.91 1.47e+00 4.63e-01 2.90e+01 ... (remaining 11123 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 4332 17.77 - 35.55: 325 35.55 - 53.32: 41 53.32 - 71.10: 10 71.10 - 88.87: 8 Dihedral angle restraints: 4716 sinusoidal: 1766 harmonic: 2950 Sorted by residual: dihedral pdb=" CA VAL C 574 " pdb=" C VAL C 574 " pdb=" N PRO C 575 " pdb=" CA PRO C 575 " ideal model delta harmonic sigma weight residual 180.00 -161.65 -18.35 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA VAL B 574 " pdb=" C VAL B 574 " pdb=" N PRO B 575 " pdb=" CA PRO B 575 " ideal model delta harmonic sigma weight residual -180.00 -161.66 -18.34 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" N PHE C 497 " pdb=" C PHE C 497 " pdb=" CA PHE C 497 " pdb=" CB PHE C 497 " ideal model delta harmonic sigma weight residual 122.80 131.72 -8.92 0 2.50e+00 1.60e-01 1.27e+01 ... (remaining 4713 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 1264 0.087 - 0.175: 58 0.175 - 0.262: 10 0.262 - 0.349: 4 0.349 - 0.436: 2 Chirality restraints: 1338 Sorted by residual: chirality pdb=" CA LEU B 501 " pdb=" N LEU B 501 " pdb=" C LEU B 501 " pdb=" CB LEU B 501 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.76e+00 chirality pdb=" CA LEU C 501 " pdb=" N LEU C 501 " pdb=" C LEU C 501 " pdb=" CB LEU C 501 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.71e+00 chirality pdb=" CA PHE C 497 " pdb=" N PHE C 497 " pdb=" C PHE C 497 " pdb=" CB PHE C 497 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.31e+00 ... (remaining 1335 not shown) Planarity restraints: 1324 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER C 502 " 0.080 5.00e-02 4.00e+02 1.21e-01 2.35e+01 pdb=" N PRO C 503 " -0.209 5.00e-02 4.00e+02 pdb=" CA PRO C 503 " 0.061 5.00e-02 4.00e+02 pdb=" CD PRO C 503 " 0.068 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 502 " -0.080 5.00e-02 4.00e+02 1.21e-01 2.34e+01 pdb=" N PRO B 503 " 0.209 5.00e-02 4.00e+02 pdb=" CA PRO B 503 " -0.061 5.00e-02 4.00e+02 pdb=" CD PRO B 503 " -0.068 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 498 " 0.061 5.00e-02 4.00e+02 9.08e-02 1.32e+01 pdb=" N PRO C 499 " -0.157 5.00e-02 4.00e+02 pdb=" CA PRO C 499 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO C 499 " 0.053 5.00e-02 4.00e+02 ... (remaining 1321 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 2385 2.82 - 3.34: 8231 3.34 - 3.86: 12891 3.86 - 4.38: 14917 4.38 - 4.90: 25340 Nonbonded interactions: 63764 Sorted by model distance: nonbonded pdb=" O LEU B 567 " pdb=" OG1 THR B 571 " model vdw 2.298 3.040 nonbonded pdb=" O LEU C 567 " pdb=" OG1 THR C 571 " model vdw 2.298 3.040 nonbonded pdb=" NE1 TRP C 424 " pdb=" OD1 ASP B 434 " model vdw 2.311 3.120 nonbonded pdb=" OD1 ASP C 434 " pdb=" NE1 TRP B 424 " model vdw 2.312 3.120 nonbonded pdb=" OG1 THR B 259 " pdb=" O3 SO4 B 601 " model vdw 2.319 3.040 ... (remaining 63759 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: 0.02 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.530 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: 0.020 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 9.390 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8144 Z= 0.278 Angle : 0.681 9.072 11128 Z= 0.412 Chirality : 0.049 0.436 1338 Planarity : 0.008 0.121 1324 Dihedral : 13.068 88.872 2800 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.60 % Allowed : 4.22 % Favored : 95.18 % Rotamer: Outliers : 0.46 % Allowed : 1.04 % Favored : 98.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.04 (0.27), residues: 996 helix: 0.76 (0.20), residues: 670 sheet: None (None), residues: 0 loop : -1.64 (0.36), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 237 TYR 0.007 0.001 TYR B 580 PHE 0.039 0.001 PHE B 430 TRP 0.009 0.001 TRP C 372 HIS 0.004 0.001 HIS B 509 Details of bonding type rmsd covalent geometry : bond 0.00415 ( 8144) covalent geometry : angle 0.68074 (11128) hydrogen bonds : bond 0.26398 ( 481) hydrogen bonds : angle 6.86162 ( 1425) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 188 time to evaluate : 0.330 Fit side-chains REVERT: C 237 ARG cc_start: 0.6782 (ptt180) cc_final: 0.5818 (ptp-110) REVERT: C 509 HIS cc_start: 0.7412 (OUTLIER) cc_final: 0.7044 (t70) REVERT: B 237 ARG cc_start: 0.6760 (ptt180) cc_final: 0.5827 (ptp-110) REVERT: B 509 HIS cc_start: 0.7463 (OUTLIER) cc_final: 0.7228 (t70) outliers start: 4 outliers final: 0 residues processed: 192 average time/residue: 0.0679 time to fit residues: 19.1445 Evaluate side-chains 164 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 162 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 509 HIS Chi-restraints excluded: chain B residue 509 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 6.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.182159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.137055 restraints weight = 11688.094| |-----------------------------------------------------------------------------| r_work (start): 0.3741 rms_B_bonded: 2.20 r_work: 0.3614 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 8144 Z= 0.161 Angle : 0.625 6.985 11128 Z= 0.330 Chirality : 0.044 0.230 1338 Planarity : 0.006 0.054 1324 Dihedral : 4.790 41.747 1054 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.60 % Allowed : 4.22 % Favored : 95.18 % Rotamer: Outliers : 2.55 % Allowed : 11.23 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.74 (0.28), residues: 996 helix: 1.33 (0.20), residues: 704 sheet: None (None), residues: 0 loop : -1.60 (0.40), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 11 TYR 0.010 0.001 TYR C 39 PHE 0.012 0.001 PHE C 285 TRP 0.013 0.001 TRP C 424 HIS 0.008 0.002 HIS C 234 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 8144) covalent geometry : angle 0.62472 (11128) hydrogen bonds : bond 0.05898 ( 481) hydrogen bonds : angle 4.41984 ( 1425) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 175 time to evaluate : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 473 ILE cc_start: 0.8377 (mt) cc_final: 0.8067 (mm) REVERT: B 431 MET cc_start: 0.8812 (tpt) cc_final: 0.7345 (tpt) REVERT: B 473 ILE cc_start: 0.8395 (mt) cc_final: 0.8085 (mm) outliers start: 22 outliers final: 16 residues processed: 183 average time/residue: 0.0591 time to fit residues: 16.4743 Evaluate side-chains 173 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 157 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 156 GLN Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 368 PHE Chi-restraints excluded: chain C residue 434 ASP Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 368 PHE Chi-restraints excluded: chain B residue 434 ASP Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 569 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 41 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 97 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 71 optimal weight: 10.0000 chunk 78 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 39 optimal weight: 0.3980 chunk 73 optimal weight: 0.9990 chunk 68 optimal weight: 0.9980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.173342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.130763 restraints weight = 11618.410| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 2.51 r_work: 0.3500 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8144 Z= 0.145 Angle : 0.618 8.130 11128 Z= 0.316 Chirality : 0.044 0.190 1338 Planarity : 0.006 0.054 1324 Dihedral : 4.548 24.277 1050 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.60 % Allowed : 3.92 % Favored : 95.48 % Rotamer: Outliers : 3.01 % Allowed : 14.58 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.65 (0.28), residues: 996 helix: 1.34 (0.20), residues: 712 sheet: None (None), residues: 0 loop : -1.95 (0.39), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 11 TYR 0.009 0.001 TYR B 39 PHE 0.009 0.001 PHE B 82 TRP 0.015 0.001 TRP B 424 HIS 0.007 0.002 HIS B 234 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 8144) covalent geometry : angle 0.61764 (11128) hydrogen bonds : bond 0.04525 ( 481) hydrogen bonds : angle 4.10864 ( 1425) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 171 time to evaluate : 0.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 115 MET cc_start: 0.8325 (OUTLIER) cc_final: 0.8068 (mmt) REVERT: C 471 TRP cc_start: 0.7782 (p-90) cc_final: 0.7263 (p-90) REVERT: C 473 ILE cc_start: 0.8431 (mt) cc_final: 0.8122 (mm) REVERT: B 115 MET cc_start: 0.8369 (ttm) cc_final: 0.8164 (mmt) REVERT: B 471 TRP cc_start: 0.7812 (p-90) cc_final: 0.7189 (p-90) REVERT: B 473 ILE cc_start: 0.8491 (mt) cc_final: 0.8202 (mm) outliers start: 26 outliers final: 17 residues processed: 185 average time/residue: 0.0555 time to fit residues: 15.4576 Evaluate side-chains 168 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 150 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 156 GLN Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 368 PHE Chi-restraints excluded: chain C residue 379 TYR Chi-restraints excluded: chain C residue 434 ASP Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 540 PHE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 368 PHE Chi-restraints excluded: chain B residue 379 TYR Chi-restraints excluded: chain B residue 434 ASP Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 540 PHE Chi-restraints excluded: chain B residue 569 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 61 optimal weight: 0.8980 chunk 79 optimal weight: 0.0470 chunk 74 optimal weight: 0.0970 chunk 26 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 69 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 24 optimal weight: 0.0170 chunk 45 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 overall best weight: 0.3714 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.175222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.133187 restraints weight = 11976.288| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 2.55 r_work: 0.3528 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8144 Z= 0.122 Angle : 0.581 6.973 11128 Z= 0.301 Chirality : 0.044 0.328 1338 Planarity : 0.005 0.052 1324 Dihedral : 4.481 23.566 1050 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.60 % Allowed : 4.12 % Favored : 95.28 % Rotamer: Outliers : 3.12 % Allowed : 15.51 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.58 (0.28), residues: 996 helix: 1.31 (0.20), residues: 722 sheet: None (None), residues: 0 loop : -2.16 (0.39), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 107 TYR 0.015 0.001 TYR B 273 PHE 0.009 0.001 PHE B 525 TRP 0.014 0.001 TRP C 424 HIS 0.005 0.001 HIS C 234 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 8144) covalent geometry : angle 0.58139 (11128) hydrogen bonds : bond 0.03969 ( 481) hydrogen bonds : angle 3.99742 ( 1425) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 163 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 294 ILE cc_start: 0.8725 (mt) cc_final: 0.8468 (mt) REVERT: C 473 ILE cc_start: 0.8487 (mt) cc_final: 0.8206 (mm) REVERT: B 294 ILE cc_start: 0.8744 (mt) cc_final: 0.8484 (mt) REVERT: B 473 ILE cc_start: 0.8484 (mt) cc_final: 0.8208 (mm) outliers start: 27 outliers final: 16 residues processed: 178 average time/residue: 0.0566 time to fit residues: 15.3423 Evaluate side-chains 163 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 147 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 112 MET Chi-restraints excluded: chain C residue 156 GLN Chi-restraints excluded: chain C residue 234 HIS Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 368 PHE Chi-restraints excluded: chain C residue 379 TYR Chi-restraints excluded: chain C residue 434 ASP Chi-restraints excluded: chain B residue 112 MET Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 234 HIS Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 368 PHE Chi-restraints excluded: chain B residue 379 TYR Chi-restraints excluded: chain B residue 434 ASP Chi-restraints excluded: chain B residue 517 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 47 optimal weight: 3.9990 chunk 84 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 7.9990 chunk 54 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 chunk 50 optimal weight: 0.0670 chunk 93 optimal weight: 3.9990 overall best weight: 0.6720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.173780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.129690 restraints weight = 11866.927| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 2.23 r_work: 0.3514 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8144 Z= 0.133 Angle : 0.622 10.680 11128 Z= 0.309 Chirality : 0.044 0.251 1338 Planarity : 0.005 0.054 1324 Dihedral : 4.494 21.913 1050 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.60 % Allowed : 3.92 % Favored : 95.48 % Rotamer: Outliers : 4.05 % Allowed : 14.35 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.63 (0.28), residues: 996 helix: 1.39 (0.20), residues: 708 sheet: None (None), residues: 0 loop : -2.11 (0.38), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 344 TYR 0.012 0.001 TYR B 273 PHE 0.009 0.001 PHE B 525 TRP 0.038 0.001 TRP B 471 HIS 0.006 0.001 HIS B 234 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 8144) covalent geometry : angle 0.62193 (11128) hydrogen bonds : bond 0.03959 ( 481) hydrogen bonds : angle 3.96334 ( 1425) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 153 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 28 ILE cc_start: 0.8076 (OUTLIER) cc_final: 0.7687 (mp) REVERT: C 294 ILE cc_start: 0.8784 (mt) cc_final: 0.8552 (mt) REVERT: C 473 ILE cc_start: 0.8645 (mt) cc_final: 0.8405 (mm) REVERT: C 497 PHE cc_start: 0.6156 (m-10) cc_final: 0.5741 (m-10) REVERT: C 576 MET cc_start: 0.7735 (pmm) cc_final: 0.7525 (pmm) REVERT: B 28 ILE cc_start: 0.8083 (OUTLIER) cc_final: 0.7660 (mp) REVERT: B 294 ILE cc_start: 0.8759 (mt) cc_final: 0.8466 (mt) REVERT: B 473 ILE cc_start: 0.8654 (mt) cc_final: 0.8417 (mm) REVERT: B 497 PHE cc_start: 0.6124 (m-10) cc_final: 0.5702 (m-10) outliers start: 35 outliers final: 22 residues processed: 174 average time/residue: 0.0504 time to fit residues: 13.6279 Evaluate side-chains 172 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 148 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 112 MET Chi-restraints excluded: chain C residue 156 GLN Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 287 PHE Chi-restraints excluded: chain C residue 368 PHE Chi-restraints excluded: chain C residue 379 TYR Chi-restraints excluded: chain C residue 434 ASP Chi-restraints excluded: chain C residue 517 ILE Chi-restraints excluded: chain C residue 540 PHE Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 287 PHE Chi-restraints excluded: chain B residue 368 PHE Chi-restraints excluded: chain B residue 379 TYR Chi-restraints excluded: chain B residue 434 ASP Chi-restraints excluded: chain B residue 540 PHE Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 569 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 65 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 91 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 45 optimal weight: 0.4980 chunk 47 optimal weight: 0.8980 chunk 50 optimal weight: 0.9980 chunk 87 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 16 optimal weight: 0.4980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 234 HIS C 544 HIS B 234 HIS B 544 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.174141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.131903 restraints weight = 11739.142| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 2.44 r_work: 0.3501 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8144 Z= 0.132 Angle : 0.624 8.879 11128 Z= 0.309 Chirality : 0.044 0.219 1338 Planarity : 0.005 0.053 1324 Dihedral : 4.503 22.852 1050 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.60 % Allowed : 3.92 % Favored : 95.48 % Rotamer: Outliers : 3.94 % Allowed : 15.05 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.70 (0.28), residues: 996 helix: 1.43 (0.20), residues: 700 sheet: None (None), residues: 0 loop : -1.94 (0.38), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 272 TYR 0.010 0.001 TYR B 273 PHE 0.009 0.001 PHE B 525 TRP 0.037 0.001 TRP B 471 HIS 0.005 0.001 HIS B 234 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 8144) covalent geometry : angle 0.62382 (11128) hydrogen bonds : bond 0.03928 ( 481) hydrogen bonds : angle 3.94882 ( 1425) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 159 time to evaluate : 0.280 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 28 ILE cc_start: 0.8100 (OUTLIER) cc_final: 0.7699 (mp) REVERT: B 28 ILE cc_start: 0.8058 (OUTLIER) cc_final: 0.7662 (mp) outliers start: 34 outliers final: 27 residues processed: 175 average time/residue: 0.0579 time to fit residues: 15.4682 Evaluate side-chains 178 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 149 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 112 MET Chi-restraints excluded: chain C residue 156 GLN Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 287 PHE Chi-restraints excluded: chain C residue 368 PHE Chi-restraints excluded: chain C residue 379 TYR Chi-restraints excluded: chain C residue 434 ASP Chi-restraints excluded: chain C residue 517 ILE Chi-restraints excluded: chain C residue 531 VAL Chi-restraints excluded: chain C residue 540 PHE Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 112 MET Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 287 PHE Chi-restraints excluded: chain B residue 368 PHE Chi-restraints excluded: chain B residue 379 TYR Chi-restraints excluded: chain B residue 434 ASP Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 540 PHE Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain B residue 569 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 0.0270 chunk 43 optimal weight: 0.5980 chunk 54 optimal weight: 0.5980 chunk 47 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 chunk 99 optimal weight: 0.0970 chunk 34 optimal weight: 0.0980 chunk 92 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 46 optimal weight: 0.0370 chunk 26 optimal weight: 2.9990 overall best weight: 0.1714 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 157 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.176973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.134423 restraints weight = 11728.371| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 2.50 r_work: 0.3544 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8144 Z= 0.118 Angle : 0.623 8.944 11128 Z= 0.309 Chirality : 0.043 0.221 1338 Planarity : 0.005 0.052 1324 Dihedral : 4.474 23.575 1050 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.60 % Allowed : 3.51 % Favored : 95.88 % Rotamer: Outliers : 3.59 % Allowed : 15.86 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.57 (0.28), residues: 996 helix: 1.35 (0.20), residues: 712 sheet: None (None), residues: 0 loop : -2.19 (0.37), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 272 TYR 0.010 0.001 TYR B 273 PHE 0.017 0.001 PHE C 285 TRP 0.034 0.001 TRP B 471 HIS 0.002 0.001 HIS B 509 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 8144) covalent geometry : angle 0.62292 (11128) hydrogen bonds : bond 0.03612 ( 481) hydrogen bonds : angle 3.91883 ( 1425) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 159 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 28 ILE cc_start: 0.8033 (OUTLIER) cc_final: 0.7635 (mp) REVERT: B 28 ILE cc_start: 0.8080 (OUTLIER) cc_final: 0.7644 (mp) outliers start: 31 outliers final: 24 residues processed: 176 average time/residue: 0.0592 time to fit residues: 15.8290 Evaluate side-chains 175 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 149 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 112 MET Chi-restraints excluded: chain C residue 156 GLN Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 287 PHE Chi-restraints excluded: chain C residue 368 PHE Chi-restraints excluded: chain C residue 379 TYR Chi-restraints excluded: chain C residue 434 ASP Chi-restraints excluded: chain C residue 517 ILE Chi-restraints excluded: chain C residue 531 VAL Chi-restraints excluded: chain C residue 540 PHE Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 112 MET Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 287 PHE Chi-restraints excluded: chain B residue 368 PHE Chi-restraints excluded: chain B residue 379 TYR Chi-restraints excluded: chain B residue 434 ASP Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 540 PHE Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain B residue 569 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 96 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 24 optimal weight: 0.2980 chunk 94 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 81 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.174717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.130455 restraints weight = 11816.268| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 2.22 r_work: 0.3514 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.3087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8144 Z= 0.134 Angle : 0.671 14.295 11128 Z= 0.323 Chirality : 0.044 0.228 1338 Planarity : 0.005 0.052 1324 Dihedral : 4.453 18.901 1050 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.60 % Allowed : 4.62 % Favored : 94.78 % Rotamer: Outliers : 3.47 % Allowed : 16.90 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.66 (0.28), residues: 996 helix: 1.39 (0.20), residues: 704 sheet: None (None), residues: 0 loop : -1.98 (0.38), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 272 TYR 0.010 0.001 TYR B 246 PHE 0.009 0.001 PHE C 525 TRP 0.028 0.001 TRP B 471 HIS 0.003 0.001 HIS B 86 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 8144) covalent geometry : angle 0.67125 (11128) hydrogen bonds : bond 0.03829 ( 481) hydrogen bonds : angle 3.99234 ( 1425) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 151 time to evaluate : 0.268 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 28 ILE cc_start: 0.8086 (OUTLIER) cc_final: 0.7648 (mp) REVERT: B 28 ILE cc_start: 0.8088 (OUTLIER) cc_final: 0.7652 (mp) outliers start: 30 outliers final: 24 residues processed: 165 average time/residue: 0.0571 time to fit residues: 14.2676 Evaluate side-chains 171 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 145 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 112 MET Chi-restraints excluded: chain C residue 156 GLN Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 287 PHE Chi-restraints excluded: chain C residue 368 PHE Chi-restraints excluded: chain C residue 379 TYR Chi-restraints excluded: chain C residue 434 ASP Chi-restraints excluded: chain C residue 531 VAL Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 112 MET Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 287 PHE Chi-restraints excluded: chain B residue 368 PHE Chi-restraints excluded: chain B residue 379 TYR Chi-restraints excluded: chain B residue 434 ASP Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain B residue 569 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 88 optimal weight: 0.7980 chunk 81 optimal weight: 0.6980 chunk 46 optimal weight: 4.9990 chunk 6 optimal weight: 0.6980 chunk 61 optimal weight: 0.2980 chunk 95 optimal weight: 2.9990 chunk 71 optimal weight: 0.0270 chunk 2 optimal weight: 0.7980 chunk 96 optimal weight: 0.9980 chunk 52 optimal weight: 0.0020 chunk 69 optimal weight: 0.9980 overall best weight: 0.3446 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 157 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.175926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.132182 restraints weight = 11781.426| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 2.23 r_work: 0.3537 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.3177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8144 Z= 0.122 Angle : 0.661 13.526 11128 Z= 0.318 Chirality : 0.044 0.224 1338 Planarity : 0.005 0.052 1324 Dihedral : 4.601 23.298 1050 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.60 % Allowed : 3.61 % Favored : 95.78 % Rotamer: Outliers : 3.01 % Allowed : 17.94 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.49 (0.28), residues: 996 helix: 1.28 (0.20), residues: 712 sheet: None (None), residues: 0 loop : -2.20 (0.37), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 272 TYR 0.009 0.001 TYR B 273 PHE 0.009 0.001 PHE C 525 TRP 0.021 0.001 TRP B 471 HIS 0.002 0.001 HIS B 544 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 8144) covalent geometry : angle 0.66075 (11128) hydrogen bonds : bond 0.03668 ( 481) hydrogen bonds : angle 4.00875 ( 1425) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 152 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 28 ILE cc_start: 0.8052 (OUTLIER) cc_final: 0.7613 (mp) REVERT: C 285 PHE cc_start: 0.7593 (t80) cc_final: 0.6913 (t80) REVERT: B 28 ILE cc_start: 0.8025 (OUTLIER) cc_final: 0.7588 (mp) REVERT: B 272 ARG cc_start: 0.8049 (ttt90) cc_final: 0.7590 (ttt-90) outliers start: 26 outliers final: 23 residues processed: 164 average time/residue: 0.0550 time to fit residues: 13.7573 Evaluate side-chains 171 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 146 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 112 MET Chi-restraints excluded: chain C residue 156 GLN Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 287 PHE Chi-restraints excluded: chain C residue 368 PHE Chi-restraints excluded: chain C residue 379 TYR Chi-restraints excluded: chain C residue 434 ASP Chi-restraints excluded: chain C residue 531 VAL Chi-restraints excluded: chain C residue 540 PHE Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 112 MET Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 287 PHE Chi-restraints excluded: chain B residue 368 PHE Chi-restraints excluded: chain B residue 379 TYR Chi-restraints excluded: chain B residue 434 ASP Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 540 PHE Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain B residue 569 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 43 optimal weight: 0.0470 chunk 23 optimal weight: 0.6980 chunk 55 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 51 optimal weight: 0.5980 chunk 68 optimal weight: 0.7980 chunk 61 optimal weight: 0.0770 overall best weight: 0.4436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 157 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.176207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.134048 restraints weight = 11732.850| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 2.52 r_work: 0.3534 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.3299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8144 Z= 0.128 Angle : 0.701 13.499 11128 Z= 0.336 Chirality : 0.046 0.259 1338 Planarity : 0.005 0.051 1324 Dihedral : 4.754 33.782 1050 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.40 % Allowed : 4.82 % Favored : 94.78 % Rotamer: Outliers : 3.01 % Allowed : 18.40 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.59 (0.28), residues: 996 helix: 1.37 (0.20), residues: 698 sheet: None (None), residues: 0 loop : -2.04 (0.37), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 272 TYR 0.011 0.001 TYR C 246 PHE 0.012 0.001 PHE C 289 TRP 0.019 0.001 TRP B 471 HIS 0.002 0.001 HIS C 86 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 8144) covalent geometry : angle 0.70145 (11128) hydrogen bonds : bond 0.03693 ( 481) hydrogen bonds : angle 4.04410 ( 1425) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 146 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 28 ILE cc_start: 0.8088 (OUTLIER) cc_final: 0.7642 (mp) REVERT: C 285 PHE cc_start: 0.7295 (t80) cc_final: 0.7086 (t80) REVERT: C 431 MET cc_start: 0.8991 (tpt) cc_final: 0.7543 (tpt) REVERT: B 28 ILE cc_start: 0.8053 (OUTLIER) cc_final: 0.7610 (mp) outliers start: 26 outliers final: 23 residues processed: 158 average time/residue: 0.0625 time to fit residues: 14.8994 Evaluate side-chains 170 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 145 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 112 MET Chi-restraints excluded: chain C residue 156 GLN Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 287 PHE Chi-restraints excluded: chain C residue 368 PHE Chi-restraints excluded: chain C residue 379 TYR Chi-restraints excluded: chain C residue 531 VAL Chi-restraints excluded: chain C residue 540 PHE Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 112 MET Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 287 PHE Chi-restraints excluded: chain B residue 368 PHE Chi-restraints excluded: chain B residue 379 TYR Chi-restraints excluded: chain B residue 434 ASP Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 540 PHE Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain B residue 569 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 3.9990 chunk 11 optimal weight: 0.0670 chunk 43 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 70 optimal weight: 7.9990 chunk 98 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 chunk 89 optimal weight: 5.9990 chunk 19 optimal weight: 0.3980 chunk 51 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.175756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.131741 restraints weight = 11713.090| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 2.20 r_work: 0.3540 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.3346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8144 Z= 0.131 Angle : 0.713 13.140 11128 Z= 0.341 Chirality : 0.046 0.273 1338 Planarity : 0.005 0.050 1324 Dihedral : 4.749 34.390 1050 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.40 % Allowed : 4.42 % Favored : 95.18 % Rotamer: Outliers : 3.36 % Allowed : 18.06 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.40 (0.28), residues: 996 helix: 1.26 (0.20), residues: 710 sheet: None (None), residues: 0 loop : -2.35 (0.37), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 272 TYR 0.011 0.001 TYR B 246 PHE 0.008 0.001 PHE C 525 TRP 0.052 0.001 TRP B 471 HIS 0.002 0.001 HIS B 86 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 8144) covalent geometry : angle 0.71256 (11128) hydrogen bonds : bond 0.03747 ( 481) hydrogen bonds : angle 4.08444 ( 1425) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1614.55 seconds wall clock time: 28 minutes 27.53 seconds (1707.53 seconds total)