Starting phenix.real_space_refine on Mon Apr 28 18:07:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y5y_38959/04_2025/8y5y_38959.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y5y_38959/04_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_38959/04_2025/8y5y_38959.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y5y_38959/04_2025/8y5y_38959.map" model { file = "/net/cci-nas-00/data/ceres_data/8y5y_38959/04_2025/8y5y_38959.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y5y_38959/04_2025/8y5y_38959.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: 7.49, per 1000 atoms: 0.95 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: 1.96 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 0.74 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: 2.01 Time building geometry restraints manager: 2.34 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: 0.04 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: 1.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.100 Process input model: 23.460 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.960 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.009 0.001 TRP C 372 HIS 0.004 0.001 HIS B 509 PHE 0.039 0.001 PHE B 430 TYR 0.007 0.001 TYR B 580 ARG 0.001 0.000 ARG B 237 Details of bonding type rmsd hydrogen bonds : bond 0.26398 ( 481) hydrogen bonds : angle 6.86162 ( 1425) covalent geometry : bond 0.00415 ( 8144) covalent geometry : angle 0.68074 (11128) *********************** 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 : 0.895 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: 0.1584 time to fit residues: 43.5675 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 : 0.866 ------------------------------------------------------------------------------- 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 84 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 51 optimal weight: 0.4980 chunk 40 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 30 optimal weight: 0.1980 chunk 47 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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 = 0.4136 r_free = 0.4136 target = 0.172972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.128321 restraints weight = 11591.853| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 2.20 r_work: 0.3493 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8144 Z= 0.176 Angle : 0.650 6.959 11128 Z= 0.341 Chirality : 0.045 0.234 1338 Planarity : 0.006 0.055 1324 Dihedral : 4.896 40.457 1054 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.60 % Allowed : 4.42 % Favored : 94.98 % Rotamer: Outliers : 2.78 % Allowed : 11.11 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.28), residues: 996 helix: 1.23 (0.20), residues: 700 sheet: None (None), residues: 0 loop : -1.53 (0.40), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 424 HIS 0.008 0.002 HIS C 234 PHE 0.013 0.001 PHE B 82 TYR 0.011 0.001 TYR B 542 ARG 0.002 0.001 ARG B 11 Details of bonding type rmsd hydrogen bonds : bond 0.05031 ( 481) hydrogen bonds : angle 4.33647 ( 1425) covalent geometry : bond 0.00412 ( 8144) covalent geometry : angle 0.64963 (11128) *********************** 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 196 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 172 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 115 MET cc_start: 0.8286 (mtm) cc_final: 0.8004 (mmt) REVERT: C 473 ILE cc_start: 0.8443 (mt) cc_final: 0.8168 (mm) REVERT: B 289 PHE cc_start: 0.7316 (t80) cc_final: 0.7082 (t80) REVERT: B 431 MET cc_start: 0.8898 (tpt) cc_final: 0.7474 (tpt) REVERT: B 473 ILE cc_start: 0.8473 (mt) cc_final: 0.8202 (mm) outliers start: 24 outliers final: 18 residues processed: 183 average time/residue: 0.1408 time to fit residues: 38.3910 Evaluate side-chains 171 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 153 time to evaluate : 0.830 ------------------------------------------------------------------------------- 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 379 TYR 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 379 TYR 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 61 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 73 optimal weight: 0.6980 chunk 76 optimal weight: 0.5980 chunk 3 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.173150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.131751 restraints weight = 11785.023| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 2.60 r_work: 0.3504 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8144 Z= 0.140 Angle : 0.610 8.169 11128 Z= 0.311 Chirality : 0.043 0.191 1338 Planarity : 0.006 0.054 1324 Dihedral : 4.572 24.397 1050 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.60 % Allowed : 3.51 % Favored : 95.88 % Rotamer: Outliers : 3.12 % Allowed : 13.77 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.28), residues: 996 helix: 1.30 (0.20), residues: 712 sheet: None (None), residues: 0 loop : -2.01 (0.39), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 424 HIS 0.007 0.002 HIS C 234 PHE 0.008 0.001 PHE C 82 TYR 0.009 0.001 TYR B 39 ARG 0.001 0.000 ARG B 11 Details of bonding type rmsd hydrogen bonds : bond 0.04558 ( 481) hydrogen bonds : angle 4.11970 ( 1425) covalent geometry : bond 0.00316 ( 8144) covalent geometry : angle 0.61048 (11128) *********************** 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 195 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 168 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 115 MET cc_start: 0.8325 (mtm) cc_final: 0.8104 (mmt) REVERT: C 471 TRP cc_start: 0.7774 (p-90) cc_final: 0.7325 (p-90) REVERT: C 473 ILE cc_start: 0.8501 (mt) cc_final: 0.8204 (mm) REVERT: B 115 MET cc_start: 0.8423 (ttm) cc_final: 0.8219 (mmt) REVERT: B 431 MET cc_start: 0.8850 (tpt) cc_final: 0.7368 (tpt) REVERT: B 471 TRP cc_start: 0.7763 (p-90) cc_final: 0.7211 (p-90) REVERT: B 473 ILE cc_start: 0.8492 (mt) cc_final: 0.8200 (mm) outliers start: 27 outliers final: 17 residues processed: 183 average time/residue: 0.1813 time to fit residues: 48.7724 Evaluate side-chains 167 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 150 time to evaluate : 0.866 ------------------------------------------------------------------------------- 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 259 THR 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 8 optimal weight: 0.5980 chunk 96 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 92 optimal weight: 0.0670 chunk 86 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 39 optimal weight: 0.8980 chunk 90 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- 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 = 0.4139 r_free = 0.4139 target = 0.173286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.129607 restraints weight = 11643.636| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 2.23 r_work: 0.3516 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8144 Z= 0.130 Angle : 0.590 6.831 11128 Z= 0.305 Chirality : 0.044 0.330 1338 Planarity : 0.005 0.053 1324 Dihedral : 4.527 22.792 1050 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.60 % Allowed : 4.72 % Favored : 94.68 % Rotamer: Outliers : 3.24 % Allowed : 15.16 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.28), residues: 996 helix: 1.29 (0.20), residues: 720 sheet: None (None), residues: 0 loop : -2.14 (0.39), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 424 HIS 0.006 0.001 HIS C 234 PHE 0.010 0.001 PHE B 525 TYR 0.014 0.001 TYR B 273 ARG 0.001 0.000 ARG B 107 Details of bonding type rmsd hydrogen bonds : bond 0.04085 ( 481) hydrogen bonds : angle 3.99175 ( 1425) covalent geometry : bond 0.00293 ( 8144) covalent geometry : angle 0.59003 (11128) *********************** 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 186 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 158 time to evaluate : 0.872 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 115 MET cc_start: 0.8317 (mtm) cc_final: 0.8115 (mmt) REVERT: C 473 ILE cc_start: 0.8506 (mt) cc_final: 0.8215 (mm) REVERT: B 294 ILE cc_start: 0.8798 (mt) cc_final: 0.8536 (mt) REVERT: B 473 ILE cc_start: 0.8494 (mt) cc_final: 0.8213 (mm) outliers start: 28 outliers final: 20 residues processed: 172 average time/residue: 0.1476 time to fit residues: 37.6543 Evaluate side-chains 166 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 146 time to evaluate : 0.841 ------------------------------------------------------------------------------- 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 239 LEU Chi-restraints excluded: chain C residue 259 THR 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 4 optimal weight: 0.7980 chunk 74 optimal weight: 6.9990 chunk 37 optimal weight: 0.0870 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 88 optimal weight: 0.8980 chunk 65 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 18 optimal weight: 3.9990 chunk 34 optimal weight: 0.0970 chunk 6 optimal weight: 1.9990 overall best weight: 0.4756 ------------------------------------------------------------------------------- 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 = 0.173927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.130071 restraints weight = 11660.568| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 2.21 r_work: 0.3530 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2679 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= 0.126 Angle : 0.630 10.227 11128 Z= 0.311 Chirality : 0.043 0.246 1338 Planarity : 0.005 0.053 1324 Dihedral : 4.520 21.381 1050 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.60 % Allowed : 3.51 % Favored : 95.88 % Rotamer: Outliers : 3.82 % Allowed : 15.62 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.28), residues: 996 helix: 1.46 (0.20), residues: 708 sheet: None (None), residues: 0 loop : -1.85 (0.39), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP B 471 HIS 0.006 0.001 HIS B 234 PHE 0.015 0.001 PHE C 285 TYR 0.013 0.001 TYR B 273 ARG 0.001 0.000 ARG B 344 Details of bonding type rmsd hydrogen bonds : bond 0.03913 ( 481) hydrogen bonds : angle 3.95117 ( 1425) covalent geometry : bond 0.00279 ( 8144) covalent geometry : angle 0.63034 (11128) *********************** 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 191 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 158 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 28 ILE cc_start: 0.8068 (OUTLIER) cc_final: 0.7681 (mp) REVERT: C 473 ILE cc_start: 0.8649 (mt) cc_final: 0.8410 (mm) REVERT: C 497 PHE cc_start: 0.6062 (m-10) cc_final: 0.5639 (m-10) REVERT: B 28 ILE cc_start: 0.8064 (OUTLIER) cc_final: 0.7671 (mp) REVERT: B 294 ILE cc_start: 0.8767 (mt) cc_final: 0.8470 (mt) REVERT: B 431 MET cc_start: 0.8879 (tpt) cc_final: 0.7328 (tpt) REVERT: B 473 ILE cc_start: 0.8651 (mt) cc_final: 0.8411 (mm) REVERT: B 497 PHE cc_start: 0.6067 (m-10) cc_final: 0.5658 (m-10) outliers start: 33 outliers final: 20 residues processed: 179 average time/residue: 0.1373 time to fit residues: 37.4124 Evaluate side-chains 169 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 147 time to evaluate : 0.882 ------------------------------------------------------------------------------- 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 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 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 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 555 LEU 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 9 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 99 optimal weight: 0.3980 chunk 38 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 75 optimal weight: 9.9990 chunk 14 optimal weight: 0.5980 chunk 73 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 90 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 234 HIS C 338 GLN C 544 HIS B 157 GLN B 234 HIS B 544 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.173319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.131945 restraints weight = 11598.409| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 2.42 r_work: 0.3492 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2878 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 : 0.614 8.968 11128 Z= 0.309 Chirality : 0.044 0.219 1338 Planarity : 0.005 0.053 1324 Dihedral : 4.527 22.631 1050 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.60 % Allowed : 4.52 % Favored : 94.88 % Rotamer: Outliers : 4.17 % Allowed : 15.16 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.28), residues: 996 helix: 1.36 (0.20), residues: 712 sheet: None (None), residues: 0 loop : -2.28 (0.37), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP B 471 HIS 0.004 0.001 HIS C 234 PHE 0.008 0.001 PHE B 82 TYR 0.010 0.001 TYR B 273 ARG 0.001 0.000 ARG B 344 Details of bonding type rmsd hydrogen bonds : bond 0.03947 ( 481) hydrogen bonds : angle 3.93261 ( 1425) covalent geometry : bond 0.00306 ( 8144) covalent geometry : angle 0.61390 (11128) *********************** 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 196 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 160 time to evaluate : 0.800 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 28 ILE cc_start: 0.8072 (OUTLIER) cc_final: 0.7687 (mp) REVERT: C 115 MET cc_start: 0.7627 (mmt) cc_final: 0.7423 (mmt) REVERT: B 28 ILE cc_start: 0.8057 (OUTLIER) cc_final: 0.7662 (mp) REVERT: B 294 ILE cc_start: 0.8816 (mt) cc_final: 0.8609 (mt) outliers start: 36 outliers final: 25 residues processed: 178 average time/residue: 0.1398 time to fit residues: 36.8994 Evaluate side-chains 175 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 148 time to evaluate : 0.875 ------------------------------------------------------------------------------- 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 97 optimal weight: 0.8980 chunk 54 optimal weight: 0.7980 chunk 85 optimal weight: 0.6980 chunk 87 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 chunk 79 optimal weight: 0.0470 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 overall best weight: 0.5878 ------------------------------------------------------------------------------- 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 = 0.4149 r_free = 0.4149 target = 0.174160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.131205 restraints weight = 11754.510| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 2.45 r_work: 0.3504 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.2962 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= 0.130 Angle : 0.660 8.968 11128 Z= 0.323 Chirality : 0.043 0.219 1338 Planarity : 0.005 0.052 1324 Dihedral : 4.556 23.452 1050 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.60 % Allowed : 3.82 % Favored : 95.58 % Rotamer: Outliers : 4.05 % Allowed : 16.55 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.28), residues: 996 helix: 1.34 (0.20), residues: 716 sheet: None (None), residues: 0 loop : -2.32 (0.37), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP B 471 HIS 0.002 0.001 HIS B 86 PHE 0.016 0.001 PHE B 285 TYR 0.009 0.001 TYR B 273 ARG 0.002 0.000 ARG C 272 Details of bonding type rmsd hydrogen bonds : bond 0.03844 ( 481) hydrogen bonds : angle 3.94737 ( 1425) covalent geometry : bond 0.00291 ( 8144) covalent geometry : angle 0.66003 (11128) *********************** 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 188 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 153 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 28 ILE cc_start: 0.8025 (OUTLIER) cc_final: 0.7639 (mp) REVERT: B 28 ILE cc_start: 0.8026 (OUTLIER) cc_final: 0.7640 (mp) REVERT: B 294 ILE cc_start: 0.8764 (mt) cc_final: 0.8508 (mt) REVERT: B 431 MET cc_start: 0.9032 (tpt) cc_final: 0.7738 (tpt) outliers start: 35 outliers final: 26 residues processed: 173 average time/residue: 0.1434 time to fit residues: 36.9381 Evaluate side-chains 179 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 151 time to evaluate : 0.823 ------------------------------------------------------------------------------- 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 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 479 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 53 optimal weight: 0.4980 chunk 52 optimal weight: 0.7980 chunk 92 optimal weight: 0.7980 chunk 30 optimal weight: 0.0060 chunk 28 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 157 GLN B 338 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.174349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.131433 restraints weight = 11675.396| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 2.49 r_work: 0.3500 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.3075 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= 0.131 Angle : 0.668 14.366 11128 Z= 0.323 Chirality : 0.044 0.221 1338 Planarity : 0.005 0.053 1324 Dihedral : 4.543 20.376 1050 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.60 % Allowed : 4.42 % Favored : 94.98 % Rotamer: Outliers : 3.59 % Allowed : 17.13 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.28), residues: 996 helix: 1.32 (0.20), residues: 716 sheet: None (None), residues: 0 loop : -2.34 (0.36), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP B 471 HIS 0.003 0.001 HIS C 86 PHE 0.007 0.001 PHE C 525 TYR 0.009 0.001 TYR B 273 ARG 0.005 0.000 ARG C 272 Details of bonding type rmsd hydrogen bonds : bond 0.03848 ( 481) hydrogen bonds : angle 3.96314 ( 1425) covalent geometry : bond 0.00296 ( 8144) covalent geometry : angle 0.66808 (11128) *********************** 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 190 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 159 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 28 ILE cc_start: 0.8057 (OUTLIER) cc_final: 0.7658 (mp) REVERT: B 28 ILE cc_start: 0.8035 (OUTLIER) cc_final: 0.7633 (mp) REVERT: B 294 ILE cc_start: 0.8778 (mt) cc_final: 0.8566 (mt) REVERT: B 431 MET cc_start: 0.8997 (tpt) cc_final: 0.7642 (tpt) outliers start: 31 outliers final: 27 residues processed: 175 average time/residue: 0.1425 time to fit residues: 37.0718 Evaluate side-chains 179 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 150 time to evaluate : 0.819 ------------------------------------------------------------------------------- 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 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 479 LEU Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 540 PHE Chi-restraints excluded: chain B residue 545 LEU 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 66 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 46 optimal weight: 4.9990 chunk 10 optimal weight: 0.2980 chunk 44 optimal weight: 0.0470 chunk 79 optimal weight: 0.0970 chunk 20 optimal weight: 3.9990 overall best weight: 0.4278 ------------------------------------------------------------------------------- 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 = 0.4163 r_free = 0.4163 target = 0.175542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.134006 restraints weight = 11925.357| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 2.39 r_work: 0.3517 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.3135 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= 0.125 Angle : 0.679 14.033 11128 Z= 0.324 Chirality : 0.044 0.221 1338 Planarity : 0.005 0.052 1324 Dihedral : 4.598 24.996 1050 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.30 % Allowed : 4.42 % Favored : 95.28 % Rotamer: Outliers : 3.24 % Allowed : 18.29 % Favored : 78.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.28), residues: 996 helix: 1.29 (0.20), residues: 716 sheet: None (None), residues: 0 loop : -2.30 (0.37), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 471 HIS 0.002 0.001 HIS C 86 PHE 0.007 0.001 PHE C 525 TYR 0.009 0.001 TYR B 273 ARG 0.004 0.000 ARG B 272 Details of bonding type rmsd hydrogen bonds : bond 0.03728 ( 481) hydrogen bonds : angle 3.98888 ( 1425) covalent geometry : bond 0.00277 ( 8144) covalent geometry : angle 0.67916 (11128) *********************** 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 182 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 154 time to evaluate : 0.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 28 ILE cc_start: 0.8025 (OUTLIER) cc_final: 0.7621 (mp) REVERT: C 285 PHE cc_start: 0.7644 (t80) cc_final: 0.6964 (t80) REVERT: B 28 ILE cc_start: 0.8022 (OUTLIER) cc_final: 0.7623 (mp) REVERT: B 294 ILE cc_start: 0.8788 (mt) cc_final: 0.8510 (mt) REVERT: B 431 MET cc_start: 0.8970 (tpt) cc_final: 0.7591 (tpt) outliers start: 28 outliers final: 24 residues processed: 169 average time/residue: 0.1466 time to fit residues: 36.7904 Evaluate side-chains 174 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 148 time to evaluate : 0.881 ------------------------------------------------------------------------------- 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 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 479 LEU Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 540 PHE Chi-restraints excluded: chain B residue 545 LEU 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 26 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 37 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 27 optimal weight: 0.3980 chunk 28 optimal weight: 0.6980 chunk 73 optimal weight: 3.9990 chunk 52 optimal weight: 0.0070 chunk 8 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 157 GLN B 338 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.175306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.131362 restraints weight = 11693.868| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 2.21 r_work: 0.3537 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.3280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8144 Z= 0.132 Angle : 0.692 13.977 11128 Z= 0.335 Chirality : 0.046 0.265 1338 Planarity : 0.005 0.051 1324 Dihedral : 4.772 34.168 1050 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.40 % Allowed : 4.82 % Favored : 94.78 % Rotamer: Outliers : 3.36 % Allowed : 17.94 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.28), residues: 996 helix: 1.32 (0.20), residues: 710 sheet: None (None), residues: 0 loop : -2.39 (0.36), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP C 471 HIS 0.002 0.001 HIS B 86 PHE 0.016 0.001 PHE B 285 TYR 0.008 0.001 TYR B 273 ARG 0.003 0.000 ARG B 272 Details of bonding type rmsd hydrogen bonds : bond 0.03779 ( 481) hydrogen bonds : angle 4.05247 ( 1425) covalent geometry : bond 0.00300 ( 8144) covalent geometry : angle 0.69195 (11128) ********************** 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: 29 poor density : 143 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 28 ILE cc_start: 0.8048 (OUTLIER) cc_final: 0.7627 (mp) REVERT: C 285 PHE cc_start: 0.7440 (t80) cc_final: 0.7228 (t80) REVERT: C 294 ILE cc_start: 0.8788 (mt) cc_final: 0.8574 (mt) REVERT: B 28 ILE cc_start: 0.8072 (OUTLIER) cc_final: 0.7621 (mp) REVERT: B 294 ILE cc_start: 0.8723 (mt) cc_final: 0.8454 (mt) outliers start: 29 outliers final: 26 residues processed: 158 average time/residue: 0.1314 time to fit residues: 31.6554 Evaluate side-chains 170 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 142 time to evaluate : 0.814 ------------------------------------------------------------------------------- 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 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 479 LEU 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 158 ILE 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 479 LEU 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 87 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 68 optimal weight: 0.2980 chunk 90 optimal weight: 2.9990 chunk 96 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 76 optimal weight: 0.9980 chunk 84 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 42 optimal weight: 0.4980 chunk 47 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.4150 r_free = 0.4150 target = 0.174555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.132388 restraints weight = 11739.921| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 2.39 r_work: 0.3515 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.3338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8144 Z= 0.136 Angle : 0.731 14.445 11128 Z= 0.348 Chirality : 0.046 0.290 1338 Planarity : 0.005 0.051 1324 Dihedral : 4.748 36.217 1050 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.40 % Allowed : 4.22 % Favored : 95.38 % Rotamer: Outliers : 3.36 % Allowed : 18.29 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.28), residues: 996 helix: 1.28 (0.20), residues: 710 sheet: None (None), residues: 0 loop : -2.41 (0.36), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP B 471 HIS 0.002 0.001 HIS B 86 PHE 0.011 0.001 PHE C 497 TYR 0.007 0.001 TYR B 39 ARG 0.004 0.000 ARG B 272 Details of bonding type rmsd hydrogen bonds : bond 0.03856 ( 481) hydrogen bonds : angle 4.10309 ( 1425) covalent geometry : bond 0.00315 ( 8144) covalent geometry : angle 0.73143 (11128) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3734.72 seconds wall clock time: 64 minutes 50.16 seconds (3890.16 seconds total)