Starting phenix.real_space_refine on Wed Feb 12 12:37:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y5y_38959/02_2025/8y5y_38959.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y5y_38959/02_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_38959/02_2025/8y5y_38959.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y5y_38959/02_2025/8y5y_38959.map" model { file = "/net/cci-nas-00/data/ceres_data/8y5y_38959/02_2025/8y5y_38959.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y5y_38959/02_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-5592/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: 7.29, per 1000 atoms: 0.92 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: 1.84 Conformation dependent library (CDL) restraints added in 1.0 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: 0.79 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: 2.45 Time building geometry restraints manager: 2.17 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: 1.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 23.630 Find NCS groups from input model: 0.130 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.320 ------------------------------------------------------------------------------- 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= 0.264 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 *********************** 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 : 0.820 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: 0.1653 time to fit residues: 45.3917 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 : 0.951 ------------------------------------------------------------------------------- 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 = 0.128322 restraints weight = 11591.843| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 2.20 r_work: 0.3493 rms_B_bonded: 3.13 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= 0.267 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 *********************** 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 : 0.903 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 115 MET cc_start: 0.8285 (mtm) cc_final: 0.8005 (mmt) REVERT: C 473 ILE cc_start: 0.8440 (mt) cc_final: 0.8165 (mm) REVERT: B 289 PHE cc_start: 0.7316 (t80) cc_final: 0.7082 (t80) REVERT: B 431 MET cc_start: 0.8897 (tpt) cc_final: 0.7471 (tpt) REVERT: B 473 ILE cc_start: 0.8473 (mt) cc_final: 0.8201 (mm) outliers start: 24 outliers final: 18 residues processed: 183 average time/residue: 0.1475 time to fit residues: 39.8156 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 : 0.839 ------------------------------------------------------------------------------- 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: 0.9980 chunk 6 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 76 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 chunk 40 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.4127 r_free = 0.4127 target = 0.172219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.130737 restraints weight = 11791.654| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 2.57 r_work: 0.3489 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.2279 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= 0.221 Angle : 0.620 7.917 11128 Z= 0.317 Chirality : 0.044 0.189 1338 Planarity : 0.006 0.054 1324 Dihedral : 4.598 23.999 1050 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.60 % Allowed : 3.82 % Favored : 95.58 % Rotamer: Outliers : 3.12 % Allowed : 13.89 % Favored : 82.99 % 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: 0.54 (0.28), residues: 996 helix: 1.27 (0.20), residues: 712 sheet: None (None), residues: 0 loop : -2.03 (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 0.010 0.001 PHE C 82 TYR 0.009 0.001 TYR B 39 ARG 0.001 0.000 ARG B 11 *********************** 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 192 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 165 time to evaluate : 0.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 115 MET cc_start: 0.8331 (mtm) cc_final: 0.8074 (mmt) REVERT: C 471 TRP cc_start: 0.7796 (p-90) cc_final: 0.7203 (p-90) REVERT: C 473 ILE cc_start: 0.8511 (mt) cc_final: 0.8219 (mm) REVERT: B 115 MET cc_start: 0.8432 (ttm) cc_final: 0.8209 (mmt) REVERT: B 431 MET cc_start: 0.8861 (tpt) cc_final: 0.7372 (tpt) REVERT: B 471 TRP cc_start: 0.7789 (p-90) cc_final: 0.7150 (p-90) REVERT: B 473 ILE cc_start: 0.8479 (mt) cc_final: 0.8182 (mm) outliers start: 27 outliers final: 19 residues processed: 180 average time/residue: 0.1568 time to fit residues: 40.7889 Evaluate side-chains 171 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 152 time to evaluate : 0.855 ------------------------------------------------------------------------------- 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 522 CYS 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 522 CYS 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: 0.9990 chunk 96 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 3 optimal weight: 0.7980 chunk 60 optimal weight: 0.9980 chunk 92 optimal weight: 0.0980 chunk 86 optimal weight: 0.9980 chunk 47 optimal weight: 5.9990 chunk 39 optimal weight: 0.2980 chunk 90 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.4141 r_free = 0.4141 target = 0.173543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.129908 restraints weight = 11662.478| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 2.23 r_work: 0.3519 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8144 Z= 0.185 Angle : 0.587 6.863 11128 Z= 0.303 Chirality : 0.044 0.323 1338 Planarity : 0.005 0.053 1324 Dihedral : 4.529 22.937 1050 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.60 % Allowed : 4.52 % Favored : 94.88 % Rotamer: Outliers : 3.70 % Allowed : 14.70 % 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: 0.55 (0.28), residues: 996 helix: 1.28 (0.20), residues: 720 sheet: None (None), residues: 0 loop : -2.14 (0.38), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 424 HIS 0.005 0.001 HIS C 234 PHE 0.010 0.001 PHE B 525 TYR 0.014 0.001 TYR C 273 ARG 0.001 0.000 ARG B 107 *********************** 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 194 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 162 time to evaluate : 0.790 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 28 ILE cc_start: 0.8128 (OUTLIER) cc_final: 0.7715 (mp) REVERT: C 294 ILE cc_start: 0.8714 (mt) cc_final: 0.8481 (mt) REVERT: C 473 ILE cc_start: 0.8498 (mt) cc_final: 0.8208 (mm) REVERT: B 28 ILE cc_start: 0.8099 (OUTLIER) cc_final: 0.7687 (mp) REVERT: B 473 ILE cc_start: 0.8485 (mt) cc_final: 0.8207 (mm) outliers start: 32 outliers final: 20 residues processed: 179 average time/residue: 0.1485 time to fit residues: 39.1052 Evaluate side-chains 168 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 146 time to evaluate : 0.779 ------------------------------------------------------------------------------- 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 479 LEU Chi-restraints excluded: chain C residue 540 PHE 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 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: 0.5980 chunk 74 optimal weight: 2.9990 chunk 37 optimal weight: 0.2980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 6 optimal weight: 0.0970 overall best weight: 0.5578 ------------------------------------------------------------------------------- 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 = 0.4147 r_free = 0.4147 target = 0.173447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.129703 restraints weight = 11660.548| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 2.19 r_work: 0.3526 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8144 Z= 0.186 Angle : 0.639 10.739 11128 Z= 0.314 Chirality : 0.043 0.244 1338 Planarity : 0.005 0.053 1324 Dihedral : 4.532 21.167 1050 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.60 % Allowed : 3.51 % Favored : 95.88 % Rotamer: Outliers : 4.05 % Allowed : 15.39 % 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: 0.67 (0.28), residues: 996 helix: 1.38 (0.20), residues: 718 sheet: None (None), residues: 0 loop : -2.10 (0.38), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP B 471 HIS 0.006 0.001 HIS C 234 PHE 0.016 0.001 PHE C 285 TYR 0.012 0.001 TYR C 273 ARG 0.001 0.000 ARG B 344 *********************** 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 195 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 160 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 294 ILE cc_start: 0.8781 (mt) cc_final: 0.8556 (mt) REVERT: C 473 ILE cc_start: 0.8681 (mt) cc_final: 0.8447 (mm) REVERT: C 497 PHE cc_start: 0.6139 (m-10) cc_final: 0.5732 (m-10) REVERT: B 294 ILE cc_start: 0.8761 (mt) cc_final: 0.8480 (mt) REVERT: B 431 MET cc_start: 0.8836 (tpt) cc_final: 0.7351 (tpt) REVERT: B 497 PHE cc_start: 0.6119 (m-10) cc_final: 0.5727 (m-10) outliers start: 35 outliers final: 26 residues processed: 179 average time/residue: 0.1332 time to fit residues: 36.0359 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 : 0.802 ------------------------------------------------------------------------------- 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 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 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 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 517 ILE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 9 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 99 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 75 optimal weight: 10.0000 chunk 14 optimal weight: 0.5980 chunk 73 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 90 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 338 GLN B 157 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.172172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.128160 restraints weight = 11655.690| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 2.21 r_work: 0.3503 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.2887 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= 0.213 Angle : 0.627 8.817 11128 Z= 0.315 Chirality : 0.044 0.250 1338 Planarity : 0.005 0.053 1324 Dihedral : 4.561 22.676 1050 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.60 % Allowed : 4.22 % Favored : 95.18 % Rotamer: Outliers : 4.40 % Allowed : 15.16 % Favored : 80.44 % 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: 1.35 (0.20), residues: 708 sheet: None (None), residues: 0 loop : -2.18 (0.37), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP B 471 HIS 0.006 0.001 HIS B 234 PHE 0.016 0.001 PHE B 285 TYR 0.010 0.001 TYR B 273 ARG 0.001 0.000 ARG B 344 *********************** 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: 38 poor density : 158 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 28 ILE cc_start: 0.8066 (OUTLIER) cc_final: 0.7679 (mp) REVERT: B 28 ILE cc_start: 0.8061 (OUTLIER) cc_final: 0.7674 (mp) outliers start: 38 outliers final: 30 residues processed: 178 average time/residue: 0.1491 time to fit residues: 39.2525 Evaluate side-chains 179 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 147 time to evaluate : 0.856 ------------------------------------------------------------------------------- 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 234 HIS 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 234 HIS 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 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=2.50 ------------------------------------------------------------------------------- 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: 0.8980 chunk 87 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 82 optimal weight: 0.4980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.4132 r_free = 0.4132 target = 0.172269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.130068 restraints weight = 11811.230| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 2.67 r_work: 0.3485 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2972 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= 0.211 Angle : 0.660 8.808 11128 Z= 0.326 Chirality : 0.044 0.252 1338 Planarity : 0.005 0.053 1324 Dihedral : 4.572 23.077 1050 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.60 % Allowed : 3.41 % Favored : 95.98 % Rotamer: Outliers : 4.40 % Allowed : 16.67 % Favored : 78.94 % 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: 0.51 (0.28), residues: 996 helix: 1.28 (0.20), residues: 724 sheet: None (None), residues: 0 loop : -2.29 (0.38), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP B 471 HIS 0.006 0.001 HIS B 234 PHE 0.037 0.001 PHE C 430 TYR 0.009 0.001 TYR C 273 ARG 0.002 0.000 ARG B 272 *********************** 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 192 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 154 time to evaluate : 0.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 28 ILE cc_start: 0.8052 (OUTLIER) cc_final: 0.7663 (mp) REVERT: C 431 MET cc_start: 0.9017 (tpt) cc_final: 0.7547 (tpt) REVERT: B 28 ILE cc_start: 0.8058 (OUTLIER) cc_final: 0.7669 (mp) REVERT: B 431 MET cc_start: 0.9068 (tpt) cc_final: 0.7691 (tpt) outliers start: 38 outliers final: 29 residues processed: 175 average time/residue: 0.1487 time to fit residues: 38.6667 Evaluate side-chains 179 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 148 time to evaluate : 0.826 ------------------------------------------------------------------------------- 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 234 HIS 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 234 HIS 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: 2.9990 chunk 52 optimal weight: 0.6980 chunk 92 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 93 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 11 optimal weight: 0.2980 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.4123 r_free = 0.4123 target = 0.171425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.127202 restraints weight = 11721.681| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 2.20 r_work: 0.3487 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.3101 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= 0.231 Angle : 0.662 9.045 11128 Z= 0.327 Chirality : 0.045 0.255 1338 Planarity : 0.005 0.053 1324 Dihedral : 4.618 25.498 1050 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.50 % Allowed : 5.32 % Favored : 94.18 % Rotamer: Outliers : 4.05 % Allowed : 16.78 % Favored : 79.17 % 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: 0.51 (0.28), residues: 996 helix: 1.26 (0.20), residues: 722 sheet: None (None), residues: 0 loop : -2.20 (0.38), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP C 471 HIS 0.006 0.001 HIS B 234 PHE 0.031 0.001 PHE C 430 TYR 0.008 0.001 TYR C 273 ARG 0.004 0.000 ARG B 272 *********************** 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 189 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 154 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 28 ILE cc_start: 0.8032 (OUTLIER) cc_final: 0.7637 (mp) REVERT: B 28 ILE cc_start: 0.8050 (OUTLIER) cc_final: 0.7654 (mp) REVERT: B 431 MET cc_start: 0.9046 (tpt) cc_final: 0.7634 (tpt) outliers start: 35 outliers final: 30 residues processed: 173 average time/residue: 0.1536 time to fit residues: 39.4232 Evaluate side-chains 178 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 146 time to evaluate : 0.841 ------------------------------------------------------------------------------- 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 234 HIS 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 522 CYS 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 234 HIS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 66 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 60 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 chunk 10 optimal weight: 0.0470 chunk 44 optimal weight: 0.0020 chunk 79 optimal weight: 0.0770 chunk 20 optimal weight: 2.9990 overall best weight: 0.3044 ------------------------------------------------------------------------------- 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 = 0.4153 r_free = 0.4153 target = 0.174532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.132185 restraints weight = 11973.539| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 2.52 r_work: 0.3516 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.3218 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= 0.176 Angle : 0.704 14.843 11128 Z= 0.334 Chirality : 0.045 0.251 1338 Planarity : 0.005 0.051 1324 Dihedral : 4.694 34.468 1050 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.30 % Allowed : 4.12 % Favored : 95.58 % Rotamer: Outliers : 3.59 % Allowed : 17.94 % Favored : 78.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 0.42 (0.28), residues: 996 helix: 1.20 (0.20), residues: 728 sheet: None (None), residues: 0 loop : -2.32 (0.38), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 471 HIS 0.005 0.001 HIS B 234 PHE 0.042 0.001 PHE B 430 TYR 0.010 0.001 TYR B 273 ARG 0.003 0.000 ARG B 272 *********************** 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: 31 poor density : 147 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 28 ILE cc_start: 0.8029 (OUTLIER) cc_final: 0.7635 (mp) REVERT: C 285 PHE cc_start: 0.7686 (t80) cc_final: 0.6966 (t80) REVERT: C 431 MET cc_start: 0.8980 (tpt) cc_final: 0.7627 (tpt) REVERT: B 28 ILE cc_start: 0.8014 (OUTLIER) cc_final: 0.7610 (mp) outliers start: 31 outliers final: 28 residues processed: 164 average time/residue: 0.1513 time to fit residues: 36.3912 Evaluate side-chains 168 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 138 time to evaluate : 0.929 ------------------------------------------------------------------------------- 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 234 HIS 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 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 156 GLN Chi-restraints excluded: chain B residue 234 HIS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 26 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 88 optimal weight: 0.0070 chunk 27 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 73 optimal weight: 0.9990 chunk 52 optimal weight: 0.0970 chunk 8 optimal weight: 0.4980 chunk 18 optimal weight: 0.0970 chunk 74 optimal weight: 0.9990 overall best weight: 0.2994 ------------------------------------------------------------------------------- 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 = 0.4155 r_free = 0.4155 target = 0.174782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.131467 restraints weight = 11748.383| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 2.20 r_work: 0.3526 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.3362 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= 0.181 Angle : 0.706 13.999 11128 Z= 0.338 Chirality : 0.046 0.262 1338 Planarity : 0.005 0.052 1324 Dihedral : 4.792 35.535 1050 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.40 % Allowed : 4.82 % Favored : 94.78 % Rotamer: Outliers : 3.36 % Allowed : 18.17 % Favored : 78.47 % 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: 0.45 (0.28), residues: 996 helix: 1.31 (0.20), residues: 710 sheet: None (None), residues: 0 loop : -2.36 (0.36), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 471 HIS 0.005 0.001 HIS B 234 PHE 0.039 0.001 PHE C 430 TYR 0.009 0.001 TYR C 273 ARG 0.005 0.000 ARG C 272 ********************** 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 170 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 141 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 28 ILE cc_start: 0.8021 (OUTLIER) cc_final: 0.7615 (mp) REVERT: C 285 PHE cc_start: 0.7412 (t80) cc_final: 0.7210 (t80) REVERT: C 294 ILE cc_start: 0.8783 (mt) cc_final: 0.8547 (mt) REVERT: C 471 TRP cc_start: 0.7186 (p-90) cc_final: 0.6943 (p-90) REVERT: B 28 ILE cc_start: 0.8070 (OUTLIER) cc_final: 0.7619 (mp) REVERT: B 431 MET cc_start: 0.9011 (tpt) cc_final: 0.7621 (tpt) outliers start: 29 outliers final: 27 residues processed: 157 average time/residue: 0.1474 time to fit residues: 34.5400 Evaluate side-chains 162 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 133 time to evaluate : 0.851 ------------------------------------------------------------------------------- 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 234 HIS 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 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 234 HIS 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: 0.9990 chunk 68 optimal weight: 0.4980 chunk 90 optimal weight: 2.9990 chunk 96 optimal weight: 0.7980 chunk 45 optimal weight: 0.6980 chunk 76 optimal weight: 0.9980 chunk 84 optimal weight: 0.1980 chunk 0 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.4144 r_free = 0.4144 target = 0.173697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.132623 restraints weight = 11832.864| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 2.73 r_work: 0.3489 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.3361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8144 Z= 0.208 Angle : 0.719 13.855 11128 Z= 0.344 Chirality : 0.047 0.275 1338 Planarity : 0.005 0.052 1324 Dihedral : 4.839 35.966 1050 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.40 % Allowed : 4.02 % Favored : 95.58 % Rotamer: Outliers : 3.47 % Allowed : 18.17 % 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: 0.38 (0.28), residues: 996 helix: 1.28 (0.20), residues: 712 sheet: None (None), residues: 0 loop : -2.48 (0.36), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP C 471 HIS 0.006 0.001 HIS B 234 PHE 0.037 0.001 PHE B 430 TYR 0.008 0.001 TYR C 39 ARG 0.004 0.000 ARG C 272 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3569.62 seconds wall clock time: 64 minutes 16.25 seconds (3856.25 seconds total)