Starting phenix.real_space_refine on Fri Aug 22 20:02:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vsb_43492/08_2025/8vsb_43492.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vsb_43492/08_2025/8vsb_43492.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8vsb_43492/08_2025/8vsb_43492.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vsb_43492/08_2025/8vsb_43492.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8vsb_43492/08_2025/8vsb_43492.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vsb_43492/08_2025/8vsb_43492.map" } resolution = 2.93 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.046 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 47 5.16 5 C 4802 2.51 5 N 1293 2.21 5 O 1377 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7519 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1525 Classifications: {'peptide': 188} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 172} Chain breaks: 6 Chain: "B" Number of atoms: 2044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 2044 Classifications: {'peptide': 249} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 17, 'TRANS': 229} Chain breaks: 8 Chain: "I" Number of atoms: 3950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 3950 Classifications: {'peptide': 532} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 29, 'TRANS': 502} Chain breaks: 2 Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 154 Unresolved non-hydrogen dihedrals: 100 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 8, 'GLN:plan1': 3, 'GLU:plan': 6, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 86 Time building chain proxies: 1.80, per 1000 atoms: 0.24 Number of scatterers: 7519 At special positions: 0 Unit cell: (90.968, 106.24, 122.176, 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 47 16.00 O 1377 8.00 N 1293 7.00 C 4802 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS A 4 " - pdb=" SG CYS I 350 " distance=2.02 Simple disulfide: pdb=" SG CYS A 284 " - pdb=" SG CYS A 293 " distance=2.04 Simple disulfide: pdb=" SG CYS A 292 " - pdb=" SG CYS A 355 " distance=2.03 Simple disulfide: pdb=" SG CYS A 321 " - pdb=" SG CYS A 386 " distance=2.03 Simple disulfide: pdb=" SG CYS A 325 " - pdb=" SG CYS A 388 " distance=2.03 Simple disulfide: pdb=" SG CYS A 354 " - pdb=" SG CYS B 354 " distance=2.03 Simple disulfide: pdb=" SG CYS B 4 " - pdb=" SG CYS I 211 " distance=2.04 Simple disulfide: pdb=" SG CYS B 284 " - pdb=" SG CYS B 293 " distance=2.03 Simple disulfide: pdb=" SG CYS B 292 " - pdb=" SG CYS B 355 " distance=2.02 Simple disulfide: pdb=" SG CYS B 321 " - pdb=" SG CYS B 386 " distance=2.03 Simple disulfide: pdb=" SG CYS B 325 " - pdb=" SG CYS B 388 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.54 Conformation dependent library (CDL) restraints added in 291.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1836 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 19 sheets defined 15.1% alpha, 14.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 8 through 29 removed outlier: 4.171A pdb=" N ILE A 12 " --> pdb=" O ASP A 8 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS A 13 " --> pdb=" O PHE A 9 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY A 22 " --> pdb=" O GLU A 18 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU A 28 " --> pdb=" O ILE A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 56 removed outlier: 3.604A pdb=" N LEU A 47 " --> pdb=" O PRO A 43 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU A 55 " --> pdb=" O ASN A 51 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LEU A 56 " --> pdb=" O SER A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 190 Processing helix chain 'A' and resid 280 through 287 Processing helix chain 'B' and resid 9 through 28 removed outlier: 3.592A pdb=" N GLY B 22 " --> pdb=" O GLU B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 52 removed outlier: 3.540A pdb=" N LEU B 47 " --> pdb=" O PRO B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 191 Processing helix chain 'B' and resid 301 through 305 Processing helix chain 'B' and resid 341 through 346 Processing helix chain 'I' and resid 65 through 71 removed outlier: 4.091A pdb=" N LEU I 69 " --> pdb=" O LEU I 65 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N PHE I 71 " --> pdb=" O SER I 67 " (cutoff:3.500A) Processing helix chain 'I' and resid 108 through 112 Processing helix chain 'I' and resid 140 through 145 Processing helix chain 'I' and resid 333 through 338 removed outlier: 3.996A pdb=" N HIS I 337 " --> pdb=" O SER I 333 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N LEU I 338 " --> pdb=" O PHE I 334 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 333 through 338' Processing helix chain 'I' and resid 509 through 513 Processing helix chain 'I' and resid 558 through 562 removed outlier: 3.607A pdb=" N THR I 561 " --> pdb=" O GLY I 558 " (cutoff:3.500A) Processing helix chain 'I' and resid 578 through 587 Processing sheet with id=AA1, first strand: chain 'A' and resid 82 through 84 Processing sheet with id=AA2, first strand: chain 'A' and resid 293 through 295 Processing sheet with id=AA3, first strand: chain 'A' and resid 298 through 300 Processing sheet with id=AA4, first strand: chain 'A' and resid 310 through 312 removed outlier: 7.395A pdb=" N VAL A 310 " --> pdb=" O TYR A 368 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N TYR A 368 " --> pdb=" O VAL A 310 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 355 through 357 Processing sheet with id=AA6, first strand: chain 'A' and resid 360 through 363 removed outlier: 5.959A pdb=" N GLU A 361 " --> pdb=" O ASN A 380 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ASN A 380 " --> pdb=" O GLU A 361 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 81 through 86 removed outlier: 3.500A pdb=" N GLU B 81 " --> pdb=" O MET B 259 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N MET B 259 " --> pdb=" O GLU B 81 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 109 through 110 Processing sheet with id=AA9, first strand: chain 'B' and resid 293 through 295 Processing sheet with id=AB1, first strand: chain 'B' and resid 298 through 300 Processing sheet with id=AB2, first strand: chain 'B' and resid 354 through 357 Processing sheet with id=AB3, first strand: chain 'B' and resid 360 through 369 removed outlier: 5.982A pdb=" N GLU B 361 " --> pdb=" O MET B 381 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N LEU B 363 " --> pdb=" O SER B 379 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N SER B 379 " --> pdb=" O LEU B 363 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ILE B 365 " --> pdb=" O GLN B 377 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N GLN B 377 " --> pdb=" O ILE B 365 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N TYR B 367 " --> pdb=" O VAL B 375 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N VAL B 375 " --> pdb=" O TYR B 367 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N VAL B 369 " --> pdb=" O PRO B 373 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 27 through 28 removed outlier: 7.177A pdb=" N VAL I 33 " --> pdb=" O ASP I 55 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N LEU I 54 " --> pdb=" O ASP I 79 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N LEU I 78 " --> pdb=" O SER I 103 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N LEU I 102 " --> pdb=" O ASP I 130 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N LEU I 129 " --> pdb=" O SER I 155 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N LEU I 154 " --> pdb=" O ASP I 179 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU I 248 " --> pdb=" O TYR I 269 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASN I 271 " --> pdb=" O LEU I 248 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N LEU I 270 " --> pdb=" O ASP I 321 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N LEU I 320 " --> pdb=" O ASN I 345 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N LEU I 344 " --> pdb=" O ASP I 369 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 63 through 64 Processing sheet with id=AB6, first strand: chain 'I' and resid 163 through 164 Processing sheet with id=AB7, first strand: chain 'I' and resid 211 through 212 Processing sheet with id=AB8, first strand: chain 'I' and resid 353 through 356 removed outlier: 7.342A pdb=" N PHE I 354 " --> pdb=" O GLU I 379 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'I' and resid 457 through 458 Processing sheet with id=AC1, first strand: chain 'I' and resid 495 through 497 removed outlier: 6.983A pdb=" N LEU I 496 " --> pdb=" O ASN I 520 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N LEU I 541 " --> pdb=" O TYR I 567 " (cutoff:3.500A) 130 hydrogen bonds defined for protein. 342 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: 0.72 Time building geometry restraints manager: 0.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1849 1.33 - 1.45: 1571 1.45 - 1.58: 4190 1.58 - 1.70: 0 1.70 - 1.83: 62 Bond restraints: 7672 Sorted by residual: bond pdb=" CB VAL B 383 " pdb=" CG2 VAL B 383 " ideal model delta sigma weight residual 1.521 1.453 0.068 3.30e-02 9.18e+02 4.21e+00 bond pdb=" CB ASN I 134 " pdb=" CG ASN I 134 " ideal model delta sigma weight residual 1.516 1.468 0.048 2.50e-02 1.60e+03 3.61e+00 bond pdb=" CA GLU A 348 " pdb=" C GLU A 348 " ideal model delta sigma weight residual 1.522 1.498 0.024 1.38e-02 5.25e+03 3.03e+00 bond pdb=" CB VAL I 451 " pdb=" CG2 VAL I 451 " ideal model delta sigma weight residual 1.521 1.466 0.055 3.30e-02 9.18e+02 2.74e+00 bond pdb=" CG LEU I 185 " pdb=" CD2 LEU I 185 " ideal model delta sigma weight residual 1.521 1.469 0.052 3.30e-02 9.18e+02 2.53e+00 ... (remaining 7667 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 9968 1.99 - 3.99: 376 3.99 - 5.98: 64 5.98 - 7.98: 18 7.98 - 9.97: 6 Bond angle restraints: 10432 Sorted by residual: angle pdb=" C LEU B 131 " pdb=" N ARG B 132 " pdb=" CA ARG B 132 " ideal model delta sigma weight residual 120.87 129.09 -8.22 1.69e+00 3.50e-01 2.36e+01 angle pdb=" C ASP B 183 " pdb=" N THR B 184 " pdb=" CA THR B 184 " ideal model delta sigma weight residual 121.54 129.20 -7.66 1.91e+00 2.74e-01 1.61e+01 angle pdb=" CA CYS B 4 " pdb=" CB CYS B 4 " pdb=" SG CYS B 4 " ideal model delta sigma weight residual 114.40 122.64 -8.24 2.30e+00 1.89e-01 1.28e+01 angle pdb=" CA GLU A 348 " pdb=" C GLU A 348 " pdb=" O GLU A 348 " ideal model delta sigma weight residual 119.05 114.75 4.30 1.30e+00 5.92e-01 1.10e+01 angle pdb=" C PRO A 347 " pdb=" N GLU A 348 " pdb=" CA GLU A 348 " ideal model delta sigma weight residual 121.18 127.43 -6.25 1.98e+00 2.55e-01 9.95e+00 ... (remaining 10427 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.52: 4230 16.52 - 33.05: 374 33.05 - 49.57: 48 49.57 - 66.10: 18 66.10 - 82.62: 6 Dihedral angle restraints: 4676 sinusoidal: 1861 harmonic: 2815 Sorted by residual: dihedral pdb=" CB CYS A 284 " pdb=" SG CYS A 284 " pdb=" SG CYS A 293 " pdb=" CB CYS A 293 " ideal model delta sinusoidal sigma weight residual -86.00 -168.62 82.62 1 1.00e+01 1.00e-02 8.37e+01 dihedral pdb=" CB CYS B 284 " pdb=" SG CYS B 284 " pdb=" SG CYS B 293 " pdb=" CB CYS B 293 " ideal model delta sinusoidal sigma weight residual 93.00 35.95 57.05 1 1.00e+01 1.00e-02 4.38e+01 dihedral pdb=" CB CYS B 4 " pdb=" SG CYS B 4 " pdb=" SG CYS I 211 " pdb=" CB CYS I 211 " ideal model delta sinusoidal sigma weight residual 93.00 42.48 50.52 1 1.00e+01 1.00e-02 3.50e+01 ... (remaining 4673 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 763 0.047 - 0.093: 372 0.093 - 0.140: 82 0.140 - 0.186: 4 0.186 - 0.233: 2 Chirality restraints: 1223 Sorted by residual: chirality pdb=" CB THR A 6 " pdb=" CA THR A 6 " pdb=" OG1 THR A 6 " pdb=" CG2 THR A 6 " both_signs ideal model delta sigma weight residual False 2.55 2.32 0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CG LEU I 566 " pdb=" CB LEU I 566 " pdb=" CD1 LEU I 566 " pdb=" CD2 LEU I 566 " both_signs ideal model delta sigma weight residual False -2.59 -2.79 0.20 2.00e-01 2.50e+01 9.65e-01 chirality pdb=" CA PRO I 90 " pdb=" N PRO I 90 " pdb=" C PRO I 90 " pdb=" CB PRO I 90 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.63e-01 ... (remaining 1220 not shown) Planarity restraints: 1335 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 316 " 0.014 2.00e-02 2.50e+03 1.95e-02 7.57e+00 pdb=" CG TYR A 316 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 TYR A 316 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TYR A 316 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 TYR A 316 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR A 316 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR A 316 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 316 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU I 529 " -0.037 5.00e-02 4.00e+02 5.62e-02 5.06e+00 pdb=" N PRO I 530 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO I 530 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO I 530 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA I 148 " -0.031 5.00e-02 4.00e+02 4.71e-02 3.54e+00 pdb=" N PRO I 149 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO I 149 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO I 149 " -0.026 5.00e-02 4.00e+02 ... (remaining 1332 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 655 2.74 - 3.28: 6887 3.28 - 3.82: 11069 3.82 - 4.36: 13466 4.36 - 4.90: 24287 Nonbonded interactions: 56364 Sorted by model distance: nonbonded pdb=" OE2 GLU B 289 " pdb=" ND2 ASN B 291 " model vdw 2.198 3.120 nonbonded pdb=" NE2 GLN I 36 " pdb=" O LEU I 38 " model vdw 2.246 3.120 nonbonded pdb=" O TYR I 404 " pdb=" ND2 ASN I 408 " model vdw 2.253 3.120 nonbonded pdb=" OD1 ASP I 179 " pdb=" ND1 HIS I 181 " model vdw 2.301 3.120 nonbonded pdb=" OE2 GLU A 348 " pdb=" NH2 ARG B 16 " model vdw 2.354 3.120 ... (remaining 56359 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: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 8.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 7.230 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 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 : 0.009 0.068 7683 Z= 0.385 Angle : 0.964 9.972 10454 Z= 0.495 Chirality : 0.052 0.233 1223 Planarity : 0.006 0.056 1335 Dihedral : 12.827 76.368 2807 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.77 (0.25), residues: 931 helix: -0.87 (0.45), residues: 118 sheet: -2.58 (0.35), residues: 177 loop : -1.89 (0.22), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 295 TYR 0.046 0.003 TYR A 316 PHE 0.022 0.003 PHE A 320 TRP 0.012 0.002 TRP I 247 HIS 0.007 0.002 HIS B 335 Details of bonding type rmsd covalent geometry : bond 0.00925 ( 7672) covalent geometry : angle 0.95364 (10432) SS BOND : bond 0.00550 ( 11) SS BOND : angle 3.23067 ( 22) hydrogen bonds : bond 0.23982 ( 130) hydrogen bonds : angle 7.80618 ( 342) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.215 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 39 MET cc_start: 0.6338 (mmp) cc_final: 0.5579 (tmm) REVERT: B 15 LYS cc_start: 0.7681 (mttt) cc_final: 0.6327 (pttp) REVERT: I 494 GLU cc_start: 0.7774 (mt-10) cc_final: 0.7564 (tt0) outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.6749 time to fit residues: 80.3813 Evaluate side-chains 86 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 HIS A 311 HIS I 59 ASN I 152 HIS I 218 GLN I 345 ASN I 546 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.186494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.132625 restraints weight = 8870.985| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 2.55 r_work: 0.3394 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3266 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.1113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7683 Z= 0.137 Angle : 0.648 7.869 10454 Z= 0.322 Chirality : 0.043 0.161 1223 Planarity : 0.005 0.050 1335 Dihedral : 5.189 28.058 1032 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.41 % Allowed : 9.29 % Favored : 88.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.24 (0.25), residues: 931 helix: -0.24 (0.48), residues: 119 sheet: -2.09 (0.36), residues: 180 loop : -1.61 (0.23), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 125 TYR 0.019 0.001 TYR A 367 PHE 0.015 0.001 PHE A 320 TRP 0.005 0.001 TRP I 247 HIS 0.003 0.001 HIS A 41 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 7672) covalent geometry : angle 0.64458 (10432) SS BOND : bond 0.00225 ( 11) SS BOND : angle 1.68013 ( 22) hydrogen bonds : bond 0.05929 ( 130) hydrogen bonds : angle 6.00785 ( 342) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 97 time to evaluate : 0.320 Fit side-chains REVERT: A 39 MET cc_start: 0.6618 (mmp) cc_final: 0.4962 (tmm) REVERT: A 81 GLU cc_start: 0.7383 (mp0) cc_final: 0.6767 (mp0) REVERT: B 15 LYS cc_start: 0.6727 (mttt) cc_final: 0.5423 (pttp) REVERT: B 39 MET cc_start: 0.6152 (mmt) cc_final: 0.4612 (pp-130) REVERT: B 309 TRP cc_start: 0.7031 (p-90) cc_final: 0.6660 (p-90) REVERT: B 359 ASP cc_start: 0.7607 (OUTLIER) cc_final: 0.7023 (m-30) REVERT: B 381 MET cc_start: 0.8012 (OUTLIER) cc_final: 0.7788 (tpp) REVERT: I 189 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.6198 (mp0) REVERT: I 494 GLU cc_start: 0.8271 (mt-10) cc_final: 0.7844 (tt0) REVERT: I 503 LEU cc_start: 0.7441 (OUTLIER) cc_final: 0.7055 (pp) outliers start: 20 outliers final: 8 residues processed: 106 average time/residue: 0.6277 time to fit residues: 69.9447 Evaluate side-chains 101 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 89 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain B residue 359 ASP Chi-restraints excluded: chain B residue 381 MET Chi-restraints excluded: chain I residue 147 GLU Chi-restraints excluded: chain I residue 189 GLU Chi-restraints excluded: chain I residue 218 GLN Chi-restraints excluded: chain I residue 268 ILE Chi-restraints excluded: chain I residue 353 THR Chi-restraints excluded: chain I residue 503 LEU Chi-restraints excluded: chain I residue 505 VAL Chi-restraints excluded: chain I residue 556 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 87 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 5 optimal weight: 7.9990 chunk 88 optimal weight: 4.9990 chunk 82 optimal weight: 0.4980 chunk 28 optimal weight: 10.0000 chunk 83 optimal weight: 3.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 152 HIS I 546 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.185744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.130948 restraints weight = 8823.016| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 2.66 r_work: 0.3375 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.1326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7683 Z= 0.168 Angle : 0.680 8.075 10454 Z= 0.330 Chirality : 0.044 0.161 1223 Planarity : 0.005 0.054 1335 Dihedral : 5.078 28.421 1032 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 2.53 % Allowed : 12.18 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.19 (0.25), residues: 931 helix: -0.40 (0.46), residues: 124 sheet: -1.90 (0.36), residues: 178 loop : -1.60 (0.23), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 125 TYR 0.016 0.001 TYR A 316 PHE 0.019 0.002 PHE A 320 TRP 0.007 0.001 TRP I 247 HIS 0.007 0.001 HIS I 528 Details of bonding type rmsd covalent geometry : bond 0.00413 ( 7672) covalent geometry : angle 0.67617 (10432) SS BOND : bond 0.00215 ( 11) SS BOND : angle 1.61753 ( 22) hydrogen bonds : bond 0.05626 ( 130) hydrogen bonds : angle 5.70838 ( 342) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 91 time to evaluate : 0.293 Fit side-chains REVERT: A 39 MET cc_start: 0.6616 (mmp) cc_final: 0.4808 (tmm) REVERT: A 81 GLU cc_start: 0.7368 (mp0) cc_final: 0.6751 (mp0) REVERT: A 288 LEU cc_start: 0.7371 (tt) cc_final: 0.6926 (mp) REVERT: A 290 GLU cc_start: 0.7115 (mm-30) cc_final: 0.6515 (tm-30) REVERT: A 361 GLU cc_start: 0.8564 (mt-10) cc_final: 0.8349 (mt-10) REVERT: B 15 LYS cc_start: 0.6770 (mttt) cc_final: 0.5418 (pttp) REVERT: B 309 TRP cc_start: 0.7001 (p-90) cc_final: 0.6662 (p-90) REVERT: B 314 LYS cc_start: 0.7502 (tppt) cc_final: 0.7170 (tptp) REVERT: I 60 GLN cc_start: 0.8463 (tp40) cc_final: 0.8020 (tt0) REVERT: I 189 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.5991 (mp0) REVERT: I 452 ASP cc_start: 0.8235 (t0) cc_final: 0.7967 (t0) outliers start: 21 outliers final: 11 residues processed: 101 average time/residue: 0.5997 time to fit residues: 63.6704 Evaluate side-chains 96 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 381 MET Chi-restraints excluded: chain I residue 143 ARG Chi-restraints excluded: chain I residue 147 GLU Chi-restraints excluded: chain I residue 184 VAL Chi-restraints excluded: chain I residue 187 ASP Chi-restraints excluded: chain I residue 189 GLU Chi-restraints excluded: chain I residue 268 ILE Chi-restraints excluded: chain I residue 353 THR Chi-restraints excluded: chain I residue 505 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 80 optimal weight: 3.9990 chunk 86 optimal weight: 0.3980 chunk 10 optimal weight: 2.9990 chunk 91 optimal weight: 0.2980 chunk 2 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 92 optimal weight: 7.9990 chunk 53 optimal weight: 4.9990 chunk 70 optimal weight: 0.3980 chunk 40 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 59 ASN I 152 HIS I 546 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.188139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.130282 restraints weight = 8938.641| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 2.28 r_work: 0.3429 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3303 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7683 Z= 0.109 Angle : 0.577 6.799 10454 Z= 0.286 Chirality : 0.041 0.144 1223 Planarity : 0.004 0.049 1335 Dihedral : 4.600 27.021 1032 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.26 % Allowed : 12.30 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.91 (0.26), residues: 931 helix: -0.09 (0.47), residues: 123 sheet: -1.71 (0.38), residues: 180 loop : -1.42 (0.23), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 21 TYR 0.011 0.001 TYR A 367 PHE 0.012 0.001 PHE A 320 TRP 0.006 0.001 TRP I 247 HIS 0.005 0.001 HIS I 528 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 7672) covalent geometry : angle 0.57493 (10432) SS BOND : bond 0.00149 ( 11) SS BOND : angle 1.12021 ( 22) hydrogen bonds : bond 0.04271 ( 130) hydrogen bonds : angle 5.38577 ( 342) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 90 time to evaluate : 0.327 Fit side-chains REVERT: A 39 MET cc_start: 0.6571 (mmp) cc_final: 0.4679 (tmm) REVERT: A 81 GLU cc_start: 0.7322 (mp0) cc_final: 0.6686 (mp0) REVERT: A 288 LEU cc_start: 0.7339 (OUTLIER) cc_final: 0.6901 (mp) REVERT: A 290 GLU cc_start: 0.7122 (OUTLIER) cc_final: 0.6464 (tm-30) REVERT: B 15 LYS cc_start: 0.6702 (mttt) cc_final: 0.5356 (pttp) REVERT: B 39 MET cc_start: 0.6162 (mmt) cc_final: 0.4485 (pp-130) REVERT: B 295 ARG cc_start: 0.5991 (mmt-90) cc_final: 0.5719 (mmt180) REVERT: B 314 LYS cc_start: 0.7393 (tppt) cc_final: 0.6292 (tptp) REVERT: B 359 ASP cc_start: 0.7668 (OUTLIER) cc_final: 0.7091 (m-30) REVERT: I 60 GLN cc_start: 0.8393 (OUTLIER) cc_final: 0.8010 (tt0) REVERT: I 189 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.5809 (mp0) REVERT: I 452 ASP cc_start: 0.8082 (t0) cc_final: 0.7799 (t0) outliers start: 27 outliers final: 9 residues processed: 104 average time/residue: 0.6305 time to fit residues: 69.1425 Evaluate side-chains 99 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain B residue 4 CYS Chi-restraints excluded: chain B residue 359 ASP Chi-restraints excluded: chain B residue 381 MET Chi-restraints excluded: chain I residue 60 GLN Chi-restraints excluded: chain I residue 143 ARG Chi-restraints excluded: chain I residue 147 GLU Chi-restraints excluded: chain I residue 184 VAL Chi-restraints excluded: chain I residue 189 GLU Chi-restraints excluded: chain I residue 353 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 58 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 10 optimal weight: 0.0980 chunk 11 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 15 optimal weight: 0.0980 chunk 88 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 90 optimal weight: 3.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 152 HIS I 546 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.186438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.130692 restraints weight = 8878.640| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 2.64 r_work: 0.3373 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7683 Z= 0.158 Angle : 0.632 5.884 10454 Z= 0.308 Chirality : 0.043 0.131 1223 Planarity : 0.005 0.048 1335 Dihedral : 4.704 27.903 1032 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 3.26 % Allowed : 13.63 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.92 (0.26), residues: 931 helix: -0.02 (0.47), residues: 123 sheet: -1.73 (0.38), residues: 176 loop : -1.45 (0.23), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG I 525 TYR 0.013 0.001 TYR A 316 PHE 0.018 0.001 PHE A 320 TRP 0.007 0.001 TRP I 247 HIS 0.004 0.001 HIS I 528 Details of bonding type rmsd covalent geometry : bond 0.00388 ( 7672) covalent geometry : angle 0.63018 (10432) SS BOND : bond 0.00198 ( 11) SS BOND : angle 1.20707 ( 22) hydrogen bonds : bond 0.05126 ( 130) hydrogen bonds : angle 5.40745 ( 342) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 86 time to evaluate : 0.307 Fit side-chains REVERT: A 39 MET cc_start: 0.6575 (mmp) cc_final: 0.4688 (tmm) REVERT: A 81 GLU cc_start: 0.7345 (mp0) cc_final: 0.6644 (mp0) REVERT: A 288 LEU cc_start: 0.7344 (tt) cc_final: 0.6902 (mp) REVERT: A 290 GLU cc_start: 0.7257 (mm-30) cc_final: 0.6558 (tm-30) REVERT: A 361 GLU cc_start: 0.8673 (mt-10) cc_final: 0.8399 (mt-10) REVERT: B 15 LYS cc_start: 0.6806 (mttt) cc_final: 0.5395 (pttp) REVERT: B 39 MET cc_start: 0.6123 (mmt) cc_final: 0.5404 (tpt) REVERT: I 60 GLN cc_start: 0.8587 (OUTLIER) cc_final: 0.8167 (tt0) REVERT: I 189 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.5849 (mp0) REVERT: I 525 ARG cc_start: 0.7499 (tmm-80) cc_final: 0.7185 (ttp80) REVERT: I 564 ARG cc_start: 0.8104 (tpp-160) cc_final: 0.7383 (mpt180) outliers start: 27 outliers final: 13 residues processed: 102 average time/residue: 0.5687 time to fit residues: 61.5069 Evaluate side-chains 99 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 84 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 258 MET Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain B residue 4 CYS Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 381 MET Chi-restraints excluded: chain I residue 60 GLN Chi-restraints excluded: chain I residue 143 ARG Chi-restraints excluded: chain I residue 184 VAL Chi-restraints excluded: chain I residue 189 GLU Chi-restraints excluded: chain I residue 353 THR Chi-restraints excluded: chain I residue 468 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 13 optimal weight: 3.9990 chunk 54 optimal weight: 0.0970 chunk 30 optimal weight: 3.9990 chunk 32 optimal weight: 0.3980 chunk 3 optimal weight: 0.1980 chunk 37 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 42 optimal weight: 0.0170 chunk 12 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 overall best weight: 0.3416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 GLN I 152 HIS I 546 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.189569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.131797 restraints weight = 8901.160| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 2.28 r_work: 0.3449 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3326 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 7683 Z= 0.094 Angle : 0.550 8.653 10454 Z= 0.275 Chirality : 0.040 0.126 1223 Planarity : 0.004 0.046 1335 Dihedral : 4.238 25.191 1032 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.29 % Allowed : 14.96 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.70 (0.26), residues: 931 helix: 0.17 (0.48), residues: 124 sheet: -1.62 (0.39), residues: 179 loop : -1.29 (0.24), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 525 TYR 0.010 0.001 TYR A 367 PHE 0.013 0.001 PHE B 124 TRP 0.006 0.001 TRP I 247 HIS 0.004 0.001 HIS I 528 Details of bonding type rmsd covalent geometry : bond 0.00218 ( 7672) covalent geometry : angle 0.54917 (10432) SS BOND : bond 0.00134 ( 11) SS BOND : angle 0.91600 ( 22) hydrogen bonds : bond 0.03672 ( 130) hydrogen bonds : angle 5.13153 ( 342) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 90 time to evaluate : 0.352 Fit side-chains REVERT: A 39 MET cc_start: 0.6678 (mmp) cc_final: 0.4595 (tmm) REVERT: A 81 GLU cc_start: 0.7375 (mp0) cc_final: 0.6694 (mp0) REVERT: A 288 LEU cc_start: 0.7155 (OUTLIER) cc_final: 0.6773 (mp) REVERT: A 290 GLU cc_start: 0.7200 (mm-30) cc_final: 0.6465 (tm-30) REVERT: A 361 GLU cc_start: 0.8654 (mt-10) cc_final: 0.8377 (mt-10) REVERT: B 15 LYS cc_start: 0.6698 (mttt) cc_final: 0.5307 (pttp) REVERT: B 39 MET cc_start: 0.5956 (mmt) cc_final: 0.5316 (tpt) REVERT: B 314 LYS cc_start: 0.7316 (tppt) cc_final: 0.6239 (tptp) REVERT: B 359 ASP cc_start: 0.7638 (m-30) cc_final: 0.7072 (m-30) REVERT: I 60 GLN cc_start: 0.8425 (OUTLIER) cc_final: 0.7976 (tt0) REVERT: I 546 ASN cc_start: 0.7832 (m-40) cc_final: 0.7079 (m-40) outliers start: 19 outliers final: 8 residues processed: 101 average time/residue: 0.5760 time to fit residues: 61.6196 Evaluate side-chains 96 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 86 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain B residue 4 CYS Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain I residue 60 GLN Chi-restraints excluded: chain I residue 184 VAL Chi-restraints excluded: chain I residue 353 THR Chi-restraints excluded: chain I residue 468 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 25 optimal weight: 6.9990 chunk 44 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 63 optimal weight: 0.5980 chunk 76 optimal weight: 1.9990 chunk 94 optimal weight: 6.9990 chunk 72 optimal weight: 0.0040 chunk 16 optimal weight: 0.8980 chunk 67 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 39 optimal weight: 0.2980 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 GLN I 152 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.189322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.131531 restraints weight = 8886.409| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 2.27 r_work: 0.3438 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3315 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 7683 Z= 0.103 Angle : 0.563 8.197 10454 Z= 0.276 Chirality : 0.040 0.143 1223 Planarity : 0.004 0.047 1335 Dihedral : 4.168 24.714 1032 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.05 % Allowed : 15.80 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.70 (0.27), residues: 931 helix: -0.04 (0.46), residues: 131 sheet: -1.60 (0.38), residues: 188 loop : -1.24 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 525 TYR 0.014 0.001 TYR A 342 PHE 0.012 0.001 PHE B 124 TRP 0.006 0.000 TRP I 247 HIS 0.005 0.001 HIS I 528 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 7672) covalent geometry : angle 0.56176 (10432) SS BOND : bond 0.00135 ( 11) SS BOND : angle 0.91887 ( 22) hydrogen bonds : bond 0.03857 ( 130) hydrogen bonds : angle 5.02124 ( 342) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 84 time to evaluate : 0.270 Fit side-chains REVERT: A 39 MET cc_start: 0.6637 (mmp) cc_final: 0.5974 (mpm) REVERT: A 81 GLU cc_start: 0.7339 (mp0) cc_final: 0.6638 (mp0) REVERT: A 288 LEU cc_start: 0.7088 (OUTLIER) cc_final: 0.6685 (mp) REVERT: A 290 GLU cc_start: 0.7217 (mm-30) cc_final: 0.6480 (tm-30) REVERT: A 361 GLU cc_start: 0.8694 (mt-10) cc_final: 0.8389 (mt-10) REVERT: B 15 LYS cc_start: 0.6701 (mttt) cc_final: 0.5306 (pttp) REVERT: B 39 MET cc_start: 0.5889 (mmt) cc_final: 0.5346 (tpt) REVERT: B 314 LYS cc_start: 0.7221 (tppt) cc_final: 0.6251 (tptp) REVERT: B 359 ASP cc_start: 0.7657 (OUTLIER) cc_final: 0.7106 (m-30) REVERT: I 60 GLN cc_start: 0.8490 (OUTLIER) cc_final: 0.8041 (tt0) REVERT: I 189 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.5820 (mp0) REVERT: I 546 ASN cc_start: 0.7844 (m-40) cc_final: 0.7228 (m-40) REVERT: I 564 ARG cc_start: 0.8032 (tpp-160) cc_final: 0.7340 (mpt180) outliers start: 17 outliers final: 10 residues processed: 97 average time/residue: 0.5504 time to fit residues: 56.7641 Evaluate side-chains 97 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain B residue 4 CYS Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 359 ASP Chi-restraints excluded: chain I residue 60 GLN Chi-restraints excluded: chain I residue 184 VAL Chi-restraints excluded: chain I residue 189 GLU Chi-restraints excluded: chain I residue 353 THR Chi-restraints excluded: chain I residue 468 LEU Chi-restraints excluded: chain I residue 503 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 37 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 27 optimal weight: 6.9990 chunk 30 optimal weight: 0.8980 chunk 93 optimal weight: 4.9990 chunk 87 optimal weight: 0.8980 chunk 22 optimal weight: 5.9990 chunk 90 optimal weight: 0.4980 chunk 75 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 42 optimal weight: 0.3980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 GLN I 152 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.187835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.129701 restraints weight = 8848.004| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 2.27 r_work: 0.3417 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3292 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7683 Z= 0.135 Angle : 0.600 8.024 10454 Z= 0.293 Chirality : 0.042 0.166 1223 Planarity : 0.004 0.047 1335 Dihedral : 4.338 24.392 1032 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 2.17 % Allowed : 15.92 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.69 (0.27), residues: 931 helix: 0.14 (0.48), residues: 124 sheet: -1.57 (0.38), residues: 189 loop : -1.27 (0.24), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 525 TYR 0.011 0.001 TYR I 269 PHE 0.029 0.001 PHE B 111 TRP 0.006 0.001 TRP I 247 HIS 0.005 0.001 HIS I 528 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 7672) covalent geometry : angle 0.59853 (10432) SS BOND : bond 0.00170 ( 11) SS BOND : angle 1.02148 ( 22) hydrogen bonds : bond 0.04584 ( 130) hydrogen bonds : angle 5.06313 ( 342) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 82 time to evaluate : 0.310 Fit side-chains REVERT: A 39 MET cc_start: 0.6629 (mmp) cc_final: 0.5933 (mpm) REVERT: A 81 GLU cc_start: 0.7370 (mp0) cc_final: 0.6673 (mp0) REVERT: A 288 LEU cc_start: 0.7076 (OUTLIER) cc_final: 0.6817 (mp) REVERT: A 361 GLU cc_start: 0.8689 (mt-10) cc_final: 0.8387 (mt-10) REVERT: B 15 LYS cc_start: 0.6741 (mttt) cc_final: 0.5336 (pttp) REVERT: B 39 MET cc_start: 0.5894 (mmt) cc_final: 0.5366 (tpt) REVERT: B 314 LYS cc_start: 0.7184 (tppt) cc_final: 0.6255 (tptp) REVERT: I 60 GLN cc_start: 0.8473 (OUTLIER) cc_final: 0.8026 (tt0) REVERT: I 189 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.5786 (mp0) REVERT: I 546 ASN cc_start: 0.7854 (m-40) cc_final: 0.7209 (m-40) REVERT: I 564 ARG cc_start: 0.8033 (tpp-160) cc_final: 0.7335 (mpt180) outliers start: 18 outliers final: 10 residues processed: 97 average time/residue: 0.5090 time to fit residues: 52.5390 Evaluate side-chains 93 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 80 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain B residue 4 CYS Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain I residue 60 GLN Chi-restraints excluded: chain I residue 184 VAL Chi-restraints excluded: chain I residue 189 GLU Chi-restraints excluded: chain I residue 353 THR Chi-restraints excluded: chain I residue 468 LEU Chi-restraints excluded: chain I residue 503 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 75 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 69 optimal weight: 0.1980 chunk 68 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 44 optimal weight: 0.6980 chunk 64 optimal weight: 0.7980 chunk 60 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 61 optimal weight: 0.1980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 GLN I 152 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.189321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.138249 restraints weight = 8847.871| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 2.14 r_work: 0.3448 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3328 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 7683 Z= 0.104 Angle : 0.568 11.124 10454 Z= 0.278 Chirality : 0.040 0.140 1223 Planarity : 0.004 0.046 1335 Dihedral : 4.200 23.795 1032 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.81 % Allowed : 16.28 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.69 (0.27), residues: 931 helix: -0.02 (0.46), residues: 131 sheet: -1.56 (0.38), residues: 188 loop : -1.24 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 125 TYR 0.010 0.001 TYR A 367 PHE 0.015 0.001 PHE B 179 TRP 0.006 0.001 TRP I 247 HIS 0.004 0.001 HIS I 528 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 7672) covalent geometry : angle 0.56705 (10432) SS BOND : bond 0.00187 ( 11) SS BOND : angle 0.99923 ( 22) hydrogen bonds : bond 0.03915 ( 130) hydrogen bonds : angle 4.93916 ( 342) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 83 time to evaluate : 0.306 Fit side-chains REVERT: A 39 MET cc_start: 0.6625 (mmp) cc_final: 0.5956 (mpm) REVERT: A 81 GLU cc_start: 0.7374 (mp0) cc_final: 0.6612 (mp0) REVERT: A 288 LEU cc_start: 0.7008 (OUTLIER) cc_final: 0.6753 (mp) REVERT: A 361 GLU cc_start: 0.8685 (mt-10) cc_final: 0.8390 (mt-10) REVERT: A 366 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.8106 (tp) REVERT: B 15 LYS cc_start: 0.6779 (mttt) cc_final: 0.5350 (pttp) REVERT: B 39 MET cc_start: 0.5831 (mmt) cc_final: 0.5342 (tpt) REVERT: B 314 LYS cc_start: 0.7059 (tppt) cc_final: 0.6194 (tptp) REVERT: B 359 ASP cc_start: 0.7678 (m-30) cc_final: 0.7110 (m-30) REVERT: I 60 GLN cc_start: 0.8441 (OUTLIER) cc_final: 0.8010 (tt0) REVERT: I 189 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.5712 (mp0) REVERT: I 546 ASN cc_start: 0.7815 (m-40) cc_final: 0.7219 (m-40) outliers start: 15 outliers final: 10 residues processed: 96 average time/residue: 0.4640 time to fit residues: 47.5900 Evaluate side-chains 94 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain B residue 4 CYS Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain I residue 60 GLN Chi-restraints excluded: chain I residue 184 VAL Chi-restraints excluded: chain I residue 189 GLU Chi-restraints excluded: chain I residue 353 THR Chi-restraints excluded: chain I residue 468 LEU Chi-restraints excluded: chain I residue 503 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 4 optimal weight: 0.9980 chunk 21 optimal weight: 0.0010 chunk 32 optimal weight: 0.0060 chunk 24 optimal weight: 0.0270 chunk 63 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 89 optimal weight: 0.0980 chunk 11 optimal weight: 0.5980 chunk 55 optimal weight: 1.9990 chunk 41 optimal weight: 5.9990 overall best weight: 0.1460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 GLN I 59 ASN I 152 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.192764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.135071 restraints weight = 8857.321| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 2.28 r_work: 0.3493 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3369 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 7683 Z= 0.088 Angle : 0.547 11.904 10454 Z= 0.265 Chirality : 0.039 0.156 1223 Planarity : 0.004 0.045 1335 Dihedral : 3.828 20.819 1032 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.45 % Allowed : 16.77 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.43 (0.27), residues: 931 helix: 0.10 (0.47), residues: 131 sheet: -1.49 (0.38), residues: 211 loop : -0.97 (0.25), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 525 TYR 0.008 0.001 TYR A 367 PHE 0.026 0.001 PHE B 111 TRP 0.007 0.001 TRP I 247 HIS 0.003 0.000 HIS I 528 Details of bonding type rmsd covalent geometry : bond 0.00196 ( 7672) covalent geometry : angle 0.54564 (10432) SS BOND : bond 0.00118 ( 11) SS BOND : angle 0.87715 ( 22) hydrogen bonds : bond 0.02853 ( 130) hydrogen bonds : angle 4.64954 ( 342) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 90 time to evaluate : 0.295 Fit side-chains REVERT: A 39 MET cc_start: 0.6565 (mmp) cc_final: 0.5886 (mpm) REVERT: A 81 GLU cc_start: 0.7200 (mp0) cc_final: 0.6470 (mp0) REVERT: A 288 LEU cc_start: 0.6943 (OUTLIER) cc_final: 0.6712 (mp) REVERT: A 302 ARG cc_start: 0.8006 (mtp85) cc_final: 0.7757 (mtp180) REVERT: A 361 GLU cc_start: 0.8722 (mt-10) cc_final: 0.8414 (mt-10) REVERT: B 15 LYS cc_start: 0.6643 (mttt) cc_final: 0.5285 (pttp) REVERT: B 39 MET cc_start: 0.5860 (mmt) cc_final: 0.5343 (tpt) REVERT: B 314 LYS cc_start: 0.6882 (tppt) cc_final: 0.6134 (tptp) REVERT: B 359 ASP cc_start: 0.7667 (m-30) cc_final: 0.7127 (m-30) REVERT: B 387 LYS cc_start: 0.6995 (tttm) cc_final: 0.6762 (ptmm) REVERT: I 28 MET cc_start: 0.7878 (mpt) cc_final: 0.7521 (mpt) REVERT: I 60 GLN cc_start: 0.8390 (OUTLIER) cc_final: 0.7939 (tt0) REVERT: I 452 ASP cc_start: 0.7970 (t0) cc_final: 0.7672 (t0) REVERT: I 546 ASN cc_start: 0.7702 (m-40) cc_final: 0.7084 (m-40) outliers start: 12 outliers final: 8 residues processed: 101 average time/residue: 0.4538 time to fit residues: 48.8802 Evaluate side-chains 94 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 84 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain B residue 4 CYS Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain I residue 60 GLN Chi-restraints excluded: chain I residue 184 VAL Chi-restraints excluded: chain I residue 468 LEU Chi-restraints excluded: chain I residue 503 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 28 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 chunk 37 optimal weight: 0.3980 chunk 56 optimal weight: 2.9990 chunk 9 optimal weight: 0.0370 chunk 13 optimal weight: 0.9990 chunk 48 optimal weight: 0.2980 chunk 29 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 overall best weight: 0.5260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 59 ASN I 152 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.190566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.139127 restraints weight = 8815.111| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 2.24 r_work: 0.3467 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3346 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 7683 Z= 0.105 Angle : 0.601 12.420 10454 Z= 0.289 Chirality : 0.041 0.182 1223 Planarity : 0.004 0.051 1335 Dihedral : 3.993 21.704 1032 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 1.21 % Allowed : 17.61 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.37 (0.27), residues: 931 helix: 0.28 (0.48), residues: 124 sheet: -1.42 (0.38), residues: 206 loop : -0.97 (0.24), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 125 TYR 0.011 0.001 TYR I 567 PHE 0.016 0.001 PHE B 179 TRP 0.005 0.000 TRP I 247 HIS 0.004 0.001 HIS I 528 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 7672) covalent geometry : angle 0.60010 (10432) SS BOND : bond 0.00121 ( 11) SS BOND : angle 0.88776 ( 22) hydrogen bonds : bond 0.03680 ( 130) hydrogen bonds : angle 4.68190 ( 342) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3424.31 seconds wall clock time: 58 minutes 49.39 seconds (3529.39 seconds total)