Starting phenix.real_space_refine on Mon Apr 28 12:37:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vsb_43492/04_2025/8vsb_43492.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vsb_43492/04_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8vsb_43492/04_2025/8vsb_43492.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vsb_43492/04_2025/8vsb_43492.map" model { file = "/net/cci-nas-00/data/ceres_data/8vsb_43492/04_2025/8vsb_43492.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vsb_43492/04_2025/8vsb_43492.cif" } resolution = 2.93 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= -0.000 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: {'GLN:plan1': 3, 'GLU:plan': 6, 'HIS:plan': 1, 'ARG:plan': 8, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 86 Time building chain proxies: 5.81, per 1000 atoms: 0.77 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: 1.64 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.82 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: 1.95 Time building geometry restraints manager: 2.00 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: 3.950 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: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 21.250 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 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:12.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.400 ------------------------------------------------------------------------------- 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 (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: -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 TRP 0.012 0.002 TRP I 247 HIS 0.007 0.002 HIS B 335 PHE 0.022 0.003 PHE A 320 TYR 0.046 0.003 TYR A 316 ARG 0.005 0.001 ARG A 295 Details of bonding type rmsd hydrogen bonds : bond 0.23982 ( 130) hydrogen bonds : angle 7.80618 ( 342) SS BOND : bond 0.00550 ( 11) SS BOND : angle 3.23067 ( 22) covalent geometry : bond 0.00925 ( 7672) covalent geometry : angle 0.95364 (10432) *********************** 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 : 0.810 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: 1.4516 time to fit residues: 173.5663 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 : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 80 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 24 optimal weight: 5.9990 chunk 48 optimal weight: 0.7980 chunk 38 optimal weight: 0.2980 chunk 74 optimal weight: 1.9990 chunk 28 optimal weight: 8.9990 chunk 45 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 86 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.4201 r_free = 0.4201 target = 0.186519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.133526 restraints weight = 8788.242| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 2.55 r_work: 0.3397 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.1125 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 : 0.647 7.826 10454 Z= 0.321 Chirality : 0.043 0.159 1223 Planarity : 0.005 0.050 1335 Dihedral : 5.177 28.022 1032 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % 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 (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: -2.23 (0.25), residues: 931 helix: -0.22 (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 TRP 0.006 0.001 TRP I 247 HIS 0.003 0.001 HIS A 41 PHE 0.015 0.001 PHE A 320 TYR 0.019 0.001 TYR A 367 ARG 0.006 0.001 ARG I 125 Details of bonding type rmsd hydrogen bonds : bond 0.05733 ( 130) hydrogen bonds : angle 5.97239 ( 342) SS BOND : bond 0.00233 ( 11) SS BOND : angle 1.67259 ( 22) covalent geometry : bond 0.00319 ( 7672) covalent geometry : angle 0.64356 (10432) *********************** 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 : 0.914 Fit side-chains REVERT: A 39 MET cc_start: 0.6621 (mmp) cc_final: 0.4964 (tmm) REVERT: A 81 GLU cc_start: 0.7390 (mp0) cc_final: 0.6775 (mp0) REVERT: B 15 LYS cc_start: 0.6762 (mttt) cc_final: 0.5446 (pttp) REVERT: B 39 MET cc_start: 0.6140 (mmt) cc_final: 0.4604 (pp-130) REVERT: B 359 ASP cc_start: 0.7631 (OUTLIER) cc_final: 0.7052 (m-30) REVERT: B 381 MET cc_start: 0.8011 (OUTLIER) cc_final: 0.7786 (tpp) REVERT: I 189 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.6183 (mp0) REVERT: I 494 GLU cc_start: 0.8288 (mt-10) cc_final: 0.7868 (tt0) REVERT: I 503 LEU cc_start: 0.7481 (OUTLIER) cc_final: 0.7147 (pp) outliers start: 20 outliers final: 8 residues processed: 106 average time/residue: 1.3501 time to fit residues: 151.0083 Evaluate side-chains 100 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 0.929 ------------------------------------------------------------------------------- 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 83 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 30 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 55 optimal weight: 0.3980 chunk 77 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 = 0.4192 r_free = 0.4192 target = 0.185797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.127565 restraints weight = 8918.219| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 2.28 r_work: 0.3389 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3263 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.1343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7683 Z= 0.165 Angle : 0.674 7.962 10454 Z= 0.327 Chirality : 0.044 0.155 1223 Planarity : 0.005 0.051 1335 Dihedral : 5.053 28.375 1032 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 2.65 % Allowed : 12.18 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.11 % 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: -2.19 (0.25), residues: 931 helix: -0.37 (0.46), residues: 124 sheet: -1.91 (0.36), residues: 178 loop : -1.60 (0.23), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 247 HIS 0.006 0.001 HIS I 528 PHE 0.018 0.002 PHE A 320 TYR 0.015 0.001 TYR A 316 ARG 0.007 0.001 ARG B 125 Details of bonding type rmsd hydrogen bonds : bond 0.05611 ( 130) hydrogen bonds : angle 5.68870 ( 342) SS BOND : bond 0.00299 ( 11) SS BOND : angle 1.65063 ( 22) covalent geometry : bond 0.00403 ( 7672) covalent geometry : angle 0.67002 (10432) *********************** 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: 22 poor density : 90 time to evaluate : 0.902 Fit side-chains REVERT: A 39 MET cc_start: 0.6601 (mmp) cc_final: 0.4786 (tmm) REVERT: A 81 GLU cc_start: 0.7350 (mp0) cc_final: 0.6732 (mp0) REVERT: A 288 LEU cc_start: 0.7365 (tt) cc_final: 0.6921 (mp) REVERT: A 290 GLU cc_start: 0.7190 (OUTLIER) cc_final: 0.6591 (tm-30) REVERT: A 361 GLU cc_start: 0.8546 (mt-10) cc_final: 0.8336 (mt-10) REVERT: B 15 LYS cc_start: 0.6737 (mttt) cc_final: 0.5382 (pttp) REVERT: B 309 TRP cc_start: 0.6993 (p-90) cc_final: 0.6654 (p-90) REVERT: B 314 LYS cc_start: 0.7496 (tppt) cc_final: 0.7157 (tptp) REVERT: I 60 GLN cc_start: 0.8473 (tp40) cc_final: 0.8034 (tt0) REVERT: I 189 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.5968 (mp0) REVERT: I 266 ARG cc_start: 0.8010 (mmt90) cc_final: 0.7594 (mtt90) outliers start: 22 outliers final: 12 residues processed: 100 average time/residue: 1.4331 time to fit residues: 150.9245 Evaluate side-chains 98 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 84 time to evaluate : 0.908 ------------------------------------------------------------------------------- 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 290 GLU 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 218 GLN 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 75 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 26 optimal weight: 0.8980 chunk 54 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 88 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 48 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- 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 = 0.4202 r_free = 0.4202 target = 0.186874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.131545 restraints weight = 8866.889| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 2.56 r_work: 0.3397 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7683 Z= 0.134 Angle : 0.612 7.692 10454 Z= 0.300 Chirality : 0.042 0.161 1223 Planarity : 0.004 0.049 1335 Dihedral : 4.760 27.770 1032 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 3.86 % Allowed : 12.18 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.11 % 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: -1.98 (0.26), residues: 931 helix: -0.13 (0.47), residues: 123 sheet: -1.71 (0.37), residues: 178 loop : -1.49 (0.23), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 247 HIS 0.005 0.001 HIS I 528 PHE 0.015 0.001 PHE A 320 TYR 0.012 0.001 TYR A 367 ARG 0.009 0.001 ARG B 125 Details of bonding type rmsd hydrogen bonds : bond 0.04798 ( 130) hydrogen bonds : angle 5.47144 ( 342) SS BOND : bond 0.00180 ( 11) SS BOND : angle 1.21911 ( 22) covalent geometry : bond 0.00323 ( 7672) covalent geometry : angle 0.60968 (10432) *********************** 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 124 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 92 time to evaluate : 0.901 Fit side-chains REVERT: A 39 MET cc_start: 0.6605 (mmp) cc_final: 0.4728 (tmm) REVERT: A 81 GLU cc_start: 0.7374 (mp0) cc_final: 0.6716 (mp0) REVERT: A 288 LEU cc_start: 0.7331 (OUTLIER) cc_final: 0.6888 (mp) REVERT: A 290 GLU cc_start: 0.7261 (OUTLIER) cc_final: 0.6602 (tm-30) REVERT: B 15 LYS cc_start: 0.6815 (mttt) cc_final: 0.5418 (pttp) REVERT: B 39 MET cc_start: 0.6092 (mmt) cc_final: 0.4498 (pp-130) REVERT: B 295 ARG cc_start: 0.6194 (OUTLIER) cc_final: 0.4705 (mtt-85) REVERT: B 309 TRP cc_start: 0.6955 (p-90) cc_final: 0.6604 (p-90) REVERT: B 359 ASP cc_start: 0.7628 (OUTLIER) cc_final: 0.7048 (m-30) REVERT: I 60 GLN cc_start: 0.8449 (OUTLIER) cc_final: 0.8003 (tt0) REVERT: I 189 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.5881 (mp0) REVERT: I 218 GLN cc_start: 0.8206 (OUTLIER) cc_final: 0.7835 (tt0) REVERT: I 452 ASP cc_start: 0.8148 (t0) cc_final: 0.7868 (t0) outliers start: 32 outliers final: 11 residues processed: 110 average time/residue: 1.2960 time to fit residues: 150.3110 Evaluate side-chains 102 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 84 time to evaluate : 0.804 ------------------------------------------------------------------------------- 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 295 ARG Chi-restraints excluded: chain B residue 332 ASP 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 218 GLN Chi-restraints excluded: chain I residue 353 THR Chi-restraints excluded: chain I residue 468 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 29 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 55 optimal weight: 0.6980 chunk 68 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 7 optimal weight: 9.9990 chunk 81 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 3 optimal weight: 0.0370 overall best weight: 0.6458 ------------------------------------------------------------------------------- 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 = 0.4215 r_free = 0.4215 target = 0.188069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.134314 restraints weight = 8798.853| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 2.52 r_work: 0.3409 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3284 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7683 Z= 0.110 Angle : 0.576 7.929 10454 Z= 0.285 Chirality : 0.041 0.129 1223 Planarity : 0.004 0.048 1335 Dihedral : 4.525 26.976 1032 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 3.38 % Allowed : 13.39 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.11 % 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: -1.85 (0.26), residues: 931 helix: 0.03 (0.47), residues: 123 sheet: -1.67 (0.38), residues: 180 loop : -1.40 (0.23), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP I 247 HIS 0.004 0.001 HIS I 528 PHE 0.013 0.001 PHE A 320 TYR 0.011 0.001 TYR A 367 ARG 0.008 0.001 ARG I 266 Details of bonding type rmsd hydrogen bonds : bond 0.04299 ( 130) hydrogen bonds : angle 5.30726 ( 342) SS BOND : bond 0.00145 ( 11) SS BOND : angle 1.07616 ( 22) covalent geometry : bond 0.00263 ( 7672) covalent geometry : angle 0.57471 (10432) *********************** 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 118 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 90 time to evaluate : 0.833 Fit side-chains REVERT: A 39 MET cc_start: 0.6590 (mmp) cc_final: 0.4581 (tmm) REVERT: A 81 GLU cc_start: 0.7368 (mp0) cc_final: 0.6700 (mp0) REVERT: A 288 LEU cc_start: 0.7324 (OUTLIER) cc_final: 0.6882 (mp) REVERT: A 290 GLU cc_start: 0.7294 (mm-30) cc_final: 0.6579 (tm-30) REVERT: A 342 TYR cc_start: 0.4579 (m-80) cc_final: 0.4222 (m-10) REVERT: A 361 GLU cc_start: 0.8586 (mt-10) cc_final: 0.8327 (mt-10) REVERT: B 15 LYS cc_start: 0.6790 (mttt) cc_final: 0.5393 (pttp) REVERT: B 39 MET cc_start: 0.6071 (mmt) cc_final: 0.5404 (tpt) REVERT: B 314 LYS cc_start: 0.7379 (tppt) cc_final: 0.6288 (tptp) REVERT: B 359 ASP cc_start: 0.7648 (OUTLIER) cc_final: 0.7072 (m-30) REVERT: I 60 GLN cc_start: 0.8497 (OUTLIER) cc_final: 0.8072 (tt0) REVERT: I 189 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.5791 (mp0) REVERT: I 218 GLN cc_start: 0.8217 (OUTLIER) cc_final: 0.7855 (tt0) REVERT: I 268 ILE cc_start: 0.8743 (OUTLIER) cc_final: 0.8339 (pt) REVERT: I 525 ARG cc_start: 0.7488 (tmm-80) cc_final: 0.7199 (ttp80) outliers start: 28 outliers final: 9 residues processed: 107 average time/residue: 1.1727 time to fit residues: 132.9155 Evaluate side-chains 105 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 90 time to evaluate : 0.805 ------------------------------------------------------------------------------- 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 359 ASP Chi-restraints excluded: chain B residue 381 MET Chi-restraints excluded: chain I residue 60 GLN 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 218 GLN Chi-restraints excluded: chain I residue 268 ILE Chi-restraints excluded: chain I residue 353 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 93 optimal weight: 7.9990 chunk 15 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 46 optimal weight: 0.0870 chunk 32 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 overall best weight: 1.3362 ------------------------------------------------------------------------------- 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 = 0.4192 r_free = 0.4192 target = 0.185832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.134827 restraints weight = 8846.846| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 2.23 r_work: 0.3398 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3277 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7683 Z= 0.176 Angle : 0.659 8.635 10454 Z= 0.321 Chirality : 0.043 0.132 1223 Planarity : 0.005 0.048 1335 Dihedral : 4.731 27.040 1032 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 2.65 % Allowed : 15.32 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.11 % 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: -1.93 (0.26), residues: 931 helix: 0.01 (0.47), residues: 123 sheet: -1.67 (0.38), residues: 178 loop : -1.48 (0.23), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 247 HIS 0.005 0.001 HIS I 528 PHE 0.019 0.001 PHE A 320 TYR 0.014 0.001 TYR I 269 ARG 0.006 0.001 ARG I 525 Details of bonding type rmsd hydrogen bonds : bond 0.05356 ( 130) hydrogen bonds : angle 5.39039 ( 342) SS BOND : bond 0.00215 ( 11) SS BOND : angle 1.21119 ( 22) covalent geometry : bond 0.00433 ( 7672) covalent geometry : angle 0.65751 (10432) *********************** 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 107 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 85 time to evaluate : 0.824 Fit side-chains REVERT: A 39 MET cc_start: 0.6646 (mmp) cc_final: 0.4718 (tmm) REVERT: A 55 GLU cc_start: 0.7403 (OUTLIER) cc_final: 0.7202 (pp20) REVERT: A 81 GLU cc_start: 0.7362 (mp0) cc_final: 0.6663 (mp0) REVERT: A 288 LEU cc_start: 0.7295 (tt) cc_final: 0.6880 (mp) REVERT: A 290 GLU cc_start: 0.7413 (mm-30) cc_final: 0.6667 (tm-30) REVERT: A 361 GLU cc_start: 0.8661 (mt-10) cc_final: 0.8402 (mt-10) REVERT: B 15 LYS cc_start: 0.6845 (mttt) cc_final: 0.5402 (pttp) REVERT: B 39 MET cc_start: 0.5989 (mmt) cc_final: 0.5430 (tpt) REVERT: B 314 LYS cc_start: 0.7276 (tppt) cc_final: 0.6258 (tptp) REVERT: I 60 GLN cc_start: 0.8587 (OUTLIER) cc_final: 0.8145 (tt0) REVERT: I 189 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.5833 (mp0) REVERT: I 218 GLN cc_start: 0.8203 (OUTLIER) cc_final: 0.7838 (tt0) REVERT: I 564 ARG cc_start: 0.8050 (tpp-160) cc_final: 0.7326 (mpt180) outliers start: 22 outliers final: 10 residues processed: 99 average time/residue: 1.1906 time to fit residues: 125.1907 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 : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR 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 184 VAL Chi-restraints excluded: chain I residue 189 GLU Chi-restraints excluded: chain I residue 218 GLN Chi-restraints excluded: chain I residue 353 THR Chi-restraints excluded: chain I residue 377 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 67 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 93 optimal weight: 6.9990 chunk 7 optimal weight: 10.0000 chunk 25 optimal weight: 0.3980 chunk 74 optimal weight: 0.0570 chunk 38 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 76 optimal weight: 0.5980 chunk 42 optimal weight: 0.0070 chunk 63 optimal weight: 0.0770 overall best weight: 0.2274 ------------------------------------------------------------------------------- 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 = 0.4242 r_free = 0.4242 target = 0.190757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.133499 restraints weight = 8762.784| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 2.25 r_work: 0.3470 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3347 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.2071 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= 0.089 Angle : 0.537 8.222 10454 Z= 0.269 Chirality : 0.039 0.126 1223 Planarity : 0.004 0.047 1335 Dihedral : 4.123 23.337 1032 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.29 % Allowed : 16.04 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.11 % 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: -1.74 (0.27), residues: 931 helix: 0.02 (0.46), residues: 131 sheet: -1.62 (0.38), residues: 183 loop : -1.30 (0.24), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP I 247 HIS 0.005 0.001 HIS I 528 PHE 0.018 0.001 PHE B 179 TYR 0.015 0.001 TYR A 342 ARG 0.009 0.001 ARG I 525 Details of bonding type rmsd hydrogen bonds : bond 0.03296 ( 130) hydrogen bonds : angle 5.03863 ( 342) SS BOND : bond 0.00118 ( 11) SS BOND : angle 0.89986 ( 22) covalent geometry : bond 0.00205 ( 7672) covalent geometry : angle 0.53627 (10432) *********************** 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 106 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 87 time to evaluate : 0.799 Fit side-chains REVERT: A 39 MET cc_start: 0.6617 (mmp) cc_final: 0.5921 (mpm) REVERT: A 81 GLU cc_start: 0.7330 (mp0) cc_final: 0.6607 (mp0) REVERT: A 288 LEU cc_start: 0.7048 (OUTLIER) cc_final: 0.6785 (mp) REVERT: A 361 GLU cc_start: 0.8636 (mt-10) cc_final: 0.8342 (mt-10) REVERT: B 15 LYS cc_start: 0.6682 (mttt) cc_final: 0.5293 (pttp) REVERT: B 39 MET cc_start: 0.5867 (mmt) cc_final: 0.5305 (tpt) REVERT: B 314 LYS cc_start: 0.7083 (tppt) cc_final: 0.6213 (tptp) REVERT: B 359 ASP cc_start: 0.7647 (m-30) cc_final: 0.7100 (m-30) REVERT: I 60 GLN cc_start: 0.8396 (OUTLIER) cc_final: 0.7955 (tt0) REVERT: I 268 ILE cc_start: 0.8685 (OUTLIER) cc_final: 0.8350 (pt) REVERT: I 546 ASN cc_start: 0.7803 (m-40) cc_final: 0.7076 (m-40) REVERT: I 564 ARG cc_start: 0.8023 (tpp-160) cc_final: 0.7336 (mpt180) outliers start: 19 outliers final: 9 residues processed: 100 average time/residue: 1.1131 time to fit residues: 118.5215 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 : 0.880 ------------------------------------------------------------------------------- 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 143 ARG Chi-restraints excluded: chain I residue 184 VAL Chi-restraints excluded: chain I residue 268 ILE Chi-restraints excluded: chain I residue 353 THR Chi-restraints excluded: chain I residue 468 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 76 optimal weight: 0.0570 chunk 75 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 93 optimal weight: 5.9990 chunk 68 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 chunk 32 optimal weight: 0.3980 chunk 89 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 overall best weight: 0.6700 ------------------------------------------------------------------------------- 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 218 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.188932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.137521 restraints weight = 8909.713| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 2.27 r_work: 0.3431 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3310 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7683 Z= 0.113 Angle : 0.577 8.729 10454 Z= 0.280 Chirality : 0.041 0.152 1223 Planarity : 0.004 0.048 1335 Dihedral : 4.182 24.727 1032 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 2.17 % Allowed : 16.41 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.11 % 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: -1.75 (0.27), residues: 931 helix: -0.11 (0.46), residues: 131 sheet: -1.57 (0.38), residues: 189 loop : -1.29 (0.24), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP I 247 HIS 0.004 0.001 HIS I 528 PHE 0.014 0.001 PHE A 320 TYR 0.010 0.001 TYR A 367 ARG 0.007 0.001 ARG B 125 Details of bonding type rmsd hydrogen bonds : bond 0.03987 ( 130) hydrogen bonds : angle 5.01437 ( 342) SS BOND : bond 0.00134 ( 11) SS BOND : angle 0.94983 ( 22) covalent geometry : bond 0.00274 ( 7672) covalent geometry : angle 0.57610 (10432) *********************** 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 104 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 86 time to evaluate : 0.814 Fit side-chains REVERT: A 39 MET cc_start: 0.6644 (mmp) cc_final: 0.5963 (mpm) REVERT: A 81 GLU cc_start: 0.7374 (mp0) cc_final: 0.6698 (mp0) REVERT: A 288 LEU cc_start: 0.7080 (OUTLIER) cc_final: 0.6806 (mp) REVERT: A 361 GLU cc_start: 0.8684 (mt-10) cc_final: 0.8393 (mt-10) REVERT: B 15 LYS cc_start: 0.6782 (mttt) cc_final: 0.5365 (pttp) REVERT: B 39 MET cc_start: 0.5857 (mmt) cc_final: 0.5367 (tpt) REVERT: B 314 LYS cc_start: 0.7087 (tppt) cc_final: 0.6235 (tptp) REVERT: B 359 ASP cc_start: 0.7668 (m-30) cc_final: 0.7107 (m-30) REVERT: I 60 GLN cc_start: 0.8490 (OUTLIER) cc_final: 0.8059 (tt0) REVERT: I 189 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.5855 (mp0) REVERT: I 268 ILE cc_start: 0.8714 (OUTLIER) cc_final: 0.8368 (pt) REVERT: I 546 ASN cc_start: 0.7865 (m-40) cc_final: 0.7266 (m-40) REVERT: I 564 ARG cc_start: 0.8065 (tpp-160) cc_final: 0.7398 (mpt180) outliers start: 18 outliers final: 10 residues processed: 100 average time/residue: 1.0291 time to fit residues: 110.0307 Evaluate side-chains 100 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 86 time to evaluate : 0.879 ------------------------------------------------------------------------------- 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 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 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 87 optimal weight: 0.5980 chunk 77 optimal weight: 2.9990 chunk 74 optimal weight: 0.0050 chunk 75 optimal weight: 0.8980 chunk 62 optimal weight: 0.4980 chunk 22 optimal weight: 4.9990 chunk 85 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 chunk 6 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 GLN ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 152 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.189617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.131521 restraints weight = 8928.093| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 2.29 r_work: 0.3441 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3318 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.2148 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= 0.102 Angle : 0.567 11.857 10454 Z= 0.276 Chirality : 0.040 0.130 1223 Planarity : 0.004 0.047 1335 Dihedral : 4.140 23.587 1032 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.93 % Allowed : 16.65 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.11 % 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: -1.73 (0.27), residues: 931 helix: -0.14 (0.46), residues: 131 sheet: -1.58 (0.39), residues: 188 loop : -1.25 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP I 247 HIS 0.004 0.001 HIS I 528 PHE 0.022 0.001 PHE B 111 TYR 0.010 0.001 TYR I 567 ARG 0.007 0.000 ARG I 525 Details of bonding type rmsd hydrogen bonds : bond 0.03769 ( 130) hydrogen bonds : angle 4.94853 ( 342) SS BOND : bond 0.00130 ( 11) SS BOND : angle 0.90058 ( 22) covalent geometry : bond 0.00245 ( 7672) covalent geometry : angle 0.56597 (10432) *********************** 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 102 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 0.857 Fit side-chains REVERT: A 39 MET cc_start: 0.6608 (mmp) cc_final: 0.5927 (mpm) REVERT: A 81 GLU cc_start: 0.7382 (mp0) cc_final: 0.6691 (mp0) REVERT: A 288 LEU cc_start: 0.7054 (OUTLIER) cc_final: 0.6798 (mp) REVERT: A 302 ARG cc_start: 0.8025 (mtp85) cc_final: 0.7763 (mtp180) REVERT: A 361 GLU cc_start: 0.8690 (mt-10) cc_final: 0.8401 (mt-10) REVERT: B 15 LYS cc_start: 0.6712 (mttt) cc_final: 0.5323 (pttp) REVERT: B 39 MET cc_start: 0.5838 (mmt) cc_final: 0.5360 (tpt) REVERT: B 314 LYS cc_start: 0.6976 (tppt) cc_final: 0.6171 (tptp) REVERT: B 359 ASP cc_start: 0.7673 (m-30) cc_final: 0.7122 (m-30) REVERT: I 60 GLN cc_start: 0.8426 (OUTLIER) cc_final: 0.7988 (tt0) REVERT: I 268 ILE cc_start: 0.8684 (OUTLIER) cc_final: 0.8337 (pt) REVERT: I 546 ASN cc_start: 0.7809 (m-40) cc_final: 0.7216 (m-40) REVERT: I 564 ARG cc_start: 0.8029 (tpp-160) cc_final: 0.7337 (mpt180) outliers start: 16 outliers final: 10 residues processed: 99 average time/residue: 1.1145 time to fit residues: 117.7932 Evaluate side-chains 98 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.810 ------------------------------------------------------------------------------- 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 268 ILE 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 26 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 64 optimal weight: 0.3980 chunk 2 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 chunk 21 optimal weight: 0.4980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 218 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.188776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.134896 restraints weight = 8822.857| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 2.29 r_work: 0.3438 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3317 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.2145 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= 0.118 Angle : 0.601 12.545 10454 Z= 0.288 Chirality : 0.041 0.216 1223 Planarity : 0.004 0.047 1335 Dihedral : 4.240 23.961 1032 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 1.81 % Allowed : 16.65 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.11 % 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: -1.75 (0.27), residues: 931 helix: -0.17 (0.46), residues: 131 sheet: -1.58 (0.39), residues: 186 loop : -1.27 (0.24), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP I 247 HIS 0.004 0.001 HIS I 528 PHE 0.014 0.001 PHE A 320 TYR 0.010 0.001 TYR B 283 ARG 0.007 0.000 ARG B 125 Details of bonding type rmsd hydrogen bonds : bond 0.04119 ( 130) hydrogen bonds : angle 4.95093 ( 342) SS BOND : bond 0.00169 ( 11) SS BOND : angle 1.05040 ( 22) covalent geometry : bond 0.00288 ( 7672) covalent geometry : angle 0.59966 (10432) ********************** 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 101 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 86 time to evaluate : 0.844 Fit side-chains REVERT: A 39 MET cc_start: 0.6652 (mmp) cc_final: 0.5519 (mpm) REVERT: A 81 GLU cc_start: 0.7376 (mp0) cc_final: 0.6682 (mp0) REVERT: A 288 LEU cc_start: 0.7014 (OUTLIER) cc_final: 0.6729 (mp) REVERT: A 361 GLU cc_start: 0.8664 (mt-10) cc_final: 0.8370 (mt-10) REVERT: A 366 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.8156 (tp) REVERT: B 15 LYS cc_start: 0.6839 (mttt) cc_final: 0.5407 (pttp) REVERT: B 39 MET cc_start: 0.5801 (mmt) cc_final: 0.5358 (tpt) REVERT: B 314 LYS cc_start: 0.6932 (tppt) cc_final: 0.6100 (tptp) REVERT: B 359 ASP cc_start: 0.7697 (m-30) cc_final: 0.7139 (m-30) REVERT: I 28 MET cc_start: 0.7893 (mpt) cc_final: 0.7536 (mpt) REVERT: I 60 GLN cc_start: 0.8473 (OUTLIER) cc_final: 0.8071 (tt0) REVERT: I 268 ILE cc_start: 0.8717 (OUTLIER) cc_final: 0.8387 (pt) REVERT: I 546 ASN cc_start: 0.7785 (m-40) cc_final: 0.7212 (m-40) outliers start: 15 outliers final: 9 residues processed: 98 average time/residue: 1.0373 time to fit residues: 108.8129 Evaluate side-chains 95 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 0.811 ------------------------------------------------------------------------------- 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 I residue 60 GLN Chi-restraints excluded: chain I residue 184 VAL Chi-restraints excluded: chain I residue 268 ILE 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 23 optimal weight: 0.0170 chunk 52 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 59 optimal weight: 0.4980 chunk 42 optimal weight: 0.0470 chunk 65 optimal weight: 0.5980 chunk 1 optimal weight: 0.9980 chunk 39 optimal weight: 0.5980 chunk 35 optimal weight: 0.5980 chunk 36 optimal weight: 0.5980 chunk 72 optimal weight: 1.9990 overall best weight: 0.3516 ------------------------------------------------------------------------------- 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 = 0.4242 r_free = 0.4242 target = 0.190912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.136890 restraints weight = 8807.130| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 2.38 r_work: 0.3479 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3357 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 7683 Z= 0.092 Angle : 0.565 12.456 10454 Z= 0.271 Chirality : 0.040 0.205 1223 Planarity : 0.004 0.047 1335 Dihedral : 4.012 21.940 1032 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.81 % Allowed : 17.25 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.11 % 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: -1.58 (0.27), residues: 931 helix: -0.14 (0.46), residues: 131 sheet: -1.62 (0.38), residues: 210 loop : -1.02 (0.25), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.000 TRP I 247 HIS 0.003 0.001 HIS I 528 PHE 0.024 0.001 PHE B 111 TYR 0.009 0.001 TYR A 367 ARG 0.007 0.000 ARG I 525 Details of bonding type rmsd hydrogen bonds : bond 0.03381 ( 130) hydrogen bonds : angle 4.79396 ( 342) SS BOND : bond 0.00152 ( 11) SS BOND : angle 0.92401 ( 22) covalent geometry : bond 0.00215 ( 7672) covalent geometry : angle 0.56371 (10432) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6947.39 seconds wall clock time: 118 minutes 32.57 seconds (7112.57 seconds total)