Starting phenix.real_space_refine on Sun May 11 05:12:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vsb_43492/05_2025/8vsb_43492.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vsb_43492/05_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_43492/05_2025/8vsb_43492.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vsb_43492/05_2025/8vsb_43492.map" model { file = "/net/cci-nas-00/data/ceres_data/8vsb_43492/05_2025/8vsb_43492.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vsb_43492/05_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-5687/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: 5.87, per 1000 atoms: 0.78 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: 1.68 Conformation dependent library (CDL) restraints added in 1.5 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: 0.92 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: 2.01 Time building geometry restraints manager: 2.02 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: 4.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 21.260 Find NCS groups from input model: 0.060 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: 0.000 Load rotamer database and sin/cos tables:11.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.620 ------------------------------------------------------------------------------- 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 : 0.830 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: 1.3652 time to fit residues: 163.7008 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 : 0.846 ------------------------------------------------------------------------------- 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: 0.3269 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 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 : 0.901 Fit side-chains REVERT: A 39 MET cc_start: 0.6631 (mmp) cc_final: 0.4981 (tmm) REVERT: A 81 GLU cc_start: 0.7404 (mp0) cc_final: 0.6791 (mp0) REVERT: B 15 LYS cc_start: 0.6787 (mttt) cc_final: 0.5462 (pttp) REVERT: B 39 MET cc_start: 0.6128 (mmt) cc_final: 0.4604 (pp-130) REVERT: B 359 ASP cc_start: 0.7644 (OUTLIER) cc_final: 0.7062 (m-30) REVERT: B 381 MET cc_start: 0.8013 (OUTLIER) cc_final: 0.7790 (tpp) REVERT: I 189 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.6181 (mp0) REVERT: I 494 GLU cc_start: 0.8290 (mt-10) cc_final: 0.7869 (tt0) REVERT: I 503 LEU cc_start: 0.7483 (OUTLIER) cc_final: 0.7150 (pp) outliers start: 20 outliers final: 8 residues processed: 106 average time/residue: 1.3043 time to fit residues: 146.0329 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 : 0.889 ------------------------------------------------------------------------------- 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: 2.9990 chunk 64 optimal weight: 0.9980 chunk 30 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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 = 0.4181 r_free = 0.4181 target = 0.184772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.132563 restraints weight = 8917.098| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 2.55 r_work: 0.3366 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3239 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.1294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 7683 Z= 0.203 Angle : 0.717 8.144 10454 Z= 0.347 Chirality : 0.045 0.156 1223 Planarity : 0.005 0.050 1335 Dihedral : 5.202 28.859 1032 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 2.77 % Allowed : 11.94 % 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 (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: -2.29 (0.25), residues: 931 helix: -0.46 (0.46), residues: 125 sheet: -2.01 (0.36), residues: 178 loop : -1.66 (0.23), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 247 HIS 0.006 0.001 HIS I 528 PHE 0.021 0.002 PHE A 320 TYR 0.017 0.002 TYR A 316 ARG 0.006 0.001 ARG B 302 Details of bonding type rmsd hydrogen bonds : bond 0.06107 ( 130) hydrogen bonds : angle 5.76895 ( 342) SS BOND : bond 0.00294 ( 11) SS BOND : angle 1.75443 ( 22) covalent geometry : bond 0.00501 ( 7672) covalent geometry : angle 0.71357 (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 115 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 92 time to evaluate : 0.852 Fit side-chains REVERT: A 39 MET cc_start: 0.6618 (mmp) cc_final: 0.4809 (tmm) REVERT: A 81 GLU cc_start: 0.7359 (mp0) cc_final: 0.6713 (mp0) REVERT: A 288 LEU cc_start: 0.7378 (tt) cc_final: 0.6934 (mp) REVERT: A 290 GLU cc_start: 0.7242 (OUTLIER) cc_final: 0.6620 (tm-30) REVERT: B 15 LYS cc_start: 0.6812 (mttt) cc_final: 0.5426 (pttp) REVERT: B 39 MET cc_start: 0.6075 (mmt) cc_final: 0.4603 (pp-130) REVERT: B 314 LYS cc_start: 0.7504 (tppt) cc_final: 0.7155 (tptp) REVERT: I 60 GLN cc_start: 0.8497 (tp40) cc_final: 0.8063 (tt0) REVERT: I 189 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.5996 (mp0) outliers start: 23 outliers final: 12 residues processed: 102 average time/residue: 1.3296 time to fit residues: 143.0835 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 : 0.869 ------------------------------------------------------------------------------- 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 290 GLU 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: 0.9990 chunk 28 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 64 optimal weight: 0.6980 chunk 88 optimal weight: 0.5980 chunk 4 optimal weight: 0.6980 chunk 48 optimal weight: 3.9990 chunk 90 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.4206 r_free = 0.4206 target = 0.187287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.131782 restraints weight = 8869.927| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 2.61 r_work: 0.3395 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.1569 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= 0.121 Angle : 0.599 7.986 10454 Z= 0.296 Chirality : 0.042 0.172 1223 Planarity : 0.004 0.049 1335 Dihedral : 4.747 27.442 1032 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 3.62 % Allowed : 12.06 % Favored : 84.32 % 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: -1.99 (0.26), residues: 931 helix: -0.13 (0.47), residues: 123 sheet: -1.75 (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 0.014 0.001 PHE A 320 TYR 0.012 0.001 TYR A 367 ARG 0.007 0.001 ARG B 21 Details of bonding type rmsd hydrogen bonds : bond 0.04594 ( 130) hydrogen bonds : angle 5.45430 ( 342) SS BOND : bond 0.00163 ( 11) SS BOND : angle 1.18787 ( 22) covalent geometry : bond 0.00288 ( 7672) covalent geometry : angle 0.59752 (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 121 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 91 time to evaluate : 0.875 Fit side-chains REVERT: A 39 MET cc_start: 0.6567 (mmp) cc_final: 0.4696 (tmm) REVERT: A 81 GLU cc_start: 0.7368 (mp0) cc_final: 0.6694 (mp0) REVERT: A 288 LEU cc_start: 0.7336 (OUTLIER) cc_final: 0.6892 (mp) REVERT: A 290 GLU cc_start: 0.7267 (mm-30) cc_final: 0.6603 (tm-30) REVERT: B 15 LYS cc_start: 0.6782 (mttt) cc_final: 0.5399 (pttp) REVERT: B 39 MET cc_start: 0.6019 (mmt) cc_final: 0.5424 (tpt) REVERT: B 295 ARG cc_start: 0.6173 (OUTLIER) cc_final: 0.4766 (mtt-85) REVERT: B 309 TRP cc_start: 0.6950 (p-90) cc_final: 0.6582 (p-90) REVERT: B 359 ASP cc_start: 0.7611 (OUTLIER) cc_final: 0.7044 (m-30) REVERT: I 60 GLN cc_start: 0.8430 (OUTLIER) cc_final: 0.7985 (tt0) REVERT: I 189 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.5874 (mp0) REVERT: I 218 GLN cc_start: 0.8194 (OUTLIER) cc_final: 0.7848 (tt0) outliers start: 30 outliers final: 10 residues processed: 109 average time/residue: 1.2859 time to fit residues: 148.0483 Evaluate side-chains 101 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 85 time to evaluate : 0.891 ------------------------------------------------------------------------------- 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 294 VAL Chi-restraints excluded: chain B residue 4 CYS Chi-restraints excluded: chain B residue 295 ARG 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: 0.7980 chunk 62 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 55 optimal weight: 0.3980 chunk 68 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 7 optimal weight: 8.9990 chunk 81 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.4209 r_free = 0.4209 target = 0.187672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.129704 restraints weight = 8790.362| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 2.28 r_work: 0.3419 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3296 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7683 Z= 0.118 Angle : 0.586 8.090 10454 Z= 0.288 Chirality : 0.041 0.129 1223 Planarity : 0.004 0.047 1335 Dihedral : 4.532 27.355 1032 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 3.26 % Allowed : 13.15 % Favored : 83.59 % 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: -1.86 (0.26), residues: 931 helix: 0.02 (0.47), residues: 123 sheet: -1.69 (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 0.015 0.001 PHE B 124 TYR 0.010 0.001 TYR A 367 ARG 0.016 0.001 ARG I 525 Details of bonding type rmsd hydrogen bonds : bond 0.04411 ( 130) hydrogen bonds : angle 5.30250 ( 342) SS BOND : bond 0.00158 ( 11) SS BOND : angle 1.09838 ( 22) covalent geometry : bond 0.00286 ( 7672) covalent geometry : angle 0.58397 (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 112 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 85 time to evaluate : 0.980 Fit side-chains REVERT: A 39 MET cc_start: 0.6586 (mmp) cc_final: 0.4675 (tmm) REVERT: A 81 GLU cc_start: 0.7350 (mp0) cc_final: 0.6679 (mp0) REVERT: A 288 LEU cc_start: 0.7270 (tt) cc_final: 0.6825 (mp) REVERT: A 290 GLU cc_start: 0.7284 (mm-30) cc_final: 0.6602 (tm-30) REVERT: A 342 TYR cc_start: 0.4611 (m-80) cc_final: 0.4236 (m-10) REVERT: A 361 GLU cc_start: 0.8509 (mt-10) cc_final: 0.8188 (mp0) REVERT: B 15 LYS cc_start: 0.6752 (mttt) cc_final: 0.5354 (pttp) REVERT: B 39 MET cc_start: 0.5991 (mmt) cc_final: 0.5482 (tpt) REVERT: B 309 TRP cc_start: 0.6912 (p-90) cc_final: 0.6537 (p-90) REVERT: B 314 LYS cc_start: 0.7336 (tppt) cc_final: 0.6236 (tptp) REVERT: B 359 ASP cc_start: 0.7626 (OUTLIER) cc_final: 0.7045 (m-30) REVERT: I 60 GLN cc_start: 0.8507 (OUTLIER) cc_final: 0.8093 (tt0) REVERT: I 189 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.5750 (mp0) REVERT: I 218 GLN cc_start: 0.8219 (OUTLIER) cc_final: 0.7835 (tt0) REVERT: I 268 ILE cc_start: 0.8737 (OUTLIER) cc_final: 0.8332 (pt) REVERT: I 525 ARG cc_start: 0.7534 (tmm-80) cc_final: 0.7279 (ttp80) REVERT: I 564 ARG cc_start: 0.8067 (tpp-160) cc_final: 0.7351 (mpt180) outliers start: 27 outliers final: 10 residues processed: 103 average time/residue: 1.1246 time to fit residues: 123.2914 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 : 0.859 ------------------------------------------------------------------------------- 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 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 93 optimal weight: 8.9990 chunk 15 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 46 optimal weight: 0.8980 chunk 32 optimal weight: 0.0060 chunk 45 optimal weight: 3.9990 chunk 16 optimal weight: 0.1980 chunk 20 optimal weight: 0.8980 chunk 26 optimal weight: 0.0870 chunk 65 optimal weight: 1.9990 overall best weight: 0.4174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 GLN I 94 GLN I 152 HIS I 546 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.189731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.136817 restraints weight = 8852.596| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 2.42 r_work: 0.3449 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3325 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.1984 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= 0.096 Angle : 0.545 8.881 10454 Z= 0.272 Chirality : 0.040 0.127 1223 Planarity : 0.004 0.047 1335 Dihedral : 4.165 24.843 1032 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.41 % Allowed : 14.84 % 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 (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: -1.70 (0.27), residues: 931 helix: 0.23 (0.48), residues: 124 sheet: -1.77 (0.38), residues: 184 loop : -1.24 (0.24), residues: 623 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 B 124 TYR 0.009 0.001 TYR A 367 ARG 0.006 0.000 ARG I 525 Details of bonding type rmsd hydrogen bonds : bond 0.03625 ( 130) hydrogen bonds : angle 5.05080 ( 342) SS BOND : bond 0.00137 ( 11) SS BOND : angle 0.91906 ( 22) covalent geometry : bond 0.00225 ( 7672) covalent geometry : angle 0.54437 (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 109 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 89 time to evaluate : 0.830 Fit side-chains REVERT: A 39 MET cc_start: 0.6679 (mmp) cc_final: 0.4581 (tmm) REVERT: A 52 SER cc_start: 0.8537 (OUTLIER) cc_final: 0.8317 (p) REVERT: A 81 GLU cc_start: 0.7421 (mp0) cc_final: 0.6689 (mp0) REVERT: A 288 LEU cc_start: 0.7146 (OUTLIER) cc_final: 0.6751 (mp) REVERT: A 290 GLU cc_start: 0.7297 (mm-30) cc_final: 0.6592 (tm-30) REVERT: A 361 GLU cc_start: 0.8524 (mt-10) cc_final: 0.8278 (mp0) REVERT: B 15 LYS cc_start: 0.6747 (mttt) cc_final: 0.5348 (pttp) REVERT: B 39 MET cc_start: 0.5920 (mmt) cc_final: 0.5428 (tpt) REVERT: B 309 TRP cc_start: 0.6892 (p-90) cc_final: 0.6472 (p-90) REVERT: B 314 LYS cc_start: 0.7164 (tppt) cc_final: 0.6251 (tptp) REVERT: B 359 ASP cc_start: 0.7665 (OUTLIER) cc_final: 0.7075 (m-30) REVERT: I 60 GLN cc_start: 0.8422 (OUTLIER) cc_final: 0.7983 (tt0) REVERT: I 268 ILE cc_start: 0.8712 (OUTLIER) cc_final: 0.8348 (pt) REVERT: I 452 ASP cc_start: 0.8062 (t0) cc_final: 0.7783 (t0) REVERT: I 564 ARG cc_start: 0.8061 (tpp-160) cc_final: 0.7371 (mpt180) outliers start: 20 outliers final: 7 residues processed: 101 average time/residue: 1.1630 time to fit residues: 124.7288 Evaluate side-chains 99 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 87 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 SER 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 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 503 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 67 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 93 optimal weight: 5.9990 chunk 7 optimal weight: 10.0000 chunk 25 optimal weight: 0.9980 chunk 74 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 chunk 26 optimal weight: 0.0870 chunk 76 optimal weight: 0.0020 chunk 42 optimal weight: 6.9990 chunk 63 optimal weight: 0.9980 overall best weight: 0.5166 ------------------------------------------------------------------------------- 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 I 152 HIS I 218 GLN I 546 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.189553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.136876 restraints weight = 8755.101| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 2.25 r_work: 0.3434 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3313 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.2046 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= 0.100 Angle : 0.553 8.889 10454 Z= 0.271 Chirality : 0.040 0.129 1223 Planarity : 0.004 0.048 1335 Dihedral : 4.110 24.338 1032 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 2.53 % Allowed : 14.84 % Favored : 82.63 % 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: -1.72 (0.27), residues: 931 helix: -0.05 (0.46), residues: 131 sheet: -1.61 (0.38), residues: 188 loop : -1.26 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP I 247 HIS 0.006 0.001 HIS I 528 PHE 0.012 0.001 PHE B 124 TYR 0.009 0.001 TYR A 367 ARG 0.008 0.000 ARG I 525 Details of bonding type rmsd hydrogen bonds : bond 0.03736 ( 130) hydrogen bonds : angle 5.00253 ( 342) SS BOND : bond 0.00128 ( 11) SS BOND : angle 0.91309 ( 22) covalent geometry : bond 0.00239 ( 7672) covalent geometry : angle 0.55240 (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 104 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 83 time to evaluate : 0.900 Fit side-chains REVERT: A 39 MET cc_start: 0.6655 (mmp) cc_final: 0.5984 (mpm) REVERT: A 81 GLU cc_start: 0.7393 (mp0) cc_final: 0.6695 (mp0) REVERT: A 288 LEU cc_start: 0.7071 (OUTLIER) cc_final: 0.6691 (mp) REVERT: A 290 GLU cc_start: 0.7268 (mm-30) cc_final: 0.6510 (tm-30) REVERT: B 15 LYS cc_start: 0.6792 (mttt) cc_final: 0.5375 (pttp) REVERT: B 39 MET cc_start: 0.5864 (mmt) cc_final: 0.5374 (tpt) REVERT: B 309 TRP cc_start: 0.6906 (p-90) cc_final: 0.6497 (p-90) REVERT: B 314 LYS cc_start: 0.7073 (tppt) cc_final: 0.6229 (tptp) REVERT: B 359 ASP cc_start: 0.7682 (OUTLIER) cc_final: 0.7105 (m-30) REVERT: I 60 GLN cc_start: 0.8493 (OUTLIER) cc_final: 0.8058 (tt0) REVERT: I 189 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.5890 (mp0) REVERT: I 268 ILE cc_start: 0.8741 (OUTLIER) cc_final: 0.8382 (pt) REVERT: I 564 ARG cc_start: 0.8066 (tpp-160) cc_final: 0.7391 (mpt180) outliers start: 21 outliers final: 14 residues processed: 98 average time/residue: 1.0893 time to fit residues: 113.8435 Evaluate side-chains 100 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 81 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 258 MET 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 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 143 ARG 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 76 optimal weight: 0.9990 chunk 75 optimal weight: 0.8980 chunk 18 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 93 optimal weight: 5.9990 chunk 68 optimal weight: 0.8980 chunk 17 optimal weight: 0.2980 chunk 32 optimal weight: 0.9980 chunk 89 optimal weight: 0.7980 chunk 40 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 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 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 = 0.4225 r_free = 0.4225 target = 0.189077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.136378 restraints weight = 8906.541| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 2.40 r_work: 0.3434 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3311 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3311 ------------------------------------------------------------------------------- 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 : 0.003 0.034 7683 Z= 0.119 Angle : 0.574 8.269 10454 Z= 0.280 Chirality : 0.041 0.168 1223 Planarity : 0.004 0.047 1335 Dihedral : 4.182 23.998 1032 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 2.77 % Allowed : 15.68 % 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: -1.70 (0.27), residues: 931 helix: 0.05 (0.48), residues: 124 sheet: -1.62 (0.38), residues: 188 loop : -1.24 (0.24), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 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 A 367 ARG 0.006 0.000 ARG I 525 Details of bonding type rmsd hydrogen bonds : bond 0.04098 ( 130) hydrogen bonds : angle 4.98909 ( 342) SS BOND : bond 0.00149 ( 11) SS BOND : angle 0.94056 ( 22) covalent geometry : bond 0.00288 ( 7672) covalent geometry : angle 0.57256 (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: 23 poor density : 81 time to evaluate : 0.884 Fit side-chains REVERT: A 39 MET cc_start: 0.6653 (mmp) cc_final: 0.5973 (mpm) REVERT: A 81 GLU cc_start: 0.7391 (mp0) cc_final: 0.6651 (mp0) REVERT: A 288 LEU cc_start: 0.7078 (OUTLIER) cc_final: 0.6806 (mp) REVERT: B 15 LYS cc_start: 0.6786 (mttt) cc_final: 0.5367 (pttp) REVERT: B 39 MET cc_start: 0.5847 (mmt) cc_final: 0.5409 (tpt) REVERT: B 309 TRP cc_start: 0.6911 (p-90) cc_final: 0.6516 (p-90) REVERT: B 314 LYS cc_start: 0.7047 (tppt) cc_final: 0.6243 (tptp) REVERT: B 359 ASP cc_start: 0.7673 (OUTLIER) cc_final: 0.7108 (m-30) REVERT: I 60 GLN cc_start: 0.8464 (OUTLIER) cc_final: 0.8033 (tt0) REVERT: I 189 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.5797 (mp0) REVERT: I 268 ILE cc_start: 0.8739 (OUTLIER) cc_final: 0.8354 (pt) REVERT: I 564 ARG cc_start: 0.8063 (tpp-160) cc_final: 0.7392 (mpt180) outliers start: 23 outliers final: 13 residues processed: 98 average time/residue: 1.0881 time to fit residues: 113.7934 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 : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 258 MET 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 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 143 ARG Chi-restraints excluded: chain I residue 184 VAL 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 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: 0.9990 chunk 77 optimal weight: 2.9990 chunk 74 optimal weight: 0.0770 chunk 75 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 chunk 22 optimal weight: 7.9990 chunk 85 optimal weight: 0.9980 chunk 7 optimal weight: 10.0000 chunk 66 optimal weight: 0.9980 chunk 6 optimal weight: 4.9990 chunk 19 optimal weight: 0.8980 overall best weight: 0.7338 ------------------------------------------------------------------------------- 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 = 0.4223 r_free = 0.4223 target = 0.188948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.134711 restraints weight = 8937.646| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 2.54 r_work: 0.3409 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3284 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.2104 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= 0.117 Angle : 0.583 12.376 10454 Z= 0.283 Chirality : 0.041 0.129 1223 Planarity : 0.004 0.047 1335 Dihedral : 4.234 23.949 1032 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 2.41 % Allowed : 15.80 % 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 (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: -1.70 (0.27), residues: 931 helix: 0.01 (0.48), residues: 124 sheet: -1.61 (0.39), residues: 186 loop : -1.24 (0.24), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP I 247 HIS 0.004 0.001 HIS I 528 PHE 0.015 0.001 PHE B 179 TYR 0.010 0.001 TYR A 367 ARG 0.007 0.000 ARG I 525 Details of bonding type rmsd hydrogen bonds : bond 0.04120 ( 130) hydrogen bonds : angle 4.92894 ( 342) SS BOND : bond 0.00148 ( 11) SS BOND : angle 0.94298 ( 22) covalent geometry : bond 0.00282 ( 7672) covalent geometry : angle 0.58194 (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 99 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 79 time to evaluate : 0.945 Fit side-chains REVERT: A 39 MET cc_start: 0.6619 (mmp) cc_final: 0.5928 (mpm) REVERT: A 81 GLU cc_start: 0.7405 (mp0) cc_final: 0.6720 (mp0) REVERT: A 288 LEU cc_start: 0.7064 (OUTLIER) cc_final: 0.6803 (mp) REVERT: B 15 LYS cc_start: 0.6806 (mttt) cc_final: 0.5392 (pttp) REVERT: B 39 MET cc_start: 0.5832 (mmt) cc_final: 0.5405 (tpt) REVERT: B 309 TRP cc_start: 0.6932 (p-90) cc_final: 0.6541 (p-90) REVERT: B 314 LYS cc_start: 0.6973 (tppt) cc_final: 0.6225 (tptp) REVERT: B 359 ASP cc_start: 0.7689 (OUTLIER) cc_final: 0.7128 (m-30) REVERT: I 60 GLN cc_start: 0.8488 (OUTLIER) cc_final: 0.8052 (tt0) REVERT: I 189 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.5772 (mp0) REVERT: I 268 ILE cc_start: 0.8747 (OUTLIER) cc_final: 0.8350 (pt) REVERT: I 564 ARG cc_start: 0.8063 (tpp-160) cc_final: 0.7377 (mpt180) outliers start: 20 outliers final: 13 residues processed: 93 average time/residue: 1.0793 time to fit residues: 107.5029 Evaluate side-chains 96 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 78 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 258 MET 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 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 143 ARG Chi-restraints excluded: chain I residue 184 VAL 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 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: 0.0670 chunk 73 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 33 optimal weight: 0.0870 chunk 20 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 41 optimal weight: 0.5980 chunk 49 optimal weight: 0.0070 chunk 21 optimal weight: 0.0010 overall best weight: 0.1520 ------------------------------------------------------------------------------- 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 I 546 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.192173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.138697 restraints weight = 8841.471| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 2.51 r_work: 0.3490 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3365 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.2399 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= 0.087 Angle : 0.551 12.196 10454 Z= 0.266 Chirality : 0.039 0.165 1223 Planarity : 0.004 0.046 1335 Dihedral : 3.923 21.268 1032 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.05 % Allowed : 16.41 % 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: -1.55 (0.27), residues: 931 helix: -0.06 (0.47), residues: 131 sheet: -1.57 (0.38), residues: 211 loop : -1.02 (0.25), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP I 247 HIS 0.003 0.000 HIS I 528 PHE 0.025 0.001 PHE B 111 TYR 0.008 0.001 TYR A 367 ARG 0.010 0.000 ARG B 125 Details of bonding type rmsd hydrogen bonds : bond 0.03022 ( 130) hydrogen bonds : angle 4.66646 ( 342) SS BOND : bond 0.00125 ( 11) SS BOND : angle 0.94485 ( 22) covalent geometry : bond 0.00196 ( 7672) covalent geometry : angle 0.54954 (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: 17 poor density : 84 time to evaluate : 0.834 Fit side-chains REVERT: A 39 MET cc_start: 0.6579 (mmp) cc_final: 0.5719 (mpm) REVERT: A 81 GLU cc_start: 0.7263 (mp0) cc_final: 0.6543 (mp0) REVERT: A 288 LEU cc_start: 0.6946 (OUTLIER) cc_final: 0.6696 (mp) REVERT: A 302 ARG cc_start: 0.8001 (mtp85) cc_final: 0.7765 (mtp180) REVERT: B 15 LYS cc_start: 0.6712 (mttt) cc_final: 0.5348 (pttp) REVERT: B 39 MET cc_start: 0.5768 (mmt) cc_final: 0.5285 (tpt) REVERT: B 309 TRP cc_start: 0.6844 (p-90) cc_final: 0.6443 (p-90) REVERT: B 359 ASP cc_start: 0.7685 (OUTLIER) cc_final: 0.7137 (m-30) REVERT: I 28 MET cc_start: 0.7901 (mpt) cc_final: 0.7540 (mpt) REVERT: I 60 GLN cc_start: 0.8383 (OUTLIER) cc_final: 0.7926 (tt0) REVERT: I 268 ILE cc_start: 0.8661 (OUTLIER) cc_final: 0.8312 (pt) REVERT: I 452 ASP cc_start: 0.8044 (t0) cc_final: 0.7756 (t0) REVERT: I 546 ASN cc_start: 0.7751 (m-40) cc_final: 0.6978 (m-40) outliers start: 17 outliers final: 9 residues processed: 96 average time/residue: 0.9245 time to fit residues: 95.5313 Evaluate side-chains 91 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 78 time to evaluate : 0.862 ------------------------------------------------------------------------------- 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 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 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: 2.9990 chunk 52 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 42 optimal weight: 0.0670 chunk 65 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 35 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 72 optimal weight: 0.0980 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 152 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.190999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.133008 restraints weight = 8809.699| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 2.28 r_work: 0.3462 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3335 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7683 Z= 0.099 Angle : 0.578 12.772 10454 Z= 0.273 Chirality : 0.040 0.207 1223 Planarity : 0.004 0.047 1335 Dihedral : 3.961 21.814 1032 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.81 % Allowed : 17.01 % 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 (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: -1.51 (0.27), residues: 931 helix: -0.02 (0.47), residues: 131 sheet: -1.47 (0.38), residues: 206 loop : -1.05 (0.24), residues: 594 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 0.014 0.001 PHE B 179 TYR 0.010 0.001 TYR I 567 ARG 0.007 0.000 ARG B 125 Details of bonding type rmsd hydrogen bonds : bond 0.03484 ( 130) hydrogen bonds : angle 4.67914 ( 342) SS BOND : bond 0.00127 ( 11) SS BOND : angle 0.88517 ( 22) covalent geometry : bond 0.00239 ( 7672) covalent geometry : angle 0.57729 (10432) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6755.23 seconds wall clock time: 116 minutes 48.28 seconds (7008.28 seconds total)