Starting phenix.real_space_refine on Thu Oct 10 11:20:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vsb_43492/10_2024/8vsb_43492.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vsb_43492/10_2024/8vsb_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vsb_43492/10_2024/8vsb_43492.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vsb_43492/10_2024/8vsb_43492.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vsb_43492/10_2024/8vsb_43492.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vsb_43492/10_2024/8vsb_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/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: 6.25, per 1000 atoms: 0.83 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: 1.86 Conformation dependent library (CDL) restraints added in 1.1 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: 0.89 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: 2.14 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: 3.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 21.780 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:11.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.930 ------------------------------------------------------------------------------- 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 7672 Z= 0.626 Angle : 0.954 9.972 10432 Z= 0.490 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 0.806 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: 1.4525 time to fit residues: 173.9751 Evaluate side-chains 86 residues out of total 867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 0.973 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 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 7672 Z= 0.211 Angle : 0.644 7.826 10432 Z= 0.320 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 *********************** 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 fitting. rotamer outliers: 20 poor density : 97 time to evaluate : 0.830 Fit side-chains REVERT: A 39 MET cc_start: 0.6476 (mmp) cc_final: 0.5609 (tmm) REVERT: A 81 GLU cc_start: 0.7238 (mp0) cc_final: 0.6813 (mp0) REVERT: B 15 LYS cc_start: 0.7671 (mttt) cc_final: 0.6323 (pttp) REVERT: B 39 MET cc_start: 0.5219 (mmt) cc_final: 0.4545 (pp-130) REVERT: B 359 ASP cc_start: 0.7756 (OUTLIER) cc_final: 0.7334 (m-30) REVERT: I 189 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.6113 (mp0) REVERT: I 494 GLU cc_start: 0.7675 (mt-10) cc_final: 0.7467 (tt0) REVERT: I 503 LEU cc_start: 0.7948 (OUTLIER) cc_final: 0.7733 (pp) outliers start: 20 outliers final: 8 residues processed: 106 average time/residue: 1.3977 time to fit residues: 156.2394 Evaluate side-chains 99 residues out of total 867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 88 time to evaluate : 0.887 ------------------------------------------------------------------------------- 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 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 47 optimal weight: 5.9990 chunk 26 optimal weight: 0.0030 chunk 71 optimal weight: 0.6980 chunk 58 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 86 optimal weight: 6.9990 chunk 93 optimal weight: 0.8980 chunk 76 optimal weight: 0.5980 chunk 85 optimal weight: 0.6980 chunk 29 optimal weight: 0.2980 chunk 69 optimal weight: 2.9990 overall best weight: 0.4590 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 7672 Z= 0.163 Angle : 0.596 7.777 10432 Z= 0.294 Chirality : 0.041 0.151 1223 Planarity : 0.004 0.054 1335 Dihedral : 4.745 27.121 1032 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.69 % Allowed : 12.91 % Favored : 85.40 % 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: -2.01 (0.26), residues: 931 helix: -0.22 (0.46), residues: 123 sheet: -1.75 (0.37), residues: 180 loop : -1.49 (0.23), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP I 247 HIS 0.006 0.001 HIS I 528 PHE 0.015 0.001 PHE B 179 TYR 0.013 0.001 TYR A 367 ARG 0.006 0.000 ARG B 302 *********************** 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 111 residues out of total 867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 97 time to evaluate : 0.833 Fit side-chains REVERT: A 39 MET cc_start: 0.6511 (mmp) cc_final: 0.5440 (tmm) REVERT: A 81 GLU cc_start: 0.7160 (mp0) cc_final: 0.6746 (mp0) REVERT: A 288 LEU cc_start: 0.7245 (tt) cc_final: 0.6810 (mp) REVERT: B 15 LYS cc_start: 0.7659 (mttt) cc_final: 0.6279 (pttp) REVERT: B 314 LYS cc_start: 0.6725 (tppt) cc_final: 0.5789 (tptp) REVERT: B 359 ASP cc_start: 0.7784 (OUTLIER) cc_final: 0.7329 (m-30) REVERT: I 189 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.5978 (mp0) REVERT: I 494 GLU cc_start: 0.7639 (mt-10) cc_final: 0.7419 (tt0) outliers start: 14 outliers final: 5 residues processed: 105 average time/residue: 1.3480 time to fit residues: 149.4135 Evaluate side-chains 91 residues out of total 867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 84 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain B residue 359 ASP 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 353 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 85 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 86 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 82 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7672 Z= 0.233 Angle : 0.626 6.686 10432 Z= 0.305 Chirality : 0.042 0.137 1223 Planarity : 0.005 0.049 1335 Dihedral : 4.708 27.506 1032 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 3.26 % Allowed : 12.18 % Favored : 84.56 % 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: -1.95 (0.26), residues: 931 helix: -0.18 (0.46), residues: 124 sheet: -1.74 (0.38), residues: 180 loop : -1.44 (0.23), residues: 627 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 0.017 0.001 PHE A 320 TYR 0.014 0.001 TYR A 316 ARG 0.007 0.001 ARG B 125 *********************** 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 111 residues out of total 867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 84 time to evaluate : 0.795 Fit side-chains REVERT: A 39 MET cc_start: 0.6492 (mmp) cc_final: 0.5367 (tmm) REVERT: A 81 GLU cc_start: 0.7241 (mp0) cc_final: 0.6799 (mp0) REVERT: A 288 LEU cc_start: 0.7239 (OUTLIER) cc_final: 0.6827 (mp) REVERT: B 15 LYS cc_start: 0.7730 (mttt) cc_final: 0.6295 (pttp) REVERT: B 39 MET cc_start: 0.5263 (mmt) cc_final: 0.4438 (pp-130) REVERT: B 314 LYS cc_start: 0.6692 (OUTLIER) cc_final: 0.5828 (tptp) REVERT: I 82 THR cc_start: 0.8628 (OUTLIER) cc_final: 0.8416 (m) REVERT: I 189 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.5897 (mp0) REVERT: I 218 GLN cc_start: 0.7700 (OUTLIER) cc_final: 0.7429 (tt0) outliers start: 27 outliers final: 10 residues processed: 99 average time/residue: 1.3018 time to fit residues: 136.0260 Evaluate side-chains 97 residues out of total 867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 82 time to evaluate : 0.917 ------------------------------------------------------------------------------- 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 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 314 LYS Chi-restraints excluded: chain I residue 82 THR 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 353 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 76 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 63 optimal weight: 0.0870 chunk 0 optimal weight: 0.6980 chunk 46 optimal weight: 0.2980 chunk 82 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 94 GLN I 152 HIS I 546 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 7672 Z= 0.161 Angle : 0.554 6.278 10432 Z= 0.275 Chirality : 0.040 0.129 1223 Planarity : 0.004 0.052 1335 Dihedral : 4.394 26.171 1032 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.38 % Allowed : 13.27 % Favored : 83.35 % 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: -1.78 (0.26), residues: 931 helix: -0.01 (0.47), residues: 124 sheet: -1.59 (0.39), residues: 180 loop : -1.35 (0.24), residues: 627 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 0.010 0.001 ARG I 525 *********************** 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 115 residues out of total 867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 87 time to evaluate : 0.854 Fit side-chains REVERT: A 39 MET cc_start: 0.6513 (mmp) cc_final: 0.5328 (tmm) REVERT: A 81 GLU cc_start: 0.7190 (mp0) cc_final: 0.6759 (mp0) REVERT: A 288 LEU cc_start: 0.7200 (OUTLIER) cc_final: 0.6803 (mp) REVERT: B 15 LYS cc_start: 0.7721 (mttt) cc_final: 0.6262 (pttp) REVERT: B 314 LYS cc_start: 0.6572 (OUTLIER) cc_final: 0.5749 (tptp) REVERT: B 359 ASP cc_start: 0.7805 (OUTLIER) cc_final: 0.7399 (m-30) REVERT: I 189 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.5816 (mp0) REVERT: I 218 GLN cc_start: 0.7714 (OUTLIER) cc_final: 0.7422 (tt0) outliers start: 28 outliers final: 10 residues processed: 106 average time/residue: 1.2118 time to fit residues: 136.0284 Evaluate side-chains 98 residues out of total 867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 83 time to evaluate : 0.853 ------------------------------------------------------------------------------- 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 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 314 LYS Chi-restraints excluded: chain B residue 359 ASP 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 Chi-restraints excluded: chain I residue 504 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 30 optimal weight: 6.9990 chunk 82 optimal weight: 0.2980 chunk 18 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 91 optimal weight: 8.9990 chunk 76 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 88 optimal weight: 0.0270 overall best weight: 0.8640 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7672 Z= 0.211 Angle : 0.597 7.735 10432 Z= 0.293 Chirality : 0.041 0.130 1223 Planarity : 0.004 0.048 1335 Dihedral : 4.394 25.984 1032 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % 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: -1.79 (0.26), residues: 931 helix: 0.05 (0.47), residues: 124 sheet: -1.57 (0.39), residues: 180 loop : -1.37 (0.23), residues: 627 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 A 320 TYR 0.011 0.001 TYR I 269 ARG 0.007 0.001 ARG B 21 *********************** 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 102 residues out of total 867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 82 time to evaluate : 0.836 Fit side-chains REVERT: A 39 MET cc_start: 0.6533 (mmp) cc_final: 0.5309 (tmm) REVERT: A 81 GLU cc_start: 0.7233 (mp0) cc_final: 0.6777 (mp0) REVERT: A 288 LEU cc_start: 0.7216 (tt) cc_final: 0.6811 (mp) REVERT: B 15 LYS cc_start: 0.7730 (mttt) cc_final: 0.6249 (pttp) REVERT: B 314 LYS cc_start: 0.6563 (tppt) cc_final: 0.5786 (tptp) REVERT: I 189 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.5795 (mp0) REVERT: I 564 ARG cc_start: 0.7504 (tpp-160) cc_final: 0.7052 (mpt180) outliers start: 20 outliers final: 12 residues processed: 97 average time/residue: 1.1972 time to fit residues: 123.2205 Evaluate side-chains 95 residues out of total 867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 82 time to evaluate : 0.868 ------------------------------------------------------------------------------- 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 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 294 VAL Chi-restraints excluded: chain I residue 147 GLU Chi-restraints excluded: chain I residue 184 VAL Chi-restraints excluded: chain I residue 189 GLU Chi-restraints excluded: chain I residue 353 THR Chi-restraints excluded: chain I residue 468 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 10 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 51 optimal weight: 0.4980 chunk 91 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 42 optimal weight: 0.0770 chunk 56 optimal weight: 0.5980 chunk 36 optimal weight: 0.5980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 152 HIS I 218 GLN I 546 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 7672 Z= 0.162 Angle : 0.555 7.530 10432 Z= 0.275 Chirality : 0.040 0.127 1223 Planarity : 0.004 0.047 1335 Dihedral : 4.205 24.462 1032 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.29 % Allowed : 15.32 % Favored : 82.39 % 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 (0.26), residues: 931 helix: 0.06 (0.48), residues: 124 sheet: -1.62 (0.38), residues: 188 loop : -1.29 (0.24), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP I 247 HIS 0.005 0.001 HIS I 528 PHE 0.026 0.001 PHE B 111 TYR 0.012 0.001 TYR A 342 ARG 0.007 0.000 ARG I 525 *********************** 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 fitting. rotamer outliers: 19 poor density : 85 time to evaluate : 0.837 Fit side-chains REVERT: A 39 MET cc_start: 0.6575 (mmp) cc_final: 0.5200 (tmm) REVERT: A 81 GLU cc_start: 0.7217 (mp0) cc_final: 0.6754 (mp0) REVERT: A 288 LEU cc_start: 0.7205 (OUTLIER) cc_final: 0.6788 (mp) REVERT: B 15 LYS cc_start: 0.7725 (mttt) cc_final: 0.6239 (pttp) REVERT: B 39 MET cc_start: 0.4300 (tpt) cc_final: 0.2079 (pp-130) REVERT: B 314 LYS cc_start: 0.6529 (tppt) cc_final: 0.5820 (tptp) REVERT: I 189 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.5707 (mp0) outliers start: 19 outliers final: 12 residues processed: 100 average time/residue: 1.1234 time to fit residues: 119.6205 Evaluate side-chains 96 residues out of total 867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 82 time to evaluate : 0.865 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 54 optimal weight: 0.2980 chunk 27 optimal weight: 7.9990 chunk 17 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 8 optimal weight: 0.3980 chunk 71 optimal weight: 0.5980 chunk 83 optimal weight: 3.9990 chunk 87 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7672 Z= 0.181 Angle : 0.579 8.902 10432 Z= 0.284 Chirality : 0.041 0.224 1223 Planarity : 0.004 0.047 1335 Dihedral : 4.200 24.409 1032 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 2.41 % Allowed : 15.08 % Favored : 82.51 % 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: 0.03 (0.47), residues: 124 sheet: -1.60 (0.38), residues: 188 loop : -1.28 (0.24), residues: 619 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 0.015 0.001 TYR A 342 ARG 0.007 0.000 ARG B 125 *********************** 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 101 residues out of total 867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 81 time to evaluate : 0.874 Fit side-chains REVERT: A 39 MET cc_start: 0.6582 (mmp) cc_final: 0.6236 (mpm) REVERT: A 81 GLU cc_start: 0.7209 (mp0) cc_final: 0.6774 (mp0) REVERT: A 288 LEU cc_start: 0.7157 (OUTLIER) cc_final: 0.6783 (mp) REVERT: B 15 LYS cc_start: 0.7720 (mttt) cc_final: 0.6234 (pttp) REVERT: B 39 MET cc_start: 0.4243 (tpt) cc_final: 0.1967 (pp-130) REVERT: B 314 LYS cc_start: 0.6437 (tppt) cc_final: 0.5717 (tptp) REVERT: B 359 ASP cc_start: 0.7778 (m-30) cc_final: 0.7354 (m-30) REVERT: I 189 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.5702 (mp0) REVERT: I 564 ARG cc_start: 0.7467 (tpp-160) cc_final: 0.7013 (mpt180) outliers start: 20 outliers final: 14 residues processed: 97 average time/residue: 1.1179 time to fit residues: 115.6488 Evaluate side-chains 96 residues out of total 867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 80 time to evaluate : 0.984 ------------------------------------------------------------------------------- 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 I residue 143 ARG Chi-restraints excluded: chain I residue 147 GLU Chi-restraints excluded: chain I residue 184 VAL Chi-restraints excluded: chain I residue 189 GLU Chi-restraints excluded: chain I residue 353 THR 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 85 optimal weight: 0.0870 chunk 87 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 overall best weight: 0.9962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 152 HIS I 218 GLN I 546 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7672 Z= 0.231 Angle : 0.625 10.734 10432 Z= 0.300 Chirality : 0.042 0.167 1223 Planarity : 0.004 0.047 1335 Dihedral : 4.412 24.760 1032 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 2.41 % Allowed : 15.44 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.79 (0.26), residues: 931 helix: -0.01 (0.48), residues: 124 sheet: -1.58 (0.39), residues: 189 loop : -1.35 (0.24), residues: 618 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 0.027 0.002 PHE B 111 TYR 0.012 0.001 TYR I 269 ARG 0.008 0.001 ARG B 125 *********************** 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 100 residues out of total 867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 80 time to evaluate : 0.849 Fit side-chains REVERT: A 39 MET cc_start: 0.6563 (mmp) cc_final: 0.6216 (mpm) REVERT: A 81 GLU cc_start: 0.7248 (mp0) cc_final: 0.6790 (mp0) REVERT: A 288 LEU cc_start: 0.7067 (OUTLIER) cc_final: 0.6672 (mp) REVERT: B 15 LYS cc_start: 0.7753 (mttt) cc_final: 0.6236 (pttp) REVERT: I 189 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.5763 (mp0) outliers start: 20 outliers final: 12 residues processed: 96 average time/residue: 1.1311 time to fit residues: 115.7247 Evaluate side-chains 92 residues out of total 867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 78 time to evaluate : 0.939 ------------------------------------------------------------------------------- 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 I residue 184 VAL Chi-restraints excluded: chain I residue 189 GLU Chi-restraints excluded: chain I residue 353 THR Chi-restraints excluded: chain I residue 377 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 42 optimal weight: 0.0070 chunk 62 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 7 optimal weight: 8.9990 chunk 58 optimal weight: 0.7980 chunk 46 optimal weight: 0.6980 chunk 59 optimal weight: 0.7980 chunk 80 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 overall best weight: 0.6600 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7672 Z= 0.183 Angle : 0.610 11.438 10432 Z= 0.294 Chirality : 0.041 0.208 1223 Planarity : 0.004 0.046 1335 Dihedral : 4.298 24.217 1032 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 1.57 % Allowed : 16.53 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.00 (0.48), residues: 124 sheet: -1.57 (0.39), residues: 186 loop : -1.30 (0.24), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP I 247 HIS 0.003 0.001 HIS I 528 PHE 0.030 0.001 PHE B 111 TYR 0.010 0.001 TYR A 367 ARG 0.006 0.000 ARG I 525 ********************** 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 92 residues out of total 867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 79 time to evaluate : 0.784 Fit side-chains REVERT: A 39 MET cc_start: 0.6549 (mmp) cc_final: 0.6219 (mpm) REVERT: A 81 GLU cc_start: 0.7198 (mp0) cc_final: 0.6714 (mp0) REVERT: A 288 LEU cc_start: 0.7123 (OUTLIER) cc_final: 0.6734 (mp) REVERT: B 15 LYS cc_start: 0.7750 (mttt) cc_final: 0.6238 (pttp) REVERT: B 314 LYS cc_start: 0.6432 (tppt) cc_final: 0.5625 (tptp) REVERT: I 189 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.5664 (mp0) REVERT: I 218 GLN cc_start: 0.7730 (OUTLIER) cc_final: 0.7233 (tt0) outliers start: 13 outliers final: 10 residues processed: 90 average time/residue: 1.0148 time to fit residues: 98.0701 Evaluate side-chains 89 residues out of total 867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 76 time to evaluate : 0.827 ------------------------------------------------------------------------------- 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 123 LEU Chi-restraints excluded: chain B residue 294 VAL 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 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 69 optimal weight: 0.0970 chunk 11 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 77 optimal weight: 0.4980 chunk 9 optimal weight: 0.9980 chunk 13 optimal weight: 0.5980 chunk 66 optimal weight: 0.9980 chunk 4 optimal weight: 0.0570 chunk 54 optimal weight: 0.3980 overall best weight: 0.3296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 152 HIS I 218 GLN I 546 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.190880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.133175 restraints weight = 8755.131| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 2.27 r_work: 0.3466 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3343 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 7672 Z= 0.147 Angle : 0.571 10.947 10432 Z= 0.275 Chirality : 0.040 0.165 1223 Planarity : 0.004 0.046 1335 Dihedral : 4.066 22.627 1032 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.81 % Allowed : 16.04 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.61 (0.27), residues: 931 helix: -0.10 (0.46), residues: 131 sheet: -1.59 (0.38), residues: 210 loop : -1.09 (0.24), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.000 TRP I 247 HIS 0.002 0.000 HIS I 528 PHE 0.017 0.001 PHE B 179 TYR 0.009 0.001 TYR I 567 ARG 0.007 0.000 ARG I 525 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3354.47 seconds wall clock time: 60 minutes 57.61 seconds (3657.61 seconds total)