Starting phenix.real_space_refine on Sun Mar 10 17:03:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f63_31471/03_2024/7f63_31471.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f63_31471/03_2024/7f63_31471.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f63_31471/03_2024/7f63_31471.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f63_31471/03_2024/7f63_31471.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f63_31471/03_2024/7f63_31471.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f63_31471/03_2024/7f63_31471.pdb" } resolution = 3.9 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= 0.031 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 15 5.16 5 C 2149 2.51 5 N 555 2.21 5 O 656 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 3375 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1578 Classifications: {'peptide': 199} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 187} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "H" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 945 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "L" Number of atoms: 852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 852 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 4, 'TRANS': 105} Time building chain proxies: 2.36, per 1000 atoms: 0.70 Number of scatterers: 3375 At special positions: 0 Unit cell: (67.1, 80.3, 115.5, 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 15 16.00 O 656 8.00 N 555 7.00 C 2149 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 1.30 Conformation dependent library (CDL) restraints added in 553.8 milliseconds 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 790 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 7 sheets defined 8.6% alpha, 23.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 337 through 342 removed outlier: 4.402A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 371 removed outlier: 4.479A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N SER A 371 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.599A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 410 removed outlier: 3.721A pdb=" N GLU A 406 " --> pdb=" O ARG A 403 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 439 through 442 Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 removed outlier: 5.006A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 453 through 454 Processing sheet with id=AA3, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 6 removed outlier: 4.127A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N SER H 25 " --> pdb=" O GLN H 3 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS H 23 " --> pdb=" O GLN H 5 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.760A pdb=" N LYS H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N TRP H 47 " --> pdb=" O LYS H 38 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.750A pdb=" N ALA L 34 " --> pdb=" O GLN L 89 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N VAL L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N TYR L 49 " --> pdb=" O VAL L 33 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 19 through 22 removed outlier: 4.198A pdb=" N VAL L 19 " --> pdb=" O ILE L 75 " (cutoff:3.500A) 82 hydrogen bonds defined for protein. 192 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.85 Time building geometry restraints manager: 1.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1061 1.34 - 1.46: 912 1.46 - 1.58: 1472 1.58 - 1.70: 0 1.70 - 1.82: 18 Bond restraints: 3463 Sorted by residual: bond pdb=" C ALA A 520 " pdb=" N PRO A 521 " ideal model delta sigma weight residual 1.334 1.356 -0.022 2.34e-02 1.83e+03 9.23e-01 bond pdb=" CA ASN A 394 " pdb=" CB ASN A 394 " ideal model delta sigma weight residual 1.527 1.542 -0.015 1.61e-02 3.86e+03 8.66e-01 bond pdb=" CB CYS A 379 " pdb=" SG CYS A 379 " ideal model delta sigma weight residual 1.808 1.779 0.029 3.30e-02 9.18e+02 7.56e-01 bond pdb=" N ASN A 394 " pdb=" CA ASN A 394 " ideal model delta sigma weight residual 1.460 1.472 -0.012 1.42e-02 4.96e+03 7.05e-01 bond pdb=" CA ILE L 75 " pdb=" C ILE L 75 " ideal model delta sigma weight residual 1.523 1.532 -0.009 1.16e-02 7.43e+03 6.11e-01 ... (remaining 3458 not shown) Histogram of bond angle deviations from ideal: 100.62 - 107.30: 102 107.30 - 113.97: 1831 113.97 - 120.65: 1320 120.65 - 127.33: 1418 127.33 - 134.01: 33 Bond angle restraints: 4704 Sorted by residual: angle pdb=" C LEU H 70 " pdb=" N THR H 71 " pdb=" CA THR H 71 " ideal model delta sigma weight residual 121.75 117.03 4.72 1.73e+00 3.34e-01 7.43e+00 angle pdb=" C TYR H 80 " pdb=" N MET H 81 " pdb=" CA MET H 81 " ideal model delta sigma weight residual 122.65 126.43 -3.78 1.49e+00 4.50e-01 6.45e+00 angle pdb=" C THR A 393 " pdb=" N ASN A 394 " pdb=" CA ASN A 394 " ideal model delta sigma weight residual 122.82 126.21 -3.39 1.42e+00 4.96e-01 5.72e+00 angle pdb=" CA LEU H 70 " pdb=" CB LEU H 70 " pdb=" CG LEU H 70 " ideal model delta sigma weight residual 116.30 124.61 -8.31 3.50e+00 8.16e-02 5.64e+00 angle pdb=" C ASN A 331 " pdb=" N ILE A 332 " pdb=" CA ILE A 332 " ideal model delta sigma weight residual 121.97 125.97 -4.00 1.80e+00 3.09e-01 4.94e+00 ... (remaining 4699 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.04: 1824 16.04 - 32.08: 153 32.08 - 48.12: 47 48.12 - 64.15: 8 64.15 - 80.19: 4 Dihedral angle restraints: 2036 sinusoidal: 788 harmonic: 1248 Sorted by residual: dihedral pdb=" CB CYS A 336 " pdb=" SG CYS A 336 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual 93.00 12.81 80.19 1 1.00e+01 1.00e-02 7.96e+01 dihedral pdb=" CB CYS A 480 " pdb=" SG CYS A 480 " pdb=" SG CYS A 488 " pdb=" CB CYS A 488 " ideal model delta sinusoidal sigma weight residual 93.00 154.13 -61.13 1 1.00e+01 1.00e-02 4.96e+01 dihedral pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " pdb=" SG CYS A 525 " pdb=" CB CYS A 525 " ideal model delta sinusoidal sigma weight residual -86.00 -46.16 -39.84 1 1.00e+01 1.00e-02 2.23e+01 ... (remaining 2033 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 304 0.032 - 0.064: 132 0.064 - 0.096: 37 0.096 - 0.128: 23 0.128 - 0.160: 5 Chirality restraints: 501 Sorted by residual: chirality pdb=" CB ILE A 332 " pdb=" CA ILE A 332 " pdb=" CG1 ILE A 332 " pdb=" CG2 ILE A 332 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.41e-01 chirality pdb=" CG LEU H 70 " pdb=" CB LEU H 70 " pdb=" CD1 LEU H 70 " pdb=" CD2 LEU H 70 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.13 2.00e-01 2.50e+01 4.53e-01 chirality pdb=" CA ASN A 394 " pdb=" N ASN A 394 " pdb=" C ASN A 394 " pdb=" CB ASN A 394 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.39e-01 ... (remaining 498 not shown) Planarity restraints: 605 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE H 64 " 0.014 2.00e-02 2.50e+03 2.31e-02 9.32e+00 pdb=" CG PHE H 64 " -0.052 2.00e-02 2.50e+03 pdb=" CD1 PHE H 64 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 PHE H 64 " 0.022 2.00e-02 2.50e+03 pdb=" CE1 PHE H 64 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE H 64 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE H 64 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS A 336 " -0.031 5.00e-02 4.00e+02 4.68e-02 3.50e+00 pdb=" N PRO A 337 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 337 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 337 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE H 29 " 0.006 2.00e-02 2.50e+03 8.93e-03 1.40e+00 pdb=" CG PHE H 29 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 PHE H 29 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE H 29 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE H 29 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE H 29 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE H 29 " -0.000 2.00e-02 2.50e+03 ... (remaining 602 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 92 2.69 - 3.24: 3188 3.24 - 3.79: 5100 3.79 - 4.35: 6634 4.35 - 4.90: 10708 Nonbonded interactions: 25722 Sorted by model distance: nonbonded pdb=" O HIS L 61 " pdb=" OG SER L 76 " model vdw 2.136 2.440 nonbonded pdb=" O ALA H 106 " pdb=" OH TYR L 36 " model vdw 2.141 2.440 nonbonded pdb=" OG1 THR H 28 " pdb=" OE2 GLU H 31 " model vdw 2.170 2.440 nonbonded pdb=" O CYS H 22 " pdb=" OG1 THR H 78 " model vdw 2.290 2.440 nonbonded pdb=" NH2 ARG A 346 " pdb=" OH TYR A 451 " model vdw 2.330 2.520 ... (remaining 25717 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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 group one per residue 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: 2.630 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: 11.580 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 14.270 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6102 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 : 0.002 0.029 3463 Z= 0.130 Angle : 0.575 8.312 4704 Z= 0.299 Chirality : 0.044 0.160 501 Planarity : 0.004 0.047 605 Dihedral : 13.336 74.505 1228 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.31 % Favored : 91.45 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.31 (0.39), residues: 421 helix: -3.88 (0.95), residues: 12 sheet: 0.31 (0.48), residues: 132 loop : -2.56 (0.33), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 36 HIS 0.000 0.000 HIS A 519 PHE 0.052 0.002 PHE H 64 TYR 0.016 0.001 TYR L 49 ARG 0.002 0.000 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 405 ASP cc_start: 0.7649 (m-30) cc_final: 0.6909 (m-30) REVERT: A 406 GLU cc_start: 0.8120 (mp0) cc_final: 0.7712 (mp0) REVERT: H 101 TYR cc_start: 0.6569 (t80) cc_final: 0.6301 (t80) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.2163 time to fit residues: 29.0376 Evaluate side-chains 67 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 10 optimal weight: 0.6980 chunk 21 optimal weight: 7.9990 chunk 32 optimal weight: 0.5980 chunk 12 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 38 optimal weight: 0.0970 chunk 11 optimal weight: 0.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 ASN A 487 ASN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6658 moved from start: 0.4633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3463 Z= 0.280 Angle : 0.787 10.142 4704 Z= 0.412 Chirality : 0.049 0.206 501 Planarity : 0.005 0.043 605 Dihedral : 5.593 27.827 472 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 17.61 Ramachandran Plot: Outliers : 0.48 % Allowed : 11.88 % Favored : 87.65 % Rotamer: Outliers : 3.50 % Allowed : 14.82 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.42 (0.39), residues: 421 helix: -3.20 (0.95), residues: 20 sheet: 0.35 (0.49), residues: 129 loop : -2.67 (0.33), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP L 35 HIS 0.001 0.000 HIS A 519 PHE 0.019 0.002 PHE H 29 TYR 0.018 0.002 TYR H 103 ARG 0.007 0.001 ARG L 54 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 74 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 406 GLU cc_start: 0.7927 (mp0) cc_final: 0.7703 (mp0) REVERT: A 417 LYS cc_start: 0.8625 (tppt) cc_final: 0.8228 (tppt) REVERT: A 484 GLU cc_start: 0.7311 (mt-10) cc_final: 0.6994 (mt-10) REVERT: A 493 GLN cc_start: 0.6866 (mp10) cc_final: 0.6223 (mp10) REVERT: H 57 ASP cc_start: 0.8598 (t0) cc_final: 0.8073 (t0) REVERT: L 83 LEU cc_start: 0.6858 (tt) cc_final: 0.6437 (pp) outliers start: 13 outliers final: 7 residues processed: 83 average time/residue: 0.1920 time to fit residues: 18.7287 Evaluate side-chains 62 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 55 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 99 ASP Chi-restraints excluded: chain L residue 32 ASN Chi-restraints excluded: chain L residue 93 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 4.9990 chunk 25 optimal weight: 0.2980 chunk 10 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 37 optimal weight: 0.4980 chunk 13 optimal weight: 7.9990 chunk 30 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 19 optimal weight: 8.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6670 moved from start: 0.5132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3463 Z= 0.187 Angle : 0.689 14.989 4704 Z= 0.353 Chirality : 0.046 0.210 501 Planarity : 0.004 0.034 605 Dihedral : 5.147 18.212 472 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 16.09 Ramachandran Plot: Outliers : 0.48 % Allowed : 9.74 % Favored : 89.79 % Rotamer: Outliers : 2.43 % Allowed : 19.68 % Favored : 77.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.45 (0.39), residues: 421 helix: -3.17 (0.99), residues: 20 sheet: 0.17 (0.48), residues: 131 loop : -2.63 (0.34), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 36 HIS 0.003 0.001 HIS L 61 PHE 0.016 0.001 PHE H 29 TYR 0.008 0.001 TYR H 103 ARG 0.005 0.001 ARG L 54 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 69 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 356 LYS cc_start: 0.8621 (tppt) cc_final: 0.8418 (tppt) REVERT: A 484 GLU cc_start: 0.7159 (mt-10) cc_final: 0.6796 (mt-10) REVERT: A 493 GLN cc_start: 0.6905 (mp10) cc_final: 0.6311 (mp10) REVERT: H 57 ASP cc_start: 0.8772 (t0) cc_final: 0.8248 (t0) REVERT: L 55 TYR cc_start: 0.2447 (OUTLIER) cc_final: 0.1914 (m-10) REVERT: L 83 LEU cc_start: 0.7156 (tt) cc_final: 0.6593 (pp) REVERT: L 85 GLU cc_start: 0.6785 (tp30) cc_final: 0.6436 (tm-30) outliers start: 9 outliers final: 5 residues processed: 76 average time/residue: 0.1604 time to fit residues: 14.8806 Evaluate side-chains 60 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 54 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 55 TYR Chi-restraints excluded: chain L residue 93 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 5.9990 chunk 18 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 20 optimal weight: 0.0670 chunk 36 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 overall best weight: 1.4124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 GLN ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 61 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6808 moved from start: 0.6379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3463 Z= 0.283 Angle : 0.753 12.179 4704 Z= 0.402 Chirality : 0.049 0.215 501 Planarity : 0.006 0.077 605 Dihedral : 6.007 21.455 472 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 18.67 Ramachandran Plot: Outliers : 0.48 % Allowed : 14.25 % Favored : 85.27 % Rotamer: Outliers : 5.12 % Allowed : 19.68 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.80 (0.38), residues: 421 helix: -3.33 (0.69), residues: 26 sheet: -0.02 (0.48), residues: 131 loop : -2.88 (0.33), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP H 36 HIS 0.001 0.001 HIS L 61 PHE 0.012 0.002 PHE H 29 TYR 0.020 0.002 TYR L 55 ARG 0.005 0.001 ARG L 54 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 63 time to evaluate : 0.431 Fit side-chains REVERT: A 408 ARG cc_start: 0.8592 (tpt170) cc_final: 0.8352 (tpt90) REVERT: A 493 GLN cc_start: 0.7146 (mp10) cc_final: 0.6407 (mp10) REVERT: H 57 ASP cc_start: 0.8906 (t0) cc_final: 0.8568 (t0) REVERT: H 62 GLN cc_start: 0.8028 (tm-30) cc_final: 0.7808 (tm-30) REVERT: H 109 PHE cc_start: 0.7480 (t80) cc_final: 0.7278 (t80) REVERT: L 24 LYS cc_start: 0.0889 (OUTLIER) cc_final: 0.0185 (tmtt) REVERT: L 55 TYR cc_start: 0.2447 (OUTLIER) cc_final: 0.1508 (m-10) REVERT: L 83 LEU cc_start: 0.7324 (tt) cc_final: 0.6848 (pp) REVERT: L 85 GLU cc_start: 0.7276 (tp30) cc_final: 0.6346 (tm-30) outliers start: 19 outliers final: 11 residues processed: 77 average time/residue: 0.1810 time to fit residues: 16.6936 Evaluate side-chains 65 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 52 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 414 GLN Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 99 ASP Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 24 LYS Chi-restraints excluded: chain L residue 32 ASN Chi-restraints excluded: chain L residue 55 TYR Chi-restraints excluded: chain L residue 93 ASN Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 20 optimal weight: 0.0980 chunk 36 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 8 optimal weight: 7.9990 chunk 23 optimal weight: 5.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 GLN ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 55 ASN L 89 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6809 moved from start: 0.6838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3463 Z= 0.266 Angle : 0.747 11.929 4704 Z= 0.396 Chirality : 0.049 0.210 501 Planarity : 0.005 0.058 605 Dihedral : 5.949 20.547 472 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 18.82 Ramachandran Plot: Outliers : 0.48 % Allowed : 12.35 % Favored : 87.17 % Rotamer: Outliers : 4.85 % Allowed : 22.10 % Favored : 73.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.91 (0.38), residues: 421 helix: -3.69 (0.66), residues: 26 sheet: -0.08 (0.48), residues: 132 loop : -2.95 (0.33), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP H 36 HIS 0.003 0.001 HIS L 61 PHE 0.014 0.002 PHE H 64 TYR 0.034 0.002 TYR H 103 ARG 0.003 0.001 ARG H 98 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 57 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 484 GLU cc_start: 0.7639 (mt-10) cc_final: 0.7438 (mt-10) REVERT: A 493 GLN cc_start: 0.7098 (mp10) cc_final: 0.6382 (mp10) REVERT: H 57 ASP cc_start: 0.8844 (t0) cc_final: 0.8623 (t0) REVERT: H 103 TYR cc_start: 0.5825 (t80) cc_final: 0.5521 (t80) REVERT: H 108 ASP cc_start: 0.8290 (p0) cc_final: 0.8037 (p0) REVERT: H 109 PHE cc_start: 0.7702 (t80) cc_final: 0.7481 (t80) REVERT: L 55 TYR cc_start: 0.2203 (OUTLIER) cc_final: 0.0992 (m-10) REVERT: L 85 GLU cc_start: 0.7347 (tp30) cc_final: 0.6330 (tm-30) REVERT: L 89 GLN cc_start: 0.7934 (OUTLIER) cc_final: 0.7726 (mt0) outliers start: 18 outliers final: 14 residues processed: 72 average time/residue: 0.1581 time to fit residues: 13.9854 Evaluate side-chains 68 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 52 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 414 GLN Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 55 ASN Chi-restraints excluded: chain H residue 99 ASP Chi-restraints excluded: chain H residue 104 TYR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 32 ASN Chi-restraints excluded: chain L residue 55 TYR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 93 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 3 optimal weight: 7.9990 chunk 13 optimal weight: 5.9990 chunk 21 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 23 optimal weight: 0.4980 chunk 29 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6788 moved from start: 0.6943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3463 Z= 0.204 Angle : 0.717 12.120 4704 Z= 0.372 Chirality : 0.048 0.207 501 Planarity : 0.005 0.044 605 Dihedral : 5.678 22.111 472 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 16.70 Ramachandran Plot: Outliers : 0.48 % Allowed : 13.54 % Favored : 85.99 % Rotamer: Outliers : 4.85 % Allowed : 22.64 % Favored : 72.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.95 (0.39), residues: 421 helix: -4.02 (0.56), residues: 26 sheet: -0.09 (0.48), residues: 132 loop : -2.95 (0.33), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 35 HIS 0.003 0.001 HIS L 61 PHE 0.011 0.001 PHE H 64 TYR 0.020 0.001 TYR H 103 ARG 0.003 0.000 ARG H 98 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 60 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 357 ARG cc_start: 0.6118 (OUTLIER) cc_final: 0.5743 (tmm160) REVERT: A 408 ARG cc_start: 0.8542 (tpt170) cc_final: 0.8329 (tpt170) REVERT: A 493 GLN cc_start: 0.7052 (mp10) cc_final: 0.6336 (mp10) REVERT: H 57 ASP cc_start: 0.8867 (t0) cc_final: 0.8507 (t0) REVERT: H 73 ASP cc_start: 0.7141 (t0) cc_final: 0.6898 (t0) REVERT: H 108 ASP cc_start: 0.8202 (p0) cc_final: 0.7937 (p0) REVERT: H 109 PHE cc_start: 0.7702 (t80) cc_final: 0.7476 (t80) REVERT: L 4 MET cc_start: 0.5972 (mmm) cc_final: 0.5631 (mpp) REVERT: L 9 LYS cc_start: 0.4720 (tmtt) cc_final: 0.3742 (mmmt) REVERT: L 24 LYS cc_start: 0.1000 (OUTLIER) cc_final: 0.0105 (tmtt) REVERT: L 55 TYR cc_start: 0.1957 (OUTLIER) cc_final: 0.0699 (m-10) REVERT: L 85 GLU cc_start: 0.7327 (tp30) cc_final: 0.6304 (tm-30) outliers start: 18 outliers final: 12 residues processed: 77 average time/residue: 0.1641 time to fit residues: 15.3567 Evaluate side-chains 69 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 54 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 357 ARG Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 99 ASP Chi-restraints excluded: chain H residue 104 TYR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 24 LYS Chi-restraints excluded: chain L residue 32 ASN Chi-restraints excluded: chain L residue 55 TYR Chi-restraints excluded: chain L residue 93 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6804 moved from start: 0.7122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3463 Z= 0.233 Angle : 0.728 12.125 4704 Z= 0.382 Chirality : 0.047 0.218 501 Planarity : 0.005 0.043 605 Dihedral : 5.776 26.637 472 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 18.37 Ramachandran Plot: Outliers : 0.48 % Allowed : 13.06 % Favored : 86.46 % Rotamer: Outliers : 5.39 % Allowed : 22.10 % Favored : 72.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.05 (0.38), residues: 421 helix: -4.08 (0.55), residues: 26 sheet: -0.19 (0.48), residues: 132 loop : -2.99 (0.33), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 35 HIS 0.003 0.001 HIS L 61 PHE 0.012 0.001 PHE H 64 TYR 0.018 0.001 TYR L 55 ARG 0.002 0.000 ARG H 98 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 58 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 357 ARG cc_start: 0.6134 (OUTLIER) cc_final: 0.5796 (tmm160) REVERT: A 408 ARG cc_start: 0.8541 (tpt170) cc_final: 0.8313 (tpt170) REVERT: A 493 GLN cc_start: 0.6962 (mp10) cc_final: 0.6281 (mp10) REVERT: H 57 ASP cc_start: 0.8771 (t0) cc_final: 0.8496 (t0) REVERT: H 103 TYR cc_start: 0.5429 (t80) cc_final: 0.4944 (t80) REVERT: L 4 MET cc_start: 0.6081 (mmm) cc_final: 0.5680 (mpp) REVERT: L 24 LYS cc_start: 0.1107 (OUTLIER) cc_final: 0.0204 (tmtt) REVERT: L 55 TYR cc_start: 0.2024 (OUTLIER) cc_final: 0.0607 (m-10) REVERT: L 79 GLN cc_start: -0.1114 (OUTLIER) cc_final: -0.2476 (mt0) REVERT: L 85 GLU cc_start: 0.7395 (tp30) cc_final: 0.6421 (tm-30) outliers start: 20 outliers final: 13 residues processed: 77 average time/residue: 0.1577 time to fit residues: 14.9798 Evaluate side-chains 72 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 55 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 357 ARG Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 99 ASP Chi-restraints excluded: chain H residue 104 TYR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 24 LYS Chi-restraints excluded: chain L residue 32 ASN Chi-restraints excluded: chain L residue 55 TYR Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 79 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 0.5980 chunk 31 optimal weight: 4.9990 chunk 36 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 35 optimal weight: 4.9990 chunk 37 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 11 optimal weight: 0.4980 chunk 34 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6789 moved from start: 0.7219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3463 Z= 0.219 Angle : 0.742 12.205 4704 Z= 0.387 Chirality : 0.048 0.225 501 Planarity : 0.005 0.040 605 Dihedral : 5.759 25.370 472 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 18.22 Ramachandran Plot: Outliers : 0.48 % Allowed : 12.83 % Favored : 86.70 % Rotamer: Outliers : 4.85 % Allowed : 24.26 % Favored : 70.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.05 (0.38), residues: 421 helix: -4.01 (0.58), residues: 26 sheet: -0.25 (0.47), residues: 132 loop : -2.96 (0.34), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 96 HIS 0.002 0.001 HIS L 61 PHE 0.011 0.001 PHE H 64 TYR 0.018 0.001 TYR L 94 ARG 0.002 0.000 ARG A 457 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 59 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 357 ARG cc_start: 0.6102 (OUTLIER) cc_final: 0.5727 (tmm160) REVERT: A 408 ARG cc_start: 0.8533 (tpt170) cc_final: 0.8315 (tpt170) REVERT: A 417 LYS cc_start: 0.8568 (tppt) cc_final: 0.8305 (tppt) REVERT: A 493 GLN cc_start: 0.6918 (mp10) cc_final: 0.6238 (mp10) REVERT: H 57 ASP cc_start: 0.8665 (t0) cc_final: 0.8386 (t0) REVERT: H 73 ASP cc_start: 0.7269 (t0) cc_final: 0.7059 (t0) REVERT: L 4 MET cc_start: 0.5983 (mmm) cc_final: 0.5564 (mpp) REVERT: L 9 LYS cc_start: 0.4596 (tmtt) cc_final: 0.3688 (mmmt) REVERT: L 24 LYS cc_start: 0.1238 (OUTLIER) cc_final: 0.0285 (tmtt) REVERT: L 79 GLN cc_start: -0.1030 (OUTLIER) cc_final: -0.2368 (mt0) REVERT: L 85 GLU cc_start: 0.7348 (tp30) cc_final: 0.7037 (tp30) outliers start: 18 outliers final: 15 residues processed: 75 average time/residue: 0.1433 time to fit residues: 13.4679 Evaluate side-chains 74 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 56 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 357 ARG Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 99 ASP Chi-restraints excluded: chain H residue 104 TYR Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 24 LYS Chi-restraints excluded: chain L residue 32 ASN Chi-restraints excluded: chain L residue 55 TYR Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 79 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.0270 chunk 37 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 27 optimal weight: 0.0030 chunk 41 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 3 optimal weight: 6.9990 chunk 25 optimal weight: 0.9980 overall best weight: 0.5648 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6763 moved from start: 0.7285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3463 Z= 0.207 Angle : 0.728 12.439 4704 Z= 0.378 Chirality : 0.047 0.228 501 Planarity : 0.004 0.037 605 Dihedral : 5.566 24.697 472 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 17.46 Ramachandran Plot: Outliers : 0.48 % Allowed : 11.88 % Favored : 87.65 % Rotamer: Outliers : 4.04 % Allowed : 24.80 % Favored : 71.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.00 (0.39), residues: 421 helix: -4.00 (0.57), residues: 26 sheet: -0.17 (0.47), residues: 132 loop : -2.95 (0.34), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 96 HIS 0.002 0.001 HIS L 61 PHE 0.031 0.002 PHE H 109 TYR 0.012 0.001 TYR L 55 ARG 0.002 0.000 ARG H 98 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 62 time to evaluate : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 357 ARG cc_start: 0.6042 (OUTLIER) cc_final: 0.5647 (tmm160) REVERT: A 408 ARG cc_start: 0.8517 (tpt170) cc_final: 0.8288 (tpt170) REVERT: A 417 LYS cc_start: 0.8601 (tppt) cc_final: 0.8168 (tppt) REVERT: A 493 GLN cc_start: 0.6804 (mp10) cc_final: 0.6173 (mp10) REVERT: A 498 GLN cc_start: 0.7363 (mp10) cc_final: 0.6519 (mp10) REVERT: H 57 ASP cc_start: 0.8603 (t0) cc_final: 0.8299 (t0) REVERT: L 4 MET cc_start: 0.5868 (mmm) cc_final: 0.5349 (mpp) REVERT: L 9 LYS cc_start: 0.4576 (tmtt) cc_final: 0.3688 (mmmt) REVERT: L 24 LYS cc_start: 0.2078 (OUTLIER) cc_final: 0.0992 (tmtt) REVERT: L 79 GLN cc_start: -0.0854 (OUTLIER) cc_final: -0.2093 (mt0) REVERT: L 85 GLU cc_start: 0.7366 (tp30) cc_final: 0.7023 (tp30) REVERT: L 94 TYR cc_start: 0.6985 (m-80) cc_final: 0.6710 (t80) outliers start: 15 outliers final: 11 residues processed: 76 average time/residue: 0.1541 time to fit residues: 14.5231 Evaluate side-chains 70 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 56 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 357 ARG Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 99 ASP Chi-restraints excluded: chain H residue 104 TYR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 24 LYS Chi-restraints excluded: chain L residue 55 TYR Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 79 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 0.0970 chunk 26 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6760 moved from start: 0.7365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3463 Z= 0.222 Angle : 0.763 12.802 4704 Z= 0.398 Chirality : 0.048 0.224 501 Planarity : 0.005 0.041 605 Dihedral : 5.733 24.019 472 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 17.46 Ramachandran Plot: Outliers : 0.48 % Allowed : 12.59 % Favored : 86.94 % Rotamer: Outliers : 4.58 % Allowed : 25.07 % Favored : 70.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.03 (0.39), residues: 421 helix: -4.23 (0.45), residues: 26 sheet: -0.21 (0.47), residues: 132 loop : -2.95 (0.34), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 36 HIS 0.002 0.001 HIS L 61 PHE 0.011 0.001 PHE H 29 TYR 0.021 0.002 TYR H 103 ARG 0.002 0.000 ARG L 54 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 59 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 357 ARG cc_start: 0.6000 (OUTLIER) cc_final: 0.5627 (tmm160) REVERT: A 408 ARG cc_start: 0.8544 (tpt170) cc_final: 0.8307 (tpt170) REVERT: A 417 LYS cc_start: 0.8562 (tppt) cc_final: 0.8307 (tppt) REVERT: A 493 GLN cc_start: 0.6804 (mp10) cc_final: 0.6178 (mp10) REVERT: A 498 GLN cc_start: 0.7368 (mp10) cc_final: 0.6534 (mp10) REVERT: L 9 LYS cc_start: 0.4648 (tmtt) cc_final: 0.3752 (mmmt) REVERT: L 24 LYS cc_start: 0.2037 (OUTLIER) cc_final: 0.0991 (tmtt) REVERT: L 55 TYR cc_start: 0.2266 (OUTLIER) cc_final: 0.0805 (m-10) REVERT: L 79 GLN cc_start: -0.0951 (OUTLIER) cc_final: -0.2193 (mt0) REVERT: L 85 GLU cc_start: 0.7330 (tp30) cc_final: 0.7007 (tp30) REVERT: L 94 TYR cc_start: 0.7021 (m-80) cc_final: 0.6771 (t80) outliers start: 17 outliers final: 12 residues processed: 75 average time/residue: 0.1713 time to fit residues: 15.8622 Evaluate side-chains 74 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 58 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 357 ARG Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 99 ASP Chi-restraints excluded: chain H residue 104 TYR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 24 LYS Chi-restraints excluded: chain L residue 32 ASN Chi-restraints excluded: chain L residue 55 TYR Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 79 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 38 optimal weight: 0.0570 chunk 22 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 chunk 16 optimal weight: 0.4980 chunk 15 optimal weight: 0.4980 chunk 41 optimal weight: 2.9990 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.110273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.100672 restraints weight = 11750.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.102414 restraints weight = 7373.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.103596 restraints weight = 5139.249| |-----------------------------------------------------------------------------| r_work (final): 0.3884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7045 moved from start: 0.7403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3463 Z= 0.215 Angle : 0.755 12.793 4704 Z= 0.392 Chirality : 0.048 0.219 501 Planarity : 0.005 0.040 605 Dihedral : 5.664 23.824 472 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 17.16 Ramachandran Plot: Outliers : 0.48 % Allowed : 11.64 % Favored : 87.89 % Rotamer: Outliers : 4.31 % Allowed : 24.53 % Favored : 71.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.04 (0.39), residues: 421 helix: -4.43 (0.37), residues: 26 sheet: -0.07 (0.48), residues: 130 loop : -2.99 (0.34), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 36 HIS 0.002 0.001 HIS L 61 PHE 0.018 0.001 PHE H 109 TYR 0.015 0.001 TYR H 60 ARG 0.002 0.000 ARG H 98 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1366.08 seconds wall clock time: 25 minutes 5.17 seconds (1505.17 seconds total)