Starting phenix.real_space_refine on Tue Feb 13 09:05:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bvs_16270/02_2024/8bvs_16270_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bvs_16270/02_2024/8bvs_16270.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bvs_16270/02_2024/8bvs_16270_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bvs_16270/02_2024/8bvs_16270_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bvs_16270/02_2024/8bvs_16270_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bvs_16270/02_2024/8bvs_16270.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bvs_16270/02_2024/8bvs_16270.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bvs_16270/02_2024/8bvs_16270_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bvs_16270/02_2024/8bvs_16270_updated.pdb" } resolution = 3.61 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= 0.001 sd= 0.047 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: 6 Type Number sf(0) Gaussians P 1 5.49 5 S 35 5.16 5 Cl 1 4.86 5 C 3100 2.51 5 N 816 2.21 5 O 846 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 5": "OD1" <-> "OD2" Residue "A PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 488": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 514": "OD1" <-> "OD2" Residue "B GLU 32": "OE1" <-> "OE2" Residue "B TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 4799 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 502, 3884 Classifications: {'peptide': 502} Link IDs: {'PTRANS': 25, 'TRANS': 476} Chain breaks: 2 Chain: "B" Number of atoms: 895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 895 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 3, 'TRANS': 111} Chain: "A" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 20 Unusual residues: {' CL': 1, 'TFO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.50, per 1000 atoms: 0.73 Number of scatterers: 4799 At special positions: 0 Unit cell: (116.48, 69.888, 81.536, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 1 17.00 S 35 16.00 P 1 15.00 O 846 8.00 N 816 7.00 C 3100 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 105 " distance=2.03 Simple disulfide: pdb=" SG CYS A 78 " - pdb=" SG CYS A 128 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " 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: 1.98 Conformation dependent library (CDL) restraints added in 867.4 milliseconds 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1134 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 23 helices and 3 sheets defined 57.7% alpha, 7.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'A' and resid 3 through 10 Processing helix chain 'A' and resid 15 through 41 removed outlier: 4.051A pdb=" N VAL A 21 " --> pdb=" O GLN A 17 " (cutoff:3.500A) Proline residue: A 27 - end of helix removed outlier: 4.792A pdb=" N LEU A 30 " --> pdb=" O ALA A 26 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N GLN A 38 " --> pdb=" O HIS A 34 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ASN A 39 " --> pdb=" O ASN A 35 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N PHE A 40 " --> pdb=" O THR A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 65 No H-bonds generated for 'chain 'A' and resid 63 through 65' Processing helix chain 'A' and resid 120 through 124 Processing helix chain 'A' and resid 132 through 159 removed outlier: 4.404A pdb=" N ALA A 137 " --> pdb=" O ARG A 134 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL A 151 " --> pdb=" O GLY A 148 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N PHE A 152 " --> pdb=" O ALA A 149 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU A 159 " --> pdb=" O ALA A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 180 Processing helix chain 'A' and resid 185 through 212 removed outlier: 3.973A pdb=" N SER A 201 " --> pdb=" O MET A 197 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N MET A 207 " --> pdb=" O ALA A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 243 removed outlier: 3.604A pdb=" N ARG A 219 " --> pdb=" O ILE A 216 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N ALA A 220 " --> pdb=" O HIS A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 264 removed outlier: 3.546A pdb=" N LEU A 252 " --> pdb=" O ARG A 248 " (cutoff:3.500A) Proline residue: A 257 - end of helix Processing helix chain 'A' and resid 272 through 278 Processing helix chain 'A' and resid 282 through 295 Processing helix chain 'A' and resid 306 through 312 removed outlier: 3.952A pdb=" N ARG A 310 " --> pdb=" O ILE A 306 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N THR A 311 " --> pdb=" O GLU A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 331 Processing helix chain 'A' and resid 333 through 357 Processing helix chain 'A' and resid 361 through 363 No H-bonds generated for 'chain 'A' and resid 361 through 363' Processing helix chain 'A' and resid 367 through 391 removed outlier: 3.867A pdb=" N ASP A 378 " --> pdb=" O PHE A 374 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N LEU A 379 " --> pdb=" O GLY A 375 " (cutoff:3.500A) Proline residue: A 380 - end of helix Processing helix chain 'A' and resid 395 through 414 Processing helix chain 'A' and resid 421 through 446 Processing helix chain 'A' and resid 454 through 480 Proline residue: A 473 - end of helix removed outlier: 4.146A pdb=" N THR A 478 " --> pdb=" O LEU A 474 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N ALA A 479 " --> pdb=" O VAL A 475 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N GLU A 480 " --> pdb=" O SER A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 500 Proline residue: A 494 - end of helix Processing helix chain 'A' and resid 516 through 525 removed outlier: 3.580A pdb=" N LYS A 520 " --> pdb=" O VAL A 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 55 No H-bonds generated for 'chain 'B' and resid 53 through 55' Processing helix chain 'B' and resid 88 through 90 No H-bonds generated for 'chain 'B' and resid 88 through 90' Processing sheet with id= A, first strand: chain 'A' and resid 47 through 49 Processing sheet with id= B, first strand: chain 'B' and resid 3 through 7 removed outlier: 3.896A pdb=" N GLN B 3 " --> pdb=" O SER B 25 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL B 5 " --> pdb=" O ALA B 23 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N THR B 78 " --> pdb=" O ASP B 73 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 10 through 13 removed outlier: 3.627A pdb=" N GLY B 10 " --> pdb=" O GLN B 110 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL B 12 " --> pdb=" O THR B 112 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL B 111 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA B 92 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL B 93 " --> pdb=" O GLN B 39 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU B 97 " --> pdb=" O GLU B 35 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ALA B 49 " --> pdb=" O TRP B 36 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N ARG B 38 " --> pdb=" O TRP B 47 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N TRP B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) 259 hydrogen bonds defined for protein. 636 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: 1.08 Time building geometry restraints manager: 2.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1519 1.35 - 1.48: 1281 1.48 - 1.61: 2057 1.61 - 1.73: 0 1.73 - 1.86: 56 Bond restraints: 4913 Sorted by residual: bond pdb=" C5 TFO A 601 " pdb=" C4 TFO A 601 " ideal model delta sigma weight residual 1.335 1.379 -0.044 2.00e-02 2.50e+03 4.82e+00 bond pdb=" C2 TFO A 601 " pdb=" N3 TFO A 601 " ideal model delta sigma weight residual 1.352 1.319 0.033 2.00e-02 2.50e+03 2.72e+00 bond pdb=" N1 TFO A 601 " pdb=" C2 TFO A 601 " ideal model delta sigma weight residual 1.354 1.324 0.030 2.00e-02 2.50e+03 2.20e+00 bond pdb=" C5 TFO A 601 " pdb=" C6 TFO A 601 " ideal model delta sigma weight residual 1.378 1.404 -0.026 2.00e-02 2.50e+03 1.69e+00 bond pdb=" CB ASP B 62 " pdb=" CG ASP B 62 " ideal model delta sigma weight residual 1.516 1.543 -0.027 2.50e-02 1.60e+03 1.16e+00 ... (remaining 4908 not shown) Histogram of bond angle deviations from ideal: 98.91 - 106.25: 138 106.25 - 113.59: 2709 113.59 - 120.92: 2461 120.92 - 128.26: 1325 128.26 - 135.60: 47 Bond angle restraints: 6680 Sorted by residual: angle pdb=" N6 TFO A 601 " pdb=" C6 TFO A 601 " pdb=" N1 TFO A 601 " ideal model delta sigma weight residual 104.35 120.34 -15.99 3.00e+00 1.11e-01 2.84e+01 angle pdb=" C5 TFO A 601 " pdb=" C6 TFO A 601 " pdb=" N6 TFO A 601 " ideal model delta sigma weight residual 134.91 120.05 14.86 3.00e+00 1.11e-01 2.45e+01 angle pdb=" CB MET A 31 " pdb=" CG MET A 31 " pdb=" SD MET A 31 " ideal model delta sigma weight residual 112.70 126.61 -13.91 3.00e+00 1.11e-01 2.15e+01 angle pdb=" C8 TFO A 601 " pdb=" N9 TFO A 601 " pdb=" C6' TFO A 601 " ideal model delta sigma weight residual 112.18 125.43 -13.25 3.00e+00 1.11e-01 1.95e+01 angle pdb=" CB MET A 327 " pdb=" CG MET A 327 " pdb=" SD MET A 327 " ideal model delta sigma weight residual 112.70 122.43 -9.73 3.00e+00 1.11e-01 1.05e+01 ... (remaining 6675 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.30: 2400 17.30 - 34.60: 351 34.60 - 51.90: 108 51.90 - 69.20: 23 69.20 - 86.49: 6 Dihedral angle restraints: 2888 sinusoidal: 1115 harmonic: 1773 Sorted by residual: dihedral pdb=" CB CYS A 78 " pdb=" SG CYS A 78 " pdb=" SG CYS A 128 " pdb=" CB CYS A 128 " ideal model delta sinusoidal sigma weight residual 93.00 8.88 84.12 1 1.00e+01 1.00e-02 8.62e+01 dihedral pdb=" CB CYS A 49 " pdb=" SG CYS A 49 " pdb=" SG CYS A 105 " pdb=" CB CYS A 105 " ideal model delta sinusoidal sigma weight residual -86.00 -152.52 66.52 1 1.00e+01 1.00e-02 5.78e+01 dihedral pdb=" CA PHE A 152 " pdb=" C PHE A 152 " pdb=" N GLY A 153 " pdb=" CA GLY A 153 " ideal model delta harmonic sigma weight residual 180.00 164.01 15.99 0 5.00e+00 4.00e-02 1.02e+01 ... (remaining 2885 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 398 0.024 - 0.048: 206 0.048 - 0.072: 92 0.072 - 0.096: 48 0.096 - 0.120: 19 Chirality restraints: 763 Sorted by residual: chirality pdb=" CA ASP B 62 " pdb=" N ASP B 62 " pdb=" C ASP B 62 " pdb=" CB ASP B 62 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.57e-01 chirality pdb=" CA VAL B 93 " pdb=" N VAL B 93 " pdb=" C VAL B 93 " pdb=" CB VAL B 93 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.56e-01 chirality pdb=" CB ILE A 453 " pdb=" CA ILE A 453 " pdb=" CG1 ILE A 453 " pdb=" CG2 ILE A 453 " both_signs ideal model delta sigma weight residual False 2.64 2.53 0.12 2.00e-01 2.50e+01 3.48e-01 ... (remaining 760 not shown) Planarity restraints: 831 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER B 114 " 0.027 2.00e-02 2.50e+03 5.43e-02 2.95e+01 pdb=" C SER B 114 " -0.094 2.00e-02 2.50e+03 pdb=" O SER B 114 " 0.035 2.00e-02 2.50e+03 pdb=" N ALA B 115 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 339 " 0.010 2.00e-02 2.50e+03 2.09e-02 4.35e+00 pdb=" C PHE A 339 " -0.036 2.00e-02 2.50e+03 pdb=" O PHE A 339 " 0.014 2.00e-02 2.50e+03 pdb=" N LEU A 340 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 45 " 0.029 5.00e-02 4.00e+02 4.48e-02 3.21e+00 pdb=" N PRO A 46 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 46 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 46 " 0.025 5.00e-02 4.00e+02 ... (remaining 828 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 163 2.70 - 3.25: 5036 3.25 - 3.80: 8230 3.80 - 4.35: 9638 4.35 - 4.90: 16055 Nonbonded interactions: 39122 Sorted by model distance: nonbonded pdb=" OE1 GLU B 35 " pdb=" OH TYR B 37 " model vdw 2.147 2.440 nonbonded pdb=" O CYS B 22 " pdb=" OG1 THR B 78 " model vdw 2.181 2.440 nonbonded pdb=" OH TYR A 444 " pdb=" O PRO A 505 " model vdw 2.210 2.440 nonbonded pdb=" OH TYR B 80 " pdb=" OE1 GLN B 82 " model vdw 2.228 2.440 nonbonded pdb=" O TYR A 275 " pdb=" OG SER A 278 " model vdw 2.234 2.440 ... (remaining 39117 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: 2.050 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: 5.070 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 19.090 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 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 : 0.004 0.044 4913 Z= 0.238 Angle : 0.749 15.987 6680 Z= 0.338 Chirality : 0.039 0.120 763 Planarity : 0.005 0.054 831 Dihedral : 18.236 86.494 1745 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.58 % Allowed : 40.08 % Favored : 59.34 % 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: 1.20 (0.36), residues: 609 helix: 1.45 (0.28), residues: 366 sheet: -1.28 (0.67), residues: 55 loop : 0.34 (0.50), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 36 HIS 0.002 0.001 HIS B 105 PHE 0.020 0.001 PHE A 351 TYR 0.021 0.001 TYR A 169 ARG 0.003 0.000 ARG A 219 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 108 time to evaluate : 0.551 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 110 average time/residue: 0.1193 time to fit residues: 18.2748 Evaluate side-chains 108 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 107 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 365 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 51 optimal weight: 7.9990 chunk 46 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 18 optimal weight: 0.5980 chunk 29 optimal weight: 0.0870 chunk 35 optimal weight: 0.1980 chunk 55 optimal weight: 10.0000 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 135 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.0720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 4913 Z= 0.166 Angle : 0.564 7.199 6680 Z= 0.289 Chirality : 0.038 0.117 763 Planarity : 0.005 0.049 831 Dihedral : 4.078 24.514 677 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 5.45 % Allowed : 34.63 % Favored : 59.92 % 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: 0.98 (0.35), residues: 609 helix: 1.22 (0.27), residues: 367 sheet: -1.47 (0.61), residues: 64 loop : 0.56 (0.52), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 36 HIS 0.002 0.000 HIS A 47 PHE 0.016 0.001 PHE A 351 TYR 0.017 0.001 TYR A 169 ARG 0.002 0.000 ARG A 219 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 118 time to evaluate : 0.545 Fit side-chains REVERT: A 5 ASP cc_start: 0.8624 (t0) cc_final: 0.8401 (t0) REVERT: A 294 ILE cc_start: 0.8761 (tt) cc_final: 0.8509 (tp) outliers start: 28 outliers final: 17 residues processed: 137 average time/residue: 0.1308 time to fit residues: 24.3355 Evaluate side-chains 128 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 111 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 386 PHE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 439 ASN Chi-restraints excluded: chain A residue 460 MET Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain B residue 39 GLN Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 96 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 30 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 55 optimal weight: 0.8980 chunk 59 optimal weight: 0.0980 chunk 49 optimal weight: 5.9990 chunk 18 optimal weight: 0.5980 chunk 44 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 135 GLN B 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.0920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4913 Z= 0.171 Angle : 0.569 7.626 6680 Z= 0.284 Chirality : 0.038 0.132 763 Planarity : 0.005 0.047 831 Dihedral : 3.919 24.793 676 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 4.86 % Allowed : 35.60 % Favored : 59.53 % 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: 0.80 (0.35), residues: 609 helix: 1.02 (0.27), residues: 367 sheet: -1.32 (0.62), residues: 64 loop : 0.53 (0.52), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 36 HIS 0.002 0.001 HIS A 48 PHE 0.017 0.001 PHE A 351 TYR 0.012 0.001 TYR A 169 ARG 0.002 0.000 ARG A 280 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 117 time to evaluate : 0.575 Fit side-chains REVERT: A 5 ASP cc_start: 0.8682 (t0) cc_final: 0.8446 (t0) REVERT: A 142 MET cc_start: 0.9221 (tpp) cc_final: 0.8297 (mpp) REVERT: A 294 ILE cc_start: 0.8722 (tt) cc_final: 0.8481 (tp) REVERT: B 87 LYS cc_start: 0.8379 (OUTLIER) cc_final: 0.8059 (mtmm) outliers start: 25 outliers final: 18 residues processed: 134 average time/residue: 0.1584 time to fit residues: 28.4192 Evaluate side-chains 129 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 110 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 383 PHE Chi-restraints excluded: chain A residue 386 PHE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 460 MET Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain B residue 39 GLN Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 87 LYS Chi-restraints excluded: chain B residue 96 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 41 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 55 optimal weight: 9.9990 chunk 58 optimal weight: 6.9990 chunk 29 optimal weight: 4.9990 chunk 52 optimal weight: 8.9990 chunk 15 optimal weight: 4.9990 chunk 49 optimal weight: 7.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 510 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.1334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 4913 Z= 0.328 Angle : 0.652 7.080 6680 Z= 0.325 Chirality : 0.040 0.119 763 Planarity : 0.005 0.045 831 Dihedral : 4.118 24.981 676 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 15.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 9.14 % Allowed : 31.52 % Favored : 59.34 % 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: 0.44 (0.35), residues: 609 helix: 0.76 (0.27), residues: 366 sheet: -1.58 (0.69), residues: 54 loop : 0.24 (0.49), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 36 HIS 0.004 0.001 HIS A 47 PHE 0.023 0.002 PHE A 351 TYR 0.015 0.002 TYR A 169 ARG 0.005 0.001 ARG A 280 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 112 time to evaluate : 0.575 Fit side-chains REVERT: A 5 ASP cc_start: 0.8768 (t0) cc_final: 0.8533 (t0) REVERT: A 142 MET cc_start: 0.9155 (tpp) cc_final: 0.8236 (mpp) REVERT: A 294 ILE cc_start: 0.8823 (tt) cc_final: 0.8595 (tp) REVERT: A 399 MET cc_start: 0.7487 (mmt) cc_final: 0.6622 (mmt) REVERT: B 20 LEU cc_start: 0.8459 (mm) cc_final: 0.7971 (mm) REVERT: B 32 GLU cc_start: 0.7425 (mp0) cc_final: 0.7214 (mp0) REVERT: B 60 TYR cc_start: 0.7282 (m-10) cc_final: 0.6742 (m-10) REVERT: B 87 LYS cc_start: 0.8409 (OUTLIER) cc_final: 0.8043 (mtmm) outliers start: 47 outliers final: 32 residues processed: 145 average time/residue: 0.1317 time to fit residues: 26.0911 Evaluate side-chains 140 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 107 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 386 PHE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 433 CYS Chi-restraints excluded: chain A residue 460 MET Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain B residue 39 GLN Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 87 LYS Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 100 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 33 optimal weight: 0.6980 chunk 0 optimal weight: 7.9990 chunk 43 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 50 optimal weight: 0.9980 chunk 40 optimal weight: 0.6980 chunk 30 optimal weight: 4.9990 chunk 52 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 53 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.1337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4913 Z= 0.187 Angle : 0.612 7.943 6680 Z= 0.297 Chirality : 0.039 0.121 763 Planarity : 0.005 0.046 831 Dihedral : 4.005 23.084 676 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 5.64 % Allowed : 34.82 % Favored : 59.53 % 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: 0.58 (0.35), residues: 609 helix: 0.80 (0.27), residues: 366 sheet: -1.19 (0.67), residues: 64 loop : 0.47 (0.52), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 36 HIS 0.002 0.001 HIS A 47 PHE 0.017 0.001 PHE A 351 TYR 0.014 0.001 TYR A 169 ARG 0.004 0.000 ARG A 394 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 119 time to evaluate : 0.574 Fit side-chains REVERT: A 5 ASP cc_start: 0.8749 (t0) cc_final: 0.8505 (t0) REVERT: A 23 MET cc_start: 0.8120 (tpt) cc_final: 0.7902 (tpt) REVERT: A 142 MET cc_start: 0.9135 (tpp) cc_final: 0.8219 (mpp) REVERT: A 294 ILE cc_start: 0.8767 (tt) cc_final: 0.8533 (tp) REVERT: A 399 MET cc_start: 0.7522 (mmt) cc_final: 0.7162 (mmt) REVERT: B 20 LEU cc_start: 0.8450 (mm) cc_final: 0.7992 (mm) REVERT: B 60 TYR cc_start: 0.7250 (m-10) cc_final: 0.6634 (m-10) REVERT: B 84 ASN cc_start: 0.7864 (p0) cc_final: 0.7616 (p0) REVERT: B 87 LYS cc_start: 0.8431 (OUTLIER) cc_final: 0.7992 (mtmm) REVERT: B 103 TRP cc_start: 0.5734 (OUTLIER) cc_final: 0.3449 (m100) outliers start: 29 outliers final: 23 residues processed: 137 average time/residue: 0.1445 time to fit residues: 26.5734 Evaluate side-chains 136 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 111 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 383 PHE Chi-restraints excluded: chain A residue 386 PHE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 447 GLU Chi-restraints excluded: chain A residue 460 MET Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain B residue 39 GLN Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 87 LYS Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 103 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 11 optimal weight: 0.9990 chunk 34 optimal weight: 0.1980 chunk 14 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 27 optimal weight: 0.0370 chunk 4 optimal weight: 0.0670 chunk 19 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 56 optimal weight: 6.9990 chunk 6 optimal weight: 3.9990 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4913 Z= 0.177 Angle : 0.637 9.105 6680 Z= 0.304 Chirality : 0.038 0.140 763 Planarity : 0.005 0.046 831 Dihedral : 3.938 22.451 676 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 6.61 % Allowed : 34.24 % Favored : 59.14 % 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: 0.56 (0.35), residues: 609 helix: 0.82 (0.27), residues: 365 sheet: -1.30 (0.73), residues: 54 loop : 0.29 (0.50), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 36 HIS 0.002 0.001 HIS A 48 PHE 0.016 0.001 PHE A 351 TYR 0.013 0.001 TYR A 169 ARG 0.003 0.000 ARG A 394 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 119 time to evaluate : 0.578 Fit side-chains REVERT: A 5 ASP cc_start: 0.8763 (t0) cc_final: 0.8521 (t0) REVERT: A 142 MET cc_start: 0.9124 (tpp) cc_final: 0.8220 (mpp) REVERT: A 165 LEU cc_start: 0.9224 (OUTLIER) cc_final: 0.8793 (tt) REVERT: A 294 ILE cc_start: 0.8745 (tt) cc_final: 0.8518 (tp) REVERT: A 399 MET cc_start: 0.7550 (mmt) cc_final: 0.7293 (mmt) REVERT: B 20 LEU cc_start: 0.8435 (mm) cc_final: 0.7974 (mm) REVERT: B 60 TYR cc_start: 0.7347 (m-10) cc_final: 0.6765 (m-10) REVERT: B 84 ASN cc_start: 0.7838 (p0) cc_final: 0.7594 (p0) REVERT: B 87 LYS cc_start: 0.8450 (OUTLIER) cc_final: 0.8015 (mtmm) REVERT: B 103 TRP cc_start: 0.5711 (OUTLIER) cc_final: 0.3473 (m100) outliers start: 34 outliers final: 27 residues processed: 139 average time/residue: 0.1418 time to fit residues: 26.4791 Evaluate side-chains 145 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 115 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 383 PHE Chi-restraints excluded: chain A residue 386 PHE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 447 GLU Chi-restraints excluded: chain A residue 460 MET Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain B residue 39 GLN Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 87 LYS Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 103 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 33 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 49 optimal weight: 9.9990 chunk 32 optimal weight: 0.9980 chunk 58 optimal weight: 0.0000 chunk 36 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 23 optimal weight: 0.0000 chunk 17 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4913 Z= 0.185 Angle : 0.639 9.647 6680 Z= 0.302 Chirality : 0.038 0.117 763 Planarity : 0.005 0.046 831 Dihedral : 3.896 22.233 676 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 6.61 % Allowed : 33.85 % Favored : 59.53 % 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: 0.57 (0.35), residues: 609 helix: 0.83 (0.27), residues: 366 sheet: -1.36 (0.71), residues: 54 loop : 0.32 (0.50), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 47 HIS 0.002 0.001 HIS A 48 PHE 0.017 0.001 PHE A 351 TYR 0.014 0.001 TYR A 169 ARG 0.003 0.000 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 117 time to evaluate : 0.560 Fit side-chains REVERT: A 5 ASP cc_start: 0.8776 (t0) cc_final: 0.8532 (t0) REVERT: A 142 MET cc_start: 0.9132 (tpp) cc_final: 0.8202 (mpp) REVERT: A 165 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.8987 (tt) REVERT: A 294 ILE cc_start: 0.8763 (tt) cc_final: 0.8547 (tp) REVERT: A 399 MET cc_start: 0.7565 (mmt) cc_final: 0.7000 (mmt) REVERT: B 20 LEU cc_start: 0.8495 (mm) cc_final: 0.8040 (mm) REVERT: B 60 TYR cc_start: 0.7389 (m-10) cc_final: 0.6876 (m-10) REVERT: B 87 LYS cc_start: 0.8435 (OUTLIER) cc_final: 0.7978 (mtmm) REVERT: B 95 TYR cc_start: 0.7443 (m-80) cc_final: 0.7226 (m-80) REVERT: B 103 TRP cc_start: 0.5683 (OUTLIER) cc_final: 0.3448 (m100) outliers start: 34 outliers final: 29 residues processed: 140 average time/residue: 0.1434 time to fit residues: 26.7886 Evaluate side-chains 144 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 112 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 341 CYS Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 383 PHE Chi-restraints excluded: chain A residue 386 PHE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 460 MET Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain B residue 39 GLN Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 87 LYS Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 103 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 11 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 29 optimal weight: 0.1980 chunk 5 optimal weight: 9.9990 chunk 46 optimal weight: 0.9990 chunk 53 optimal weight: 7.9990 chunk 56 optimal weight: 7.9990 chunk 51 optimal weight: 0.0470 chunk 54 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4913 Z= 0.186 Angle : 0.643 9.569 6680 Z= 0.304 Chirality : 0.039 0.131 763 Planarity : 0.005 0.046 831 Dihedral : 3.836 21.900 676 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 6.42 % Allowed : 34.05 % Favored : 59.53 % 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: 0.52 (0.35), residues: 609 helix: 0.82 (0.27), residues: 366 sheet: -1.30 (0.69), residues: 56 loop : 0.22 (0.50), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP B 47 HIS 0.002 0.001 HIS A 48 PHE 0.017 0.001 PHE A 351 TYR 0.017 0.001 TYR A 169 ARG 0.006 0.000 ARG B 59 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 120 time to evaluate : 0.563 Fit side-chains REVERT: A 5 ASP cc_start: 0.8781 (t0) cc_final: 0.8541 (t0) REVERT: A 142 MET cc_start: 0.9123 (tpp) cc_final: 0.8199 (mpp) REVERT: A 294 ILE cc_start: 0.8776 (tt) cc_final: 0.8559 (tp) REVERT: A 398 GLN cc_start: 0.8214 (mm110) cc_final: 0.8009 (tp40) REVERT: A 399 MET cc_start: 0.7517 (mmt) cc_final: 0.6896 (mmt) REVERT: A 464 MET cc_start: 0.8457 (mmm) cc_final: 0.8240 (mmt) REVERT: B 20 LEU cc_start: 0.8476 (mm) cc_final: 0.8038 (mm) REVERT: B 60 TYR cc_start: 0.7395 (m-10) cc_final: 0.6926 (m-10) REVERT: B 87 LYS cc_start: 0.8465 (OUTLIER) cc_final: 0.8025 (mtmm) REVERT: B 95 TYR cc_start: 0.7466 (m-80) cc_final: 0.7218 (m-80) REVERT: B 103 TRP cc_start: 0.5643 (OUTLIER) cc_final: 0.3417 (m100) outliers start: 33 outliers final: 30 residues processed: 141 average time/residue: 0.1376 time to fit residues: 26.0948 Evaluate side-chains 147 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 115 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 49 CYS Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 383 PHE Chi-restraints excluded: chain A residue 386 PHE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 433 CYS Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 447 GLU Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain B residue 39 GLN Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 87 LYS Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 103 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 23 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 49 optimal weight: 10.0000 chunk 51 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 chunk 57 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4913 Z= 0.237 Angle : 0.684 10.449 6680 Z= 0.322 Chirality : 0.039 0.120 763 Planarity : 0.005 0.046 831 Dihedral : 3.889 22.352 676 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 15.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 6.61 % Allowed : 33.85 % Favored : 59.53 % 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: 0.48 (0.35), residues: 609 helix: 0.81 (0.28), residues: 366 sheet: -1.34 (0.69), residues: 56 loop : 0.17 (0.49), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP B 47 HIS 0.002 0.001 HIS B 105 PHE 0.019 0.001 PHE A 351 TYR 0.018 0.001 TYR A 169 ARG 0.006 0.000 ARG B 59 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 119 time to evaluate : 0.624 Fit side-chains REVERT: A 5 ASP cc_start: 0.8776 (t0) cc_final: 0.8539 (t0) REVERT: A 142 MET cc_start: 0.9130 (tpp) cc_final: 0.8209 (mpp) REVERT: A 165 LEU cc_start: 0.9224 (OUTLIER) cc_final: 0.8808 (tt) REVERT: A 294 ILE cc_start: 0.8786 (tt) cc_final: 0.8560 (tp) REVERT: A 398 GLN cc_start: 0.8206 (mm110) cc_final: 0.8004 (tp40) REVERT: A 399 MET cc_start: 0.7571 (mmt) cc_final: 0.6956 (mmt) REVERT: A 464 MET cc_start: 0.8501 (mmm) cc_final: 0.8287 (mmt) REVERT: B 20 LEU cc_start: 0.8490 (mm) cc_final: 0.8048 (mm) REVERT: B 60 TYR cc_start: 0.7583 (m-10) cc_final: 0.7034 (m-10) REVERT: B 87 LYS cc_start: 0.8479 (OUTLIER) cc_final: 0.8055 (mtmm) REVERT: B 103 TRP cc_start: 0.5645 (OUTLIER) cc_final: 0.3331 (m100) outliers start: 34 outliers final: 30 residues processed: 141 average time/residue: 0.1406 time to fit residues: 26.6198 Evaluate side-chains 149 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 116 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 49 CYS Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 341 CYS Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 383 PHE Chi-restraints excluded: chain A residue 386 PHE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 433 CYS Chi-restraints excluded: chain A residue 460 MET Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain B residue 39 GLN Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 87 LYS Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 103 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 55 optimal weight: 6.9990 chunk 48 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 29 optimal weight: 8.9990 chunk 38 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 14 optimal weight: 0.0970 chunk 44 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4913 Z= 0.198 Angle : 0.683 9.715 6680 Z= 0.324 Chirality : 0.039 0.125 763 Planarity : 0.005 0.046 831 Dihedral : 3.915 21.755 676 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 6.61 % Allowed : 34.44 % Favored : 58.95 % 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: 0.48 (0.35), residues: 609 helix: 0.87 (0.28), residues: 360 sheet: -1.37 (0.69), residues: 56 loop : 0.05 (0.48), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP B 47 HIS 0.002 0.000 HIS A 48 PHE 0.021 0.001 PHE A 16 TYR 0.018 0.001 TYR A 169 ARG 0.006 0.000 ARG B 59 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 118 time to evaluate : 0.596 Fit side-chains REVERT: A 5 ASP cc_start: 0.8778 (t0) cc_final: 0.8551 (t0) REVERT: A 31 MET cc_start: 0.8042 (tpp) cc_final: 0.7810 (tpp) REVERT: A 142 MET cc_start: 0.9114 (tpp) cc_final: 0.8198 (mpp) REVERT: A 165 LEU cc_start: 0.9202 (OUTLIER) cc_final: 0.8775 (tt) REVERT: A 294 ILE cc_start: 0.8761 (tt) cc_final: 0.8536 (tp) REVERT: A 398 GLN cc_start: 0.8145 (mm110) cc_final: 0.7943 (tp40) REVERT: A 399 MET cc_start: 0.7579 (mmt) cc_final: 0.6973 (mmt) REVERT: A 464 MET cc_start: 0.8467 (mmm) cc_final: 0.8263 (mmt) REVERT: B 20 LEU cc_start: 0.8516 (mm) cc_final: 0.8102 (mm) REVERT: B 60 TYR cc_start: 0.7446 (m-10) cc_final: 0.6974 (m-10) REVERT: B 87 LYS cc_start: 0.8464 (OUTLIER) cc_final: 0.8004 (mtmm) REVERT: B 103 TRP cc_start: 0.5628 (OUTLIER) cc_final: 0.3369 (m100) outliers start: 34 outliers final: 29 residues processed: 142 average time/residue: 0.1371 time to fit residues: 26.1205 Evaluate side-chains 148 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 116 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 49 CYS Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 341 CYS Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 383 PHE Chi-restraints excluded: chain A residue 386 PHE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 460 MET Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain B residue 39 GLN Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 87 LYS Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 103 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 48 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 49 optimal weight: 6.9990 chunk 6 optimal weight: 0.1980 chunk 8 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 2 optimal weight: 0.2980 chunk 35 optimal weight: 0.8980 chunk 55 optimal weight: 8.9990 chunk 32 optimal weight: 0.6980 chunk 41 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 4 ASN ** 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 = 0.4086 r_free = 0.4086 target = 0.147601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.118935 restraints weight = 8991.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.122606 restraints weight = 4266.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.125075 restraints weight = 2650.646| |-----------------------------------------------------------------------------| r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4913 Z= 0.193 Angle : 0.678 9.998 6680 Z= 0.319 Chirality : 0.039 0.124 763 Planarity : 0.005 0.046 831 Dihedral : 3.879 21.714 676 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 6.42 % Allowed : 34.82 % Favored : 58.75 % 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: 0.50 (0.35), residues: 609 helix: 0.90 (0.28), residues: 360 sheet: -1.39 (0.68), residues: 56 loop : 0.04 (0.48), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP B 47 HIS 0.002 0.001 HIS A 48 PHE 0.017 0.001 PHE A 351 TYR 0.019 0.001 TYR A 169 ARG 0.004 0.000 ARG B 59 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1402.48 seconds wall clock time: 26 minutes 0.84 seconds (1560.84 seconds total)