Starting phenix.real_space_refine on Sun Mar 10 23:38:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gyw_34378/03_2024/8gyw_34378_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gyw_34378/03_2024/8gyw_34378.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/8gyw_34378/03_2024/8gyw_34378.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gyw_34378/03_2024/8gyw_34378.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gyw_34378/03_2024/8gyw_34378_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gyw_34378/03_2024/8gyw_34378_updated.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= 0.005 sd= 0.102 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 4 5.49 5 Mg 4 5.21 5 S 48 5.16 5 C 3994 2.51 5 N 984 2.21 5 O 1042 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 52": "OE1" <-> "OE2" Residue "B PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 383": "OD1" <-> "OD2" Residue "B TYR 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 52": "OE1" <-> "OE2" Residue "A PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 383": "OD1" <-> "OD2" Residue "A TYR 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 6076 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 3005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 3005 Classifications: {'peptide': 380} Link IDs: {'PTRANS': 17, 'TRANS': 362} Chain: "A" Number of atoms: 3005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 3005 Classifications: {'peptide': 380} Link IDs: {'PTRANS': 17, 'TRANS': 362} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 2, 'CDC': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 2, 'CDC': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 3.87, per 1000 atoms: 0.64 Number of scatterers: 6076 At special positions: 0 Unit cell: (97.37, 101.65, 71.69, 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) S 48 16.00 P 4 15.00 Mg 4 11.99 O 1042 8.00 N 984 7.00 C 3994 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 2.37 Conformation dependent library (CDL) restraints added in 1.3 seconds 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1424 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 32 helices and 2 sheets defined 72.9% alpha, 1.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'B' and resid 29 through 36 Processing helix chain 'B' and resid 45 through 52 Processing helix chain 'B' and resid 65 through 78 removed outlier: 4.253A pdb=" N GLY B 70 " --> pdb=" O PRO B 66 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N TYR B 71 " --> pdb=" O LEU B 67 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG B 77 " --> pdb=" O GLU B 73 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG B 78 " --> pdb=" O TRP B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 106 Processing helix chain 'B' and resid 116 through 142 removed outlier: 4.374A pdb=" N GLY B 137 " --> pdb=" O ASP B 133 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N LYS B 138 " --> pdb=" O ALA B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 172 removed outlier: 3.583A pdb=" N LEU B 160 " --> pdb=" O GLY B 156 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N VAL B 163 " --> pdb=" O SER B 159 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N PHE B 164 " --> pdb=" O LEU B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 177 No H-bonds generated for 'chain 'B' and resid 175 through 177' Processing helix chain 'B' and resid 179 through 203 Processing helix chain 'B' and resid 213 through 236 Proline residue: B 232 - end of helix Processing helix chain 'B' and resid 246 through 271 Proline residue: B 250 - end of helix removed outlier: 3.942A pdb=" N VAL B 268 " --> pdb=" O ASN B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 278 No H-bonds generated for 'chain 'B' and resid 276 through 278' Processing helix chain 'B' and resid 288 through 306 removed outlier: 4.229A pdb=" N HIS B 292 " --> pdb=" O SER B 288 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE B 293 " --> pdb=" O PRO B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 314 No H-bonds generated for 'chain 'B' and resid 311 through 314' Processing helix chain 'B' and resid 316 through 339 Processing helix chain 'B' and resid 349 through 362 removed outlier: 4.030A pdb=" N GLY B 353 " --> pdb=" O ALA B 350 " (cutoff:3.500A) Proline residue: B 354 - end of helix removed outlier: 3.539A pdb=" N LEU B 359 " --> pdb=" O LEU B 356 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN B 361 " --> pdb=" O PHE B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 399 Processing helix chain 'A' and resid 29 through 36 Processing helix chain 'A' and resid 45 through 52 Processing helix chain 'A' and resid 65 through 78 removed outlier: 4.253A pdb=" N GLY A 70 " --> pdb=" O PRO A 66 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N TYR A 71 " --> pdb=" O LEU A 67 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG A 78 " --> pdb=" O TRP A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 106 Processing helix chain 'A' and resid 116 through 142 removed outlier: 4.374A pdb=" N GLY A 137 " --> pdb=" O ASP A 133 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N LYS A 138 " --> pdb=" O ALA A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 172 removed outlier: 3.583A pdb=" N LEU A 160 " --> pdb=" O GLY A 156 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N VAL A 163 " --> pdb=" O SER A 159 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N PHE A 164 " --> pdb=" O LEU A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 177 No H-bonds generated for 'chain 'A' and resid 175 through 177' Processing helix chain 'A' and resid 179 through 203 Processing helix chain 'A' and resid 213 through 236 Proline residue: A 232 - end of helix Processing helix chain 'A' and resid 246 through 271 Proline residue: A 250 - end of helix removed outlier: 3.942A pdb=" N VAL A 268 " --> pdb=" O ASN A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 278 No H-bonds generated for 'chain 'A' and resid 276 through 278' Processing helix chain 'A' and resid 288 through 306 removed outlier: 4.229A pdb=" N HIS A 292 " --> pdb=" O SER A 288 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE A 293 " --> pdb=" O PRO A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 314 No H-bonds generated for 'chain 'A' and resid 311 through 314' Processing helix chain 'A' and resid 316 through 339 Processing helix chain 'A' and resid 349 through 362 removed outlier: 4.030A pdb=" N GLY A 353 " --> pdb=" O ALA A 350 " (cutoff:3.500A) Proline residue: A 354 - end of helix removed outlier: 3.539A pdb=" N LEU A 359 " --> pdb=" O LEU A 356 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN A 361 " --> pdb=" O PHE A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 399 Processing sheet with id= A, first strand: chain 'B' and resid 58 through 60 removed outlier: 5.790A pdb=" N LEU B 206 " --> pdb=" O ALA B 59 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 58 through 60 removed outlier: 5.791A pdb=" N LEU A 206 " --> pdb=" O ALA A 59 " (cutoff:3.500A) No H-bonds generated for sheet with id= B 384 hydrogen bonds defined for protein. 1122 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: 1.77 Time building geometry restraints manager: 2.56 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: 1379 1.34 - 1.45: 1411 1.45 - 1.57: 3380 1.57 - 1.69: 12 1.69 - 1.81: 66 Bond restraints: 6248 Sorted by residual: bond pdb=" CB PRO A 115 " pdb=" CG PRO A 115 " ideal model delta sigma weight residual 1.492 1.638 -0.146 5.00e-02 4.00e+02 8.56e+00 bond pdb=" CB PRO B 115 " pdb=" CG PRO B 115 " ideal model delta sigma weight residual 1.492 1.638 -0.146 5.00e-02 4.00e+02 8.55e+00 bond pdb=" CA PRO A 108 " pdb=" C PRO A 108 " ideal model delta sigma weight residual 1.517 1.559 -0.042 1.54e-02 4.22e+03 7.49e+00 bond pdb=" CA PRO B 108 " pdb=" C PRO B 108 " ideal model delta sigma weight residual 1.517 1.558 -0.042 1.54e-02 4.22e+03 7.39e+00 bond pdb=" CB PRO B 108 " pdb=" CG PRO B 108 " ideal model delta sigma weight residual 1.492 1.612 -0.120 5.00e-02 4.00e+02 5.74e+00 ... (remaining 6243 not shown) Histogram of bond angle deviations from ideal: 94.38 - 102.56: 52 102.56 - 110.73: 1929 110.73 - 118.91: 3102 118.91 - 127.08: 3341 127.08 - 135.26: 100 Bond angle restraints: 8524 Sorted by residual: angle pdb=" CA PRO A 115 " pdb=" N PRO A 115 " pdb=" CD PRO A 115 " ideal model delta sigma weight residual 112.00 99.70 12.30 1.40e+00 5.10e-01 7.72e+01 angle pdb=" CA PRO B 115 " pdb=" N PRO B 115 " pdb=" CD PRO B 115 " ideal model delta sigma weight residual 112.00 99.71 12.29 1.40e+00 5.10e-01 7.71e+01 angle pdb=" CA PRO A 108 " pdb=" N PRO A 108 " pdb=" CD PRO A 108 " ideal model delta sigma weight residual 112.00 100.26 11.74 1.40e+00 5.10e-01 7.03e+01 angle pdb=" CA PRO B 108 " pdb=" N PRO B 108 " pdb=" CD PRO B 108 " ideal model delta sigma weight residual 112.00 100.28 11.72 1.40e+00 5.10e-01 7.01e+01 angle pdb=" CA LEU A 48 " pdb=" CB LEU A 48 " pdb=" CG LEU A 48 " ideal model delta sigma weight residual 116.30 135.26 -18.96 3.50e+00 8.16e-02 2.93e+01 ... (remaining 8519 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.52: 3182 16.52 - 33.04: 286 33.04 - 49.56: 98 49.56 - 66.08: 54 66.08 - 82.61: 14 Dihedral angle restraints: 3634 sinusoidal: 1426 harmonic: 2208 Sorted by residual: dihedral pdb=" C PRO B 108 " pdb=" N PRO B 108 " pdb=" CA PRO B 108 " pdb=" CB PRO B 108 " ideal model delta harmonic sigma weight residual -120.70 -129.60 8.90 0 2.50e+00 1.60e-01 1.27e+01 dihedral pdb=" C PRO A 108 " pdb=" N PRO A 108 " pdb=" CA PRO A 108 " pdb=" CB PRO A 108 " ideal model delta harmonic sigma weight residual -120.70 -129.55 8.85 0 2.50e+00 1.60e-01 1.25e+01 dihedral pdb=" CA ASP A 348 " pdb=" CB ASP A 348 " pdb=" CG ASP A 348 " pdb=" OD1 ASP A 348 " ideal model delta sinusoidal sigma weight residual -30.00 -89.32 59.32 1 2.00e+01 2.50e-03 1.18e+01 ... (remaining 3631 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 758 0.081 - 0.162: 188 0.162 - 0.244: 30 0.244 - 0.325: 6 0.325 - 0.406: 2 Chirality restraints: 984 Sorted by residual: chirality pdb=" CA PRO B 108 " pdb=" N PRO B 108 " pdb=" C PRO B 108 " pdb=" CB PRO B 108 " both_signs ideal model delta sigma weight residual False 2.72 2.31 0.41 2.00e-01 2.50e+01 4.12e+00 chirality pdb=" CA PRO A 108 " pdb=" N PRO A 108 " pdb=" C PRO A 108 " pdb=" CB PRO A 108 " both_signs ideal model delta sigma weight residual False 2.72 2.32 0.40 2.00e-01 2.50e+01 4.04e+00 chirality pdb=" CB THR A 214 " pdb=" CA THR A 214 " pdb=" OG1 THR A 214 " pdb=" CG2 THR A 214 " both_signs ideal model delta sigma weight residual False 2.55 2.26 0.29 2.00e-01 2.50e+01 2.13e+00 ... (remaining 981 not shown) Planarity restraints: 1036 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 114 " 0.103 5.00e-02 4.00e+02 1.45e-01 3.39e+01 pdb=" N PRO A 115 " -0.251 5.00e-02 4.00e+02 pdb=" CA PRO A 115 " 0.074 5.00e-02 4.00e+02 pdb=" CD PRO A 115 " 0.075 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 114 " 0.102 5.00e-02 4.00e+02 1.45e-01 3.37e+01 pdb=" N PRO B 115 " -0.251 5.00e-02 4.00e+02 pdb=" CA PRO B 115 " 0.073 5.00e-02 4.00e+02 pdb=" CD PRO B 115 " 0.075 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS A 107 " -0.094 5.00e-02 4.00e+02 1.33e-01 2.83e+01 pdb=" N PRO A 108 " 0.230 5.00e-02 4.00e+02 pdb=" CA PRO A 108 " -0.064 5.00e-02 4.00e+02 pdb=" CD PRO A 108 " -0.071 5.00e-02 4.00e+02 ... (remaining 1033 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 40 2.59 - 3.17: 5070 3.17 - 3.74: 9924 3.74 - 4.32: 12183 4.32 - 4.90: 20526 Nonbonded interactions: 47743 Sorted by model distance: nonbonded pdb=" OD1 ASP B 154 " pdb="MG MG B 502 " model vdw 2.008 2.170 nonbonded pdb=" OD1 ASP A 154 " pdb="MG MG A 502 " model vdw 2.009 2.170 nonbonded pdb="MG MG B 502 " pdb=" O2B CDC B 503 " model vdw 2.085 2.170 nonbonded pdb="MG MG A 502 " pdb=" O2B CDC A 503 " model vdw 2.086 2.170 nonbonded pdb=" OD1 ASP A 180 " pdb=" OH TYR A 304 " model vdw 2.269 2.440 ... (remaining 47738 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 0.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.080 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 21.120 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 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 : 0.008 0.146 6248 Z= 0.529 Angle : 1.459 18.960 8524 Z= 0.833 Chirality : 0.077 0.406 984 Planarity : 0.015 0.199 1036 Dihedral : 16.780 82.606 2210 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 0.30 % Allowed : 19.94 % Favored : 79.76 % 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: 1.24 (0.29), residues: 756 helix: 0.99 (0.20), residues: 554 sheet: None (None), residues: 0 loop : 0.67 (0.47), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.004 TRP B 181 HIS 0.007 0.002 HIS A 46 PHE 0.069 0.004 PHE B 234 TYR 0.047 0.006 TYR A 362 ARG 0.010 0.002 ARG A 77 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 190 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 69 GLN cc_start: 0.8807 (mt0) cc_final: 0.8524 (mt0) REVERT: B 82 TRP cc_start: 0.8514 (p90) cc_final: 0.8297 (p90) REVERT: B 130 GLN cc_start: 0.8216 (tp40) cc_final: 0.7863 (tp-100) REVERT: B 344 MET cc_start: 0.7872 (mtp) cc_final: 0.7572 (mtt) REVERT: B 361 GLN cc_start: 0.8418 (mm-40) cc_final: 0.8108 (mm-40) REVERT: A 82 TRP cc_start: 0.8500 (p90) cc_final: 0.8279 (p90) REVERT: A 130 GLN cc_start: 0.8265 (tp40) cc_final: 0.7914 (tp-100) REVERT: A 361 GLN cc_start: 0.8537 (mm-40) cc_final: 0.8294 (mm-40) outliers start: 2 outliers final: 0 residues processed: 192 average time/residue: 0.1993 time to fit residues: 48.4345 Evaluate side-chains 172 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 172 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 64 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 31 optimal weight: 0.1980 chunk 19 optimal weight: 2.9990 chunk 38 optimal weight: 10.0000 chunk 30 optimal weight: 0.9990 chunk 59 optimal weight: 0.0370 chunk 23 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 44 optimal weight: 0.6980 chunk 69 optimal weight: 0.5980 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 197 HIS A 69 GLN A 197 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 6248 Z= 0.173 Angle : 0.589 6.935 8524 Z= 0.303 Chirality : 0.041 0.126 984 Planarity : 0.005 0.051 1036 Dihedral : 7.670 53.521 874 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 3.63 % Allowed : 16.77 % Favored : 79.61 % 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: 2.78 (0.29), residues: 756 helix: 2.20 (0.20), residues: 544 sheet: None (None), residues: 0 loop : 1.07 (0.46), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 117 HIS 0.002 0.000 HIS B 46 PHE 0.014 0.002 PHE B 404 TYR 0.012 0.001 TYR B 387 ARG 0.007 0.001 ARG B 141 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 178 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 45 ARG cc_start: 0.7328 (ttt90) cc_final: 0.6942 (tmm160) REVERT: B 68 MET cc_start: 0.8872 (OUTLIER) cc_final: 0.8585 (mmm) REVERT: B 142 ARG cc_start: 0.8162 (tpt90) cc_final: 0.7843 (tpt90) REVERT: B 260 PHE cc_start: 0.8627 (OUTLIER) cc_final: 0.8327 (t80) REVERT: B 302 MET cc_start: 0.8761 (mmm) cc_final: 0.8556 (mmt) REVERT: B 359 LEU cc_start: 0.8304 (mt) cc_final: 0.7850 (tp) REVERT: A 45 ARG cc_start: 0.7310 (ttt90) cc_final: 0.6901 (tmm160) REVERT: A 142 ARG cc_start: 0.8261 (tpt90) cc_final: 0.7933 (tpt90) REVERT: A 260 PHE cc_start: 0.8572 (OUTLIER) cc_final: 0.8345 (t80) REVERT: A 359 LEU cc_start: 0.8263 (mt) cc_final: 0.7800 (tp) outliers start: 24 outliers final: 14 residues processed: 189 average time/residue: 0.2151 time to fit residues: 50.8515 Evaluate side-chains 185 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 168 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 68 MET Chi-restraints excluded: chain B residue 153 PHE Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 260 PHE Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 153 PHE Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 260 PHE Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 378 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 38 optimal weight: 10.0000 chunk 21 optimal weight: 8.9990 chunk 57 optimal weight: 7.9990 chunk 46 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 69 optimal weight: 0.8980 chunk 74 optimal weight: 0.9990 chunk 61 optimal weight: 7.9990 chunk 68 optimal weight: 0.7980 chunk 23 optimal weight: 7.9990 chunk 55 optimal weight: 3.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 69 GLN A 69 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.3220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 6248 Z= 0.326 Angle : 0.647 7.207 8524 Z= 0.336 Chirality : 0.044 0.166 984 Planarity : 0.004 0.032 1036 Dihedral : 5.640 37.931 874 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.13 % Allowed : 1.19 % Favored : 98.68 % Rotamer: Outliers : 6.34 % Allowed : 17.67 % Favored : 75.98 % 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: 2.63 (0.29), residues: 756 helix: 2.02 (0.20), residues: 554 sheet: None (None), residues: 0 loop : 1.18 (0.47), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 374 HIS 0.004 0.001 HIS B 315 PHE 0.020 0.002 PHE A 234 TYR 0.018 0.002 TYR B 304 ARG 0.005 0.001 ARG A 50 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 190 time to evaluate : 0.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 45 ARG cc_start: 0.7489 (ttt90) cc_final: 0.6984 (tmm160) REVERT: B 98 CYS cc_start: 0.7742 (m) cc_final: 0.7389 (p) REVERT: B 142 ARG cc_start: 0.8416 (tpt90) cc_final: 0.8089 (tpt90) REVERT: B 260 PHE cc_start: 0.8679 (OUTLIER) cc_final: 0.8248 (t80) REVERT: B 302 MET cc_start: 0.8863 (mmm) cc_final: 0.8474 (mtt) REVERT: B 307 SER cc_start: 0.9108 (t) cc_final: 0.8838 (t) REVERT: A 45 ARG cc_start: 0.7611 (ttt90) cc_final: 0.7118 (tmm160) REVERT: A 98 CYS cc_start: 0.7749 (m) cc_final: 0.7348 (p) REVERT: A 127 PHE cc_start: 0.8779 (t80) cc_final: 0.8543 (t80) REVERT: A 142 ARG cc_start: 0.8403 (tpt90) cc_final: 0.7998 (tpt90) REVERT: A 260 PHE cc_start: 0.8701 (OUTLIER) cc_final: 0.8328 (t80) REVERT: A 307 SER cc_start: 0.9108 (t) cc_final: 0.8829 (t) outliers start: 42 outliers final: 34 residues processed: 210 average time/residue: 0.2104 time to fit residues: 55.7054 Evaluate side-chains 205 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 169 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 153 PHE Chi-restraints excluded: chain B residue 170 CYS Chi-restraints excluded: chain B residue 186 CYS Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 253 CYS Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 260 PHE Chi-restraints excluded: chain B residue 288 SER Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 388 CYS Chi-restraints excluded: chain B residue 392 CYS Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 153 PHE Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain A residue 186 CYS Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 253 CYS Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 260 PHE Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 388 CYS Chi-restraints excluded: chain A residue 392 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 68 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 7 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 69 GLN A 69 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.3436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6248 Z= 0.202 Angle : 0.557 7.621 8524 Z= 0.289 Chirality : 0.041 0.156 984 Planarity : 0.004 0.032 1036 Dihedral : 5.686 41.072 874 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 6.19 % Allowed : 20.39 % Favored : 73.41 % 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: 2.90 (0.30), residues: 756 helix: 2.20 (0.21), residues: 550 sheet: None (None), residues: 0 loop : 1.37 (0.48), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 374 HIS 0.003 0.001 HIS B 46 PHE 0.019 0.002 PHE B 234 TYR 0.016 0.001 TYR B 304 ARG 0.003 0.000 ARG B 50 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 170 time to evaluate : 0.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 45 ARG cc_start: 0.7461 (ttt90) cc_final: 0.6960 (tmm160) REVERT: B 127 PHE cc_start: 0.8833 (t80) cc_final: 0.8589 (t80) REVERT: B 142 ARG cc_start: 0.8402 (tpt90) cc_final: 0.8111 (tpt90) REVERT: B 260 PHE cc_start: 0.8660 (OUTLIER) cc_final: 0.8170 (t80) REVERT: B 302 MET cc_start: 0.8858 (mmm) cc_final: 0.8532 (mtt) REVERT: B 307 SER cc_start: 0.9119 (t) cc_final: 0.8886 (t) REVERT: A 45 ARG cc_start: 0.7541 (ttt90) cc_final: 0.7069 (tmm160) REVERT: A 127 PHE cc_start: 0.8813 (t80) cc_final: 0.8600 (t80) REVERT: A 307 SER cc_start: 0.9055 (t) cc_final: 0.8814 (t) outliers start: 41 outliers final: 30 residues processed: 188 average time/residue: 0.2226 time to fit residues: 52.0833 Evaluate side-chains 197 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 166 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 153 PHE Chi-restraints excluded: chain B residue 170 CYS Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 253 CYS Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 260 PHE Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 153 PHE Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 253 CYS Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 390 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 61 optimal weight: 7.9990 chunk 41 optimal weight: 2.9990 chunk 1 optimal weight: 0.0970 chunk 54 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 37 optimal weight: 7.9990 chunk 65 optimal weight: 2.9990 chunk 18 optimal weight: 8.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.3996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 6248 Z= 0.354 Angle : 0.656 7.438 8524 Z= 0.340 Chirality : 0.044 0.151 984 Planarity : 0.004 0.031 1036 Dihedral : 5.679 37.385 874 Min Nonbonded Distance : 1.258 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 8.61 % Allowed : 20.09 % Favored : 71.30 % 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: 2.37 (0.30), residues: 756 helix: 1.77 (0.21), residues: 562 sheet: None (None), residues: 0 loop : 1.24 (0.50), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 374 HIS 0.004 0.001 HIS B 398 PHE 0.014 0.002 PHE A 184 TYR 0.022 0.002 TYR B 129 ARG 0.003 0.000 ARG A 50 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 185 time to evaluate : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 127 PHE cc_start: 0.8816 (t80) cc_final: 0.8552 (t80) REVERT: B 130 GLN cc_start: 0.8157 (tp40) cc_final: 0.7891 (tp-100) REVERT: B 182 MET cc_start: 0.8635 (OUTLIER) cc_final: 0.8101 (ttp) REVERT: B 260 PHE cc_start: 0.8704 (OUTLIER) cc_final: 0.8151 (t80) REVERT: A 45 ARG cc_start: 0.7580 (ttt90) cc_final: 0.7079 (tmm160) REVERT: A 55 ARG cc_start: 0.7986 (tpp80) cc_final: 0.7742 (mpt-90) REVERT: A 127 PHE cc_start: 0.8884 (t80) cc_final: 0.8644 (t80) REVERT: A 182 MET cc_start: 0.8625 (OUTLIER) cc_final: 0.8158 (ttp) REVERT: A 260 PHE cc_start: 0.8705 (OUTLIER) cc_final: 0.8187 (t80) outliers start: 57 outliers final: 44 residues processed: 214 average time/residue: 0.2068 time to fit residues: 55.5021 Evaluate side-chains 220 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 172 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 153 PHE Chi-restraints excluded: chain B residue 170 CYS Chi-restraints excluded: chain B residue 182 MET Chi-restraints excluded: chain B residue 186 CYS Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 253 CYS Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 260 PHE Chi-restraints excluded: chain B residue 288 SER Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 388 CYS Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 392 CYS Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 153 PHE Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain A residue 182 MET Chi-restraints excluded: chain A residue 186 CYS Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 253 CYS Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 260 PHE Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 388 CYS Chi-restraints excluded: chain A residue 390 SER Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 392 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 24 optimal weight: 0.7980 chunk 66 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 43 optimal weight: 9.9990 chunk 18 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 chunk 61 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 38 optimal weight: 10.0000 chunk 70 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.4132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6248 Z= 0.199 Angle : 0.589 8.093 8524 Z= 0.298 Chirality : 0.040 0.137 984 Planarity : 0.004 0.031 1036 Dihedral : 5.861 41.795 874 Min Nonbonded Distance : 1.184 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 6.34 % Allowed : 25.53 % Favored : 68.13 % 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: 2.54 (0.30), residues: 756 helix: 1.93 (0.21), residues: 560 sheet: None (None), residues: 0 loop : 1.17 (0.51), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 181 HIS 0.002 0.001 HIS A 315 PHE 0.018 0.001 PHE B 234 TYR 0.018 0.002 TYR A 129 ARG 0.003 0.000 ARG B 142 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 181 time to evaluate : 0.668 Fit side-chains revert: symmetry clash REVERT: B 127 PHE cc_start: 0.8823 (t80) cc_final: 0.8583 (t80) REVERT: B 130 GLN cc_start: 0.8184 (tp40) cc_final: 0.7853 (tp-100) REVERT: B 260 PHE cc_start: 0.8683 (OUTLIER) cc_final: 0.8149 (t80) REVERT: A 127 PHE cc_start: 0.8813 (t80) cc_final: 0.8588 (t80) REVERT: A 260 PHE cc_start: 0.8684 (OUTLIER) cc_final: 0.8087 (t80) outliers start: 42 outliers final: 34 residues processed: 194 average time/residue: 0.1977 time to fit residues: 49.3239 Evaluate side-chains 207 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 171 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 153 PHE Chi-restraints excluded: chain B residue 170 CYS Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 260 PHE Chi-restraints excluded: chain B residue 288 SER Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 392 CYS Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 153 PHE Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 260 PHE Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 392 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 8 optimal weight: 0.3980 chunk 41 optimal weight: 10.0000 chunk 53 optimal weight: 2.9990 chunk 61 optimal weight: 7.9990 chunk 73 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 33 optimal weight: 0.0980 chunk 29 optimal weight: 0.9980 chunk 43 optimal weight: 9.9990 chunk 22 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.4257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 6248 Z= 0.226 Angle : 0.618 8.877 8524 Z= 0.308 Chirality : 0.040 0.132 984 Planarity : 0.004 0.031 1036 Dihedral : 5.794 41.973 874 Min Nonbonded Distance : 1.222 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 7.25 % Allowed : 24.47 % Favored : 68.28 % 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: 2.52 (0.30), residues: 756 helix: 1.93 (0.21), residues: 560 sheet: None (None), residues: 0 loop : 1.14 (0.51), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 82 HIS 0.002 0.001 HIS B 315 PHE 0.016 0.001 PHE A 234 TYR 0.019 0.002 TYR A 129 ARG 0.001 0.000 ARG A 61 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 179 time to evaluate : 0.698 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 182 MET cc_start: 0.8482 (OUTLIER) cc_final: 0.7988 (ttp) REVERT: B 260 PHE cc_start: 0.8677 (OUTLIER) cc_final: 0.8141 (t80) REVERT: A 127 PHE cc_start: 0.8953 (t80) cc_final: 0.8729 (t80) REVERT: A 130 GLN cc_start: 0.8226 (tp40) cc_final: 0.7920 (tp40) REVERT: A 182 MET cc_start: 0.8503 (OUTLIER) cc_final: 0.7945 (ttp) REVERT: A 260 PHE cc_start: 0.8676 (OUTLIER) cc_final: 0.8087 (t80) outliers start: 48 outliers final: 41 residues processed: 197 average time/residue: 0.1946 time to fit residues: 48.9815 Evaluate side-chains 214 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 169 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 153 PHE Chi-restraints excluded: chain B residue 170 CYS Chi-restraints excluded: chain B residue 182 MET Chi-restraints excluded: chain B residue 185 CYS Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 260 PHE Chi-restraints excluded: chain B residue 288 SER Chi-restraints excluded: chain B residue 307 SER Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 392 CYS Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 153 PHE Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain A residue 182 MET Chi-restraints excluded: chain A residue 185 CYS Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 260 PHE Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 392 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 14 optimal weight: 0.3980 chunk 46 optimal weight: 1.9990 chunk 49 optimal weight: 9.9990 chunk 36 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 chunk 57 optimal weight: 0.7980 chunk 66 optimal weight: 0.9990 chunk 70 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 41 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.4365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6248 Z= 0.194 Angle : 0.622 10.290 8524 Z= 0.308 Chirality : 0.040 0.133 984 Planarity : 0.004 0.031 1036 Dihedral : 5.856 43.118 874 Min Nonbonded Distance : 1.203 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 5.59 % Allowed : 26.89 % Favored : 67.52 % 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: 2.59 (0.30), residues: 756 helix: 1.98 (0.21), residues: 560 sheet: None (None), residues: 0 loop : 1.13 (0.51), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 235 HIS 0.002 0.001 HIS A 315 PHE 0.019 0.001 PHE B 234 TYR 0.020 0.002 TYR A 129 ARG 0.004 0.000 ARG B 61 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 174 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 130 GLN cc_start: 0.8216 (tp40) cc_final: 0.7971 (tp-100) REVERT: B 182 MET cc_start: 0.8416 (OUTLIER) cc_final: 0.7965 (ttp) REVERT: B 260 PHE cc_start: 0.8694 (OUTLIER) cc_final: 0.8066 (t80) REVERT: A 127 PHE cc_start: 0.8993 (t80) cc_final: 0.8754 (t80) REVERT: A 182 MET cc_start: 0.8464 (OUTLIER) cc_final: 0.7946 (ttp) REVERT: A 260 PHE cc_start: 0.8715 (OUTLIER) cc_final: 0.8132 (t80) outliers start: 37 outliers final: 33 residues processed: 188 average time/residue: 0.1827 time to fit residues: 44.2519 Evaluate side-chains 203 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 166 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 153 PHE Chi-restraints excluded: chain B residue 170 CYS Chi-restraints excluded: chain B residue 182 MET Chi-restraints excluded: chain B residue 185 CYS Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 260 PHE Chi-restraints excluded: chain B residue 288 SER Chi-restraints excluded: chain B residue 307 SER Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 153 PHE Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain A residue 182 MET Chi-restraints excluded: chain A residue 185 CYS Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 260 PHE Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 359 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 29 optimal weight: 0.8980 chunk 53 optimal weight: 0.5980 chunk 20 optimal weight: 6.9990 chunk 61 optimal weight: 10.0000 chunk 64 optimal weight: 0.4980 chunk 68 optimal weight: 0.6980 chunk 44 optimal weight: 0.8980 chunk 72 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 chunk 75 optimal weight: 0.4980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.4439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6248 Z= 0.191 Angle : 0.617 9.543 8524 Z= 0.306 Chirality : 0.040 0.134 984 Planarity : 0.004 0.032 1036 Dihedral : 5.837 44.116 874 Min Nonbonded Distance : 1.193 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 6.04 % Allowed : 27.19 % Favored : 66.77 % 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: 2.70 (0.31), residues: 756 helix: 2.08 (0.21), residues: 560 sheet: None (None), residues: 0 loop : 1.13 (0.53), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 117 HIS 0.002 0.000 HIS A 315 PHE 0.018 0.001 PHE A 234 TYR 0.020 0.002 TYR A 129 ARG 0.003 0.000 ARG B 61 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 163 time to evaluate : 0.699 Fit side-chains REVERT: B 182 MET cc_start: 0.8424 (OUTLIER) cc_final: 0.7979 (ttp) REVERT: B 260 PHE cc_start: 0.8662 (OUTLIER) cc_final: 0.8015 (t80) REVERT: A 127 PHE cc_start: 0.8962 (t80) cc_final: 0.8732 (t80) REVERT: A 128 ILE cc_start: 0.9460 (mt) cc_final: 0.9184 (mt) REVERT: A 130 GLN cc_start: 0.8234 (tp40) cc_final: 0.7990 (tp40) REVERT: A 182 MET cc_start: 0.8469 (OUTLIER) cc_final: 0.7954 (ttp) REVERT: A 223 MET cc_start: 0.8462 (ttm) cc_final: 0.8157 (ttm) REVERT: A 246 MET cc_start: 0.7919 (tpp) cc_final: 0.7662 (tpp) REVERT: A 260 PHE cc_start: 0.8665 (OUTLIER) cc_final: 0.8093 (t80) outliers start: 40 outliers final: 35 residues processed: 183 average time/residue: 0.1775 time to fit residues: 42.1761 Evaluate side-chains 201 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 162 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 153 PHE Chi-restraints excluded: chain B residue 170 CYS Chi-restraints excluded: chain B residue 182 MET Chi-restraints excluded: chain B residue 185 CYS Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 260 PHE Chi-restraints excluded: chain B residue 307 SER Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 153 PHE Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain A residue 182 MET Chi-restraints excluded: chain A residue 185 CYS Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 260 PHE Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 390 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 69 optimal weight: 7.9990 chunk 60 optimal weight: 0.7980 chunk 6 optimal weight: 0.7980 chunk 46 optimal weight: 0.4980 chunk 36 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 64 optimal weight: 0.4980 chunk 18 optimal weight: 9.9990 chunk 55 optimal weight: 0.9990 chunk 8 optimal weight: 0.2980 chunk 16 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 197 HIS A 197 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.4496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6248 Z= 0.186 Angle : 0.613 9.979 8524 Z= 0.304 Chirality : 0.039 0.142 984 Planarity : 0.004 0.032 1036 Dihedral : 5.817 44.922 874 Min Nonbonded Distance : 1.189 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 6.50 % Allowed : 27.04 % Favored : 66.47 % 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: 2.83 (0.31), residues: 756 helix: 2.22 (0.21), residues: 550 sheet: None (None), residues: 0 loop : 1.09 (0.51), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 117 HIS 0.002 0.000 HIS A 197 PHE 0.022 0.001 PHE B 234 TYR 0.021 0.002 TYR A 129 ARG 0.003 0.000 ARG B 61 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 168 time to evaluate : 0.681 Fit side-chains REVERT: B 61 ARG cc_start: 0.7680 (mtp85) cc_final: 0.7375 (mtp85) REVERT: B 130 GLN cc_start: 0.8204 (tp40) cc_final: 0.7987 (tp40) REVERT: B 182 MET cc_start: 0.8449 (OUTLIER) cc_final: 0.8018 (ttp) REVERT: B 260 PHE cc_start: 0.8642 (OUTLIER) cc_final: 0.7988 (t80) REVERT: A 52 GLU cc_start: 0.8730 (tp30) cc_final: 0.8423 (tm-30) REVERT: A 127 PHE cc_start: 0.8988 (t80) cc_final: 0.8749 (t80) REVERT: A 128 ILE cc_start: 0.9444 (mt) cc_final: 0.9163 (mt) REVERT: A 130 GLN cc_start: 0.8274 (tp40) cc_final: 0.8013 (tp40) REVERT: A 182 MET cc_start: 0.8489 (OUTLIER) cc_final: 0.8018 (ttp) REVERT: A 223 MET cc_start: 0.8431 (ttm) cc_final: 0.8105 (ttm) REVERT: A 246 MET cc_start: 0.7922 (tpp) cc_final: 0.7659 (tpp) REVERT: A 260 PHE cc_start: 0.8620 (OUTLIER) cc_final: 0.8075 (t80) outliers start: 43 outliers final: 36 residues processed: 189 average time/residue: 0.1814 time to fit residues: 44.2498 Evaluate side-chains 207 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 167 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 153 PHE Chi-restraints excluded: chain B residue 170 CYS Chi-restraints excluded: chain B residue 182 MET Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 260 PHE Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 288 SER Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain A residue 182 MET Chi-restraints excluded: chain A residue 185 CYS Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 260 PHE Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 390 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 60 optimal weight: 0.9980 chunk 25 optimal weight: 7.9990 chunk 62 optimal weight: 0.0050 chunk 7 optimal weight: 0.6980 chunk 11 optimal weight: 10.0000 chunk 53 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 43 optimal weight: 0.0070 chunk 69 optimal weight: 7.9990 chunk 40 optimal weight: 0.2980 chunk 51 optimal weight: 0.6980 overall best weight: 0.3412 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.176985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.139387 restraints weight = 8231.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.144877 restraints weight = 4425.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.148582 restraints weight = 2930.369| |-----------------------------------------------------------------------------| r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.4590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6248 Z= 0.175 Angle : 0.611 9.663 8524 Z= 0.304 Chirality : 0.041 0.375 984 Planarity : 0.004 0.033 1036 Dihedral : 5.853 45.898 874 Min Nonbonded Distance : 1.211 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 5.14 % Allowed : 29.00 % Favored : 65.86 % 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: 2.94 (0.31), residues: 756 helix: 2.30 (0.21), residues: 550 sheet: None (None), residues: 0 loop : 1.12 (0.52), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 198 HIS 0.003 0.001 HIS B 197 PHE 0.025 0.001 PHE A 234 TYR 0.021 0.002 TYR B 129 ARG 0.007 0.000 ARG B 55 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1601.31 seconds wall clock time: 29 minutes 50.92 seconds (1790.92 seconds total)