Starting phenix.real_space_refine on Mon Feb 10 22:11:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rtv_24690/02_2025/7rtv_24690.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rtv_24690/02_2025/7rtv_24690.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7rtv_24690/02_2025/7rtv_24690.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rtv_24690/02_2025/7rtv_24690.map" model { file = "/net/cci-nas-00/data/ceres_data/7rtv_24690/02_2025/7rtv_24690.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rtv_24690/02_2025/7rtv_24690.cif" } resolution = 3.96 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.044 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 25 5.16 5 C 1846 2.51 5 N 460 2.21 5 O 550 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 2881 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2803 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 7, 'TRANS': 358} Chain breaks: 1 Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 2.21, per 1000 atoms: 0.77 Number of scatterers: 2881 At special positions: 0 Unit cell: (62.863, 52.669, 135.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 25 16.00 O 550 8.00 N 460 7.00 C 1846 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 274 " - pdb=" SG CYS A 382 " distance=2.03 Simple disulfide: pdb=" SG CYS A 300 " - pdb=" SG CYS A 367 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " NAG-ASN " NAG B 1 " - " ASN A 129 " " NAG C 1 " - " ASN A 352 " Time building additional restraints: 1.02 Conformation dependent library (CDL) restraints added in 355.7 milliseconds 724 Ramachandran restraints generated. 362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 680 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 0 sheets defined 92.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 39 through 73 removed outlier: 4.152A pdb=" N CYS A 73 " --> pdb=" O CYS A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 161 Processing helix chain 'A' and resid 162 through 164 No H-bonds generated for 'chain 'A' and resid 162 through 164' Processing helix chain 'A' and resid 167 through 187 Processing helix chain 'A' and resid 191 through 236 Processing helix chain 'A' and resid 240 through 274 removed outlier: 3.951A pdb=" N LEU A 246 " --> pdb=" O LEU A 242 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N CYS A 247 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N CYS A 248 " --> pdb=" O SER A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 286 removed outlier: 4.318A pdb=" N TYR A 280 " --> pdb=" O ALA A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 299 removed outlier: 3.530A pdb=" N THR A 294 " --> pdb=" O ASN A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 333 removed outlier: 3.507A pdb=" N LEU A 312 " --> pdb=" O PHE A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 366 removed outlier: 3.618A pdb=" N GLU A 341 " --> pdb=" O PHE A 337 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASP A 366 " --> pdb=" O THR A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 409 removed outlier: 4.054A pdb=" N ASP A 384 " --> pdb=" O GLY A 380 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N GLU A 387 " --> pdb=" O TYR A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 414 280 hydrogen bonds defined for protein. 834 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.79 Time building geometry restraints manager: 1.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 903 1.34 - 1.46: 530 1.46 - 1.58: 1465 1.58 - 1.69: 0 1.69 - 1.81: 34 Bond restraints: 2932 Sorted by residual: bond pdb=" C1 BMA B 3 " pdb=" C2 BMA B 3 " ideal model delta sigma weight residual 1.519 1.574 -0.055 2.00e-02 2.50e+03 7.58e+00 bond pdb=" C1 BMA B 3 " pdb=" O5 BMA B 3 " ideal model delta sigma weight residual 1.410 1.452 -0.042 2.00e-02 2.50e+03 4.32e+00 bond pdb=" C1 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 4.09e+00 bond pdb=" C1 BMA C 3 " pdb=" C2 BMA C 3 " ideal model delta sigma weight residual 1.519 1.549 -0.030 2.00e-02 2.50e+03 2.26e+00 bond pdb=" C1 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.14e+00 ... (remaining 2927 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.76: 3857 1.76 - 3.52: 101 3.52 - 5.28: 16 5.28 - 7.05: 10 7.05 - 8.81: 5 Bond angle restraints: 3989 Sorted by residual: angle pdb=" C GLN A 176 " pdb=" N MET A 177 " pdb=" CA MET A 177 " ideal model delta sigma weight residual 121.58 113.37 8.21 1.95e+00 2.63e-01 1.77e+01 angle pdb=" CA MET A 177 " pdb=" CB MET A 177 " pdb=" CG MET A 177 " ideal model delta sigma weight residual 114.10 120.21 -6.11 2.00e+00 2.50e-01 9.33e+00 angle pdb=" CB MET A 174 " pdb=" CG MET A 174 " pdb=" SD MET A 174 " ideal model delta sigma weight residual 112.70 121.51 -8.81 3.00e+00 1.11e-01 8.62e+00 angle pdb=" N MET A 177 " pdb=" CA MET A 177 " pdb=" CB MET A 177 " ideal model delta sigma weight residual 110.41 115.33 -4.92 1.68e+00 3.54e-01 8.59e+00 angle pdb=" CA GLN A 144 " pdb=" CB GLN A 144 " pdb=" CG GLN A 144 " ideal model delta sigma weight residual 114.10 119.15 -5.05 2.00e+00 2.50e-01 6.37e+00 ... (remaining 3984 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.21: 1630 24.21 - 48.42: 102 48.42 - 72.63: 32 72.63 - 96.84: 10 96.84 - 121.05: 30 Dihedral angle restraints: 1804 sinusoidal: 746 harmonic: 1058 Sorted by residual: dihedral pdb=" CB CYS A 274 " pdb=" SG CYS A 274 " pdb=" SG CYS A 382 " pdb=" CB CYS A 382 " ideal model delta sinusoidal sigma weight residual 93.00 172.83 -79.83 1 1.00e+01 1.00e-02 7.90e+01 dihedral pdb=" CB CYS A 300 " pdb=" SG CYS A 300 " pdb=" SG CYS A 367 " pdb=" CB CYS A 367 " ideal model delta sinusoidal sigma weight residual 93.00 132.56 -39.56 1 1.00e+01 1.00e-02 2.20e+01 dihedral pdb=" O4 BMA B 3 " pdb=" C4 BMA B 3 " pdb=" C5 BMA B 3 " pdb=" O5 BMA B 3 " ideal model delta sinusoidal sigma weight residual 288.71 167.66 121.05 1 3.00e+01 1.11e-03 1.62e+01 ... (remaining 1801 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 412 0.054 - 0.107: 78 0.107 - 0.161: 7 0.161 - 0.214: 3 0.214 - 0.268: 2 Chirality restraints: 502 Sorted by residual: chirality pdb=" C5 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C6 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" C5 BMA B 3 " pdb=" C4 BMA B 3 " pdb=" C6 BMA B 3 " pdb=" O5 BMA B 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" C1 NAG B 1 " pdb=" ND2 ASN A 129 " pdb=" C2 NAG B 1 " pdb=" O5 NAG B 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 9.52e-01 ... (remaining 499 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 410 " -0.053 5.00e-02 4.00e+02 8.01e-02 1.03e+01 pdb=" N PRO A 411 " 0.139 5.00e-02 4.00e+02 pdb=" CA PRO A 411 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO A 411 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 381 " 0.007 2.00e-02 2.50e+03 1.47e-02 2.17e+00 pdb=" C ILE A 381 " -0.026 2.00e-02 2.50e+03 pdb=" O ILE A 381 " 0.010 2.00e-02 2.50e+03 pdb=" N CYS A 382 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 382 " -0.007 2.00e-02 2.50e+03 1.45e-02 2.11e+00 pdb=" C CYS A 382 " 0.025 2.00e-02 2.50e+03 pdb=" O CYS A 382 " -0.009 2.00e-02 2.50e+03 pdb=" N TYR A 383 " -0.008 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 387 2.75 - 3.28: 3201 3.28 - 3.82: 5090 3.82 - 4.36: 5147 4.36 - 4.90: 8800 Nonbonded interactions: 22625 Sorted by model distance: nonbonded pdb=" O SER A 256 " pdb=" OG SER A 396 " model vdw 2.207 3.040 nonbonded pdb=" O GLY A 117 " pdb=" NE2 GLN A 120 " model vdw 2.228 3.120 nonbonded pdb=" O SER A 183 " pdb=" OG SER A 186 " model vdw 2.259 3.040 nonbonded pdb=" O CYS A 300 " pdb=" NH2 ARG A 368 " model vdw 2.308 3.120 nonbonded pdb=" ND2 ASN A 115 " pdb=" OE2 GLU A 209 " model vdw 2.319 3.120 ... (remaining 22620 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' } 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: 0.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.650 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6368 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 0.055 2932 Z= 0.257 Angle : 0.763 8.808 3989 Z= 0.350 Chirality : 0.045 0.268 502 Planarity : 0.005 0.080 486 Dihedral : 24.992 121.052 1118 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.32 % Allowed : 1.95 % Favored : 97.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.61 (0.44), residues: 362 helix: 2.84 (0.28), residues: 321 sheet: None (None), residues: 0 loop : -1.76 (1.14), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 257 HIS 0.003 0.001 HIS A 359 PHE 0.022 0.002 PHE A 220 TYR 0.015 0.001 TYR A 66 ARG 0.003 0.001 ARG A 192 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 724 Ramachandran restraints generated. 362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 724 Ramachandran restraints generated. 362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 93 time to evaluate : 0.310 Fit side-chains REVERT: A 127 ASN cc_start: 0.7972 (m110) cc_final: 0.7152 (m-40) REVERT: A 132 PHE cc_start: 0.7293 (m-80) cc_final: 0.7026 (m-10) REVERT: A 177 MET cc_start: 0.7020 (pmm) cc_final: 0.6597 (pmm) REVERT: A 372 LYS cc_start: 0.8838 (tttp) cc_final: 0.8365 (tttm) outliers start: 1 outliers final: 0 residues processed: 94 average time/residue: 0.1352 time to fit residues: 15.4664 Evaluate side-chains 76 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 30 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 18 optimal weight: 4.9990 chunk 14 optimal weight: 0.2980 chunk 28 optimal weight: 0.0030 chunk 10 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 21 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 overall best weight: 0.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 ASN A 152 GLN A 359 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4703 r_free = 0.4703 target = 0.233393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.199612 restraints weight = 4581.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.205863 restraints weight = 2915.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4495 r_free = 0.4495 target = 0.210064 restraints weight = 2061.945| |-----------------------------------------------------------------------------| r_work (final): 0.4481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6410 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2932 Z= 0.179 Angle : 0.740 8.162 3989 Z= 0.341 Chirality : 0.046 0.252 502 Planarity : 0.004 0.049 486 Dihedral : 24.738 111.752 511 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.92 % Allowed : 12.66 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.62 (0.43), residues: 362 helix: 2.85 (0.27), residues: 322 sheet: None (None), residues: 0 loop : -1.81 (1.13), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 257 HIS 0.003 0.001 HIS A 359 PHE 0.017 0.002 PHE A 395 TYR 0.019 0.001 TYR A 296 ARG 0.003 0.000 ARG A 236 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 724 Ramachandran restraints generated. 362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 724 Ramachandran restraints generated. 362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 90 time to evaluate : 0.284 Fit side-chains REVERT: A 127 ASN cc_start: 0.7617 (m110) cc_final: 0.6747 (m-40) REVERT: A 177 MET cc_start: 0.7133 (pmm) cc_final: 0.6521 (pmm) REVERT: A 401 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8512 (mp) outliers start: 9 outliers final: 5 residues processed: 91 average time/residue: 0.1210 time to fit residues: 13.5837 Evaluate side-chains 83 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 77 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 401 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 33 optimal weight: 0.7980 chunk 30 optimal weight: 10.0000 chunk 25 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 ASN ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4699 r_free = 0.4699 target = 0.232615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.199850 restraints weight = 4376.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.205581 restraints weight = 2804.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.209371 restraints weight = 1986.319| |-----------------------------------------------------------------------------| r_work (final): 0.4485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6451 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2932 Z= 0.189 Angle : 0.758 9.360 3989 Z= 0.343 Chirality : 0.045 0.247 502 Planarity : 0.004 0.037 486 Dihedral : 21.791 113.547 511 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.25 % Allowed : 17.53 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.42 (0.43), residues: 362 helix: 2.74 (0.27), residues: 321 sheet: None (None), residues: 0 loop : -2.04 (1.09), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 191 HIS 0.003 0.001 HIS A 153 PHE 0.019 0.002 PHE A 315 TYR 0.006 0.001 TYR A 66 ARG 0.003 0.001 ARG A 368 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 724 Ramachandran restraints generated. 362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 724 Ramachandran restraints generated. 362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 89 time to evaluate : 0.322 Fit side-chains revert: symmetry clash REVERT: A 127 ASN cc_start: 0.7896 (m110) cc_final: 0.7311 (m-40) REVERT: A 177 MET cc_start: 0.7166 (OUTLIER) cc_final: 0.6705 (pmm) REVERT: A 392 LEU cc_start: 0.7995 (OUTLIER) cc_final: 0.7724 (tt) outliers start: 10 outliers final: 6 residues processed: 91 average time/residue: 0.1333 time to fit residues: 14.8027 Evaluate side-chains 88 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 80 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 392 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 25 optimal weight: 8.9990 chunk 18 optimal weight: 3.9990 chunk 15 optimal weight: 0.6980 chunk 28 optimal weight: 8.9990 chunk 16 optimal weight: 0.6980 chunk 22 optimal weight: 4.9990 chunk 26 optimal weight: 0.3980 chunk 32 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 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 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4706 r_free = 0.4706 target = 0.232462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.196531 restraints weight = 4492.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.203460 restraints weight = 2724.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.208000 restraints weight = 1865.633| |-----------------------------------------------------------------------------| r_work (final): 0.4474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6451 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2932 Z= 0.185 Angle : 0.802 10.134 3989 Z= 0.351 Chirality : 0.048 0.304 502 Planarity : 0.004 0.028 486 Dihedral : 19.667 113.336 511 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 4.87 % Allowed : 18.18 % Favored : 76.95 % 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: 3.48 (0.43), residues: 362 helix: 2.77 (0.27), residues: 321 sheet: None (None), residues: 0 loop : -1.94 (1.12), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 191 HIS 0.002 0.001 HIS A 359 PHE 0.013 0.002 PHE A 395 TYR 0.005 0.001 TYR A 66 ARG 0.003 0.001 ARG A 368 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 724 Ramachandran restraints generated. 362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 724 Ramachandran restraints generated. 362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 96 time to evaluate : 0.298 Fit side-chains REVERT: A 127 ASN cc_start: 0.7649 (m110) cc_final: 0.7154 (m-40) REVERT: A 143 THR cc_start: 0.8867 (p) cc_final: 0.8442 (t) REVERT: A 177 MET cc_start: 0.7141 (OUTLIER) cc_final: 0.6704 (pmm) REVERT: A 370 LEU cc_start: 0.7082 (tp) cc_final: 0.6817 (mt) outliers start: 15 outliers final: 9 residues processed: 99 average time/residue: 0.1121 time to fit residues: 13.8507 Evaluate side-chains 92 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 82 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 274 CYS Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 389 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 11 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 2 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 17 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4697 r_free = 0.4697 target = 0.231944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.197429 restraints weight = 4460.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.203295 restraints weight = 2813.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.207242 restraints weight = 1994.867| |-----------------------------------------------------------------------------| r_work (final): 0.4454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6490 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2932 Z= 0.213 Angle : 0.821 10.569 3989 Z= 0.372 Chirality : 0.049 0.275 502 Planarity : 0.004 0.032 486 Dihedral : 17.686 112.104 511 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 4.87 % Allowed : 20.13 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.44 (0.44), residues: 362 helix: 2.73 (0.27), residues: 321 sheet: None (None), residues: 0 loop : -1.81 (1.17), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 213 HIS 0.003 0.001 HIS A 153 PHE 0.016 0.002 PHE A 308 TYR 0.006 0.001 TYR A 216 ARG 0.011 0.001 ARG A 192 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 724 Ramachandran restraints generated. 362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 724 Ramachandran restraints generated. 362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 88 time to evaluate : 0.276 Fit side-chains REVERT: A 127 ASN cc_start: 0.7502 (m110) cc_final: 0.6716 (m-40) REVERT: A 143 THR cc_start: 0.8939 (p) cc_final: 0.8498 (t) REVERT: A 150 LEU cc_start: 0.7927 (mt) cc_final: 0.7631 (mt) REVERT: A 177 MET cc_start: 0.7201 (OUTLIER) cc_final: 0.6760 (pmm) REVERT: A 236 ARG cc_start: 0.5568 (tpp80) cc_final: 0.5284 (tpp-160) REVERT: A 304 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.7841 (mt) outliers start: 15 outliers final: 12 residues processed: 94 average time/residue: 0.1282 time to fit residues: 14.7439 Evaluate side-chains 97 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 274 CYS Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 389 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 35 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 0 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 371 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4695 r_free = 0.4695 target = 0.231529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.195167 restraints weight = 4586.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.202113 restraints weight = 2782.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.206888 restraints weight = 1908.341| |-----------------------------------------------------------------------------| r_work (final): 0.4458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6466 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2932 Z= 0.183 Angle : 0.842 11.490 3989 Z= 0.371 Chirality : 0.049 0.312 502 Planarity : 0.004 0.048 486 Dihedral : 16.220 110.406 511 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 5.52 % Allowed : 22.40 % Favored : 72.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.43 (0.44), residues: 362 helix: 2.72 (0.27), residues: 321 sheet: None (None), residues: 0 loop : -1.77 (1.17), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 191 HIS 0.003 0.001 HIS A 153 PHE 0.011 0.002 PHE A 308 TYR 0.007 0.001 TYR A 41 ARG 0.009 0.001 ARG A 192 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 724 Ramachandran restraints generated. 362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 724 Ramachandran restraints generated. 362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 90 time to evaluate : 0.281 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 143 THR cc_start: 0.8935 (p) cc_final: 0.8531 (t) REVERT: A 177 MET cc_start: 0.7161 (OUTLIER) cc_final: 0.6707 (pmm) REVERT: A 236 ARG cc_start: 0.5584 (tpp80) cc_final: 0.5218 (tpp-160) REVERT: A 304 LEU cc_start: 0.8269 (OUTLIER) cc_final: 0.7817 (mt) outliers start: 17 outliers final: 14 residues processed: 97 average time/residue: 0.1253 time to fit residues: 14.9115 Evaluate side-chains 102 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 274 CYS Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 389 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 26 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 25 optimal weight: 0.1980 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 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 127 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4682 r_free = 0.4682 target = 0.229860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.195797 restraints weight = 4706.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.202041 restraints weight = 2985.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.206235 restraints weight = 2099.259| |-----------------------------------------------------------------------------| r_work (final): 0.4466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6456 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 2932 Z= 0.190 Angle : 0.851 11.633 3989 Z= 0.375 Chirality : 0.045 0.270 502 Planarity : 0.004 0.052 486 Dihedral : 14.907 107.389 511 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 5.52 % Allowed : 23.05 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.45 (0.44), residues: 362 helix: 2.74 (0.27), residues: 321 sheet: None (None), residues: 0 loop : -1.79 (1.17), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 191 HIS 0.003 0.001 HIS A 153 PHE 0.011 0.001 PHE A 308 TYR 0.015 0.001 TYR A 41 ARG 0.009 0.001 ARG A 192 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 724 Ramachandran restraints generated. 362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 724 Ramachandran restraints generated. 362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 88 time to evaluate : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 143 THR cc_start: 0.8948 (p) cc_final: 0.8538 (t) REVERT: A 177 MET cc_start: 0.7160 (OUTLIER) cc_final: 0.6701 (pmm) REVERT: A 192 ARG cc_start: 0.6764 (tmt-80) cc_final: 0.6556 (ptp-110) REVERT: A 196 THR cc_start: 0.8482 (OUTLIER) cc_final: 0.8198 (p) REVERT: A 236 ARG cc_start: 0.5616 (tpp80) cc_final: 0.5269 (tpp-160) REVERT: A 237 ARG cc_start: 0.6007 (tpt170) cc_final: 0.5612 (tpm170) REVERT: A 304 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7733 (mt) outliers start: 17 outliers final: 12 residues processed: 96 average time/residue: 0.1207 time to fit residues: 14.5994 Evaluate side-chains 98 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 83 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 274 CYS Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 389 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 19 optimal weight: 4.9990 chunk 4 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 18 optimal weight: 8.9990 chunk 9 optimal weight: 0.8980 chunk 0 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4678 r_free = 0.4678 target = 0.229562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.195951 restraints weight = 4594.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.201987 restraints weight = 2910.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.206035 restraints weight = 2058.676| |-----------------------------------------------------------------------------| r_work (final): 0.4464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6482 moved from start: 0.2752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 2932 Z= 0.204 Angle : 0.886 13.931 3989 Z= 0.393 Chirality : 0.049 0.353 502 Planarity : 0.004 0.028 486 Dihedral : 13.726 103.060 511 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 5.84 % Allowed : 25.00 % Favored : 69.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.20 (0.43), residues: 362 helix: 2.56 (0.27), residues: 321 sheet: None (None), residues: 0 loop : -1.75 (1.14), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 191 HIS 0.003 0.001 HIS A 153 PHE 0.031 0.002 PHE A 220 TYR 0.012 0.001 TYR A 296 ARG 0.006 0.001 ARG A 192 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 724 Ramachandran restraints generated. 362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 724 Ramachandran restraints generated. 362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 84 time to evaluate : 0.285 Fit side-chains REVERT: A 127 ASN cc_start: 0.7401 (m-40) cc_final: 0.7123 (m-40) REVERT: A 143 THR cc_start: 0.8962 (p) cc_final: 0.8553 (t) REVERT: A 150 LEU cc_start: 0.8079 (mt) cc_final: 0.7860 (mt) REVERT: A 177 MET cc_start: 0.7161 (OUTLIER) cc_final: 0.6704 (pmm) REVERT: A 196 THR cc_start: 0.8185 (OUTLIER) cc_final: 0.7801 (p) REVERT: A 236 ARG cc_start: 0.5616 (tpp80) cc_final: 0.5276 (tpp-160) REVERT: A 237 ARG cc_start: 0.5993 (tpt170) cc_final: 0.5769 (tpm170) REVERT: A 304 LEU cc_start: 0.8198 (OUTLIER) cc_final: 0.7716 (mt) outliers start: 18 outliers final: 14 residues processed: 92 average time/residue: 0.1249 time to fit residues: 14.1793 Evaluate side-chains 99 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 82 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 274 CYS Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 392 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 23 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4680 r_free = 0.4680 target = 0.229320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.196232 restraints weight = 4575.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.202268 restraints weight = 2884.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4470 r_free = 0.4470 target = 0.206302 restraints weight = 2033.680| |-----------------------------------------------------------------------------| r_work (final): 0.4466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6475 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 2932 Z= 0.207 Angle : 0.901 14.461 3989 Z= 0.404 Chirality : 0.047 0.296 502 Planarity : 0.004 0.052 486 Dihedral : 12.796 98.659 511 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 5.84 % Allowed : 25.65 % Favored : 68.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.19 (0.43), residues: 362 helix: 2.54 (0.27), residues: 321 sheet: None (None), residues: 0 loop : -1.69 (1.15), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 191 HIS 0.003 0.001 HIS A 153 PHE 0.026 0.002 PHE A 220 TYR 0.012 0.001 TYR A 296 ARG 0.012 0.001 ARG A 192 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 724 Ramachandran restraints generated. 362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 724 Ramachandran restraints generated. 362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 84 time to evaluate : 0.311 Fit side-chains revert: symmetry clash REVERT: A 132 PHE cc_start: 0.7192 (m-80) cc_final: 0.6823 (t80) REVERT: A 143 THR cc_start: 0.8954 (p) cc_final: 0.8538 (t) REVERT: A 150 LEU cc_start: 0.8063 (mt) cc_final: 0.7851 (mt) REVERT: A 177 MET cc_start: 0.7172 (OUTLIER) cc_final: 0.6727 (pmm) REVERT: A 192 ARG cc_start: 0.6723 (tmt-80) cc_final: 0.6518 (tmt-80) REVERT: A 196 THR cc_start: 0.8358 (OUTLIER) cc_final: 0.7857 (p) REVERT: A 236 ARG cc_start: 0.5912 (tpp80) cc_final: 0.5251 (tpp-160) REVERT: A 237 ARG cc_start: 0.5972 (tpt170) cc_final: 0.5755 (tpm170) REVERT: A 304 LEU cc_start: 0.8122 (OUTLIER) cc_final: 0.7726 (mt) REVERT: A 359 HIS cc_start: 0.7567 (m-70) cc_final: 0.7191 (m-70) outliers start: 18 outliers final: 14 residues processed: 93 average time/residue: 0.1178 time to fit residues: 13.6487 Evaluate side-chains 100 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 83 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 274 CYS Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 392 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 7 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 28 optimal weight: 6.9990 chunk 27 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 127 ASN A 359 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4685 r_free = 0.4685 target = 0.230047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.194595 restraints weight = 4644.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.201736 restraints weight = 2827.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.206252 restraints weight = 1937.928| |-----------------------------------------------------------------------------| r_work (final): 0.4455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6471 moved from start: 0.2968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 2932 Z= 0.204 Angle : 0.905 15.078 3989 Z= 0.404 Chirality : 0.047 0.297 502 Planarity : 0.004 0.041 486 Dihedral : 11.761 91.999 511 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 15.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 5.52 % Allowed : 26.62 % Favored : 67.86 % 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: 3.18 (0.43), residues: 362 helix: 2.54 (0.27), residues: 320 sheet: None (None), residues: 0 loop : -1.67 (1.12), residues: 42 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 191 HIS 0.003 0.001 HIS A 153 PHE 0.025 0.002 PHE A 220 TYR 0.011 0.001 TYR A 296 ARG 0.010 0.001 ARG A 192 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 724 Ramachandran restraints generated. 362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 724 Ramachandran restraints generated. 362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 84 time to evaluate : 0.287 Fit side-chains revert: symmetry clash REVERT: A 127 ASN cc_start: 0.7630 (m-40) cc_final: 0.7370 (m-40) REVERT: A 143 THR cc_start: 0.8979 (p) cc_final: 0.8594 (t) REVERT: A 177 MET cc_start: 0.6721 (OUTLIER) cc_final: 0.6230 (pmm) REVERT: A 192 ARG cc_start: 0.6794 (tmt-80) cc_final: 0.6547 (tmt-80) REVERT: A 196 THR cc_start: 0.8522 (OUTLIER) cc_final: 0.8105 (p) REVERT: A 236 ARG cc_start: 0.5978 (tpp80) cc_final: 0.5291 (tpp-160) REVERT: A 237 ARG cc_start: 0.6099 (tpt170) cc_final: 0.5861 (tpm170) REVERT: A 304 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.7803 (mt) outliers start: 17 outliers final: 13 residues processed: 92 average time/residue: 0.1152 time to fit residues: 13.2095 Evaluate side-chains 98 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 82 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 274 CYS Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 392 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 22 optimal weight: 0.0970 chunk 6 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 28 optimal weight: 0.0870 chunk 35 optimal weight: 1.9990 chunk 24 optimal weight: 0.0970 chunk 32 optimal weight: 0.9990 chunk 13 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 overall best weight: 0.3754 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 359 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4705 r_free = 0.4705 target = 0.232330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.198175 restraints weight = 4499.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.204973 restraints weight = 2735.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.209489 restraints weight = 1870.262| |-----------------------------------------------------------------------------| r_work (final): 0.4488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6408 moved from start: 0.3090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 2932 Z= 0.184 Angle : 0.918 14.918 3989 Z= 0.403 Chirality : 0.047 0.293 502 Planarity : 0.004 0.035 486 Dihedral : 10.786 84.061 511 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 4.87 % Allowed : 27.27 % Favored : 67.86 % 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: 3.30 (0.43), residues: 362 helix: 2.64 (0.27), residues: 320 sheet: None (None), residues: 0 loop : -1.71 (1.11), residues: 42 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 191 HIS 0.005 0.001 HIS A 359 PHE 0.022 0.001 PHE A 220 TYR 0.013 0.001 TYR A 296 ARG 0.008 0.001 ARG A 192 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1187.68 seconds wall clock time: 22 minutes 10.05 seconds (1330.05 seconds total)