Starting phenix.real_space_refine on Wed Mar 5 17:08:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rtv_24690/03_2025/7rtv_24690.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rtv_24690/03_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_24690/03_2025/7rtv_24690.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rtv_24690/03_2025/7rtv_24690.map" model { file = "/net/cci-nas-00/data/ceres_data/7rtv_24690/03_2025/7rtv_24690.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rtv_24690/03_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-5624/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: 2.45, per 1000 atoms: 0.85 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: 0.83 Conformation dependent library (CDL) restraints added in 315.3 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: 0.22 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: 0.75 Time building geometry restraints manager: 0.96 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: 0.340 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: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.590 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.290 ------------------------------------------------------------------------------- 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 : 0.297 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: 0.1245 time to fit residues: 14.3460 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 : 0.302 ------------------------------------------------------------------------------- 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: 0.0770 chunk 10 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 chunk 21 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 ASN ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.233262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.199976 restraints weight = 4578.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.206104 restraints weight = 2902.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.210287 restraints weight = 2046.949| |-----------------------------------------------------------------------------| r_work (final): 0.4491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6410 moved from start: 0.1446 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= 0.180 Angle : 0.744 8.350 3989 Z= 0.343 Chirality : 0.045 0.249 502 Planarity : 0.004 0.048 486 Dihedral : 24.778 111.491 511 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 : 2.60 % Allowed : 12.66 % Favored : 84.74 % 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: 2.84 (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 0.016 0.002 PHE A 395 TYR 0.020 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 98 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 90 time to evaluate : 0.317 Fit side-chains REVERT: A 127 ASN cc_start: 0.7643 (m110) cc_final: 0.6788 (m-40) REVERT: A 150 LEU cc_start: 0.7939 (mt) cc_final: 0.7730 (mt) REVERT: A 177 MET cc_start: 0.7168 (pmm) cc_final: 0.6560 (pmm) REVERT: A 401 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8476 (mp) outliers start: 8 outliers final: 4 residues processed: 91 average time/residue: 0.1196 time to fit residues: 13.6609 Evaluate side-chains 82 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 77 time to evaluate : 0.264 ------------------------------------------------------------------------------- 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 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: 0.5980 chunk 30 optimal weight: 10.0000 chunk 25 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 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 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 = 0.4704 r_free = 0.4704 target = 0.232750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.199053 restraints weight = 4492.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.204997 restraints weight = 2885.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.208922 restraints weight = 2066.223| |-----------------------------------------------------------------------------| r_work (final): 0.4483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6447 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2932 Z= 0.184 Angle : 0.756 9.900 3989 Z= 0.341 Chirality : 0.045 0.244 502 Planarity : 0.004 0.036 486 Dihedral : 21.826 113.403 511 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.92 % Allowed : 16.23 % Favored : 80.84 % 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 (0.43), residues: 362 helix: 2.76 (0.27), residues: 321 sheet: None (None), residues: 0 loop : -2.06 (1.09), 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 359 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 98 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 89 time to evaluate : 0.276 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 127 ASN cc_start: 0.7892 (m110) cc_final: 0.7324 (m-40) REVERT: A 132 PHE cc_start: 0.7285 (m-80) cc_final: 0.7073 (m-80) REVERT: A 177 MET cc_start: 0.7147 (OUTLIER) cc_final: 0.6685 (pmm) REVERT: A 392 LEU cc_start: 0.7989 (OUTLIER) cc_final: 0.7728 (tt) REVERT: A 401 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8410 (mp) outliers start: 9 outliers final: 5 residues processed: 91 average time/residue: 0.1242 time to fit residues: 13.8236 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 : 0.274 ------------------------------------------------------------------------------- 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 305 ILE Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 401 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 25 optimal weight: 9.9990 chunk 18 optimal weight: 6.9990 chunk 15 optimal weight: 0.6980 chunk 28 optimal weight: 0.0040 chunk 16 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 32 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 0 optimal weight: 8.9990 overall best weight: 0.5792 ------------------------------------------------------------------------------- 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 152 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4722 r_free = 0.4722 target = 0.235224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.201977 restraints weight = 4450.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.207711 restraints weight = 2819.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.211754 restraints weight = 2012.396| |-----------------------------------------------------------------------------| r_work (final): 0.4496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6425 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2932 Z= 0.171 Angle : 0.791 10.072 3989 Z= 0.347 Chirality : 0.049 0.322 502 Planarity : 0.004 0.029 486 Dihedral : 19.817 113.581 511 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 4.22 % Allowed : 18.51 % Favored : 77.27 % 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: 3.49 (0.43), residues: 362 helix: 2.78 (0.27), residues: 321 sheet: None (None), residues: 0 loop : -1.97 (1.12), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 257 HIS 0.003 0.001 HIS A 153 PHE 0.012 0.001 PHE A 395 TYR 0.005 0.001 TYR A 66 ARG 0.003 0.000 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 108 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 95 time to evaluate : 0.331 Fit side-chains REVERT: A 111 ASN cc_start: 0.7374 (t0) cc_final: 0.7166 (t0) REVERT: A 127 ASN cc_start: 0.7588 (m110) cc_final: 0.7093 (m-40) REVERT: A 143 THR cc_start: 0.8849 (p) cc_final: 0.8406 (t) REVERT: A 177 MET cc_start: 0.7139 (OUTLIER) cc_final: 0.6718 (pmm) outliers start: 13 outliers final: 9 residues processed: 98 average time/residue: 0.1153 time to fit residues: 14.1360 Evaluate side-chains 96 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 86 time to evaluate : 0.274 ------------------------------------------------------------------------------- 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: 0.0060 chunk 3 optimal weight: 0.9980 chunk 14 optimal weight: 0.5980 chunk 2 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 17 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 overall best weight: 0.6196 ------------------------------------------------------------------------------- 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 = 0.4703 r_free = 0.4703 target = 0.232743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.198391 restraints weight = 4595.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.204427 restraints weight = 2909.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.208719 restraints weight = 2068.143| |-----------------------------------------------------------------------------| r_work (final): 0.4474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6427 moved from start: 0.2265 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= 0.180 Angle : 0.812 10.509 3989 Z= 0.361 Chirality : 0.048 0.268 502 Planarity : 0.004 0.043 486 Dihedral : 18.036 112.999 511 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 4.55 % Allowed : 22.08 % Favored : 73.38 % 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: 3.52 (0.44), residues: 362 helix: 2.80 (0.27), residues: 321 sheet: None (None), residues: 0 loop : -1.92 (1.15), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 213 HIS 0.003 0.001 HIS A 153 PHE 0.012 0.001 PHE A 132 TYR 0.005 0.001 TYR A 280 ARG 0.013 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 104 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 90 time to evaluate : 0.275 Fit side-chains revert: symmetry clash REVERT: A 127 ASN cc_start: 0.7621 (m110) cc_final: 0.7109 (m-40) REVERT: A 143 THR cc_start: 0.8883 (p) cc_final: 0.8439 (t) REVERT: A 177 MET cc_start: 0.6690 (OUTLIER) cc_final: 0.6212 (pmm) REVERT: A 236 ARG cc_start: 0.5551 (tpp80) cc_final: 0.5175 (tpp-160) outliers start: 14 outliers final: 10 residues processed: 95 average time/residue: 0.1368 time to fit residues: 15.8090 Evaluate side-chains 93 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 82 time to evaluate : 0.303 ------------------------------------------------------------------------------- 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 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 350 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: 2.9990 chunk 20 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 9 optimal weight: 0.4980 chunk 0 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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 = 0.232656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.198528 restraints weight = 4608.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.204605 restraints weight = 2912.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.208854 restraints weight = 2058.013| |-----------------------------------------------------------------------------| r_work (final): 0.4473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6441 moved from start: 0.2367 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= 0.192 Angle : 0.849 11.626 3989 Z= 0.371 Chirality : 0.049 0.324 502 Planarity : 0.004 0.058 486 Dihedral : 16.264 110.660 511 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 4.87 % Allowed : 22.73 % Favored : 72.40 % 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: 3.49 (0.44), residues: 362 helix: 2.77 (0.27), residues: 321 sheet: None (None), residues: 0 loop : -1.89 (1.14), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 213 HIS 0.003 0.001 HIS A 153 PHE 0.013 0.002 PHE A 308 TYR 0.009 0.001 TYR A 41 ARG 0.011 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 103 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 88 time to evaluate : 0.296 Fit side-chains revert: symmetry clash REVERT: A 127 ASN cc_start: 0.7390 (m110) cc_final: 0.6620 (m-40) REVERT: A 143 THR cc_start: 0.8874 (p) cc_final: 0.8446 (t) REVERT: A 177 MET cc_start: 0.6686 (OUTLIER) cc_final: 0.6228 (pmm) REVERT: A 192 ARG cc_start: 0.6558 (tmt-80) cc_final: 0.6341 (tmt-80) REVERT: A 236 ARG cc_start: 0.5559 (tpp80) cc_final: 0.5188 (tpp-160) outliers start: 15 outliers final: 13 residues processed: 93 average time/residue: 0.1257 time to fit residues: 14.3753 Evaluate side-chains 98 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 84 time to evaluate : 0.269 ------------------------------------------------------------------------------- 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 274 CYS Chi-restraints excluded: chain A residue 294 THR 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: 0.9990 chunk 21 optimal weight: 0.9980 chunk 29 optimal weight: 0.1980 chunk 35 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.5980 chunk 13 optimal weight: 4.9990 chunk 25 optimal weight: 0.0570 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4714 r_free = 0.4714 target = 0.234715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.200235 restraints weight = 4603.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.206704 restraints weight = 2865.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.210917 restraints weight = 1998.997| |-----------------------------------------------------------------------------| r_work (final): 0.4481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6412 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 2932 Z= 0.180 Angle : 0.852 12.977 3989 Z= 0.372 Chirality : 0.045 0.297 502 Planarity : 0.004 0.036 486 Dihedral : 14.997 107.792 511 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 5.19 % Allowed : 23.05 % Favored : 71.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.52 (0.44), residues: 362 helix: 2.79 (0.27), residues: 321 sheet: None (None), residues: 0 loop : -1.85 (1.14), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 257 HIS 0.002 0.001 HIS A 153 PHE 0.011 0.002 PHE A 273 TYR 0.008 0.001 TYR A 280 ARG 0.006 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 102 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 0.298 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 111 ASN cc_start: 0.7699 (t0) cc_final: 0.7494 (t0) REVERT: A 132 PHE cc_start: 0.7327 (m-10) cc_final: 0.7069 (m-80) REVERT: A 143 THR cc_start: 0.8862 (p) cc_final: 0.8434 (t) REVERT: A 177 MET cc_start: 0.6643 (OUTLIER) cc_final: 0.6190 (pmm) REVERT: A 236 ARG cc_start: 0.5473 (tpp80) cc_final: 0.5109 (tpp-160) REVERT: A 237 ARG cc_start: 0.5947 (tpt170) cc_final: 0.5557 (tpm170) outliers start: 16 outliers final: 12 residues processed: 93 average time/residue: 0.1152 time to fit residues: 13.3630 Evaluate side-chains 95 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 0.303 ------------------------------------------------------------------------------- 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 253 LEU Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 294 THR 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: 0.9980 chunk 4 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 0 optimal weight: 0.8980 chunk 5 optimal weight: 4.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- 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 = 0.4685 r_free = 0.4685 target = 0.231549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.197605 restraints weight = 4498.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.203793 restraints weight = 2800.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.207889 restraints weight = 1969.205| |-----------------------------------------------------------------------------| r_work (final): 0.4457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6489 moved from start: 0.2621 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= 0.222 Angle : 0.884 12.834 3989 Z= 0.397 Chirality : 0.049 0.351 502 Planarity : 0.004 0.045 486 Dihedral : 13.739 103.430 511 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 14.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 5.19 % Allowed : 24.68 % Favored : 70.13 % 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: 3.35 (0.44), residues: 362 helix: 2.67 (0.27), residues: 321 sheet: None (None), residues: 0 loop : -1.80 (1.12), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 213 HIS 0.003 0.001 HIS A 153 PHE 0.016 0.002 PHE A 308 TYR 0.011 0.001 TYR A 296 ARG 0.014 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 99 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 83 time to evaluate : 0.288 Fit side-chains revert: symmetry clash REVERT: A 143 THR cc_start: 0.8937 (p) cc_final: 0.8512 (t) REVERT: A 177 MET cc_start: 0.7187 (OUTLIER) cc_final: 0.6735 (pmm) REVERT: A 237 ARG cc_start: 0.5993 (tpt170) cc_final: 0.5679 (tpm170) outliers start: 16 outliers final: 14 residues processed: 89 average time/residue: 0.1196 time to fit residues: 13.2859 Evaluate side-chains 94 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 0.273 ------------------------------------------------------------------------------- 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 23 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 25 optimal weight: 5.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.4684 r_free = 0.4684 target = 0.230571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.197369 restraints weight = 4638.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.203536 restraints weight = 2912.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.207592 restraints weight = 2050.745| |-----------------------------------------------------------------------------| r_work (final): 0.4461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6471 moved from start: 0.2760 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= 0.211 Angle : 0.897 13.336 3989 Z= 0.407 Chirality : 0.048 0.286 502 Planarity : 0.005 0.065 486 Dihedral : 12.955 99.595 511 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 14.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 5.52 % Allowed : 25.32 % 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: 3.29 (0.44), residues: 362 helix: 2.61 (0.27), residues: 321 sheet: None (None), residues: 0 loop : -1.68 (1.15), 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 0.012 0.001 PHE A 308 TYR 0.013 0.001 TYR A 296 ARG 0.018 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 101 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 84 time to evaluate : 0.275 Fit side-chains revert: symmetry clash REVERT: A 127 ASN cc_start: 0.7630 (m-40) cc_final: 0.6982 (m-40) REVERT: A 143 THR cc_start: 0.8957 (p) cc_final: 0.8545 (t) REVERT: A 177 MET cc_start: 0.7167 (OUTLIER) cc_final: 0.6697 (pmm) REVERT: A 237 ARG cc_start: 0.5968 (tpt170) cc_final: 0.5660 (tpm170) outliers start: 17 outliers final: 15 residues processed: 91 average time/residue: 0.1229 time to fit residues: 13.8783 Evaluate side-chains 97 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 81 time to evaluate : 0.257 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 7 optimal weight: 0.9980 chunk 32 optimal weight: 0.0870 chunk 24 optimal weight: 0.8980 chunk 28 optimal weight: 7.9990 chunk 27 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 13 optimal weight: 0.0060 chunk 18 optimal weight: 0.2980 chunk 1 optimal weight: 0.9980 overall best weight: 0.3774 ------------------------------------------------------------------------------- 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 = 0.4702 r_free = 0.4702 target = 0.233017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.198714 restraints weight = 4590.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.205922 restraints weight = 2757.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4495 r_free = 0.4495 target = 0.210580 restraints weight = 1866.511| |-----------------------------------------------------------------------------| r_work (final): 0.4486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6405 moved from start: 0.2889 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= 0.191 Angle : 0.920 14.516 3989 Z= 0.412 Chirality : 0.048 0.294 502 Planarity : 0.005 0.069 486 Dihedral : 12.038 94.263 511 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 4.87 % Allowed : 25.97 % 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: 3.19 (0.43), residues: 362 helix: 2.54 (0.27), residues: 321 sheet: None (None), residues: 0 loop : -1.67 (1.14), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 257 HIS 0.005 0.001 HIS A 359 PHE 0.030 0.002 PHE A 220 TYR 0.016 0.001 TYR A 296 ARG 0.012 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: 15 poor density : 86 time to evaluate : 0.298 Fit side-chains REVERT: A 111 ASN cc_start: 0.7447 (t0) cc_final: 0.7198 (t0) REVERT: A 132 PHE cc_start: 0.6771 (m-80) cc_final: 0.6303 (t80) REVERT: A 143 THR cc_start: 0.8927 (p) cc_final: 0.8533 (t) REVERT: A 177 MET cc_start: 0.7073 (OUTLIER) cc_final: 0.6636 (pmm) REVERT: A 237 ARG cc_start: 0.5948 (tpt170) cc_final: 0.5634 (tpm170) outliers start: 15 outliers final: 13 residues processed: 91 average time/residue: 0.1154 time to fit residues: 13.0530 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 : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE 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 253 LEU Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 294 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 22 optimal weight: 0.0020 chunk 6 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 28 optimal weight: 0.2980 chunk 35 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 13 optimal weight: 0.0570 chunk 10 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 overall best weight: 0.3906 ------------------------------------------------------------------------------- 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 = 0.4697 r_free = 0.4697 target = 0.232277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.200879 restraints weight = 4472.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.206984 restraints weight = 2801.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.210956 restraints weight = 1960.355| |-----------------------------------------------------------------------------| r_work (final): 0.4494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6395 moved from start: 0.2936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2932 Z= 0.192 Angle : 0.912 14.546 3989 Z= 0.408 Chirality : 0.048 0.291 502 Planarity : 0.004 0.060 486 Dihedral : 11.277 88.429 511 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 4.87 % Allowed : 26.62 % 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: 3.26 (0.43), residues: 362 helix: 2.60 (0.27), residues: 320 sheet: None (None), residues: 0 loop : -1.67 (1.11), residues: 42 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 213 HIS 0.004 0.001 HIS A 371 PHE 0.023 0.001 PHE A 220 TYR 0.017 0.001 TYR A 296 ARG 0.014 0.001 ARG A 192 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1219.12 seconds wall clock time: 21 minutes 51.68 seconds (1311.68 seconds total)