Starting phenix.real_space_refine on Tue Feb 3 14:33:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j02_61046/02_2026/9j02_61046.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j02_61046/02_2026/9j02_61046.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9j02_61046/02_2026/9j02_61046.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j02_61046/02_2026/9j02_61046.map" model { file = "/net/cci-nas-00/data/ceres_data/9j02_61046/02_2026/9j02_61046.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j02_61046/02_2026/9j02_61046.cif" } resolution = 3.36 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= -0.002 sd= 0.033 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 30 5.16 5 C 2442 2.51 5 N 636 2.21 5 O 656 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3764 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3764 Classifications: {'peptide': 488} Link IDs: {'PTRANS': 26, 'TRANS': 461} Chain breaks: 3 Time building chain proxies: 1.12, per 1000 atoms: 0.30 Number of scatterers: 3764 At special positions: 0 Unit cell: (103.7, 53.55, 71.4, 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 30 16.00 O 656 8.00 N 636 7.00 C 2442 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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 Time building additional restraints: 0.32 Conformation dependent library (CDL) restraints added in 156.9 milliseconds 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 904 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 1 sheets defined 77.0% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'A' and resid 2 through 11 Processing helix chain 'A' and resid 14 through 26 removed outlier: 4.319A pdb=" N THR A 22 " --> pdb=" O GLN A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 29 No H-bonds generated for 'chain 'A' and resid 27 through 29' Processing helix chain 'A' and resid 30 through 36 Processing helix chain 'A' and resid 119 through 125 Processing helix chain 'A' and resid 131 through 160 removed outlier: 4.572A pdb=" N GLN A 135 " --> pdb=" O ARG A 131 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL A 145 " --> pdb=" O TYR A 141 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N LEU A 146 " --> pdb=" O MET A 142 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU A 147 " --> pdb=" O VAL A 143 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLY A 148 " --> pdb=" O GLY A 144 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ASP A 157 " --> pdb=" O GLY A 153 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ARG A 158 " --> pdb=" O TYR A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 178 removed outlier: 3.629A pdb=" N ALA A 173 " --> pdb=" O TYR A 169 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N CYS A 178 " --> pdb=" O VAL A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 182 Processing helix chain 'A' and resid 184 through 214 removed outlier: 3.532A pdb=" N TYR A 188 " --> pdb=" O ASN A 184 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N MET A 207 " --> pdb=" O SER A 203 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU A 212 " --> pdb=" O THR A 208 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N TRP A 213 " --> pdb=" O LEU A 209 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N MET A 214 " --> pdb=" O ASN A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 232 removed outlier: 3.739A pdb=" N VAL A 222 " --> pdb=" O THR A 218 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY A 223 " --> pdb=" O ARG A 219 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N THR A 224 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU A 225 " --> pdb=" O CYS A 221 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLY A 227 " --> pdb=" O GLY A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 244 removed outlier: 3.916A pdb=" N LEU A 236 " --> pdb=" O LEU A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 256 Processing helix chain 'A' and resid 256 through 264 removed outlier: 4.245A pdb=" N ALA A 260 " --> pdb=" O ALA A 256 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N TYR A 264 " --> pdb=" O ALA A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 268 removed outlier: 3.732A pdb=" N PHE A 268 " --> pdb=" O SER A 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 265 through 268' Processing helix chain 'A' and resid 271 through 279 Processing helix chain 'A' and resid 280 through 296 removed outlier: 3.993A pdb=" N THR A 284 " --> pdb=" O ARG A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 304 removed outlier: 3.546A pdb=" N GLY A 301 " --> pdb=" O LYS A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 313 removed outlier: 3.593A pdb=" N LEU A 309 " --> pdb=" O SER A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 329 removed outlier: 3.900A pdb=" N LEU A 329 " --> pdb=" O ALA A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 357 removed outlier: 3.780A pdb=" N LEU A 338 " --> pdb=" O THR A 334 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N CYS A 341 " --> pdb=" O HIS A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 376 removed outlier: 3.610A pdb=" N VAL A 372 " --> pdb=" O TYR A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 393 removed outlier: 3.713A pdb=" N LEU A 387 " --> pdb=" O LEU A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 412 removed outlier: 3.655A pdb=" N ASN A 412 " --> pdb=" O CYS A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 449 removed outlier: 3.895A pdb=" N LEU A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TYR A 449 " --> pdb=" O THR A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 465 Processing helix chain 'A' and resid 466 through 477 Proline residue: A 473 - end of helix Processing helix chain 'A' and resid 478 through 480 No H-bonds generated for 'chain 'A' and resid 478 through 480' Processing helix chain 'A' and resid 484 through 499 removed outlier: 3.689A pdb=" N VAL A 493 " --> pdb=" O ILE A 489 " (cutoff:3.500A) Proline residue: A 494 - end of helix removed outlier: 3.950A pdb=" N ALA A 499 " --> pdb=" O VAL A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 504 removed outlier: 3.586A pdb=" N LEU A 504 " --> pdb=" O THR A 501 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 49 removed outlier: 3.545A pdb=" N HIS A 48 " --> pdb=" O ILE A 110 " (cutoff:3.500A) 223 hydrogen bonds defined for protein. 660 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: 0.63 Time building geometry restraints manager: 0.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1184 1.34 - 1.46: 650 1.46 - 1.58: 1971 1.58 - 1.69: 0 1.69 - 1.81: 47 Bond restraints: 3852 Sorted by residual: bond pdb=" N ASP A 359 " pdb=" CA ASP A 359 " ideal model delta sigma weight residual 1.457 1.482 -0.025 1.29e-02 6.01e+03 3.73e+00 bond pdb=" C TYR A 449 " pdb=" N PRO A 450 " ideal model delta sigma weight residual 1.330 1.349 -0.019 1.25e-02 6.40e+03 2.36e+00 bond pdb=" CB GLN A 417 " pdb=" CG GLN A 417 " ideal model delta sigma weight residual 1.520 1.555 -0.035 3.00e-02 1.11e+03 1.38e+00 bond pdb=" CG ARG A 219 " pdb=" CD ARG A 219 " ideal model delta sigma weight residual 1.520 1.555 -0.035 3.00e-02 1.11e+03 1.38e+00 bond pdb=" CA GLU A 447 " pdb=" CB GLU A 447 " ideal model delta sigma weight residual 1.531 1.549 -0.018 1.56e-02 4.11e+03 1.32e+00 ... (remaining 3847 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 5011 1.73 - 3.45: 179 3.45 - 5.18: 29 5.18 - 6.91: 19 6.91 - 8.63: 5 Bond angle restraints: 5243 Sorted by residual: angle pdb=" C LEU A 330 " pdb=" N ARG A 331 " pdb=" CA ARG A 331 " ideal model delta sigma weight residual 122.08 127.67 -5.59 1.47e+00 4.63e-01 1.45e+01 angle pdb=" N ILE A 453 " pdb=" CA ILE A 453 " pdb=" C ILE A 453 " ideal model delta sigma weight residual 112.83 109.07 3.76 9.90e-01 1.02e+00 1.45e+01 angle pdb=" C MET A 358 " pdb=" N ASP A 359 " pdb=" CA ASP A 359 " ideal model delta sigma weight residual 121.54 128.17 -6.63 1.91e+00 2.74e-01 1.21e+01 angle pdb=" CA GLN A 417 " pdb=" CB GLN A 417 " pdb=" CG GLN A 417 " ideal model delta sigma weight residual 114.10 120.98 -6.88 2.00e+00 2.50e-01 1.18e+01 angle pdb=" N ARG A 158 " pdb=" CA ARG A 158 " pdb=" C ARG A 158 " ideal model delta sigma weight residual 114.04 110.23 3.81 1.24e+00 6.50e-01 9.46e+00 ... (remaining 5238 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.61: 2008 15.61 - 31.22: 197 31.22 - 46.83: 55 46.83 - 62.44: 9 62.44 - 78.05: 7 Dihedral angle restraints: 2276 sinusoidal: 872 harmonic: 1404 Sorted by residual: dihedral pdb=" CA GLN A 72 " pdb=" C GLN A 72 " pdb=" N GLY A 73 " pdb=" CA GLY A 73 " ideal model delta harmonic sigma weight residual 180.00 156.78 23.22 0 5.00e+00 4.00e-02 2.16e+01 dihedral pdb=" CG ARG A 293 " pdb=" CD ARG A 293 " pdb=" NE ARG A 293 " pdb=" CZ ARG A 293 " ideal model delta sinusoidal sigma weight residual 180.00 137.22 42.78 2 1.50e+01 4.44e-03 9.84e+00 dihedral pdb=" CA VAL A 127 " pdb=" C VAL A 127 " pdb=" N CYS A 128 " pdb=" CA CYS A 128 " ideal model delta harmonic sigma weight residual 180.00 164.39 15.61 0 5.00e+00 4.00e-02 9.75e+00 ... (remaining 2273 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 417 0.040 - 0.080: 140 0.080 - 0.119: 49 0.119 - 0.159: 3 0.159 - 0.199: 4 Chirality restraints: 613 Sorted by residual: chirality pdb=" CB ILE A 415 " pdb=" CA ILE A 415 " pdb=" CG1 ILE A 415 " pdb=" CG2 ILE A 415 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.88e-01 chirality pdb=" CA ASP A 359 " pdb=" N ASP A 359 " pdb=" C ASP A 359 " pdb=" CB ASP A 359 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.20e-01 chirality pdb=" CB VAL A 25 " pdb=" CA VAL A 25 " pdb=" CG1 VAL A 25 " pdb=" CG2 VAL A 25 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.95e-01 ... (remaining 610 not shown) Planarity restraints: 658 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 244 " 0.037 5.00e-02 4.00e+02 5.54e-02 4.92e+00 pdb=" N PRO A 245 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO A 245 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 245 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 504 " 0.027 5.00e-02 4.00e+02 4.16e-02 2.77e+00 pdb=" N PRO A 505 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 505 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 505 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 103 " 0.024 5.00e-02 4.00e+02 3.64e-02 2.12e+00 pdb=" N PRO A 104 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 104 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 104 " 0.020 5.00e-02 4.00e+02 ... (remaining 655 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 1090 2.83 - 3.34: 3707 3.34 - 3.86: 5811 3.86 - 4.38: 6423 4.38 - 4.90: 11341 Nonbonded interactions: 28372 Sorted by model distance: nonbonded pdb=" O LEU A 281 " pdb=" OG1 THR A 284 " model vdw 2.307 3.040 nonbonded pdb=" OE1 GLN A 417 " pdb=" NH1 ARG A 423 " model vdw 2.353 3.120 nonbonded pdb=" OG1 THR A 515 " pdb=" OE1 GLN A 517 " model vdw 2.360 3.040 nonbonded pdb=" O ALA A 180 " pdb=" NH1 ARG A 248 " model vdw 2.398 3.120 nonbonded pdb=" OH TYR A 228 " pdb=" NZ LYS A 382 " model vdw 2.416 3.120 ... (remaining 28367 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 1.700 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 5.960 Find NCS groups from input model: 0.020 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 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 0.035 3852 Z= 0.187 Angle : 0.822 8.633 5243 Z= 0.416 Chirality : 0.044 0.199 613 Planarity : 0.006 0.055 658 Dihedral : 14.258 78.048 1372 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.37), residues: 480 helix: 0.50 (0.28), residues: 331 sheet: None (None), residues: 0 loop : -1.49 (0.49), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 219 TYR 0.011 0.001 TYR A 490 PHE 0.019 0.002 PHE A 438 TRP 0.023 0.001 TRP A 213 HIS 0.003 0.001 HIS A 217 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 3852) covalent geometry : angle 0.82174 ( 5243) hydrogen bonds : bond 0.14067 ( 223) hydrogen bonds : angle 5.32802 ( 660) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.157 Fit side-chains REVERT: A 74 GLN cc_start: 0.7182 (mp10) cc_final: 0.6859 (mp10) outliers start: 0 outliers final: 0 residues processed: 70 average time/residue: 0.0530 time to fit residues: 4.9884 Evaluate side-chains 57 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 25 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 30 optimal weight: 0.3980 chunk 22 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 ASN A 168 ASN A 412 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.170717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.129368 restraints weight = 4795.683| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 2.52 r_work: 0.3510 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3852 Z= 0.131 Angle : 0.575 6.447 5243 Z= 0.285 Chirality : 0.040 0.161 613 Planarity : 0.005 0.054 658 Dihedral : 3.632 19.650 527 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.49 % Allowed : 6.17 % Favored : 93.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.39), residues: 480 helix: 1.03 (0.29), residues: 343 sheet: None (None), residues: 0 loop : -1.36 (0.53), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 219 TYR 0.008 0.001 TYR A 188 PHE 0.016 0.001 PHE A 152 TRP 0.010 0.001 TRP A 346 HIS 0.002 0.001 HIS A 48 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 3852) covalent geometry : angle 0.57475 ( 5243) hydrogen bonds : bond 0.04323 ( 223) hydrogen bonds : angle 3.94499 ( 660) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 69 time to evaluate : 0.084 Fit side-chains REVERT: A 18 GLN cc_start: 0.8293 (mt0) cc_final: 0.8023 (mt0) REVERT: A 74 GLN cc_start: 0.7066 (mp10) cc_final: 0.6639 (mp10) REVERT: A 214 MET cc_start: 0.7679 (mmt) cc_final: 0.7428 (mmt) outliers start: 2 outliers final: 1 residues processed: 69 average time/residue: 0.0448 time to fit residues: 4.2003 Evaluate side-chains 59 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 58 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 443 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 15 optimal weight: 0.0970 chunk 33 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 20 optimal weight: 0.4980 chunk 0 optimal weight: 5.9990 chunk 16 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 ASN A 8 GLN A 275 HIS A 398 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.157560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.116857 restraints weight = 4670.649| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 2.31 r_work: 0.3341 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3852 Z= 0.139 Angle : 0.578 6.317 5243 Z= 0.288 Chirality : 0.041 0.176 613 Planarity : 0.005 0.049 658 Dihedral : 3.607 15.786 527 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.47 % Allowed : 11.36 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.39), residues: 480 helix: 1.12 (0.28), residues: 341 sheet: -0.77 (1.46), residues: 10 loop : -1.32 (0.57), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 423 TYR 0.011 0.002 TYR A 354 PHE 0.022 0.002 PHE A 152 TRP 0.010 0.001 TRP A 274 HIS 0.002 0.001 HIS A 48 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 3852) covalent geometry : angle 0.57790 ( 5243) hydrogen bonds : bond 0.04886 ( 223) hydrogen bonds : angle 3.72837 ( 660) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 68 time to evaluate : 0.166 Fit side-chains REVERT: A 74 GLN cc_start: 0.7093 (mp10) cc_final: 0.6790 (mp10) REVERT: A 263 ILE cc_start: 0.8230 (tp) cc_final: 0.8016 (tp) REVERT: A 282 ASP cc_start: 0.8978 (p0) cc_final: 0.8305 (t0) REVERT: A 289 GLN cc_start: 0.8206 (mt0) cc_final: 0.7865 (mm110) REVERT: A 386 PHE cc_start: 0.7013 (t80) cc_final: 0.6715 (t80) outliers start: 10 outliers final: 6 residues processed: 76 average time/residue: 0.0400 time to fit residues: 4.1398 Evaluate side-chains 69 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 63 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 316 GLU Chi-restraints excluded: chain A residue 438 PHE Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 500 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 32 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 chunk 37 optimal weight: 0.3980 chunk 46 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 ASN A 398 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.155150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.114437 restraints weight = 4782.726| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 2.40 r_work: 0.3298 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.3447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3852 Z= 0.130 Angle : 0.545 5.792 5243 Z= 0.270 Chirality : 0.039 0.183 613 Planarity : 0.004 0.041 658 Dihedral : 3.534 13.649 527 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.47 % Allowed : 15.56 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.40), residues: 480 helix: 1.28 (0.29), residues: 341 sheet: -0.88 (1.54), residues: 10 loop : -1.28 (0.58), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 158 TYR 0.011 0.001 TYR A 354 PHE 0.022 0.002 PHE A 152 TRP 0.011 0.001 TRP A 346 HIS 0.003 0.001 HIS A 48 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 3852) covalent geometry : angle 0.54476 ( 5243) hydrogen bonds : bond 0.04457 ( 223) hydrogen bonds : angle 3.72426 ( 660) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.145 Fit side-chains REVERT: A 74 GLN cc_start: 0.7136 (mp10) cc_final: 0.6505 (mp10) REVERT: A 214 MET cc_start: 0.8535 (mmt) cc_final: 0.8277 (mmt) REVERT: A 289 GLN cc_start: 0.8206 (mt0) cc_final: 0.7881 (mm110) REVERT: A 386 PHE cc_start: 0.6861 (t80) cc_final: 0.6553 (t80) outliers start: 10 outliers final: 6 residues processed: 69 average time/residue: 0.0581 time to fit residues: 5.1187 Evaluate side-chains 61 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 55 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 438 PHE Chi-restraints excluded: chain A residue 475 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 15 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 6 optimal weight: 9.9990 chunk 4 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 ASN A 8 GLN A 398 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.150662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.111001 restraints weight = 4694.407| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 2.29 r_work: 0.3260 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.3942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3852 Z= 0.134 Angle : 0.550 6.399 5243 Z= 0.271 Chirality : 0.039 0.159 613 Planarity : 0.004 0.043 658 Dihedral : 3.560 14.358 527 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 3.46 % Allowed : 17.28 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.40), residues: 480 helix: 1.32 (0.29), residues: 342 sheet: -1.05 (1.53), residues: 10 loop : -1.24 (0.58), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 158 TYR 0.012 0.001 TYR A 354 PHE 0.018 0.001 PHE A 152 TRP 0.011 0.001 TRP A 346 HIS 0.002 0.001 HIS A 48 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 3852) covalent geometry : angle 0.55017 ( 5243) hydrogen bonds : bond 0.04632 ( 223) hydrogen bonds : angle 3.71534 ( 660) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 60 time to evaluate : 0.141 Fit side-chains revert: symmetry clash REVERT: A 289 GLN cc_start: 0.8314 (mt0) cc_final: 0.8014 (mm110) REVERT: A 344 MET cc_start: 0.8236 (tpp) cc_final: 0.7807 (mtm) REVERT: A 507 THR cc_start: 0.7989 (p) cc_final: 0.7621 (p) outliers start: 14 outliers final: 10 residues processed: 69 average time/residue: 0.0636 time to fit residues: 5.6186 Evaluate side-chains 67 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 81 PHE Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 327 MET Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 438 PHE Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 475 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 29 optimal weight: 6.9990 chunk 40 optimal weight: 0.6980 chunk 30 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 34 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 chunk 18 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 398 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 = 0.3852 r_free = 0.3852 target = 0.152176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.111304 restraints weight = 4785.938| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 2.38 r_work: 0.3276 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.4120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3852 Z= 0.123 Angle : 0.546 6.251 5243 Z= 0.271 Chirality : 0.039 0.165 613 Planarity : 0.004 0.038 658 Dihedral : 3.507 13.452 527 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.47 % Allowed : 18.77 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.40), residues: 480 helix: 1.42 (0.29), residues: 343 sheet: -1.17 (1.49), residues: 10 loop : -1.16 (0.59), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 423 TYR 0.016 0.001 TYR A 230 PHE 0.022 0.001 PHE A 442 TRP 0.011 0.001 TRP A 346 HIS 0.002 0.001 HIS A 48 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 3852) covalent geometry : angle 0.54647 ( 5243) hydrogen bonds : bond 0.04302 ( 223) hydrogen bonds : angle 3.69382 ( 660) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 0.143 Fit side-chains revert: symmetry clash REVERT: A 289 GLN cc_start: 0.8298 (mt0) cc_final: 0.7912 (mm110) REVERT: A 344 MET cc_start: 0.8153 (tpp) cc_final: 0.7733 (mtm) REVERT: A 386 PHE cc_start: 0.7219 (OUTLIER) cc_final: 0.6709 (t80) outliers start: 10 outliers final: 9 residues processed: 63 average time/residue: 0.0599 time to fit residues: 4.8914 Evaluate side-chains 65 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 55 time to evaluate : 0.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 PHE Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 386 PHE Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 438 PHE Chi-restraints excluded: chain A residue 475 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 2 optimal weight: 0.5980 chunk 21 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 chunk 29 optimal weight: 6.9990 chunk 5 optimal weight: 0.0670 chunk 40 optimal weight: 0.8980 chunk 28 optimal weight: 0.0370 chunk 7 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 36 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 398 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 = 0.3868 r_free = 0.3868 target = 0.153315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.113773 restraints weight = 4741.769| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 2.33 r_work: 0.3312 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.4155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 3852 Z= 0.110 Angle : 0.535 7.419 5243 Z= 0.263 Chirality : 0.038 0.157 613 Planarity : 0.004 0.037 658 Dihedral : 3.455 13.411 527 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.96 % Allowed : 18.52 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.41), residues: 480 helix: 1.59 (0.29), residues: 342 sheet: -1.23 (1.49), residues: 10 loop : -1.14 (0.59), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 423 TYR 0.013 0.001 TYR A 230 PHE 0.015 0.001 PHE A 152 TRP 0.010 0.001 TRP A 346 HIS 0.001 0.000 HIS A 48 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 3852) covalent geometry : angle 0.53467 ( 5243) hydrogen bonds : bond 0.03728 ( 223) hydrogen bonds : angle 3.60373 ( 660) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 57 time to evaluate : 0.170 Fit side-chains revert: symmetry clash REVERT: A 289 GLN cc_start: 0.8287 (mt0) cc_final: 0.7940 (mm110) REVERT: A 344 MET cc_start: 0.8111 (tpp) cc_final: 0.7686 (mtm) REVERT: A 507 THR cc_start: 0.8010 (p) cc_final: 0.7652 (p) outliers start: 12 outliers final: 11 residues processed: 66 average time/residue: 0.0676 time to fit residues: 5.7004 Evaluate side-chains 67 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 56 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 81 PHE Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 438 PHE Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 475 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 16 optimal weight: 0.6980 chunk 18 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 chunk 37 optimal weight: 0.7980 chunk 44 optimal weight: 0.2980 chunk 33 optimal weight: 1.9990 chunk 32 optimal weight: 0.4980 chunk 21 optimal weight: 0.0570 chunk 1 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 chunk 10 optimal weight: 3.9990 overall best weight: 0.4298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 398 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 = 0.3884 r_free = 0.3884 target = 0.155056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.114260 restraints weight = 4820.993| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 2.42 r_work: 0.3317 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.4240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 3852 Z= 0.106 Angle : 0.537 7.910 5243 Z= 0.260 Chirality : 0.037 0.163 613 Planarity : 0.004 0.036 658 Dihedral : 3.366 13.005 527 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.72 % Allowed : 18.52 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.41), residues: 480 helix: 1.66 (0.29), residues: 342 sheet: -1.30 (1.49), residues: 10 loop : -1.09 (0.60), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 423 TYR 0.013 0.001 TYR A 230 PHE 0.014 0.001 PHE A 152 TRP 0.009 0.001 TRP A 346 HIS 0.002 0.000 HIS A 130 Details of bonding type rmsd covalent geometry : bond 0.00229 ( 3852) covalent geometry : angle 0.53676 ( 5243) hydrogen bonds : bond 0.03574 ( 223) hydrogen bonds : angle 3.54398 ( 660) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 60 time to evaluate : 0.084 Fit side-chains revert: symmetry clash REVERT: A 289 GLN cc_start: 0.8283 (mt0) cc_final: 0.8002 (mm110) REVERT: A 344 MET cc_start: 0.8098 (tpp) cc_final: 0.7689 (mtm) REVERT: A 438 PHE cc_start: 0.8116 (OUTLIER) cc_final: 0.7800 (t80) REVERT: A 507 THR cc_start: 0.8046 (p) cc_final: 0.7715 (p) outliers start: 11 outliers final: 10 residues processed: 68 average time/residue: 0.0395 time to fit residues: 3.4791 Evaluate side-chains 72 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 61 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 81 PHE Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 438 PHE Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 475 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 7 optimal weight: 6.9990 chunk 10 optimal weight: 0.2980 chunk 30 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 44 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 398 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 = 0.3864 r_free = 0.3864 target = 0.153151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.112369 restraints weight = 4757.701| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 2.38 r_work: 0.3294 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.4387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3852 Z= 0.115 Angle : 0.544 7.874 5243 Z= 0.263 Chirality : 0.038 0.154 613 Planarity : 0.004 0.037 658 Dihedral : 3.426 13.690 527 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.96 % Allowed : 18.52 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.41), residues: 480 helix: 1.66 (0.29), residues: 343 sheet: -1.20 (1.55), residues: 10 loop : -0.92 (0.60), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 423 TYR 0.013 0.001 TYR A 230 PHE 0.014 0.001 PHE A 152 TRP 0.010 0.001 TRP A 346 HIS 0.002 0.001 HIS A 48 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 3852) covalent geometry : angle 0.54358 ( 5243) hydrogen bonds : bond 0.03984 ( 223) hydrogen bonds : angle 3.57931 ( 660) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 0.085 Fit side-chains revert: symmetry clash REVERT: A 289 GLN cc_start: 0.8285 (mt0) cc_final: 0.8020 (mm110) REVERT: A 344 MET cc_start: 0.8157 (tpp) cc_final: 0.7750 (mtm) REVERT: A 507 THR cc_start: 0.8002 (p) cc_final: 0.7681 (p) outliers start: 12 outliers final: 12 residues processed: 68 average time/residue: 0.0583 time to fit residues: 5.0368 Evaluate side-chains 76 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 81 PHE Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 438 PHE Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 475 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 11 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 29 optimal weight: 4.9990 chunk 47 optimal weight: 0.0070 chunk 34 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 2 optimal weight: 0.0050 chunk 44 optimal weight: 1.9990 overall best weight: 0.5212 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 398 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 = 0.3875 r_free = 0.3875 target = 0.154247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.113338 restraints weight = 4871.358| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 2.41 r_work: 0.3291 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.4477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 3852 Z= 0.111 Angle : 0.553 8.306 5243 Z= 0.266 Chirality : 0.038 0.160 613 Planarity : 0.004 0.036 658 Dihedral : 3.366 13.111 527 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.96 % Allowed : 19.26 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.41), residues: 480 helix: 1.74 (0.29), residues: 342 sheet: -1.33 (1.52), residues: 10 loop : -0.89 (0.60), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 423 TYR 0.012 0.001 TYR A 230 PHE 0.017 0.001 PHE A 442 TRP 0.010 0.001 TRP A 346 HIS 0.002 0.001 HIS A 130 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 3852) covalent geometry : angle 0.55333 ( 5243) hydrogen bonds : bond 0.03733 ( 223) hydrogen bonds : angle 3.54428 ( 660) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 0.135 Fit side-chains revert: symmetry clash REVERT: A 289 GLN cc_start: 0.8313 (mt0) cc_final: 0.8091 (mm110) REVERT: A 344 MET cc_start: 0.8127 (tpp) cc_final: 0.7735 (mtm) outliers start: 12 outliers final: 12 residues processed: 75 average time/residue: 0.0482 time to fit residues: 4.6730 Evaluate side-chains 73 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 61 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 81 PHE Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 438 PHE Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 475 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 9 optimal weight: 0.0000 chunk 0 optimal weight: 5.9990 chunk 18 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 4 optimal weight: 0.0970 chunk 1 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 29 optimal weight: 5.9990 overall best weight: 0.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 398 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 = 0.3864 r_free = 0.3864 target = 0.152835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.113557 restraints weight = 4624.402| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.28 r_work: 0.3314 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.4514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 3852 Z= 0.113 Angle : 0.561 8.174 5243 Z= 0.271 Chirality : 0.038 0.190 613 Planarity : 0.004 0.036 658 Dihedral : 3.411 13.397 527 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.96 % Allowed : 20.49 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.41), residues: 480 helix: 1.78 (0.29), residues: 342 sheet: -1.30 (1.49), residues: 10 loop : -0.76 (0.61), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 423 TYR 0.012 0.001 TYR A 230 PHE 0.014 0.001 PHE A 152 TRP 0.010 0.001 TRP A 346 HIS 0.002 0.000 HIS A 48 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 3852) covalent geometry : angle 0.56085 ( 5243) hydrogen bonds : bond 0.03706 ( 223) hydrogen bonds : angle 3.53378 ( 660) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1051.58 seconds wall clock time: 18 minutes 41.97 seconds (1121.97 seconds total)