Starting phenix.real_space_refine on Tue Mar 3 11:52:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wsn_32761/03_2026/7wsn_32761.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wsn_32761/03_2026/7wsn_32761.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wsn_32761/03_2026/7wsn_32761.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wsn_32761/03_2026/7wsn_32761.map" model { file = "/net/cci-nas-00/data/ceres_data/7wsn_32761/03_2026/7wsn_32761.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wsn_32761/03_2026/7wsn_32761.cif" } resolution = 3.31 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= 0.116 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 14 5.16 5 C 2353 2.51 5 N 579 2.21 5 O 621 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3567 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3504 Classifications: {'peptide': 463} Link IDs: {'PTRANS': 24, 'TRANS': 438} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'5RH': 1} Classifications: {'undetermined': 1} Time building chain proxies: 0.78, per 1000 atoms: 0.22 Number of scatterers: 3567 At special positions: 0 Unit cell: (92.0125, 58.455, 72.5275, 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 14 16.00 O 621 8.00 N 579 7.00 C 2353 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 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG B 1 " - " ASN A 57 " Time building additional restraints: 0.26 Conformation dependent library (CDL) restraints added in 166.0 milliseconds 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 828 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 0 sheets defined 87.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'A' and resid 21 through 44 Processing helix chain 'A' and resid 48 through 63 removed outlier: 3.634A pdb=" N GLN A 54 " --> pdb=" O LYS A 50 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG A 63 " --> pdb=" O THR A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 107 removed outlier: 3.705A pdb=" N VAL A 85 " --> pdb=" O TRP A 81 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N PHE A 88 " --> pdb=" O SER A 84 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N SER A 89 " --> pdb=" O VAL A 85 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N PHE A 97 " --> pdb=" O MET A 93 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU A 98 " --> pdb=" O ILE A 94 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N GLY A 100 " --> pdb=" O SER A 96 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N ILE A 101 " --> pdb=" O PHE A 97 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE A 102 " --> pdb=" O LEU A 98 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N SER A 103 " --> pdb=" O ILE A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 128 Processing helix chain 'A' and resid 128 through 133 Processing helix chain 'A' and resid 135 through 164 removed outlier: 3.560A pdb=" N ILE A 139 " --> pdb=" O TYR A 135 " (cutoff:3.500A) Proline residue: A 157 - end of helix Processing helix chain 'A' and resid 168 through 174 removed outlier: 3.742A pdb=" N THR A 174 " --> pdb=" O GLY A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 190 Processing helix chain 'A' and resid 202 through 220 removed outlier: 3.822A pdb=" N LEU A 206 " --> pdb=" O TRP A 202 " (cutoff:3.500A) Proline residue: A 212 - end of helix removed outlier: 3.631A pdb=" N LEU A 215 " --> pdb=" O LEU A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 223 No H-bonds generated for 'chain 'A' and resid 221 through 223' Processing helix chain 'A' and resid 226 through 233 removed outlier: 3.572A pdb=" N ILE A 233 " --> pdb=" O TYR A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 249 Processing helix chain 'A' and resid 253 through 270 Processing helix chain 'A' and resid 274 through 281 Processing helix chain 'A' and resid 285 through 301 removed outlier: 3.520A pdb=" N SER A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 318 removed outlier: 6.833A pdb=" N THR A 311 " --> pdb=" O PHE A 307 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N SER A 312 " --> pdb=" O TYR A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 344 removed outlier: 3.501A pdb=" N ALA A 325 " --> pdb=" O GLN A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 347 No H-bonds generated for 'chain 'A' and resid 345 through 347' Processing helix chain 'A' and resid 349 through 373 Processing helix chain 'A' and resid 377 through 379 No H-bonds generated for 'chain 'A' and resid 377 through 379' Processing helix chain 'A' and resid 380 through 398 removed outlier: 3.822A pdb=" N SER A 384 " --> pdb=" O MET A 380 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE A 385 " --> pdb=" O SER A 381 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE A 397 " --> pdb=" O ALA A 393 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLY A 398 " --> pdb=" O PHE A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 410 removed outlier: 3.572A pdb=" N PHE A 405 " --> pdb=" O PRO A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 446 removed outlier: 5.161A pdb=" N GLN A 439 " --> pdb=" O GLY A 435 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N TYR A 440 " --> pdb=" O MET A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 468 removed outlier: 3.504A pdb=" N PHE A 453 " --> pdb=" O VAL A 449 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL A 468 " --> pdb=" O THR A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 483 removed outlier: 3.689A pdb=" N PHE A 483 " --> pdb=" O ILE A 479 " (cutoff:3.500A) 272 hydrogen bonds defined for protein. 816 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: 0.52 Time building geometry restraints manager: 0.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 542 1.31 - 1.43: 967 1.43 - 1.56: 2114 1.56 - 1.68: 1 1.68 - 1.81: 25 Bond restraints: 3649 Sorted by residual: bond pdb=" C ASN A 46 " pdb=" O ASN A 46 " ideal model delta sigma weight residual 1.237 1.186 0.051 1.19e-02 7.06e+03 1.82e+01 bond pdb=" C ILE A 45 " pdb=" N ASN A 46 " ideal model delta sigma weight residual 1.335 1.283 0.052 1.36e-02 5.41e+03 1.48e+01 bond pdb=" CA ASN A 46 " pdb=" CB ASN A 46 " ideal model delta sigma weight residual 1.528 1.489 0.040 1.59e-02 3.96e+03 6.18e+00 bond pdb=" N THR A 78 " pdb=" CA THR A 78 " ideal model delta sigma weight residual 1.459 1.489 -0.029 1.21e-02 6.83e+03 5.91e+00 bond pdb=" N ASP A 252 " pdb=" CA ASP A 252 " ideal model delta sigma weight residual 1.455 1.485 -0.030 1.25e-02 6.40e+03 5.70e+00 ... (remaining 3644 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.83: 4770 1.83 - 3.66: 173 3.66 - 5.50: 28 5.50 - 7.33: 2 7.33 - 9.16: 2 Bond angle restraints: 4975 Sorted by residual: angle pdb=" N ASN A 46 " pdb=" CA ASN A 46 " pdb=" CB ASN A 46 " ideal model delta sigma weight residual 110.16 103.10 7.06 1.48e+00 4.57e-01 2.27e+01 angle pdb=" CA ILE A 45 " pdb=" C ILE A 45 " pdb=" N ASN A 46 " ideal model delta sigma weight residual 118.48 122.63 -4.15 1.01e+00 9.80e-01 1.69e+01 angle pdb=" O ILE A 45 " pdb=" C ILE A 45 " pdb=" N ASN A 46 " ideal model delta sigma weight residual 122.12 117.65 4.47 1.16e+00 7.43e-01 1.49e+01 angle pdb=" CA ASN A 46 " pdb=" C ASN A 46 " pdb=" O ASN A 46 " ideal model delta sigma weight residual 120.42 116.59 3.83 1.06e+00 8.90e-01 1.31e+01 angle pdb=" CA SER A 412 " pdb=" C SER A 412 " pdb=" O SER A 412 " ideal model delta sigma weight residual 122.01 118.23 3.78 1.05e+00 9.07e-01 1.29e+01 ... (remaining 4970 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.67: 2137 35.67 - 71.33: 58 71.33 - 107.00: 3 107.00 - 142.67: 0 142.67 - 178.33: 2 Dihedral angle restraints: 2200 sinusoidal: 897 harmonic: 1303 Sorted by residual: dihedral pdb=" C19 5RH A 601 " pdb=" C17 5RH A 601 " pdb=" C18 5RH A 601 " pdb=" O3 5RH A 601 " ideal model delta sinusoidal sigma weight residual 193.05 14.72 178.33 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C19 5RH A 601 " pdb=" C17 5RH A 601 " pdb=" C18 5RH A 601 " pdb=" O2 5RH A 601 " ideal model delta sinusoidal sigma weight residual 11.42 -165.41 176.83 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" CA PRO A 401 " pdb=" C PRO A 401 " pdb=" N ILE A 402 " pdb=" CA ILE A 402 " ideal model delta harmonic sigma weight residual -180.00 -161.98 -18.02 0 5.00e+00 4.00e-02 1.30e+01 ... (remaining 2197 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 381 0.038 - 0.075: 169 0.075 - 0.113: 44 0.113 - 0.150: 8 0.150 - 0.188: 1 Chirality restraints: 603 Sorted by residual: chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.42 0.02 2.00e-02 2.50e+03 1.24e+00 chirality pdb=" CG LEU A 206 " pdb=" CB LEU A 206 " pdb=" CD1 LEU A 206 " pdb=" CD2 LEU A 206 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.81e-01 chirality pdb=" CA PHE A 336 " pdb=" N PHE A 336 " pdb=" C PHE A 336 " pdb=" CB PHE A 336 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.87e-01 ... (remaining 600 not shown) Planarity restraints: 617 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 57 " 0.062 2.00e-02 2.50e+03 6.25e-02 4.88e+01 pdb=" CG ASN A 57 " -0.033 2.00e-02 2.50e+03 pdb=" OD1 ASN A 57 " -0.017 2.00e-02 2.50e+03 pdb=" ND2 ASN A 57 " -0.090 2.00e-02 2.50e+03 pdb=" C1 NAG B 1 " 0.078 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C17 5RH A 601 " -0.027 2.00e-02 2.50e+03 4.87e-02 2.37e+01 pdb=" C18 5RH A 601 " 0.064 2.00e-02 2.50e+03 pdb=" C19 5RH A 601 " -0.063 2.00e-02 2.50e+03 pdb=" C20 5RH A 601 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" N 5RH A 601 " 0.066 2.00e-02 2.50e+03 4.30e-02 2.31e+01 pdb=" C15 5RH A 601 " 0.005 2.00e-02 2.50e+03 pdb=" C16 5RH A 601 " 0.021 2.00e-02 2.50e+03 pdb=" C7 5RH A 601 " -0.053 2.00e-02 2.50e+03 pdb=" O1 5RH A 601 " -0.039 2.00e-02 2.50e+03 ... (remaining 614 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 865 2.78 - 3.31: 3862 3.31 - 3.84: 5928 3.84 - 4.37: 6613 4.37 - 4.90: 11300 Nonbonded interactions: 28568 Sorted by model distance: nonbonded pdb=" OG SER A 89 " pdb=" ND2 ASN A 431 " model vdw 2.248 3.120 nonbonded pdb=" O GLY A 100 " pdb=" OG SER A 103 " model vdw 2.256 3.040 nonbonded pdb=" OG1 THR A 79 " pdb=" OH TYR A 440 " model vdw 2.261 3.040 nonbonded pdb=" O GLY A 92 " pdb=" OG SER A 95 " model vdw 2.372 3.040 nonbonded pdb=" NH2 ARG A 350 " pdb=" O PHE A 465 " model vdw 2.375 3.120 ... (remaining 28563 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 ========== 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: 0.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.510 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 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:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 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 : 0.007 0.052 3651 Z= 0.340 Angle : 0.840 9.162 4981 Z= 0.461 Chirality : 0.044 0.188 603 Planarity : 0.006 0.049 616 Dihedral : 17.546 178.332 1372 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 1.08 % Allowed : 0.27 % Favored : 98.65 % 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: -0.44 (0.39), residues: 461 helix: 0.35 (0.27), residues: 375 sheet: None (None), residues: 0 loop : -2.88 (0.62), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 285 TYR 0.015 0.002 TYR A 148 PHE 0.014 0.002 PHE A 391 TRP 0.011 0.002 TRP A 202 HIS 0.004 0.001 HIS A 353 Details of bonding type rmsd covalent geometry : bond 0.00720 ( 3649) covalent geometry : angle 0.82698 ( 4975) hydrogen bonds : bond 0.13925 ( 272) hydrogen bonds : angle 7.18828 ( 816) link_BETA1-4 : bond 0.00113 ( 1) link_BETA1-4 : angle 3.70338 ( 3) link_NAG-ASN : bond 0.00981 ( 1) link_NAG-ASN : angle 4.81094 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 55 time to evaluate : 0.171 Fit side-chains REVERT: A 264 LYS cc_start: 0.6249 (ttpt) cc_final: 0.5560 (pttm) REVERT: A 412 SER cc_start: 0.8132 (OUTLIER) cc_final: 0.7872 (t) outliers start: 4 outliers final: 1 residues processed: 59 average time/residue: 0.0621 time to fit residues: 4.7085 Evaluate side-chains 45 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 43 time to evaluate : 0.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 431 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 24 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 2 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 5.9990 chunk 19 optimal weight: 0.8980 chunk 30 optimal weight: 8.9990 chunk 22 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 ASN A 177 GLN A 234 GLN A 299 GLN A 353 HIS A 413 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.142259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.109794 restraints weight = 4407.670| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 2.11 r_work: 0.2995 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3651 Z= 0.170 Angle : 0.726 10.691 4981 Z= 0.356 Chirality : 0.044 0.186 603 Planarity : 0.005 0.049 616 Dihedral : 13.099 174.477 605 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.16 % Allowed : 14.32 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 461 helix: 1.56 (0.28), residues: 378 sheet: None (None), residues: 0 loop : -2.82 (0.59), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 246 TYR 0.023 0.002 TYR A 148 PHE 0.022 0.002 PHE A 336 TRP 0.006 0.001 TRP A 250 HIS 0.001 0.000 HIS A 353 Details of bonding type rmsd covalent geometry : bond 0.00386 ( 3649) covalent geometry : angle 0.71969 ( 4975) hydrogen bonds : bond 0.05406 ( 272) hydrogen bonds : angle 4.86722 ( 816) link_BETA1-4 : bond 0.00722 ( 1) link_BETA1-4 : angle 1.75755 ( 3) link_NAG-ASN : bond 0.00057 ( 1) link_NAG-ASN : angle 3.66267 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.080 Fit side-chains REVERT: A 264 LYS cc_start: 0.5435 (ttpt) cc_final: 0.5009 (pttm) REVERT: A 431 ASN cc_start: 0.8600 (OUTLIER) cc_final: 0.8327 (t0) REVERT: A 434 ILE cc_start: 0.7327 (tp) cc_final: 0.7079 (tp) outliers start: 8 outliers final: 5 residues processed: 59 average time/residue: 0.0392 time to fit residues: 3.1934 Evaluate side-chains 53 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 431 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 40 optimal weight: 0.6980 chunk 39 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 38 optimal weight: 0.1980 chunk 25 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.144493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.111697 restraints weight = 4342.900| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.13 r_work: 0.3161 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3651 Z= 0.147 Angle : 0.656 10.768 4981 Z= 0.322 Chirality : 0.042 0.185 603 Planarity : 0.005 0.050 616 Dihedral : 12.757 169.458 604 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.70 % Allowed : 15.41 % Favored : 81.89 % 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: 1.59 (0.41), residues: 461 helix: 1.82 (0.28), residues: 380 sheet: None (None), residues: 0 loop : -2.80 (0.57), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 285 TYR 0.015 0.001 TYR A 148 PHE 0.018 0.002 PHE A 336 TRP 0.007 0.001 TRP A 202 HIS 0.001 0.000 HIS A 353 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 3649) covalent geometry : angle 0.65067 ( 4975) hydrogen bonds : bond 0.04709 ( 272) hydrogen bonds : angle 4.55559 ( 816) link_BETA1-4 : bond 0.00174 ( 1) link_BETA1-4 : angle 1.91768 ( 3) link_NAG-ASN : bond 0.00237 ( 1) link_NAG-ASN : angle 3.08595 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 0.131 Fit side-chains REVERT: A 431 ASN cc_start: 0.8656 (OUTLIER) cc_final: 0.8423 (t0) outliers start: 10 outliers final: 4 residues processed: 61 average time/residue: 0.0490 time to fit residues: 3.9802 Evaluate side-chains 55 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 50 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 431 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 3 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 42 optimal weight: 0.5980 chunk 27 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 44 optimal weight: 0.3980 chunk 9 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 413 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.145322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.113066 restraints weight = 4202.932| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 2.03 r_work: 0.3169 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3651 Z= 0.146 Angle : 0.636 8.761 4981 Z= 0.311 Chirality : 0.041 0.181 603 Planarity : 0.005 0.054 616 Dihedral : 12.578 166.844 604 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.43 % Allowed : 18.92 % Favored : 78.65 % 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: 1.66 (0.41), residues: 461 helix: 1.87 (0.27), residues: 380 sheet: None (None), residues: 0 loop : -2.77 (0.56), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 228 TYR 0.014 0.001 TYR A 148 PHE 0.017 0.002 PHE A 336 TRP 0.008 0.001 TRP A 202 HIS 0.001 0.000 HIS A 353 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 3649) covalent geometry : angle 0.63156 ( 4975) hydrogen bonds : bond 0.04529 ( 272) hydrogen bonds : angle 4.44027 ( 816) link_BETA1-4 : bond 0.00392 ( 1) link_BETA1-4 : angle 1.83123 ( 3) link_NAG-ASN : bond 0.00097 ( 1) link_NAG-ASN : angle 2.49769 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 52 time to evaluate : 0.078 Fit side-chains REVERT: A 104 GLN cc_start: 0.7829 (mt0) cc_final: 0.7569 (tt0) REVERT: A 431 ASN cc_start: 0.8658 (OUTLIER) cc_final: 0.8432 (t0) outliers start: 9 outliers final: 6 residues processed: 57 average time/residue: 0.0471 time to fit residues: 3.5237 Evaluate side-chains 56 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 49 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 431 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 2 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 GLN ** A 41 ASN ** 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 = 0.3654 r_free = 0.3654 target = 0.146000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.113506 restraints weight = 4218.113| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 2.04 r_work: 0.3176 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3651 Z= 0.148 Angle : 0.613 6.991 4981 Z= 0.303 Chirality : 0.040 0.172 603 Planarity : 0.005 0.056 616 Dihedral : 12.434 164.721 604 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.43 % Allowed : 21.35 % Favored : 76.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.74 (0.41), residues: 461 helix: 1.92 (0.28), residues: 380 sheet: None (None), residues: 0 loop : -2.68 (0.57), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 228 TYR 0.014 0.001 TYR A 229 PHE 0.016 0.001 PHE A 336 TRP 0.008 0.001 TRP A 202 HIS 0.001 0.000 HIS A 353 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 3649) covalent geometry : angle 0.60969 ( 4975) hydrogen bonds : bond 0.04520 ( 272) hydrogen bonds : angle 4.39214 ( 816) link_BETA1-4 : bond 0.00240 ( 1) link_BETA1-4 : angle 1.77661 ( 3) link_NAG-ASN : bond 0.00086 ( 1) link_NAG-ASN : angle 2.19755 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.130 Fit side-chains REVERT: A 104 GLN cc_start: 0.7546 (mt0) cc_final: 0.7281 (tt0) REVERT: A 431 ASN cc_start: 0.8651 (OUTLIER) cc_final: 0.8426 (t0) outliers start: 9 outliers final: 5 residues processed: 57 average time/residue: 0.0484 time to fit residues: 3.6963 Evaluate side-chains 57 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 51 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 431 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 8 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 2 optimal weight: 0.0020 chunk 37 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 41 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.147171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.114607 restraints weight = 4169.729| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 2.04 r_work: 0.3149 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3651 Z= 0.138 Angle : 0.619 11.753 4981 Z= 0.301 Chirality : 0.040 0.162 603 Planarity : 0.005 0.058 616 Dihedral : 12.195 161.316 604 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.43 % Allowed : 22.16 % Favored : 75.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.85 (0.41), residues: 461 helix: 1.99 (0.28), residues: 380 sheet: None (None), residues: 0 loop : -2.64 (0.58), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 285 TYR 0.014 0.001 TYR A 148 PHE 0.016 0.001 PHE A 336 TRP 0.008 0.001 TRP A 202 HIS 0.000 0.000 HIS A 353 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 3649) covalent geometry : angle 0.61581 ( 4975) hydrogen bonds : bond 0.04306 ( 272) hydrogen bonds : angle 4.32803 ( 816) link_BETA1-4 : bond 0.00344 ( 1) link_BETA1-4 : angle 1.67677 ( 3) link_NAG-ASN : bond 0.00013 ( 1) link_NAG-ASN : angle 1.86767 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.079 Fit side-chains REVERT: A 104 GLN cc_start: 0.7543 (mt0) cc_final: 0.7274 (tt0) REVERT: A 431 ASN cc_start: 0.8621 (OUTLIER) cc_final: 0.8396 (t0) outliers start: 9 outliers final: 6 residues processed: 58 average time/residue: 0.0501 time to fit residues: 3.8435 Evaluate side-chains 59 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 431 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 19 optimal weight: 0.7980 chunk 21 optimal weight: 6.9990 chunk 26 optimal weight: 0.9980 chunk 3 optimal weight: 0.5980 chunk 45 optimal weight: 8.9990 chunk 9 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 38 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 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 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 41 ASN A 177 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.148061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.114774 restraints weight = 4418.984| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 2.18 r_work: 0.3040 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7235 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3651 Z= 0.138 Angle : 0.587 6.773 4981 Z= 0.291 Chirality : 0.039 0.141 603 Planarity : 0.005 0.058 616 Dihedral : 11.801 155.064 604 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.24 % Allowed : 23.24 % Favored : 73.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.90 (0.41), residues: 461 helix: 2.01 (0.28), residues: 380 sheet: None (None), residues: 0 loop : -2.56 (0.59), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 228 TYR 0.014 0.001 TYR A 229 PHE 0.016 0.001 PHE A 336 TRP 0.008 0.001 TRP A 202 HIS 0.000 0.000 HIS A 353 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 3649) covalent geometry : angle 0.58482 ( 4975) hydrogen bonds : bond 0.04284 ( 272) hydrogen bonds : angle 4.27954 ( 816) link_BETA1-4 : bond 0.00314 ( 1) link_BETA1-4 : angle 1.67305 ( 3) link_NAG-ASN : bond 0.00021 ( 1) link_NAG-ASN : angle 1.67757 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 52 time to evaluate : 0.126 Fit side-chains REVERT: A 41 ASN cc_start: 0.8301 (OUTLIER) cc_final: 0.7993 (m110) REVERT: A 104 GLN cc_start: 0.7491 (mt0) cc_final: 0.7285 (tt0) REVERT: A 431 ASN cc_start: 0.8621 (OUTLIER) cc_final: 0.8407 (t0) outliers start: 12 outliers final: 6 residues processed: 60 average time/residue: 0.0482 time to fit residues: 3.8456 Evaluate side-chains 58 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 50 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ASN Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 431 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 28 optimal weight: 1.9990 chunk 18 optimal weight: 0.0270 chunk 23 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 1 optimal weight: 0.8980 chunk 44 optimal weight: 0.6980 chunk 45 optimal weight: 4.9990 chunk 2 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 overall best weight: 0.7038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 41 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.148837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.115572 restraints weight = 4355.501| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.17 r_work: 0.3201 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.2703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3651 Z= 0.137 Angle : 0.626 13.203 4981 Z= 0.303 Chirality : 0.040 0.148 603 Planarity : 0.005 0.061 616 Dihedral : 11.350 146.605 604 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.97 % Allowed : 22.70 % Favored : 74.32 % 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: 1.87 (0.41), residues: 461 helix: 2.01 (0.27), residues: 380 sheet: None (None), residues: 0 loop : -2.68 (0.58), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 228 TYR 0.014 0.001 TYR A 229 PHE 0.016 0.001 PHE A 336 TRP 0.008 0.001 TRP A 202 HIS 0.000 0.000 HIS A 353 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 3649) covalent geometry : angle 0.62408 ( 4975) hydrogen bonds : bond 0.04217 ( 272) hydrogen bonds : angle 4.21381 ( 816) link_BETA1-4 : bond 0.00362 ( 1) link_BETA1-4 : angle 1.62995 ( 3) link_NAG-ASN : bond 0.00010 ( 1) link_NAG-ASN : angle 1.63587 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 53 time to evaluate : 0.091 Fit side-chains REVERT: A 41 ASN cc_start: 0.8292 (OUTLIER) cc_final: 0.8038 (m110) REVERT: A 346 ARG cc_start: 0.8037 (ttt180) cc_final: 0.7175 (ttt180) REVERT: A 431 ASN cc_start: 0.8707 (OUTLIER) cc_final: 0.8493 (t0) outliers start: 11 outliers final: 6 residues processed: 61 average time/residue: 0.0467 time to fit residues: 3.7896 Evaluate side-chains 58 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 50 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ASN Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 431 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 20 optimal weight: 1.9990 chunk 35 optimal weight: 0.0970 chunk 29 optimal weight: 0.0170 chunk 19 optimal weight: 0.0870 chunk 30 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 overall best weight: 0.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 41 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.152287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.118605 restraints weight = 4315.761| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 2.18 r_work: 0.3079 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 moved from start: 0.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3651 Z= 0.123 Angle : 0.602 12.962 4981 Z= 0.292 Chirality : 0.039 0.163 603 Planarity : 0.006 0.057 616 Dihedral : 10.019 124.676 604 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.70 % Allowed : 24.05 % Favored : 73.24 % 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: 1.92 (0.41), residues: 461 helix: 2.04 (0.27), residues: 380 sheet: None (None), residues: 0 loop : -2.63 (0.59), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 228 TYR 0.013 0.001 TYR A 229 PHE 0.015 0.001 PHE A 336 TRP 0.008 0.001 TRP A 202 HIS 0.000 0.000 HIS A 167 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 3649) covalent geometry : angle 0.60042 ( 4975) hydrogen bonds : bond 0.03921 ( 272) hydrogen bonds : angle 4.13790 ( 816) link_BETA1-4 : bond 0.00362 ( 1) link_BETA1-4 : angle 1.45739 ( 3) link_NAG-ASN : bond 0.00064 ( 1) link_NAG-ASN : angle 1.43800 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 51 time to evaluate : 0.125 Fit side-chains REVERT: A 346 ARG cc_start: 0.8003 (ttt180) cc_final: 0.7129 (ttt180) REVERT: A 431 ASN cc_start: 0.8573 (OUTLIER) cc_final: 0.8357 (t0) outliers start: 10 outliers final: 7 residues processed: 57 average time/residue: 0.0509 time to fit residues: 3.8891 Evaluate side-chains 55 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 431 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 17 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 2 optimal weight: 0.2980 chunk 40 optimal weight: 3.9990 chunk 44 optimal weight: 0.0070 chunk 30 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 overall best weight: 0.5400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 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 = 0.3699 r_free = 0.3699 target = 0.150719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.117144 restraints weight = 4286.154| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 2.11 r_work: 0.3226 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3651 Z= 0.126 Angle : 0.591 12.408 4981 Z= 0.289 Chirality : 0.039 0.159 603 Planarity : 0.006 0.060 616 Dihedral : 8.996 108.224 604 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.43 % Allowed : 24.05 % Favored : 73.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.02 (0.41), residues: 461 helix: 2.10 (0.27), residues: 380 sheet: None (None), residues: 0 loop : -2.56 (0.60), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 228 TYR 0.014 0.001 TYR A 229 PHE 0.016 0.001 PHE A 336 TRP 0.009 0.001 TRP A 202 HIS 0.001 0.000 HIS A 284 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 3649) covalent geometry : angle 0.58897 ( 4975) hydrogen bonds : bond 0.04014 ( 272) hydrogen bonds : angle 4.11497 ( 816) link_BETA1-4 : bond 0.00344 ( 1) link_BETA1-4 : angle 1.50552 ( 3) link_NAG-ASN : bond 0.00035 ( 1) link_NAG-ASN : angle 1.44669 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 0.113 Fit side-chains REVERT: A 104 GLN cc_start: 0.7167 (tt0) cc_final: 0.6847 (tt0) REVERT: A 346 ARG cc_start: 0.8052 (ttt180) cc_final: 0.7127 (ttt180) REVERT: A 413 GLN cc_start: 0.7363 (tp40) cc_final: 0.6846 (pm20) REVERT: A 431 ASN cc_start: 0.8601 (OUTLIER) cc_final: 0.8361 (t0) outliers start: 9 outliers final: 7 residues processed: 52 average time/residue: 0.0502 time to fit residues: 3.4576 Evaluate side-chains 55 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 431 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 5 optimal weight: 0.0980 chunk 44 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 45 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 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 37 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 = 0.3695 r_free = 0.3695 target = 0.150188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.116810 restraints weight = 4246.839| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 2.11 r_work: 0.3225 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 moved from start: 0.3045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3651 Z= 0.130 Angle : 0.592 12.346 4981 Z= 0.289 Chirality : 0.039 0.158 603 Planarity : 0.006 0.062 616 Dihedral : 8.933 108.683 604 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.43 % Allowed : 24.32 % Favored : 73.24 % 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: 2.06 (0.41), residues: 461 helix: 2.13 (0.27), residues: 380 sheet: None (None), residues: 0 loop : -2.57 (0.60), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 228 TYR 0.013 0.001 TYR A 229 PHE 0.016 0.001 PHE A 336 TRP 0.008 0.001 TRP A 202 HIS 0.000 0.000 HIS A 284 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 3649) covalent geometry : angle 0.59001 ( 4975) hydrogen bonds : bond 0.04069 ( 272) hydrogen bonds : angle 4.12339 ( 816) link_BETA1-4 : bond 0.00334 ( 1) link_BETA1-4 : angle 1.48085 ( 3) link_NAG-ASN : bond 0.00036 ( 1) link_NAG-ASN : angle 1.43550 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 994.15 seconds wall clock time: 17 minutes 38.57 seconds (1058.57 seconds total)