Starting phenix.real_space_refine on Wed Jul 1 22:39:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7wsn_32761/07_2026/7wsn_32761.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wsn_32761/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/7wsn_32761/07_2026/7wsn_32761.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wsn_32761/07_2026/7wsn_32761.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7wsn_32761/07_2026/7wsn_32761.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7wsn_32761/07_2026/7wsn_32761.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wsn_32761/07_2026/7wsn_32761.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wsn_32761/07_2026/7wsn_32761.map" } 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-6108/lib/python3.11/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 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: 0.69, per 1000 atoms: 0.19 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: 0.35 Conformation dependent library (CDL) restraints added in 97.0 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: 0.05 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: 0.41 Time building geometry restraints manager: 0.40 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: 2096 35.67 - 71.33: 57 71.33 - 107.00: 3 107.00 - 142.67: 0 142.67 - 178.33: 2 Dihedral angle restraints: 2158 sinusoidal: 855 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 2155 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: 0.360 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: 0.030 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 4.090 Find NCS groups from input model: 0.010 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:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 5.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 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 : 17.680 178.332 1330 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/Z covalent geometry : bond 0.00720 / 0.34 ( 3649) covalent geometry : angle 0.82698 / 0.46 ( 4975) hydrogen bonds : bond 0.13925 / 8.82 ( 272) hydrogen bonds : angle 7.18828 / 4.99 ( 816) link_BETA1-4 : bond 0.00113 / 0.06 ( 1) link_BETA1-4 : angle 3.70338 / 1.87 ( 3) link_NAG-ASN : bond 0.00981 / 0.52 ( 1) link_NAG-ASN : angle 4.81094 / 2.25 ( 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 : 0.124 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: 0.0559 time to fit residues: 4.2579 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 : 0.076 ------------------------------------------------------------------------------- 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... 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 = 0.3618 r_free = 0.3618 target = 0.141836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.109658 restraints weight = 4407.955| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 2.10 r_work: 0.2992 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.1576 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= 0.168 Angle : 0.725 11.124 4981 Z= 0.353 Chirality : 0.044 0.190 603 Planarity : 0.005 0.050 616 Dihedral : 13.298 174.235 563 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.16 % Allowed : 14.05 % Favored : 83.78 % 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: 1.17 (0.41), residues: 461 helix: 1.53 (0.28), residues: 378 sheet: None (None), residues: 0 loop : -2.83 (0.59), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 246 TYR 0.023 0.002 TYR A 148 PHE 0.022 0.002 PHE A 336 TRP 0.005 0.001 TRP A 250 HIS 0.002 0.001 HIS A 353 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.17 ( 3649) covalent geometry : angle 0.71779 / 0.35 ( 4975) hydrogen bonds : bond 0.05455 / 3.63 ( 272) hydrogen bonds : angle 4.89362 / 3.39 ( 816) link_BETA1-4 : bond 0.00685 / 0.36 ( 1) link_BETA1-4 : angle 1.84653 / 0.97 ( 3) link_NAG-ASN : bond 0.00027 / 0.01 ( 1) link_NAG-ASN : angle 3.78696 / 2.07 ( 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 61 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 0.104 Fit side-chains REVERT: A 264 LYS cc_start: 0.5459 (ttpt) cc_final: 0.5022 (pttm) REVERT: A 431 ASN cc_start: 0.8611 (OUTLIER) cc_final: 0.8337 (t0) REVERT: A 434 ILE cc_start: 0.7345 (tp) cc_final: 0.7094 (tp) outliers start: 8 outliers final: 5 residues processed: 58 average time/residue: 0.0354 time to fit residues: 2.7865 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 : 0.073 ------------------------------------------------------------------------------- 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: 0.9990 chunk 39 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 22 optimal weight: 4.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.143498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.110342 restraints weight = 4361.486| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 2.16 r_work: 0.3151 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3651 Z= 0.156 Angle : 0.664 10.914 4981 Z= 0.325 Chirality : 0.042 0.188 603 Planarity : 0.005 0.051 616 Dihedral : 13.064 170.531 562 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.43 % Allowed : 16.22 % Favored : 81.35 % 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: 1.55 (0.41), residues: 461 helix: 1.78 (0.28), residues: 380 sheet: None (None), residues: 0 loop : -2.73 (0.57), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 285 TYR 0.016 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/Z covalent geometry : bond 0.00362 / 0.16 ( 3649) covalent geometry : angle 0.65790 / 0.32 ( 4975) hydrogen bonds : bond 0.04884 / 3.30 ( 272) hydrogen bonds : angle 4.60860 / 3.21 ( 816) link_BETA1-4 : bond 0.00218 / 0.11 ( 1) link_BETA1-4 : angle 1.90888 / 1.01 ( 3) link_NAG-ASN : bond 0.00218 / 0.11 ( 1) link_NAG-ASN : angle 3.25703 / 1.82 ( 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 64 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.072 Fit side-chains REVERT: A 431 ASN cc_start: 0.8597 (OUTLIER) cc_final: 0.8353 (t0) REVERT: A 434 ILE cc_start: 0.7322 (tp) cc_final: 0.7106 (tp) outliers start: 9 outliers final: 5 residues processed: 58 average time/residue: 0.0429 time to fit residues: 3.2855 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 : 0.083 ------------------------------------------------------------------------------- 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 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: 0.8980 chunk 22 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 27 optimal weight: 0.5980 chunk 35 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3639 r_free = 0.3639 target = 0.144499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.112110 restraints weight = 4208.605| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.03 r_work: 0.3166 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.2243 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 : 0.643 8.612 4981 Z= 0.315 Chirality : 0.041 0.182 603 Planarity : 0.005 0.056 616 Dihedral : 12.903 167.426 562 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.70 % Allowed : 18.65 % 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: 1.62 (0.40), residues: 461 helix: 1.84 (0.27), residues: 380 sheet: None (None), residues: 0 loop : -2.81 (0.55), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 228 TYR 0.015 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/Z covalent geometry : bond 0.00336 / 0.15 ( 3649) covalent geometry : angle 0.63850 / 0.31 ( 4975) hydrogen bonds : bond 0.04577 / 3.11 ( 272) hydrogen bonds : angle 4.45034 / 3.11 ( 816) link_BETA1-4 : bond 0.00332 / 0.17 ( 1) link_BETA1-4 : angle 1.79720 / 0.95 ( 3) link_NAG-ASN : bond 0.00073 / 0.04 ( 1) link_NAG-ASN : angle 2.63364 / 1.50 ( 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 64 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.073 Fit side-chains REVERT: A 104 GLN cc_start: 0.7860 (mt0) cc_final: 0.7598 (tt0) REVERT: A 431 ASN cc_start: 0.8660 (OUTLIER) cc_final: 0.8405 (t0) outliers start: 10 outliers final: 5 residues processed: 59 average time/residue: 0.0332 time to fit residues: 2.6327 Evaluate side-chains 56 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.117 ------------------------------------------------------------------------------- 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 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: 0.8980 chunk 30 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 14 optimal weight: 0.0040 chunk 31 optimal weight: 0.9990 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3665 r_free = 0.3665 target = 0.147170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.114776 restraints weight = 4199.417| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 2.03 r_work: 0.3075 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.2490 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= 0.135 Angle : 0.601 7.009 4981 Z= 0.297 Chirality : 0.040 0.168 603 Planarity : 0.005 0.055 616 Dihedral : 12.597 163.135 562 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.70 % Allowed : 19.46 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.40), residues: 461 helix: 1.91 (0.27), residues: 380 sheet: None (None), residues: 0 loop : -2.67 (0.58), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 228 TYR 0.013 0.001 TYR A 148 PHE 0.016 0.001 PHE A 336 TRP 0.008 0.001 TRP A 202 HIS 0.001 0.000 HIS A 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 ( 3649) covalent geometry : angle 0.59715 / 0.30 ( 4975) hydrogen bonds : bond 0.04278 / 2.92 ( 272) hydrogen bonds : angle 4.29287 / 3.01 ( 816) link_BETA1-4 : bond 0.00352 / 0.19 ( 1) link_BETA1-4 : angle 1.71881 / 0.90 ( 3) link_NAG-ASN : bond 0.00047 / 0.02 ( 1) link_NAG-ASN : angle 2.13104 / 1.23 ( 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 67 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 0.073 Fit side-chains REVERT: A 104 GLN cc_start: 0.7452 (mt0) cc_final: 0.7203 (tt0) REVERT: A 431 ASN cc_start: 0.8569 (OUTLIER) cc_final: 0.8350 (t0) outliers start: 10 outliers final: 6 residues processed: 61 average time/residue: 0.0314 time to fit residues: 2.5795 Evaluate side-chains 58 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 51 time to evaluate : 0.072 ------------------------------------------------------------------------------- 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 260 LEU 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: 0.0270 chunk 18 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 32 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 177 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.147951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.115700 restraints weight = 4158.596| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.02 r_work: 0.3200 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3651 Z= 0.137 Angle : 0.621 11.119 4981 Z= 0.302 Chirality : 0.041 0.193 603 Planarity : 0.005 0.057 616 Dihedral : 12.368 159.603 562 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.24 % Allowed : 21.35 % 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: 1.78 (0.40), residues: 461 helix: 1.94 (0.27), residues: 380 sheet: None (None), residues: 0 loop : -2.66 (0.58), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 228 TYR 0.011 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/Z covalent geometry : bond 0.00315 / 0.14 ( 3649) covalent geometry : angle 0.61789 / 0.30 ( 4975) hydrogen bonds : bond 0.04206 / 2.87 ( 272) hydrogen bonds : angle 4.27764 / 3.00 ( 816) link_BETA1-4 : bond 0.00357 / 0.19 ( 1) link_BETA1-4 : angle 1.66614 / 0.87 ( 3) link_NAG-ASN : bond 0.00023 / 0.01 ( 1) link_NAG-ASN : angle 1.92121 / 1.12 ( 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 67 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 55 time to evaluate : 0.124 Fit side-chains REVERT: A 104 GLN cc_start: 0.7569 (mt0) cc_final: 0.7307 (tt0) REVERT: A 431 ASN cc_start: 0.8650 (OUTLIER) cc_final: 0.8427 (t0) outliers start: 12 outliers final: 10 residues processed: 63 average time/residue: 0.0365 time to fit residues: 3.1008 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 : 0.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 145 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 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: 1.9990 chunk 21 optimal weight: 5.9990 chunk 26 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 45 optimal weight: 10.0000 chunk 9 optimal weight: 0.8980 chunk 17 optimal weight: 6.9990 chunk 31 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 41 ASN ** 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 = 0.3657 r_free = 0.3657 target = 0.146457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.113955 restraints weight = 4286.493| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.05 r_work: 0.3187 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.2626 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= 0.143 Angle : 0.595 6.708 4981 Z= 0.294 Chirality : 0.040 0.134 603 Planarity : 0.006 0.059 616 Dihedral : 11.981 152.941 562 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.24 % Allowed : 22.43 % 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: 1.79 (0.40), residues: 461 helix: 1.95 (0.27), residues: 380 sheet: None (None), residues: 0 loop : -2.67 (0.58), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 228 TYR 0.012 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/Z covalent geometry : bond 0.00334 / 0.14 ( 3649) covalent geometry : angle 0.59178 / 0.29 ( 4975) hydrogen bonds : bond 0.04352 / 2.97 ( 272) hydrogen bonds : angle 4.21598 / 2.99 ( 816) link_BETA1-4 : bond 0.00324 / 0.17 ( 1) link_BETA1-4 : angle 1.72003 / 0.89 ( 3) link_NAG-ASN : bond 0.00061 / 0.03 ( 1) link_NAG-ASN : angle 1.82088 / 1.07 ( 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 65 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 53 time to evaluate : 0.121 Fit side-chains REVERT: A 104 GLN cc_start: 0.7539 (mt0) cc_final: 0.7319 (tt0) REVERT: A 431 ASN cc_start: 0.8654 (OUTLIER) cc_final: 0.8426 (t0) outliers start: 12 outliers final: 9 residues processed: 62 average time/residue: 0.0466 time to fit residues: 3.8873 Evaluate side-chains 60 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 50 time to evaluate : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 145 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: 0.5980 chunk 23 optimal weight: 0.0040 chunk 0 optimal weight: 4.9990 chunk 1 optimal weight: 0.8980 chunk 44 optimal weight: 0.4980 chunk 45 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 4 optimal weight: 0.3980 chunk 35 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 overall best weight: 0.4392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3708 r_free = 0.3708 target = 0.150854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.117529 restraints weight = 4361.108| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 2.18 r_work: 0.3101 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3651 Z= 0.126 Angle : 0.612 13.155 4981 Z= 0.296 Chirality : 0.039 0.161 603 Planarity : 0.005 0.060 616 Dihedral : 10.835 133.877 562 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.70 % Allowed : 23.78 % 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: 1.89 (0.41), residues: 461 helix: 2.00 (0.27), residues: 380 sheet: None (None), residues: 0 loop : -2.55 (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 0.015 0.001 PHE A 336 TRP 0.009 0.001 TRP A 202 HIS 0.001 0.000 HIS A 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 ( 3649) covalent geometry : angle 0.61043 / 0.30 ( 4975) hydrogen bonds : bond 0.03997 / 2.72 ( 272) hydrogen bonds : angle 4.14383 / 2.95 ( 816) link_BETA1-4 : bond 0.00370 / 0.19 ( 1) link_BETA1-4 : angle 1.50719 / 0.79 ( 3) link_NAG-ASN : bond 0.00025 / 0.01 ( 1) link_NAG-ASN : angle 1.60459 / 0.94 ( 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 63 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 53 time to evaluate : 0.119 Fit side-chains REVERT: A 346 ARG cc_start: 0.8006 (ttt180) cc_final: 0.7132 (ttt180) REVERT: A 431 ASN cc_start: 0.8637 (OUTLIER) cc_final: 0.8413 (t0) outliers start: 10 outliers final: 7 residues processed: 60 average time/residue: 0.0388 time to fit residues: 3.1501 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 : 0.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ILE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 20 optimal weight: 1.9990 chunk 35 optimal weight: 0.2980 chunk 29 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 41 ASN ** 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 = 0.3666 r_free = 0.3666 target = 0.147405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.113871 restraints weight = 4258.031| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.11 r_work: 0.3183 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.2842 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= 0.143 Angle : 0.611 13.129 4981 Z= 0.296 Chirality : 0.040 0.170 603 Planarity : 0.006 0.060 616 Dihedral : 9.480 112.725 562 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.97 % Allowed : 24.05 % Favored : 72.97 % 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: 1.94 (0.41), residues: 461 helix: 2.04 (0.27), 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 0.013 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 284 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.14 ( 3649) covalent geometry : angle 0.60882 / 0.30 ( 4975) hydrogen bonds : bond 0.04291 / 2.92 ( 272) hydrogen bonds : angle 4.20486 / 2.99 ( 816) link_BETA1-4 : bond 0.00299 / 0.16 ( 1) link_BETA1-4 : angle 1.66842 / 0.86 ( 3) link_NAG-ASN : bond 0.00060 / 0.03 ( 1) link_NAG-ASN : angle 1.71798 / 1.01 ( 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 59 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 48 time to evaluate : 0.073 Fit side-chains REVERT: A 346 ARG cc_start: 0.8071 (ttt180) cc_final: 0.7129 (ttt180) REVERT: A 431 ASN cc_start: 0.8545 (OUTLIER) cc_final: 0.8295 (t0) outliers start: 11 outliers final: 8 residues processed: 54 average time/residue: 0.0374 time to fit residues: 2.6455 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 : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ILE 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: 0.9980 chunk 37 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 44 optimal weight: 0.6980 chunk 30 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 41 ASN ** 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 = 0.3670 r_free = 0.3670 target = 0.147765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.114466 restraints weight = 4321.460| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 2.11 r_work: 0.3194 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3651 Z= 0.140 Angle : 0.603 12.584 4981 Z= 0.294 Chirality : 0.040 0.160 603 Planarity : 0.005 0.063 616 Dihedral : 9.225 110.084 562 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.43 % Allowed : 24.59 % Favored : 72.97 % 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: 1.95 (0.40), residues: 461 helix: 2.05 (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 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 ( 3649) covalent geometry : angle 0.60068 / 0.29 ( 4975) hydrogen bonds : bond 0.04280 / 2.91 ( 272) hydrogen bonds : angle 4.16340 / 2.96 ( 816) link_BETA1-4 : bond 0.00326 / 0.17 ( 1) link_BETA1-4 : angle 1.63248 / 0.85 ( 3) link_NAG-ASN : bond 0.00030 / 0.02 ( 1) link_NAG-ASN : angle 1.65538 / 0.97 ( 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 : 0.074 Fit side-chains REVERT: A 346 ARG cc_start: 0.8083 (ttt180) cc_final: 0.7041 (ttt180) REVERT: A 413 GLN cc_start: 0.7399 (tp40) cc_final: 0.6887 (pm20) REVERT: A 431 ASN cc_start: 0.8601 (OUTLIER) cc_final: 0.8360 (t0) outliers start: 9 outliers final: 8 residues processed: 52 average time/residue: 0.0367 time to fit residues: 2.5467 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 : 0.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ILE 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 264 LYS 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: 0.3980 chunk 44 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 41 ASN ** 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 = 0.3673 r_free = 0.3673 target = 0.148129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.114301 restraints weight = 4280.024| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 2.17 r_work: 0.3191 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3651 Z= 0.136 Angle : 0.598 12.485 4981 Z= 0.291 Chirality : 0.040 0.161 603 Planarity : 0.005 0.061 616 Dihedral : 9.114 109.079 562 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.97 % Allowed : 24.05 % Favored : 72.97 % 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: 1.99 (0.40), residues: 461 helix: 2.07 (0.27), residues: 380 sheet: None (None), residues: 0 loop : -2.53 (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 0.007 0.001 TRP A 404 HIS 0.000 0.000 HIS A 353 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 ( 3649) covalent geometry : angle 0.59576 / 0.29 ( 4975) hydrogen bonds : bond 0.04233 / 2.88 ( 272) hydrogen bonds : angle 4.13317 / 2.93 ( 816) link_BETA1-4 : bond 0.00315 / 0.17 ( 1) link_BETA1-4 : angle 1.60287 / 0.83 ( 3) link_NAG-ASN : bond 0.00037 / 0.02 ( 1) link_NAG-ASN : angle 1.61628 / 0.95 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 735.90 seconds wall clock time: 13 minutes 15.85 seconds (795.85 seconds total)