Starting phenix.real_space_refine on Wed Jul 1 22:40:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7wsm_32760/07_2026/7wsm_32760.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wsm_32760/07_2026/7wsm_32760.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7wsm_32760/07_2026/7wsm_32760.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7wsm_32760/07_2026/7wsm_32760.cif" model { file = "/net/cci-nas-00/data/ceres_data/7wsm_32760/07_2026/7wsm_32760.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wsm_32760/07_2026/7wsm_32760.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wsm_32760/07_2026/7wsm_32760.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wsm_32760/07_2026/7wsm_32760.map" } resolution = 3.25 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= -0.003 sd= 0.090 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 2359 2.51 5 N 582 2.21 5 O 622 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 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: 3577 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3514 Classifications: {'peptide': 464} Link IDs: {'PTRANS': 24, 'TRANS': 439} 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: 0.71, per 1000 atoms: 0.20 Number of scatterers: 3577 At special positions: 0 Unit cell: (86.6, 56.29, 83.3525, 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 622 8.00 N 582 7.00 C 2359 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: 0.21 Conformation dependent library (CDL) restraints added in 82.5 milliseconds 924 Ramachandran restraints generated. 462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 830 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 0 sheets defined 88.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.07 Creating SS restraints... Processing helix chain 'A' and resid 21 through 44 Processing helix chain 'A' and resid 48 through 65 removed outlier: 4.084A pdb=" N GLN A 54 " --> pdb=" O LYS A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 68 No H-bonds generated for 'chain 'A' and resid 66 through 68' Processing helix chain 'A' and resid 73 through 99 removed outlier: 4.162A pdb=" N PHE A 88 " --> pdb=" O SER A 84 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N PHE A 97 " --> pdb=" O MET A 93 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LEU A 98 " --> pdb=" O ILE A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 107 Processing helix chain 'A' and resid 108 through 128 Processing helix chain 'A' and resid 129 through 133 Processing helix chain 'A' and resid 135 through 164 Proline residue: A 157 - end of helix Processing helix chain 'A' and resid 168 through 174 removed outlier: 3.795A pdb=" N THR A 174 " --> pdb=" O GLY A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 190 removed outlier: 3.853A pdb=" N ILE A 180 " --> pdb=" O ASN A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 209 removed outlier: 4.057A pdb=" N LEU A 205 " --> pdb=" O LEU A 201 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU A 206 " --> pdb=" O TRP A 202 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR A 209 " --> pdb=" O LEU A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 220 removed outlier: 4.265A pdb=" N ALA A 213 " --> pdb=" O THR A 209 " (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 Processing helix chain 'A' and resid 237 through 249 Processing helix chain 'A' and resid 253 through 270 removed outlier: 3.613A pdb=" N ASP A 262 " --> pdb=" O ALA A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 280 Processing helix chain 'A' and resid 281 through 283 No H-bonds generated for 'chain 'A' and resid 281 through 283' Processing helix chain 'A' and resid 284 through 300 Processing helix chain 'A' and resid 302 through 317 removed outlier: 3.640A pdb=" N VAL A 306 " --> pdb=" O GLY A 302 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N SER A 310 " --> pdb=" O VAL A 306 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N THR A 311 " --> pdb=" O PHE A 307 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N SER A 312 " --> pdb=" O TYR A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 344 removed outlier: 3.514A 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 379 through 398 removed outlier: 3.947A pdb=" N VAL A 383 " --> pdb=" O ALA A 379 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE A 389 " --> pdb=" O ILE A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 411 removed outlier: 3.562A pdb=" N PHE A 405 " --> pdb=" O PRO A 401 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE A 411 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 446 removed outlier: 5.858A pdb=" N GLN A 439 " --> pdb=" O GLY A 435 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N TYR A 440 " --> pdb=" O MET A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 468 Processing helix chain 'A' and resid 475 through 483 279 hydrogen bonds defined for protein. 831 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: 0.50 Time building geometry restraints manager: 0.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 550 1.32 - 1.44: 969 1.44 - 1.56: 2116 1.56 - 1.69: 0 1.69 - 1.81: 25 Bond restraints: 3660 Sorted by residual: bond pdb=" C TRP A 60 " pdb=" O TRP A 60 " ideal model delta sigma weight residual 1.236 1.196 0.040 1.29e-02 6.01e+03 9.64e+00 bond pdb=" C TRP A 60 " pdb=" N LEU A 61 " ideal model delta sigma weight residual 1.333 1.290 0.043 1.45e-02 4.76e+03 8.81e+00 bond pdb=" CA ALA A 364 " pdb=" CB ALA A 364 " ideal model delta sigma weight residual 1.528 1.479 0.049 1.66e-02 3.63e+03 8.69e+00 bond pdb=" N ILE A 365 " pdb=" CA ILE A 365 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.33e-02 5.65e+03 6.58e+00 bond pdb=" N ILE A 479 " pdb=" CA ILE A 479 " ideal model delta sigma weight residual 1.462 1.491 -0.029 1.14e-02 7.69e+03 6.30e+00 ... (remaining 3655 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 4803 1.92 - 3.85: 159 3.85 - 5.77: 19 5.77 - 7.69: 4 7.69 - 9.61: 5 Bond angle restraints: 4990 Sorted by residual: angle pdb=" N LEU A 61 " pdb=" CA LEU A 61 " pdb=" C LEU A 61 " ideal model delta sigma weight residual 112.45 103.58 8.87 1.39e+00 5.18e-01 4.07e+01 angle pdb=" N PHE A 476 " pdb=" CA PHE A 476 " pdb=" C PHE A 476 " ideal model delta sigma weight residual 111.75 103.68 8.07 1.28e+00 6.10e-01 3.98e+01 angle pdb=" N LEU A 366 " pdb=" CA LEU A 366 " pdb=" C LEU A 366 " ideal model delta sigma weight residual 111.14 104.95 6.19 1.08e+00 8.57e-01 3.28e+01 angle pdb=" N GLY A 62 " pdb=" CA GLY A 62 " pdb=" C GLY A 62 " ideal model delta sigma weight residual 113.27 106.78 6.49 1.33e+00 5.65e-01 2.38e+01 angle pdb=" C TRP A 60 " pdb=" N LEU A 61 " pdb=" CA LEU A 61 " ideal model delta sigma weight residual 121.64 112.03 9.61 2.13e+00 2.20e-01 2.04e+01 ... (remaining 4985 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 2116 35.97 - 71.93: 41 71.93 - 107.90: 4 107.90 - 143.87: 0 143.87 - 179.83: 2 Dihedral angle restraints: 2163 sinusoidal: 857 harmonic: 1306 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 -166.95 12.88 -179.83 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 -166.96 178.38 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 -161.64 -18.36 0 5.00e+00 4.00e-02 1.35e+01 ... (remaining 2160 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 487 0.053 - 0.106: 102 0.106 - 0.160: 11 0.160 - 0.213: 2 0.213 - 0.266: 2 Chirality restraints: 604 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 -2.67 0.27 2.00e-02 2.50e+03 1.77e+02 chirality pdb=" CA LEU A 366 " pdb=" N LEU A 366 " pdb=" C LEU A 366 " pdb=" CB LEU A 366 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CA LEU A 61 " pdb=" N LEU A 61 " pdb=" C LEU A 61 " pdb=" CB LEU A 61 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 1.01e+00 ... (remaining 601 not shown) Planarity restraints: 619 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 57 " -0.096 2.00e-02 2.50e+03 1.03e-01 1.34e+02 pdb=" CG ASN A 57 " 0.034 2.00e-02 2.50e+03 pdb=" OD1 ASN A 57 " 0.034 2.00e-02 2.50e+03 pdb=" ND2 ASN A 57 " 0.159 2.00e-02 2.50e+03 pdb=" C1 NAG B 1 " -0.129 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C17 5RH A 601 " -0.029 2.00e-02 2.50e+03 5.23e-02 2.73e+01 pdb=" C18 5RH A 601 " 0.068 2.00e-02 2.50e+03 pdb=" C19 5RH A 601 " -0.068 2.00e-02 2.50e+03 pdb=" C20 5RH A 601 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" N 5RH A 601 " 0.041 2.00e-02 2.50e+03 2.65e-02 8.76e+00 pdb=" C15 5RH A 601 " 0.003 2.00e-02 2.50e+03 pdb=" C16 5RH A 601 " 0.013 2.00e-02 2.50e+03 pdb=" C7 5RH A 601 " -0.033 2.00e-02 2.50e+03 pdb=" O1 5RH A 601 " -0.024 2.00e-02 2.50e+03 ... (remaining 616 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 951 2.78 - 3.31: 4008 3.31 - 3.84: 5987 3.84 - 4.37: 6934 4.37 - 4.90: 11613 Nonbonded interactions: 29493 Sorted by model distance: nonbonded pdb=" OD1 ASN A 46 " pdb=" OG1 THR A 311 " model vdw 2.253 3.040 nonbonded pdb=" O PRO A 69 " pdb=" OG SER A 70 " model vdw 2.253 3.040 nonbonded pdb=" O ALA A 423 " pdb=" OG SER A 426 " model vdw 2.289 3.040 nonbonded pdb=" OG1 THR A 23 " pdb=" O ARG A 246 " model vdw 2.317 3.040 nonbonded pdb=" OE2 GLU A 225 " pdb=" N SER A 226 " model vdw 2.347 3.120 ... (remaining 29488 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: 0.370 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: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 3.620 Find NCS groups from input model: 0.010 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: 0.010 Load rotamer database and sin/cos tables:1.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 5.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 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 : 0.006 0.049 3662 Z= 0.313 Angle : 0.868 10.041 4996 Z= 0.507 Chirality : 0.045 0.266 604 Planarity : 0.006 0.052 618 Dihedral : 17.424 179.833 1333 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 0.81 % Allowed : 1.35 % Favored : 97.84 % 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: -1.23 (0.39), residues: 462 helix: -0.32 (0.27), residues: 374 sheet: None (None), residues: 0 loop : -2.47 (0.63), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 142 TYR 0.026 0.002 TYR A 148 PHE 0.021 0.002 PHE A 476 TRP 0.016 0.002 TRP A 60 HIS 0.002 0.001 HIS A 284 Details of bonding type rmsd/Z covalent geometry : bond 0.00575 / 0.31 ( 3660) covalent geometry : angle 0.84233 / 0.50 ( 4990) hydrogen bonds : bond 0.16237 / 11.13 ( 279) hydrogen bonds : angle 7.91722 / 5.75 ( 831) link_BETA1-4 : bond 0.00136 / 0.07 ( 1) link_BETA1-4 : angle 6.79657 / 3.56 ( 3) link_NAG-ASN : bond 0.00318 / 0.17 ( 1) link_NAG-ASN : angle 5.39832 / 2.67 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 924 Ramachandran restraints generated. 462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 924 Ramachandran restraints generated. 462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 74 time to evaluate : 0.094 Fit side-chains REVERT: A 389 PHE cc_start: 0.7591 (m-80) cc_final: 0.7005 (m-80) REVERT: A 440 TYR cc_start: 0.8101 (m-80) cc_final: 0.7514 (m-80) outliers start: 3 outliers final: 1 residues processed: 76 average time/residue: 0.0376 time to fit residues: 3.7544 Evaluate side-chains 69 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 68 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 24 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 299 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 = 0.138109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.114734 restraints weight = 4970.281| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 2.07 r_work: 0.3269 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 3662 Z= 0.173 Angle : 0.699 8.070 4996 Z= 0.347 Chirality : 0.042 0.158 604 Planarity : 0.006 0.066 618 Dihedral : 13.274 178.669 562 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.43 % Allowed : 11.05 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.41), residues: 462 helix: 1.27 (0.28), residues: 378 sheet: None (None), residues: 0 loop : -2.04 (0.62), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 246 TYR 0.011 0.002 TYR A 148 PHE 0.023 0.002 PHE A 336 TRP 0.012 0.001 TRP A 60 HIS 0.002 0.001 HIS A 284 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.17 ( 3660) covalent geometry : angle 0.69516 / 0.35 ( 4990) hydrogen bonds : bond 0.05669 / 3.92 ( 279) hydrogen bonds : angle 4.77777 / 3.45 ( 831) link_BETA1-4 : bond 0.00279 / 0.15 ( 1) link_BETA1-4 : angle 1.58927 / 0.83 ( 3) link_NAG-ASN : bond 0.00280 / 0.15 ( 1) link_NAG-ASN : angle 2.78749 / 1.32 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 924 Ramachandran restraints generated. 462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 924 Ramachandran restraints generated. 462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 0.132 Fit side-chains REVERT: A 289 ILE cc_start: 0.8703 (OUTLIER) cc_final: 0.8456 (mp) REVERT: A 367 MET cc_start: 0.7988 (tpt) cc_final: 0.7753 (ttm) REVERT: A 389 PHE cc_start: 0.8071 (m-80) cc_final: 0.7556 (m-80) REVERT: A 440 TYR cc_start: 0.8542 (m-80) cc_final: 0.7807 (m-80) REVERT: A 466 LEU cc_start: 0.8701 (pp) cc_final: 0.8273 (mp) outliers start: 9 outliers final: 7 residues processed: 72 average time/residue: 0.0437 time to fit residues: 4.0758 Evaluate side-chains 69 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 61 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 188 GLN Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 433 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 40 optimal weight: 0.9980 chunk 38 optimal weight: 0.1980 chunk 1 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 13 optimal weight: 0.0770 chunk 44 optimal weight: 0.8980 chunk 41 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 37 GLN ** A 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 439 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.142228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.119242 restraints weight = 4938.655| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 2.08 r_work: 0.3312 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3662 Z= 0.145 Angle : 0.644 9.139 4996 Z= 0.316 Chirality : 0.040 0.160 604 Planarity : 0.005 0.068 618 Dihedral : 13.040 173.971 561 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.96 % Allowed : 15.90 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.48 (0.41), residues: 462 helix: 1.63 (0.28), residues: 378 sheet: None (None), residues: 0 loop : -2.04 (0.60), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 271 TYR 0.012 0.001 TYR A 148 PHE 0.009 0.001 PHE A 395 TRP 0.010 0.001 TRP A 60 HIS 0.002 0.000 HIS A 284 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.15 ( 3660) covalent geometry : angle 0.63964 / 0.32 ( 4990) hydrogen bonds : bond 0.04686 / 3.27 ( 279) hydrogen bonds : angle 4.46996 / 3.25 ( 831) link_BETA1-4 : bond 0.00321 / 0.17 ( 1) link_BETA1-4 : angle 1.56818 / 0.83 ( 3) link_NAG-ASN : bond 0.00144 / 0.08 ( 1) link_NAG-ASN : angle 2.68582 / 1.29 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 924 Ramachandran restraints generated. 462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 924 Ramachandran restraints generated. 462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 68 time to evaluate : 0.125 Fit side-chains REVERT: A 151 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8099 (mm) REVERT: A 289 ILE cc_start: 0.8879 (OUTLIER) cc_final: 0.8632 (mp) REVERT: A 367 MET cc_start: 0.7885 (tpt) cc_final: 0.7657 (ttm) REVERT: A 389 PHE cc_start: 0.7952 (m-80) cc_final: 0.7657 (m-80) REVERT: A 440 TYR cc_start: 0.8407 (m-80) cc_final: 0.7577 (m-80) REVERT: A 476 PHE cc_start: 0.7834 (t80) cc_final: 0.7547 (m-80) outliers start: 11 outliers final: 8 residues processed: 74 average time/residue: 0.0418 time to fit residues: 3.9856 Evaluate side-chains 66 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 0.098 ------------------------------------------------------------------------------- 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 174 THR Chi-restraints excluded: chain A residue 188 GLN Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 339 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 23 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 chunk 5 optimal weight: 5.9990 chunk 29 optimal weight: 0.0470 chunk 31 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 overall best weight: 0.7078 ------------------------------------------------------------------------------- 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 = 0.3680 r_free = 0.3680 target = 0.141574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.118504 restraints weight = 4907.482| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 2.08 r_work: 0.3301 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3662 Z= 0.146 Angle : 0.646 13.554 4996 Z= 0.310 Chirality : 0.040 0.154 604 Planarity : 0.005 0.068 618 Dihedral : 13.021 172.969 561 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 4.04 % Allowed : 16.98 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.40), residues: 462 helix: 1.61 (0.27), residues: 384 sheet: None (None), residues: 0 loop : -1.88 (0.63), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 271 TYR 0.015 0.001 TYR A 148 PHE 0.009 0.001 PHE A 438 TRP 0.008 0.001 TRP A 60 HIS 0.002 0.000 HIS A 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 ( 3660) covalent geometry : angle 0.64251 / 0.31 ( 4990) hydrogen bonds : bond 0.04588 / 3.20 ( 279) hydrogen bonds : angle 4.36362 / 3.18 ( 831) link_BETA1-4 : bond 0.00247 / 0.13 ( 1) link_BETA1-4 : angle 1.39080 / 0.73 ( 3) link_NAG-ASN : bond 0.00118 / 0.06 ( 1) link_NAG-ASN : angle 2.60510 / 1.25 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 924 Ramachandran restraints generated. 462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 924 Ramachandran restraints generated. 462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 62 time to evaluate : 0.080 Fit side-chains REVERT: A 151 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8097 (mm) REVERT: A 289 ILE cc_start: 0.8825 (OUTLIER) cc_final: 0.8621 (mp) REVERT: A 367 MET cc_start: 0.7900 (tpt) cc_final: 0.7654 (ttm) REVERT: A 440 TYR cc_start: 0.8411 (m-80) cc_final: 0.7587 (m-80) REVERT: A 476 PHE cc_start: 0.7812 (t80) cc_final: 0.7522 (m-80) outliers start: 15 outliers final: 10 residues processed: 71 average time/residue: 0.0377 time to fit residues: 3.5351 Evaluate side-chains 68 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 56 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 188 GLN Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 361 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 33 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 11 optimal weight: 0.4980 chunk 35 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 116 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.140389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.117136 restraints weight = 4962.613| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 2.07 r_work: 0.3300 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3662 Z= 0.143 Angle : 0.627 10.829 4996 Z= 0.303 Chirality : 0.040 0.148 604 Planarity : 0.005 0.069 618 Dihedral : 13.015 172.035 561 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 4.58 % Allowed : 18.60 % Favored : 76.82 % 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: 1.60 (0.40), residues: 462 helix: 1.64 (0.27), residues: 384 sheet: None (None), residues: 0 loop : -1.87 (0.63), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 271 TYR 0.011 0.001 TYR A 148 PHE 0.017 0.001 PHE A 432 TRP 0.008 0.001 TRP A 60 HIS 0.001 0.000 HIS A 284 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 ( 3660) covalent geometry : angle 0.62426 / 0.30 ( 4990) hydrogen bonds : bond 0.04485 / 3.13 ( 279) hydrogen bonds : angle 4.29347 / 3.13 ( 831) link_BETA1-4 : bond 0.00294 / 0.15 ( 1) link_BETA1-4 : angle 1.38639 / 0.74 ( 3) link_NAG-ASN : bond 0.00196 / 0.10 ( 1) link_NAG-ASN : angle 2.35241 / 1.15 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 924 Ramachandran restraints generated. 462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 924 Ramachandran restraints generated. 462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 56 time to evaluate : 0.079 Fit side-chains REVERT: A 151 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8070 (mm) REVERT: A 440 TYR cc_start: 0.8424 (m-80) cc_final: 0.7644 (m-80) REVERT: A 476 PHE cc_start: 0.7903 (t80) cc_final: 0.7529 (m-80) outliers start: 17 outliers final: 11 residues processed: 68 average time/residue: 0.0346 time to fit residues: 3.1111 Evaluate side-chains 64 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 52 time to evaluate : 0.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 ASN Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 413 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 4 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 20 optimal weight: 4.9990 chunk 11 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 116 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.140752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.117499 restraints weight = 4960.919| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.08 r_work: 0.3295 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3662 Z= 0.151 Angle : 0.623 9.824 4996 Z= 0.304 Chirality : 0.040 0.149 604 Planarity : 0.005 0.068 618 Dihedral : 13.034 171.935 561 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.77 % Allowed : 20.75 % Favored : 75.47 % 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: 1.60 (0.40), residues: 462 helix: 1.62 (0.27), residues: 385 sheet: None (None), residues: 0 loop : -1.74 (0.64), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 271 TYR 0.010 0.001 TYR A 148 PHE 0.015 0.001 PHE A 336 TRP 0.006 0.001 TRP A 60 HIS 0.001 0.000 HIS A 284 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 ( 3660) covalent geometry : angle 0.61969 / 0.30 ( 4990) hydrogen bonds : bond 0.04495 / 3.13 ( 279) hydrogen bonds : angle 4.33806 / 3.18 ( 831) link_BETA1-4 : bond 0.00363 / 0.19 ( 1) link_BETA1-4 : angle 1.41351 / 0.76 ( 3) link_NAG-ASN : bond 0.00231 / 0.12 ( 1) link_NAG-ASN : angle 2.33766 / 1.14 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 924 Ramachandran restraints generated. 462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 924 Ramachandran restraints generated. 462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 52 time to evaluate : 0.128 Fit side-chains REVERT: A 440 TYR cc_start: 0.8490 (m-80) cc_final: 0.7704 (m-80) REVERT: A 476 PHE cc_start: 0.7914 (t80) cc_final: 0.7537 (m-80) outliers start: 14 outliers final: 12 residues processed: 62 average time/residue: 0.0419 time to fit residues: 3.4910 Evaluate side-chains 61 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 49 time to evaluate : 0.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 ASN Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 413 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 31 optimal weight: 0.6980 chunk 7 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 116 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.141235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.117972 restraints weight = 5011.679| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 2.09 r_work: 0.3301 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3662 Z= 0.140 Angle : 0.612 9.060 4996 Z= 0.297 Chirality : 0.040 0.148 604 Planarity : 0.005 0.069 618 Dihedral : 12.996 171.238 561 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 4.31 % Allowed : 21.02 % Favored : 74.66 % 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: 1.65 (0.40), residues: 462 helix: 1.65 (0.27), residues: 385 sheet: None (None), residues: 0 loop : -1.72 (0.64), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 246 TYR 0.009 0.001 TYR A 148 PHE 0.016 0.001 PHE A 336 TRP 0.006 0.001 TRP A 60 HIS 0.001 0.000 HIS A 284 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 ( 3660) covalent geometry : angle 0.60880 / 0.30 ( 4990) hydrogen bonds : bond 0.04396 / 3.07 ( 279) hydrogen bonds : angle 4.29960 / 3.15 ( 831) link_BETA1-4 : bond 0.00333 / 0.18 ( 1) link_BETA1-4 : angle 1.34835 / 0.72 ( 3) link_NAG-ASN : bond 0.00197 / 0.10 ( 1) link_NAG-ASN : angle 2.32176 / 1.13 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 924 Ramachandran restraints generated. 462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 924 Ramachandran restraints generated. 462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 53 time to evaluate : 0.086 Fit side-chains REVERT: A 440 TYR cc_start: 0.8485 (m-80) cc_final: 0.7705 (m-80) REVERT: A 476 PHE cc_start: 0.7884 (t80) cc_final: 0.7567 (m-80) outliers start: 16 outliers final: 13 residues processed: 65 average time/residue: 0.0393 time to fit residues: 3.3283 Evaluate side-chains 67 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 54 time to evaluate : 0.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 413 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 26 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 42 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 36 optimal weight: 0.4980 chunk 43 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 40 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 116 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.141990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.118723 restraints weight = 5019.533| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 2.10 r_work: 0.3305 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3662 Z= 0.137 Angle : 0.629 14.407 4996 Z= 0.300 Chirality : 0.039 0.147 604 Planarity : 0.005 0.069 618 Dihedral : 12.916 170.091 561 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 4.04 % Allowed : 21.83 % Favored : 74.12 % 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: 1.69 (0.40), residues: 462 helix: 1.68 (0.27), residues: 385 sheet: None (None), residues: 0 loop : -1.73 (0.63), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 63 TYR 0.008 0.001 TYR A 148 PHE 0.017 0.001 PHE A 336 TRP 0.006 0.001 TRP A 60 HIS 0.001 0.000 HIS A 284 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 ( 3660) covalent geometry : angle 0.62673 / 0.30 ( 4990) hydrogen bonds : bond 0.04302 / 3.00 ( 279) hydrogen bonds : angle 4.23523 / 3.11 ( 831) link_BETA1-4 : bond 0.00201 / 0.11 ( 1) link_BETA1-4 : angle 1.37640 / 0.72 ( 3) link_NAG-ASN : bond 0.00136 / 0.07 ( 1) link_NAG-ASN : angle 2.13514 / 1.03 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 924 Ramachandran restraints generated. 462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 924 Ramachandran restraints generated. 462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 55 time to evaluate : 0.123 Fit side-chains REVERT: A 440 TYR cc_start: 0.8497 (m-80) cc_final: 0.7730 (m-80) outliers start: 15 outliers final: 13 residues processed: 66 average time/residue: 0.0375 time to fit residues: 3.2947 Evaluate side-chains 65 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 52 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 413 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 12 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 38 optimal weight: 0.0070 chunk 37 optimal weight: 0.8980 chunk 45 optimal weight: 0.0170 chunk 19 optimal weight: 0.0980 chunk 2 optimal weight: 3.9990 overall best weight: 0.3036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 116 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 = 0.145397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.122212 restraints weight = 4858.733| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 2.09 r_work: 0.3349 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3232 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3662 Z= 0.126 Angle : 0.621 12.255 4996 Z= 0.298 Chirality : 0.039 0.147 604 Planarity : 0.005 0.071 618 Dihedral : 12.622 166.451 561 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.70 % Allowed : 23.99 % Favored : 73.32 % 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: 1.76 (0.40), residues: 462 helix: 1.69 (0.27), residues: 387 sheet: None (None), residues: 0 loop : -1.53 (0.64), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 246 TYR 0.009 0.001 TYR A 40 PHE 0.017 0.001 PHE A 336 TRP 0.006 0.001 TRP A 202 HIS 0.001 0.000 HIS A 284 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 ( 3660) covalent geometry : angle 0.61902 / 0.30 ( 4990) hydrogen bonds : bond 0.03981 / 2.78 ( 279) hydrogen bonds : angle 4.18355 / 3.06 ( 831) link_BETA1-4 : bond 0.00411 / 0.22 ( 1) link_BETA1-4 : angle 1.19506 / 0.65 ( 3) link_NAG-ASN : bond 0.00022 / 0.01 ( 1) link_NAG-ASN : angle 2.06948 / 1.03 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 924 Ramachandran restraints generated. 462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 924 Ramachandran restraints generated. 462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 0.153 Fit side-chains REVERT: A 135 TYR cc_start: 0.8814 (p90) cc_final: 0.8570 (p90) REVERT: A 440 TYR cc_start: 0.8513 (m-80) cc_final: 0.7792 (m-80) outliers start: 10 outliers final: 8 residues processed: 72 average time/residue: 0.0407 time to fit residues: 3.8875 Evaluate side-chains 66 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 ASN Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 294 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 33 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 37 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 116 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.142872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.119394 restraints weight = 5040.991| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 2.11 r_work: 0.3314 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3662 Z= 0.148 Angle : 0.635 12.181 4996 Z= 0.308 Chirality : 0.040 0.155 604 Planarity : 0.005 0.069 618 Dihedral : 12.743 167.920 561 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.70 % Allowed : 23.18 % Favored : 74.12 % 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: 1.82 (0.40), residues: 462 helix: 1.71 (0.27), residues: 386 sheet: None (None), residues: 0 loop : -1.38 (0.63), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 271 TYR 0.008 0.001 TYR A 148 PHE 0.016 0.001 PHE A 336 TRP 0.007 0.001 TRP A 60 HIS 0.002 0.000 HIS A 353 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 ( 3660) covalent geometry : angle 0.63235 / 0.31 ( 4990) hydrogen bonds : bond 0.04239 / 2.96 ( 279) hydrogen bonds : angle 4.20706 / 3.08 ( 831) link_BETA1-4 : bond 0.00253 / 0.13 ( 1) link_BETA1-4 : angle 1.29021 / 0.69 ( 3) link_NAG-ASN : bond 0.00189 / 0.10 ( 1) link_NAG-ASN : angle 2.04681 / 1.03 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 924 Ramachandran restraints generated. 462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 924 Ramachandran restraints generated. 462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 0.080 Fit side-chains REVERT: A 440 TYR cc_start: 0.8551 (m-80) cc_final: 0.7848 (m-80) outliers start: 10 outliers final: 7 residues processed: 62 average time/residue: 0.0457 time to fit residues: 3.7059 Evaluate side-chains 63 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 56 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 294 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 43 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 22 optimal weight: 0.0670 chunk 9 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 overall best weight: 0.7718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 116 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.142323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.118823 restraints weight = 4922.850| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 2.08 r_work: 0.3309 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 3662 Z= 0.146 Angle : 0.642 11.980 4996 Z= 0.312 Chirality : 0.040 0.154 604 Planarity : 0.005 0.068 618 Dihedral : 12.810 168.834 561 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.89 % Allowed : 23.99 % Favored : 74.12 % 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: 1.76 (0.40), residues: 462 helix: 1.69 (0.27), residues: 385 sheet: None (None), residues: 0 loop : -1.46 (0.63), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 246 TYR 0.008 0.001 TYR A 148 PHE 0.016 0.001 PHE A 336 TRP 0.007 0.001 TRP A 60 HIS 0.001 0.000 HIS A 284 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 ( 3660) covalent geometry : angle 0.64006 / 0.31 ( 4990) hydrogen bonds : bond 0.04314 / 3.02 ( 279) hydrogen bonds : angle 4.28646 / 3.16 ( 831) link_BETA1-4 : bond 0.00285 / 0.15 ( 1) link_BETA1-4 : angle 1.29595 / 0.69 ( 3) link_NAG-ASN : bond 0.00163 / 0.09 ( 1) link_NAG-ASN : angle 2.08054 / 1.04 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 769.56 seconds wall clock time: 13 minutes 50.60 seconds (830.60 seconds total)