Starting phenix.real_space_refine on Wed Jul 1 23:31:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9v8x_64854/07_2026/9v8x_64854_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9v8x_64854/07_2026/9v8x_64854.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9v8x_64854/07_2026/9v8x_64854_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9v8x_64854/07_2026/9v8x_64854_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9v8x_64854/07_2026/9v8x_64854.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9v8x_64854/07_2026/9v8x_64854.map" } resolution = 2.85 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= -0.000 sd= 0.088 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: 6 Type Number sf(0) Gaussians S 35 5.16 5 Cl 1 4.86 5 Na 2 4.78 5 C 2709 2.51 5 N 610 2.21 5 O 673 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 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: 4030 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 4008 Classifications: {'peptide': 504} Link IDs: {'PTRANS': 23, 'TRANS': 480} Chain breaks: 4 Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 19 Ad-hoc single atom residues: {' NA': 2, ' CL': 1} Unusual residues: {'CRN': 1} Classifications: {'undetermined': 1, 'water': 10} Link IDs: {None: 9} Chain breaks: 3 Time building chain proxies: 1.03, per 1000 atoms: 0.26 Number of scatterers: 4030 At special positions: 0 Unit cell: (80.9568, 63.2475, 83.4867, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 1 17.00 S 35 16.00 Na 2 11.00 O 673 8.00 N 610 7.00 C 2709 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 172 " - pdb=" SG CYS A 181 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.36 Conformation dependent library (CDL) restraints added in 138.8 milliseconds 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 918 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 1 sheets defined 80.2% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'A' and resid 60 through 76 removed outlier: 4.332A pdb=" N GLY A 71 " --> pdb=" O GLY A 67 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N LEU A 72 " --> pdb=" O PHE A 68 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N GLY A 73 " --> pdb=" O ALA A 69 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASN A 74 " --> pdb=" O VAL A 70 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N VAL A 75 " --> pdb=" O GLY A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 85 removed outlier: 4.072A pdb=" N TYR A 80 " --> pdb=" O TRP A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 101 Processing helix chain 'A' and resid 101 through 117 Processing helix chain 'A' and resid 121 through 130 removed outlier: 3.589A pdb=" N TRP A 124 " --> pdb=" O ILE A 121 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE A 126 " --> pdb=" O VAL A 123 " (cutoff:3.500A) Proline residue: A 128 - end of helix Processing helix chain 'A' and resid 131 through 162 removed outlier: 3.729A pdb=" N ILE A 149 " --> pdb=" O ASN A 145 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N MET A 150 " --> pdb=" O THR A 146 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N VAL A 151 " --> pdb=" O TYR A 147 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU A 152 " --> pdb=" O TYR A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 171 removed outlier: 4.063A pdb=" N THR A 171 " --> pdb=" O PRO A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 219 Processing helix chain 'A' and resid 232 through 248 removed outlier: 3.719A pdb=" N CYS A 238 " --> pdb=" O GLU A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 263 removed outlier: 4.181A pdb=" N TYR A 262 " --> pdb=" O LYS A 259 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N PHE A 263 " --> pdb=" O ILE A 260 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 259 through 263' Processing helix chain 'A' and resid 265 through 281 removed outlier: 4.548A pdb=" N TYR A 269 " --> pdb=" O ALA A 265 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU A 281 " --> pdb=" O VAL A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 294 removed outlier: 3.619A pdb=" N GLY A 288 " --> pdb=" O GLY A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 301 Processing helix chain 'A' and resid 302 through 317 removed outlier: 4.123A pdb=" N TRP A 306 " --> pdb=" O SER A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 330 removed outlier: 3.799A pdb=" N TYR A 330 " --> pdb=" O ALA A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 371 removed outlier: 3.517A pdb=" N ASP A 340 " --> pdb=" O ASN A 336 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE A 342 " --> pdb=" O TYR A 338 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL A 358 " --> pdb=" O PHE A 354 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE A 362 " --> pdb=" O VAL A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 377 removed outlier: 3.757A pdb=" N VAL A 377 " --> pdb=" O ILE A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 393 Processing helix chain 'A' and resid 398 through 431 removed outlier: 3.896A pdb=" N SER A 417 " --> pdb=" O LEU A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 457 removed outlier: 3.954A pdb=" N ALA A 448 " --> pdb=" O GLU A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 462 removed outlier: 3.591A pdb=" N MET A 461 " --> pdb=" O ASP A 458 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL A 462 " --> pdb=" O LEU A 459 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 458 through 462' Processing helix chain 'A' and resid 465 through 477 Processing helix chain 'A' and resid 480 through 496 Processing helix chain 'A' and resid 499 through 512 Processing helix chain 'A' and resid 517 through 525 Processing helix chain 'A' and resid 525 through 541 Processing helix chain 'A' and resid 554 through 570 removed outlier: 3.634A pdb=" N MET A 560 " --> pdb=" O TRP A 556 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N SER A 568 " --> pdb=" O PHE A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 581 removed outlier: 3.577A pdb=" N LEU A 580 " --> pdb=" O LEU A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 595 removed outlier: 3.910A pdb=" N HIS A 593 " --> pdb=" O GLU A 589 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 546 through 547 259 hydrogen bonds defined for protein. 753 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: 0.58 Time building geometry restraints manager: 0.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1159 1.34 - 1.46: 1110 1.46 - 1.58: 1835 1.58 - 1.69: 0 1.69 - 1.81: 50 Bond restraints: 4154 Sorted by residual: bond pdb=" C2 CRN A 701 " pdb=" N1 CRN A 701 " ideal model delta sigma weight residual 1.371 1.461 -0.090 2.00e-02 2.50e+03 2.03e+01 bond pdb=" C2 CRN A 701 " pdb=" N3 CRN A 701 " ideal model delta sigma weight residual 1.374 1.456 -0.082 2.00e-02 2.50e+03 1.69e+01 bond pdb=" C ASP A 474 " pdb=" N TYR A 475 " ideal model delta sigma weight residual 1.333 1.308 0.025 1.43e-02 4.89e+03 3.05e+00 bond pdb=" C2 CRN A 701 " pdb=" N6 CRN A 701 " ideal model delta sigma weight residual 1.288 1.254 0.034 2.00e-02 2.50e+03 2.94e+00 bond pdb=" CB PRO A 179 " pdb=" CG PRO A 179 " ideal model delta sigma weight residual 1.492 1.557 -0.065 5.00e-02 4.00e+02 1.69e+00 ... (remaining 4149 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.40: 5436 1.40 - 2.81: 189 2.81 - 4.21: 42 4.21 - 5.61: 6 5.61 - 7.02: 4 Bond angle restraints: 5677 Sorted by residual: angle pdb=" N ILE A 260 " pdb=" CA ILE A 260 " pdb=" C ILE A 260 " ideal model delta sigma weight residual 111.91 109.10 2.81 8.90e-01 1.26e+00 9.99e+00 angle pdb=" N CYS A 249 " pdb=" CA CYS A 249 " pdb=" C CYS A 249 " ideal model delta sigma weight residual 113.89 109.48 4.41 1.58e+00 4.01e-01 7.80e+00 angle pdb=" C GLY A 102 " pdb=" N ILE A 103 " pdb=" CA ILE A 103 " ideal model delta sigma weight residual 120.33 122.44 -2.11 8.00e-01 1.56e+00 6.95e+00 angle pdb=" N ALA A 385 " pdb=" CA ALA A 385 " pdb=" CB ALA A 385 " ideal model delta sigma weight residual 114.17 111.27 2.90 1.14e+00 7.69e-01 6.46e+00 angle pdb=" CA PRO A 179 " pdb=" N PRO A 179 " pdb=" CD PRO A 179 " ideal model delta sigma weight residual 112.00 108.67 3.33 1.40e+00 5.10e-01 5.67e+00 ... (remaining 5672 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.76: 2075 15.76 - 31.52: 174 31.52 - 47.29: 33 47.29 - 63.05: 9 63.05 - 78.81: 4 Dihedral angle restraints: 2295 sinusoidal: 850 harmonic: 1445 Sorted by residual: dihedral pdb=" CB CYS A 172 " pdb=" SG CYS A 172 " pdb=" SG CYS A 181 " pdb=" CB CYS A 181 " ideal model delta sinusoidal sigma weight residual -86.00 -126.93 40.93 1 1.00e+01 1.00e-02 2.35e+01 dihedral pdb=" CA ALA A 385 " pdb=" C ALA A 385 " pdb=" N PHE A 386 " pdb=" CA PHE A 386 " ideal model delta harmonic sigma weight residual 180.00 161.24 18.76 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" CA PHE A 525 " pdb=" C PHE A 525 " pdb=" N PHE A 526 " pdb=" CA PHE A 526 " ideal model delta harmonic sigma weight residual 180.00 -164.55 -15.45 0 5.00e+00 4.00e-02 9.55e+00 ... (remaining 2292 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 315 0.025 - 0.050: 203 0.050 - 0.075: 72 0.075 - 0.099: 22 0.099 - 0.124: 12 Chirality restraints: 624 Sorted by residual: chirality pdb=" CA PRO A 79 " pdb=" N PRO A 79 " pdb=" C PRO A 79 " pdb=" CB PRO A 79 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.12 2.00e-01 2.50e+01 3.86e-01 chirality pdb=" CA PRO A 104 " pdb=" N PRO A 104 " pdb=" C PRO A 104 " pdb=" CB PRO A 104 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.44e-01 chirality pdb=" CA VAL A 546 " pdb=" N VAL A 546 " pdb=" C VAL A 546 " pdb=" CB VAL A 546 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.11 2.00e-01 2.50e+01 3.30e-01 ... (remaining 621 not shown) Planarity restraints: 687 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 178 " 0.063 5.00e-02 4.00e+02 9.41e-02 1.42e+01 pdb=" N PRO A 179 " -0.163 5.00e-02 4.00e+02 pdb=" CA PRO A 179 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO A 179 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TRP A 214 " 0.011 2.00e-02 2.50e+03 2.26e-02 5.11e+00 pdb=" C TRP A 214 " -0.039 2.00e-02 2.50e+03 pdb=" O TRP A 214 " 0.015 2.00e-02 2.50e+03 pdb=" N GLU A 215 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 527 " -0.034 5.00e-02 4.00e+02 5.23e-02 4.37e+00 pdb=" N PRO A 528 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 528 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 528 " -0.029 5.00e-02 4.00e+02 ... (remaining 684 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 34 2.52 - 3.12: 3190 3.12 - 3.71: 6351 3.71 - 4.31: 9465 4.31 - 4.90: 15804 Nonbonded interactions: 34844 Sorted by model distance: nonbonded pdb=" NH2 ARG A 77 " pdb=" OG SER A 479 " model vdw 1.929 3.120 nonbonded pdb=" O ILE A 307 " pdb=" OG1 THR A 311 " model vdw 2.039 3.040 nonbonded pdb=" O TRP A 76 " pdb=" O HOH A 801 " model vdw 2.126 3.040 nonbonded pdb=" O SER A 477 " pdb=" O HOH A 802 " model vdw 2.130 3.040 nonbonded pdb=" OD1 ASP A 505 " pdb=" NH2 ARG A 514 " model vdw 2.143 3.120 ... (remaining 34839 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.120 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.110 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:5.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 4155 Z= 0.199 Angle : 0.652 7.016 5679 Z= 0.394 Chirality : 0.038 0.124 624 Planarity : 0.006 0.094 687 Dihedral : 12.831 78.808 1374 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 21.42 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.86 % Favored : 94.94 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.39), residues: 494 helix: 0.84 (0.30), residues: 337 sheet: None (None), residues: 0 loop : -0.47 (0.51), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 77 TYR 0.016 0.001 TYR A 468 PHE 0.019 0.001 PHE A 406 TRP 0.013 0.001 TRP A 489 HIS 0.001 0.000 HIS A 593 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.20 ( 4154) covalent geometry : angle 0.65151 / 0.39 ( 5677) SS BOND : bond 0.00231 / 0.12 ( 1) SS BOND : angle 1.44174 / 0.77 ( 2) hydrogen bonds : bond 0.21673 / 13.61 ( 259) hydrogen bonds : angle 7.54998 / 5.44 ( 753) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.144 Fit side-chains REVERT: A 444 GLU cc_start: 0.7646 (mp0) cc_final: 0.7312 (mp0) outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.3306 time to fit residues: 22.1476 Evaluate side-chains 50 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 24 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 74 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.121118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.096526 restraints weight = 4912.144| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 1.61 r_work: 0.2949 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.1338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4155 Z= 0.159 Angle : 0.641 7.946 5679 Z= 0.341 Chirality : 0.041 0.138 624 Planarity : 0.007 0.088 687 Dihedral : 5.008 35.678 540 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.66 % Favored : 95.14 % Rotamer: Outliers : 1.19 % Allowed : 5.94 % Favored : 92.87 % 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: 1.14 (0.39), residues: 494 helix: 1.34 (0.28), residues: 341 sheet: None (None), residues: 0 loop : -0.49 (0.53), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 77 TYR 0.013 0.001 TYR A 468 PHE 0.024 0.002 PHE A 353 TRP 0.013 0.001 TRP A 485 HIS 0.002 0.001 HIS A 575 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.16 ( 4154) covalent geometry : angle 0.64059 / 0.34 ( 5677) SS BOND : bond 0.00368 / 0.19 ( 1) SS BOND : angle 1.78876 / 0.97 ( 2) hydrogen bonds : bond 0.05520 / 3.62 ( 259) hydrogen bonds : angle 5.02147 / 3.58 ( 753) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 57 time to evaluate : 0.128 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 59 average time/residue: 0.3219 time to fit residues: 19.8993 Evaluate side-chains 52 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 50 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain A residue 456 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 8 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 25 optimal weight: 0.0980 chunk 39 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 486 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.131657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.109079 restraints weight = 4828.966| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 1.53 r_work: 0.3060 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8849 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4155 Z= 0.145 Angle : 0.590 6.510 5679 Z= 0.313 Chirality : 0.040 0.131 624 Planarity : 0.005 0.068 687 Dihedral : 5.033 47.092 540 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.66 % Favored : 95.14 % Rotamer: Outliers : 1.43 % Allowed : 9.03 % Favored : 89.55 % 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: 1.40 (0.38), residues: 494 helix: 1.57 (0.28), residues: 345 sheet: None (None), residues: 0 loop : -0.51 (0.54), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 77 TYR 0.017 0.001 TYR A 80 PHE 0.018 0.002 PHE A 353 TRP 0.015 0.001 TRP A 485 HIS 0.001 0.000 HIS A 575 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 ( 4154) covalent geometry : angle 0.58863 / 0.31 ( 5677) SS BOND : bond 0.00000 / 0.00 ( 1) SS BOND : angle 2.09767 / 1.14 ( 2) hydrogen bonds : bond 0.04710 / 3.07 ( 259) hydrogen bonds : angle 4.66609 / 3.32 ( 753) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 55 time to evaluate : 0.143 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 59 average time/residue: 0.2477 time to fit residues: 15.4962 Evaluate side-chains 50 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 47 time to evaluate : 0.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 598 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 19 optimal weight: 2.9990 chunk 37 optimal weight: 0.0470 chunk 48 optimal weight: 0.9990 chunk 6 optimal weight: 0.3980 chunk 1 optimal weight: 0.6980 chunk 2 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 chunk 43 optimal weight: 0.6980 chunk 44 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 177 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 = 0.3468 r_free = 0.3468 target = 0.131556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.108995 restraints weight = 4742.601| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 1.53 r_work: 0.3040 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4155 Z= 0.125 Angle : 0.570 6.480 5679 Z= 0.297 Chirality : 0.039 0.126 624 Planarity : 0.005 0.062 687 Dihedral : 4.975 48.608 540 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.25 % Favored : 95.55 % Rotamer: Outliers : 1.66 % Allowed : 10.45 % Favored : 87.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.48 (0.38), residues: 494 helix: 1.65 (0.27), residues: 348 sheet: None (None), residues: 0 loop : -0.58 (0.54), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 77 TYR 0.017 0.001 TYR A 80 PHE 0.014 0.001 PHE A 406 TRP 0.016 0.001 TRP A 485 HIS 0.002 0.001 HIS A 602 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 ( 4154) covalent geometry : angle 0.56856 / 0.30 ( 5677) SS BOND : bond 0.00002 / 0.00 ( 1) SS BOND : angle 2.12294 / 1.16 ( 2) hydrogen bonds : bond 0.04295 / 2.79 ( 259) hydrogen bonds : angle 4.51366 / 3.21 ( 753) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 55 time to evaluate : 0.099 Fit side-chains REVERT: A 111 SER cc_start: 0.9054 (t) cc_final: 0.8817 (p) REVERT: A 183 GLU cc_start: 0.7743 (OUTLIER) cc_final: 0.7277 (mt-10) outliers start: 7 outliers final: 2 residues processed: 59 average time/residue: 0.2428 time to fit residues: 15.3204 Evaluate side-chains 54 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 51 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 601 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 28 optimal weight: 0.7980 chunk 15 optimal weight: 0.0470 chunk 12 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 chunk 0 optimal weight: 6.9990 chunk 43 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 22 optimal weight: 0.5980 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 232 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.131849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.109196 restraints weight = 4783.485| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 1.53 r_work: 0.3059 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4155 Z= 0.124 Angle : 0.558 6.144 5679 Z= 0.291 Chirality : 0.039 0.126 624 Planarity : 0.005 0.059 687 Dihedral : 4.907 46.811 540 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.05 % Favored : 95.75 % Rotamer: Outliers : 2.38 % Allowed : 10.93 % Favored : 86.70 % 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: 1.57 (0.38), residues: 494 helix: 1.72 (0.27), residues: 347 sheet: None (None), residues: 0 loop : -0.55 (0.53), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 77 TYR 0.017 0.001 TYR A 80 PHE 0.014 0.001 PHE A 406 TRP 0.015 0.001 TRP A 485 HIS 0.001 0.000 HIS A 575 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 ( 4154) covalent geometry : angle 0.55644 / 0.29 ( 5677) SS BOND : bond 0.00030 / 0.02 ( 1) SS BOND : angle 2.13837 / 1.16 ( 2) hydrogen bonds : bond 0.04213 / 2.73 ( 259) hydrogen bonds : angle 4.43226 / 3.14 ( 753) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 55 time to evaluate : 0.097 Fit side-chains REVERT: A 111 SER cc_start: 0.9042 (t) cc_final: 0.8810 (p) REVERT: A 183 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7282 (mt-10) REVERT: A 346 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8397 (mp) outliers start: 10 outliers final: 3 residues processed: 61 average time/residue: 0.2299 time to fit residues: 14.9426 Evaluate side-chains 55 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 50 time to evaluate : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 560 MET Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 601 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 43 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 177 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 = 0.3451 r_free = 0.3451 target = 0.130114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.107493 restraints weight = 4814.609| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 1.53 r_work: 0.3021 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4155 Z= 0.143 Angle : 0.582 6.153 5679 Z= 0.303 Chirality : 0.040 0.133 624 Planarity : 0.005 0.058 687 Dihedral : 4.983 47.712 540 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.45 % Favored : 95.34 % Rotamer: Outliers : 2.14 % Allowed : 12.59 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.38), residues: 494 helix: 1.71 (0.28), residues: 348 sheet: None (None), residues: 0 loop : -0.59 (0.53), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 77 TYR 0.020 0.001 TYR A 80 PHE 0.016 0.002 PHE A 406 TRP 0.014 0.001 TRP A 485 HIS 0.001 0.000 HIS A 575 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.14 ( 4154) covalent geometry : angle 0.58049 / 0.30 ( 5677) SS BOND : bond 0.00325 / 0.17 ( 1) SS BOND : angle 2.33331 / 1.28 ( 2) hydrogen bonds : bond 0.04391 / 2.86 ( 259) hydrogen bonds : angle 4.43795 / 3.14 ( 753) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 50 time to evaluate : 0.098 Fit side-chains REVERT: A 183 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.7289 (mt-10) REVERT: A 211 ILE cc_start: 0.8750 (OUTLIER) cc_final: 0.8473 (tt) REVERT: A 249 CYS cc_start: 0.8192 (m) cc_final: 0.7959 (m) outliers start: 9 outliers final: 6 residues processed: 56 average time/residue: 0.2854 time to fit residues: 16.9935 Evaluate side-chains 58 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 50 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 TYR Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 560 MET Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 601 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 29 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 24 optimal weight: 0.2980 chunk 14 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 177 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 = 0.3463 r_free = 0.3463 target = 0.131103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.108460 restraints weight = 4872.515| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 1.54 r_work: 0.3051 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8837 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4155 Z= 0.130 Angle : 0.563 6.089 5679 Z= 0.292 Chirality : 0.039 0.127 624 Planarity : 0.005 0.056 687 Dihedral : 4.910 45.095 540 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.45 % Favored : 95.34 % Rotamer: Outliers : 2.14 % Allowed : 13.54 % Favored : 84.32 % 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: 1.57 (0.38), residues: 494 helix: 1.73 (0.28), residues: 348 sheet: None (None), residues: 0 loop : -0.59 (0.53), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 77 TYR 0.020 0.001 TYR A 80 PHE 0.017 0.001 PHE A 419 TRP 0.015 0.001 TRP A 485 HIS 0.001 0.000 HIS A 575 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 ( 4154) covalent geometry : angle 0.56106 / 0.29 ( 5677) SS BOND : bond 0.00112 / 0.06 ( 1) SS BOND : angle 2.25204 / 1.23 ( 2) hydrogen bonds : bond 0.04221 / 2.74 ( 259) hydrogen bonds : angle 4.37932 / 3.09 ( 753) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 0.149 Fit side-chains REVERT: A 183 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.7329 (mt-10) REVERT: A 249 CYS cc_start: 0.8171 (m) cc_final: 0.7961 (m) REVERT: A 346 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8418 (mp) outliers start: 9 outliers final: 6 residues processed: 60 average time/residue: 0.2588 time to fit residues: 16.5337 Evaluate side-chains 59 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 51 time to evaluate : 0.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 TYR Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 509 CYS Chi-restraints excluded: chain A residue 560 MET Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 601 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 33 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 44 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 177 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 = 0.3467 r_free = 0.3467 target = 0.131397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.108835 restraints weight = 4743.116| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 1.51 r_work: 0.3036 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8826 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4155 Z= 0.146 Angle : 0.589 6.274 5679 Z= 0.306 Chirality : 0.040 0.134 624 Planarity : 0.005 0.057 687 Dihedral : 4.976 46.044 540 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.66 % Favored : 95.14 % Rotamer: Outliers : 2.14 % Allowed : 13.78 % Favored : 84.09 % 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: 1.49 (0.38), residues: 494 helix: 1.61 (0.28), residues: 353 sheet: None (None), residues: 0 loop : -0.55 (0.54), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 77 TYR 0.021 0.001 TYR A 80 PHE 0.021 0.002 PHE A 419 TRP 0.014 0.001 TRP A 485 HIS 0.001 0.000 HIS A 575 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 ( 4154) covalent geometry : angle 0.58762 / 0.31 ( 5677) SS BOND : bond 0.00091 / 0.05 ( 1) SS BOND : angle 2.31605 / 1.26 ( 2) hydrogen bonds : bond 0.04388 / 2.86 ( 259) hydrogen bonds : angle 4.41957 / 3.12 ( 753) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.089 Fit side-chains REVERT: A 183 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.7333 (mt-10) outliers start: 9 outliers final: 6 residues processed: 59 average time/residue: 0.2264 time to fit residues: 14.2333 Evaluate side-chains 59 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 TYR Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 509 CYS Chi-restraints excluded: chain A residue 560 MET Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 601 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 4 optimal weight: 1.9990 chunk 8 optimal weight: 0.0970 chunk 47 optimal weight: 0.7980 chunk 26 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 chunk 27 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 chunk 36 optimal weight: 0.0470 chunk 46 optimal weight: 0.9980 overall best weight: 0.4076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 177 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 = 0.3478 r_free = 0.3478 target = 0.132568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.109886 restraints weight = 4889.479| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 1.55 r_work: 0.3056 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4155 Z= 0.114 Angle : 0.555 6.160 5679 Z= 0.288 Chirality : 0.038 0.122 624 Planarity : 0.005 0.056 687 Dihedral : 4.809 40.910 540 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.05 % Favored : 95.75 % Rotamer: Outliers : 1.43 % Allowed : 15.44 % Favored : 83.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.66 (0.38), residues: 494 helix: 1.78 (0.27), residues: 349 sheet: None (None), residues: 0 loop : -0.56 (0.53), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 77 TYR 0.017 0.001 TYR A 80 PHE 0.021 0.001 PHE A 419 TRP 0.016 0.001 TRP A 485 HIS 0.001 0.000 HIS A 575 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 ( 4154) covalent geometry : angle 0.55404 / 0.29 ( 5677) SS BOND : bond 0.00062 / 0.03 ( 1) SS BOND : angle 2.04811 / 1.12 ( 2) hydrogen bonds : bond 0.03953 / 2.56 ( 259) hydrogen bonds : angle 4.30658 / 3.04 ( 753) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 56 time to evaluate : 0.090 Fit side-chains REVERT: A 111 SER cc_start: 0.9037 (t) cc_final: 0.8796 (p) REVERT: A 183 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7325 (mt-10) outliers start: 6 outliers final: 3 residues processed: 58 average time/residue: 0.2668 time to fit residues: 16.4704 Evaluate side-chains 59 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 55 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 TYR Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 601 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 25 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 14 optimal weight: 0.0970 chunk 15 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 177 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 = 0.3481 r_free = 0.3481 target = 0.132578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.109961 restraints weight = 4751.894| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 1.53 r_work: 0.3031 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4155 Z= 0.134 Angle : 0.577 6.205 5679 Z= 0.299 Chirality : 0.040 0.129 624 Planarity : 0.005 0.056 687 Dihedral : 4.938 44.933 540 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.45 % Favored : 95.34 % Rotamer: Outliers : 1.19 % Allowed : 15.91 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.38), residues: 494 helix: 1.68 (0.27), residues: 354 sheet: None (None), residues: 0 loop : -0.51 (0.55), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 77 TYR 0.021 0.001 TYR A 80 PHE 0.025 0.001 PHE A 419 TRP 0.014 0.001 TRP A 485 HIS 0.001 0.000 HIS A 575 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.13 ( 4154) covalent geometry : angle 0.57578 / 0.30 ( 5677) SS BOND : bond 0.00066 / 0.03 ( 1) SS BOND : angle 2.16689 / 1.18 ( 2) hydrogen bonds : bond 0.04215 / 2.74 ( 259) hydrogen bonds : angle 4.36153 / 3.08 ( 753) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 54 time to evaluate : 0.091 Fit side-chains REVERT: A 183 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7352 (mt-10) outliers start: 5 outliers final: 3 residues processed: 57 average time/residue: 0.2523 time to fit residues: 15.3384 Evaluate side-chains 58 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 54 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 TYR Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 601 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 4 optimal weight: 0.5980 chunk 45 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 chunk 21 optimal weight: 0.0040 chunk 13 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 37 optimal weight: 0.5980 chunk 29 optimal weight: 0.8980 chunk 12 optimal weight: 6.9990 chunk 10 optimal weight: 0.0470 overall best weight: 0.3890 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 177 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 = 0.3487 r_free = 0.3487 target = 0.133198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.110752 restraints weight = 4749.963| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 1.50 r_work: 0.3085 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4155 Z= 0.113 Angle : 0.556 6.016 5679 Z= 0.288 Chirality : 0.038 0.122 624 Planarity : 0.005 0.055 687 Dihedral : 4.808 41.321 540 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.45 % Favored : 95.34 % Rotamer: Outliers : 1.19 % Allowed : 16.15 % Favored : 82.66 % 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: 1.72 (0.38), residues: 494 helix: 1.84 (0.27), residues: 349 sheet: None (None), residues: 0 loop : -0.55 (0.53), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 77 TYR 0.017 0.001 TYR A 80 PHE 0.021 0.001 PHE A 419 TRP 0.017 0.001 TRP A 485 HIS 0.001 0.000 HIS A 575 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 ( 4154) covalent geometry : angle 0.55463 / 0.29 ( 5677) SS BOND : bond 0.00033 / 0.02 ( 1) SS BOND : angle 1.89409 / 1.04 ( 2) hydrogen bonds : bond 0.03908 / 2.52 ( 259) hydrogen bonds : angle 4.28591 / 3.03 ( 753) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1124.24 seconds wall clock time: 19 minutes 52.24 seconds (1192.24 seconds total)