Starting phenix.real_space_refine on Sat May 2 09:14:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9v8x_64854/05_2026/9v8x_64854_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9v8x_64854/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9v8x_64854/05_2026/9v8x_64854.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9v8x_64854/05_2026/9v8x_64854.map" model { file = "/net/cci-nas-00/data/ceres_data/9v8x_64854/05_2026/9v8x_64854_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9v8x_64854/05_2026/9v8x_64854_trim.cif" } 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-2.1rc2-6044/lib/python3.9/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, 22 Unusual residues: {' CL': 1, ' NA': 2, 'CRN': 1} Classifications: {'undetermined': 4, 'water': 10} Link IDs: {None: 13} Time building chain proxies: 1.22, per 1000 atoms: 0.30 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: 0.44 Conformation dependent library (CDL) restraints added in 148.8 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: 0.09 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: 0.60 Time building geometry restraints manager: 0.57 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: 0.060 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 5.920 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:7.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 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 covalent geometry : bond 0.00418 ( 4154) covalent geometry : angle 0.65151 ( 5677) SS BOND : bond 0.00231 ( 1) SS BOND : angle 1.44174 ( 2) hydrogen bonds : bond 0.21673 ( 259) hydrogen bonds : angle 7.54998 ( 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 : 0.110 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: 0.3982 time to fit residues: 26.6730 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 : 0.150 ------------------------------------------------------------------------------- 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: 2.9990 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 22 optimal weight: 0.4980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.122858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.098806 restraints weight = 4889.683| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 1.56 r_work: 0.2954 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.1394 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= 0.157 Angle : 0.644 8.129 5679 Z= 0.341 Chirality : 0.042 0.135 624 Planarity : 0.007 0.082 687 Dihedral : 5.050 36.560 540 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.06 % Favored : 94.74 % 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: 1.08 (0.38), residues: 494 helix: 1.31 (0.28), residues: 341 sheet: None (None), residues: 0 loop : -0.55 (0.52), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 77 TYR 0.016 0.001 TYR A 148 PHE 0.025 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 covalent geometry : bond 0.00359 ( 4154) covalent geometry : angle 0.64300 ( 5677) SS BOND : bond 0.00413 ( 1) SS BOND : angle 1.78148 ( 2) hydrogen bonds : bond 0.05245 ( 259) hydrogen bonds : angle 4.97152 ( 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 64 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 0.103 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 61 average time/residue: 0.3647 time to fit residues: 23.3143 Evaluate side-chains 53 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 51 time to evaluate : 0.135 ------------------------------------------------------------------------------- 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: 0.9990 chunk 33 optimal weight: 0.6980 chunk 44 optimal weight: 0.6980 chunk 35 optimal weight: 0.9990 chunk 25 optimal weight: 0.0570 chunk 39 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 overall best weight: 0.6900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 486 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.129818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.107172 restraints weight = 4857.674| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 1.55 r_work: 0.3048 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.1679 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= 0.140 Angle : 0.585 6.477 5679 Z= 0.310 Chirality : 0.040 0.132 624 Planarity : 0.006 0.067 687 Dihedral : 4.922 34.084 540 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.45 % Favored : 95.34 % Rotamer: Outliers : 1.43 % Allowed : 9.26 % Favored : 89.31 % 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: 1.58 (0.28), residues: 343 sheet: None (None), residues: 0 loop : -0.54 (0.53), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 77 TYR 0.016 0.001 TYR A 148 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 covalent geometry : bond 0.00322 ( 4154) covalent geometry : angle 0.58347 ( 5677) SS BOND : bond 0.00030 ( 1) SS BOND : angle 2.36359 ( 2) hydrogen bonds : bond 0.04790 ( 259) hydrogen bonds : angle 4.68711 ( 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 63 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 57 time to evaluate : 0.123 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 60 average time/residue: 0.2814 time to fit residues: 17.9915 Evaluate side-chains 52 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 49 time to evaluate : 0.138 ------------------------------------------------------------------------------- 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: 0.7980 chunk 37 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 2 optimal weight: 0.5980 chunk 4 optimal weight: 0.7980 chunk 43 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.3443 r_free = 0.3443 target = 0.129448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.106768 restraints weight = 4771.394| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 1.53 r_work: 0.3039 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.1786 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= 0.147 Angle : 0.590 6.816 5679 Z= 0.310 Chirality : 0.040 0.133 624 Planarity : 0.005 0.062 687 Dihedral : 4.937 31.600 540 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.66 % Favored : 95.14 % Rotamer: Outliers : 2.61 % Allowed : 10.69 % 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: 1.40 (0.38), residues: 494 helix: 1.61 (0.27), residues: 345 sheet: None (None), residues: 0 loop : -0.64 (0.53), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 77 TYR 0.018 0.001 TYR A 80 PHE 0.017 0.002 PHE A 406 TRP 0.015 0.001 TRP A 485 HIS 0.001 0.001 HIS A 602 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 4154) covalent geometry : angle 0.58845 ( 5677) SS BOND : bond 0.00099 ( 1) SS BOND : angle 2.36316 ( 2) hydrogen bonds : bond 0.04626 ( 259) hydrogen bonds : angle 4.58945 ( 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 63 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 52 time to evaluate : 0.125 Fit side-chains REVERT: A 467 MET cc_start: 0.9078 (tpp) cc_final: 0.8859 (tpt) outliers start: 11 outliers final: 5 residues processed: 58 average time/residue: 0.3212 time to fit residues: 19.7683 Evaluate side-chains 53 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 48 time to evaluate : 0.207 ------------------------------------------------------------------------------- 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 560 MET 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: 0.0040 chunk 15 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 6 optimal weight: 0.0370 chunk 44 optimal weight: 1.9990 chunk 10 optimal weight: 0.4980 chunk 0 optimal weight: 6.9990 chunk 43 optimal weight: 0.5980 chunk 39 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 overall best weight: 0.3470 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3476 r_free = 0.3476 target = 0.132390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.109942 restraints weight = 4789.116| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 1.51 r_work: 0.3091 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 4155 Z= 0.109 Angle : 0.541 6.222 5679 Z= 0.282 Chirality : 0.038 0.122 624 Planarity : 0.005 0.059 687 Dihedral : 4.811 32.540 540 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.05 % Favored : 95.75 % Rotamer: Outliers : 1.90 % Allowed : 11.88 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.38), residues: 494 helix: 1.67 (0.27), residues: 348 sheet: None (None), residues: 0 loop : -0.49 (0.53), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 77 TYR 0.016 0.001 TYR A 80 PHE 0.012 0.001 PHE A 353 TRP 0.017 0.001 TRP A 485 HIS 0.002 0.000 HIS A 575 Details of bonding type rmsd covalent geometry : bond 0.00238 ( 4154) covalent geometry : angle 0.54027 ( 5677) SS BOND : bond 0.00027 ( 1) SS BOND : angle 2.01138 ( 2) hydrogen bonds : bond 0.04055 ( 259) hydrogen bonds : angle 4.38675 ( 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 63 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 55 time to evaluate : 0.140 Fit side-chains REVERT: A 183 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.7290 (mt-10) outliers start: 8 outliers final: 2 residues processed: 59 average time/residue: 0.2851 time to fit residues: 17.9167 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 : 0.084 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- 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: 0.5980 chunk 2 optimal weight: 0.5980 chunk 20 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 43 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3455 r_free = 0.3455 target = 0.130443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.107702 restraints weight = 4828.852| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 1.53 r_work: 0.3039 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.2086 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= 0.135 Angle : 0.565 6.134 5679 Z= 0.295 Chirality : 0.039 0.130 624 Planarity : 0.005 0.057 687 Dihedral : 4.847 32.583 540 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.25 % Favored : 95.55 % Rotamer: Outliers : 1.66 % Allowed : 12.59 % Favored : 85.75 % 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: 1.54 (0.38), residues: 494 helix: 1.68 (0.27), residues: 348 sheet: None (None), residues: 0 loop : -0.53 (0.53), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 77 TYR 0.018 0.001 TYR A 80 PHE 0.015 0.001 PHE A 406 TRP 0.014 0.001 TRP A 485 HIS 0.001 0.000 HIS A 575 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 4154) covalent geometry : angle 0.56345 ( 5677) SS BOND : bond 0.00281 ( 1) SS BOND : angle 2.42108 ( 2) hydrogen bonds : bond 0.04312 ( 259) hydrogen bonds : angle 4.41641 ( 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 60 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 53 time to evaluate : 0.152 Fit side-chains REVERT: A 183 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.7291 (mt-10) outliers start: 7 outliers final: 4 residues processed: 56 average time/residue: 0.2953 time to fit residues: 17.5715 Evaluate side-chains 56 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 51 time to evaluate : 0.137 ------------------------------------------------------------------------------- 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 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: 0.7980 chunk 2 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 39 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3454 r_free = 0.3454 target = 0.130320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.107606 restraints weight = 4869.816| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 1.54 r_work: 0.3038 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.2127 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= 0.139 Angle : 0.567 6.111 5679 Z= 0.296 Chirality : 0.040 0.131 624 Planarity : 0.005 0.057 687 Dihedral : 4.872 34.823 540 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.25 % Favored : 95.55 % Rotamer: Outliers : 1.66 % Allowed : 13.78 % Favored : 84.56 % 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: 1.54 (0.38), residues: 494 helix: 1.69 (0.27), residues: 349 sheet: None (None), residues: 0 loop : -0.58 (0.53), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 77 TYR 0.019 0.001 TYR A 80 PHE 0.016 0.001 PHE A 406 TRP 0.014 0.001 TRP A 485 HIS 0.001 0.000 HIS A 575 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 4154) covalent geometry : angle 0.56496 ( 5677) SS BOND : bond 0.00077 ( 1) SS BOND : angle 2.31583 ( 2) hydrogen bonds : bond 0.04408 ( 259) hydrogen bonds : angle 4.39570 ( 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 62 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 55 time to evaluate : 0.086 Fit side-chains REVERT: A 183 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.7275 (mt-10) REVERT: A 211 ILE cc_start: 0.8774 (OUTLIER) cc_final: 0.8525 (tt) REVERT: A 249 CYS cc_start: 0.8256 (m) cc_final: 0.8041 (m) outliers start: 7 outliers final: 5 residues processed: 59 average time/residue: 0.2991 time to fit residues: 18.7515 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 : 0.143 ------------------------------------------------------------------------------- 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 211 ILE 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: 0.8980 chunk 26 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 13 optimal weight: 0.3980 chunk 11 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3447 r_free = 0.3447 target = 0.129838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.107193 restraints weight = 4756.238| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 1.52 r_work: 0.3051 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.2133 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 : 0.575 6.132 5679 Z= 0.300 Chirality : 0.040 0.137 624 Planarity : 0.005 0.057 687 Dihedral : 4.916 39.253 540 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.66 % Favored : 95.14 % Rotamer: Outliers : 1.90 % Allowed : 14.01 % 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: 1.46 (0.38), residues: 494 helix: 1.59 (0.28), residues: 354 sheet: None (None), residues: 0 loop : -0.57 (0.54), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 77 TYR 0.019 0.001 TYR A 80 PHE 0.020 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 covalent geometry : bond 0.00339 ( 4154) covalent geometry : angle 0.57334 ( 5677) SS BOND : bond 0.00040 ( 1) SS BOND : angle 2.30565 ( 2) hydrogen bonds : bond 0.04457 ( 259) hydrogen bonds : angle 4.40694 ( 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 66 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.125 Fit side-chains REVERT: A 183 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.7301 (mt-10) outliers start: 8 outliers final: 6 residues processed: 62 average time/residue: 0.2837 time to fit residues: 18.7241 Evaluate side-chains 60 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 53 time to evaluate : 0.154 ------------------------------------------------------------------------------- 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 445 ILE 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: 0.9980 chunk 8 optimal weight: 0.7980 chunk 47 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 12 optimal weight: 0.0050 chunk 21 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.132352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.109773 restraints weight = 4887.475| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 1.51 r_work: 0.3049 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.2248 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= 0.129 Angle : 0.568 6.499 5679 Z= 0.295 Chirality : 0.039 0.128 624 Planarity : 0.005 0.056 687 Dihedral : 4.908 41.547 540 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.25 % Favored : 95.55 % Rotamer: Outliers : 1.66 % Allowed : 14.73 % Favored : 83.61 % 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: 1.51 (0.38), residues: 494 helix: 1.62 (0.27), residues: 354 sheet: None (None), residues: 0 loop : -0.54 (0.54), residues: 140 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 0.023 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 covalent geometry : bond 0.00299 ( 4154) covalent geometry : angle 0.56637 ( 5677) SS BOND : bond 0.00099 ( 1) SS BOND : angle 2.24500 ( 2) hydrogen bonds : bond 0.04256 ( 259) hydrogen bonds : angle 4.36506 ( 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: 7 poor density : 55 time to evaluate : 0.169 Fit side-chains REVERT: A 183 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.7294 (mt-10) outliers start: 7 outliers final: 4 residues processed: 59 average time/residue: 0.2932 time to fit residues: 18.4862 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 : 0.095 ------------------------------------------------------------------------------- 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 509 CYS 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: 0.5980 chunk 44 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 7 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 14 optimal weight: 0.3980 chunk 15 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 chunk 41 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3465 r_free = 0.3465 target = 0.131349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.108764 restraints weight = 4764.123| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 1.52 r_work: 0.3048 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.2247 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= 0.129 Angle : 0.571 6.341 5679 Z= 0.297 Chirality : 0.040 0.127 624 Planarity : 0.005 0.056 687 Dihedral : 4.937 41.993 540 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.45 % Favored : 95.34 % Rotamer: Outliers : 1.43 % Allowed : 14.96 % Favored : 83.61 % 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: 1.51 (0.38), residues: 494 helix: 1.63 (0.27), residues: 354 sheet: None (None), residues: 0 loop : -0.55 (0.55), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 77 TYR 0.018 0.001 TYR A 80 PHE 0.025 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 covalent geometry : bond 0.00302 ( 4154) covalent geometry : angle 0.56977 ( 5677) SS BOND : bond 0.00088 ( 1) SS BOND : angle 2.16639 ( 2) hydrogen bonds : bond 0.04273 ( 259) hydrogen bonds : angle 4.36333 ( 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 62 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 56 time to evaluate : 0.181 Fit side-chains REVERT: A 183 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7316 (mt-10) outliers start: 6 outliers final: 5 residues processed: 59 average time/residue: 0.3058 time to fit residues: 19.2554 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 : 0.147 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 4 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 27 optimal weight: 0.4980 chunk 21 optimal weight: 0.0870 chunk 13 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.131530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.108991 restraints weight = 4769.293| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 1.52 r_work: 0.3051 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.2317 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= 0.129 Angle : 0.569 6.228 5679 Z= 0.296 Chirality : 0.040 0.127 624 Planarity : 0.005 0.055 687 Dihedral : 4.925 42.195 540 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.25 % Favored : 95.55 % Rotamer: Outliers : 1.43 % Allowed : 14.73 % Favored : 83.85 % 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: 1.54 (0.38), residues: 494 helix: 1.65 (0.27), residues: 354 sheet: None (None), residues: 0 loop : -0.53 (0.55), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 77 TYR 0.018 0.001 TYR A 80 PHE 0.025 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 covalent geometry : bond 0.00299 ( 4154) covalent geometry : angle 0.56740 ( 5677) SS BOND : bond 0.00074 ( 1) SS BOND : angle 2.12422 ( 2) hydrogen bonds : bond 0.04246 ( 259) hydrogen bonds : angle 4.35623 ( 753) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1311.89 seconds wall clock time: 23 minutes 5.08 seconds (1385.08 seconds total)