Starting phenix.real_space_refine on Wed Jul 1 23:50:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wtv_37843/07_2026/8wtv_37843.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wtv_37843/07_2026/8wtv_37843.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8wtv_37843/07_2026/8wtv_37843.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wtv_37843/07_2026/8wtv_37843.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wtv_37843/07_2026/8wtv_37843.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wtv_37843/07_2026/8wtv_37843.map" } resolution = 2.7 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= -0.001 sd= 0.067 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 20 5.16 5 Cl 1 4.86 5 Na 2 4.78 5 C 2897 2.51 5 N 667 2.21 5 O 738 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 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: 4325 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 536, 4281 Classifications: {'peptide': 536} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 516} Chain breaks: 1 Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 41 Ad-hoc single atom residues: {' NA': 2, ' CL': 1} Unusual residues: {'E5E': 2, 'NAG': 1} Classifications: {'undetermined': 3, 'water': 3} Link IDs: {None: 5} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 0.78, per 1000 atoms: 0.18 Number of scatterers: 4325 At special positions: 0 Unit cell: (77.35, 67.15, 90.95, 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 20 16.00 Na 2 11.00 O 738 8.00 N 667 7.00 C 2897 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 176 " - pdb=" SG CYS A 185 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 706 " - " ASN A 184 " Time building additional restraints: 0.22 Conformation dependent library (CDL) restraints added in 94.2 milliseconds 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 986 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 1 sheets defined 79.1% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'A' and resid 76 through 89 removed outlier: 4.670A pdb=" N PHE A 82 " --> pdb=" O ASN A 78 " (cutoff:3.500A) Proline residue: A 83 - end of helix Processing helix chain 'A' and resid 91 through 93 No H-bonds generated for 'chain 'A' and resid 91 through 93' Processing helix chain 'A' and resid 94 through 105 removed outlier: 3.504A pdb=" N TYR A 98 " --> pdb=" O PHE A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 121 removed outlier: 3.551A pdb=" N LEU A 109 " --> pdb=" O ALA A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 134 removed outlier: 3.662A pdb=" N TRP A 128 " --> pdb=" O ALA A 125 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS A 129 " --> pdb=" O THR A 126 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ILE A 130 " --> pdb=" O VAL A 127 " (cutoff:3.500A) Proline residue: A 132 - end of helix Processing helix chain 'A' and resid 135 through 166 removed outlier: 3.788A pdb=" N TYR A 139 " --> pdb=" O LYS A 135 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N TYR A 151 " --> pdb=" O TYR A 147 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ASN A 153 " --> pdb=" O GLY A 149 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N VAL A 154 " --> pdb=" O PHE A 150 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ILE A 155 " --> pdb=" O TYR A 151 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ILE A 156 " --> pdb=" O TYR A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 217 Processing helix chain 'A' and resid 220 through 224 Processing helix chain 'A' and resid 234 through 251 Processing helix chain 'A' and resid 261 through 267 removed outlier: 3.639A pdb=" N ILE A 265 " --> pdb=" O LYS A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 283 removed outlier: 3.620A pdb=" N PHE A 272 " --> pdb=" O THR A 268 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N THR A 283 " --> pdb=" O VAL A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 295 removed outlier: 3.761A pdb=" N GLY A 290 " --> pdb=" O GLY A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 320 removed outlier: 4.362A pdb=" N TRP A 308 " --> pdb=" O GLU A 304 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE A 316 " --> pdb=" O ALA A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 Processing helix chain 'A' and resid 338 through 373 removed outlier: 3.732A pdb=" N ASP A 342 " --> pdb=" O ASN A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 396 Proline residue: A 392 - end of helix Processing helix chain 'A' and resid 400 through 435 removed outlier: 3.525A pdb=" N TRP A 404 " --> pdb=" O GLY A 400 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ASP A 434 " --> pdb=" O GLY A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 440 Processing helix chain 'A' and resid 441 through 458 Processing helix chain 'A' and resid 459 through 462 removed outlier: 3.868A pdb=" N THR A 462 " --> pdb=" O PHE A 459 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 459 through 462' Processing helix chain 'A' and resid 464 through 476 removed outlier: 3.876A pdb=" N VAL A 468 " --> pdb=" O GLY A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 495 Processing helix chain 'A' and resid 497 through 510 removed outlier: 3.557A pdb=" N MET A 508 " --> pdb=" O ASP A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 523 Processing helix chain 'A' and resid 523 through 539 Processing helix chain 'A' and resid 551 through 567 removed outlier: 3.688A pdb=" N ASN A 555 " --> pdb=" O PRO A 551 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N SER A 565 " --> pdb=" O ILE A 561 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N MET A 566 " --> pdb=" O ALA A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 579 Processing helix chain 'A' and resid 583 through 593 removed outlier: 3.577A pdb=" N ILE A 592 " --> pdb=" O LEU A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 598 removed outlier: 3.944A pdb=" N HIS A 598 " --> pdb=" O GLU A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 604 removed outlier: 3.856A pdb=" N GLN A 603 " --> pdb=" O HIS A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 609 Processing helix chain 'A' and resid 610 through 616 removed outlier: 4.076A pdb=" N TRP A 614 " --> pdb=" O GLN A 610 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 544 through 545 265 hydrogen bonds defined for protein. 771 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: 0.44 Time building geometry restraints manager: 0.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 635 1.31 - 1.43: 1405 1.43 - 1.56: 2387 1.56 - 1.68: 1 1.68 - 1.81: 31 Bond restraints: 4459 Sorted by residual: bond pdb=" CA MET A 107 " pdb=" C MET A 107 " ideal model delta sigma weight residual 1.520 1.572 -0.052 1.23e-02 6.61e+03 1.80e+01 bond pdb=" C LYS A 576 " pdb=" O LYS A 576 " ideal model delta sigma weight residual 1.236 1.184 0.052 1.26e-02 6.30e+03 1.70e+01 bond pdb=" C LYS A 576 " pdb=" N PHE A 577 " ideal model delta sigma weight residual 1.335 1.288 0.047 1.36e-02 5.41e+03 1.19e+01 bond pdb=" C MET A 107 " pdb=" N PRO A 108 " ideal model delta sigma weight residual 1.335 1.382 -0.047 1.36e-02 5.41e+03 1.17e+01 bond pdb=" C SER A 182 " pdb=" N PRO A 183 " ideal model delta sigma weight residual 1.337 1.370 -0.033 9.80e-03 1.04e+04 1.14e+01 ... (remaining 4454 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.31: 5906 1.31 - 2.61: 139 2.61 - 3.92: 25 3.92 - 5.23: 11 5.23 - 6.53: 5 Bond angle restraints: 6086 Sorted by residual: angle pdb=" N TRP A 253 " pdb=" CA TRP A 253 " pdb=" C TRP A 253 " ideal model delta sigma weight residual 113.01 118.40 -5.39 1.20e+00 6.94e-01 2.02e+01 angle pdb=" CA SER A 182 " pdb=" C SER A 182 " pdb=" N PRO A 183 " ideal model delta sigma weight residual 117.48 122.12 -4.64 1.15e+00 7.56e-01 1.63e+01 angle pdb=" O SER A 182 " pdb=" C SER A 182 " pdb=" N PRO A 183 " ideal model delta sigma weight residual 121.53 117.15 4.38 1.12e+00 7.97e-01 1.53e+01 angle pdb=" N ASN A 184 " pdb=" CA ASN A 184 " pdb=" C ASN A 184 " ideal model delta sigma weight residual 113.38 108.98 4.40 1.23e+00 6.61e-01 1.28e+01 angle pdb=" O TYR A 575 " pdb=" C TYR A 575 " pdb=" N LYS A 576 " ideal model delta sigma weight residual 122.12 118.36 3.76 1.06e+00 8.90e-01 1.26e+01 ... (remaining 6081 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 2187 17.99 - 35.97: 236 35.97 - 53.96: 63 53.96 - 71.95: 12 71.95 - 89.94: 2 Dihedral angle restraints: 2500 sinusoidal: 951 harmonic: 1549 Sorted by residual: dihedral pdb=" CB CYS A 176 " pdb=" SG CYS A 176 " pdb=" SG CYS A 185 " pdb=" CB CYS A 185 " ideal model delta sinusoidal sigma weight residual -86.00 -175.94 89.94 1 1.00e+01 1.00e-02 9.59e+01 dihedral pdb=" CG ARG A 442 " pdb=" CD ARG A 442 " pdb=" NE ARG A 442 " pdb=" CZ ARG A 442 " ideal model delta sinusoidal sigma weight residual 90.00 132.55 -42.55 2 1.50e+01 4.44e-03 9.76e+00 dihedral pdb=" CA LYS A 576 " pdb=" CB LYS A 576 " pdb=" CG LYS A 576 " pdb=" CD LYS A 576 " ideal model delta sinusoidal sigma weight residual 180.00 120.06 59.94 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 2497 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 504 0.045 - 0.090: 148 0.090 - 0.134: 25 0.134 - 0.179: 0 0.179 - 0.224: 4 Chirality restraints: 681 Sorted by residual: chirality pdb=" C1 NAG A 706 " pdb=" ND2 ASN A 184 " pdb=" C2 NAG A 706 " pdb=" O5 NAG A 706 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CA TRP A 253 " pdb=" N TRP A 253 " pdb=" C TRP A 253 " pdb=" CB TRP A 253 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.21 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CAL E5E A 704 " pdb=" CAH E5E A 704 " pdb=" CAK E5E A 704 " pdb=" OAD E5E A 704 " both_signs ideal model delta sigma weight residual False -2.31 -2.51 0.20 2.00e-01 2.50e+01 1.00e+00 ... (remaining 678 not shown) Planarity restraints: 739 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 706 " 0.248 2.00e-02 2.50e+03 2.09e-01 5.45e+02 pdb=" C7 NAG A 706 " -0.067 2.00e-02 2.50e+03 pdb=" C8 NAG A 706 " 0.170 2.00e-02 2.50e+03 pdb=" N2 NAG A 706 " -0.351 2.00e-02 2.50e+03 pdb=" O7 NAG A 706 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 106 " -0.009 2.00e-02 2.50e+03 1.69e-02 2.87e+00 pdb=" C GLY A 106 " 0.029 2.00e-02 2.50e+03 pdb=" O GLY A 106 " -0.011 2.00e-02 2.50e+03 pdb=" N MET A 107 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 82 " -0.024 5.00e-02 4.00e+02 3.65e-02 2.13e+00 pdb=" N PRO A 83 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 83 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 83 " -0.021 5.00e-02 4.00e+02 ... (remaining 736 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 1259 2.82 - 3.34: 3885 3.34 - 3.86: 7037 3.86 - 4.38: 8265 4.38 - 4.90: 14400 Nonbonded interactions: 34846 Sorted by model distance: nonbonded pdb=" OD1 ASN A 350 " pdb="NA NA A 701 " model vdw 2.297 3.210 nonbonded pdb=" O ALA A 394 " pdb=" OG1 THR A 397 " model vdw 2.299 3.040 nonbonded pdb=" O SER A 259 " pdb=" OG SER A 259 " model vdw 2.319 3.040 nonbonded pdb=" NH2 ARG A 341 " pdb=" OD1 ASP A 342 " model vdw 2.319 3.120 nonbonded pdb=" O ARG A 442 " pdb=" OG1 THR A 446 " model vdw 2.346 3.040 ... (remaining 34841 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: 1.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 3.980 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:5.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 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 0.052 4461 Z= 0.212 Angle : 0.548 6.532 6091 Z= 0.311 Chirality : 0.043 0.224 681 Planarity : 0.009 0.209 738 Dihedral : 15.806 81.789 1511 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.22 % Allowed : 16.41 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.82 (0.38), residues: 532 helix: 1.99 (0.29), residues: 358 sheet: None (None), residues: 0 loop : -0.41 (0.48), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 216 TYR 0.016 0.001 TYR A 84 PHE 0.010 0.001 PHE A 409 TRP 0.016 0.001 TRP A 553 HIS 0.002 0.000 HIS A 599 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.21 ( 4459) covalent geometry : angle 0.54472 / 0.31 ( 6086) SS BOND : bond 0.00760 / 0.40 ( 1) SS BOND : angle 2.68512 / 1.58 ( 2) hydrogen bonds : bond 0.12253 / 7.50 ( 265) hydrogen bonds : angle 4.30574 / 2.90 ( 771) link_NAG-ASN : bond 0.00941 / 0.50 ( 1) link_NAG-ASN : angle 1.45844 / 0.80 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 45 time to evaluate : 0.130 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 46 average time/residue: 0.4852 time to fit residues: 23.3054 Evaluate side-chains 45 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 44 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 576 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 24 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 0.5980 chunk 50 optimal weight: 0.0980 chunk 19 optimal weight: 0.6980 chunk 30 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.112350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.098276 restraints weight = 4736.657| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 1.01 r_work: 0.2860 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.2759 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8902 moved from start: 0.0614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 4461 Z= 0.112 Angle : 0.458 5.549 6091 Z= 0.247 Chirality : 0.038 0.124 681 Planarity : 0.004 0.034 738 Dihedral : 5.940 50.212 614 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 1.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.77 % Allowed : 15.96 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.12 (0.39), residues: 532 helix: 2.20 (0.29), residues: 362 sheet: None (None), residues: 0 loop : -0.35 (0.49), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 604 TYR 0.017 0.001 TYR A 84 PHE 0.008 0.001 PHE A 409 TRP 0.014 0.001 TRP A 553 HIS 0.001 0.000 HIS A 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.11 ( 4459) covalent geometry : angle 0.45659 / 0.25 ( 6086) SS BOND : bond 0.00093 / 0.05 ( 1) SS BOND : angle 1.35545 / 0.77 ( 2) hydrogen bonds : bond 0.05580 / 3.64 ( 265) hydrogen bonds : angle 3.82703 / 2.56 ( 771) link_NAG-ASN : bond 0.00137 / 0.07 ( 1) link_NAG-ASN : angle 1.36300 / 0.79 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.125 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 50 average time/residue: 0.4803 time to fit residues: 25.1236 Evaluate side-chains 44 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 40 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 541 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 41 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 49 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 17 optimal weight: 0.0040 chunk 14 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 overall best weight: 1.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.108538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.096306 restraints weight = 4637.598| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 0.92 r_work: 0.2806 rms_B_bonded: 1.33 restraints_weight: 0.5000 r_work: 0.2710 rms_B_bonded: 2.31 restraints_weight: 0.2500 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8964 moved from start: 0.0650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4461 Z= 0.150 Angle : 0.525 5.496 6091 Z= 0.283 Chirality : 0.041 0.143 681 Planarity : 0.004 0.034 738 Dihedral : 5.670 45.573 610 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 0.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.00 % Allowed : 15.30 % Favored : 82.71 % 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: 1.84 (0.38), residues: 532 helix: 2.00 (0.28), residues: 364 sheet: None (None), residues: 0 loop : -0.49 (0.49), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 604 TYR 0.019 0.002 TYR A 84 PHE 0.015 0.002 PHE A 409 TRP 0.013 0.001 TRP A 553 HIS 0.002 0.001 HIS A 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.15 ( 4459) covalent geometry : angle 0.52319 / 0.28 ( 6086) SS BOND : bond 0.00216 / 0.11 ( 1) SS BOND : angle 1.47760 / 0.83 ( 2) hydrogen bonds : bond 0.07443 / 4.83 ( 265) hydrogen bonds : angle 4.04214 / 2.70 ( 771) link_NAG-ASN : bond 0.00045 / 0.02 ( 1) link_NAG-ASN : angle 1.47773 / 0.85 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 41 time to evaluate : 0.118 Fit side-chains outliers start: 9 outliers final: 5 residues processed: 47 average time/residue: 0.4625 time to fit residues: 22.7626 Evaluate side-chains 45 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 40 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 541 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 35 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 21 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 18 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.106882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.092021 restraints weight = 4659.029| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 1.06 r_work: 0.2779 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.2675 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8937 moved from start: 0.0731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4461 Z= 0.150 Angle : 0.525 5.769 6091 Z= 0.285 Chirality : 0.041 0.144 681 Planarity : 0.005 0.035 738 Dihedral : 5.662 43.245 610 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 0.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.77 % Allowed : 15.08 % Favored : 83.15 % 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: 1.84 (0.38), residues: 532 helix: 2.01 (0.28), residues: 363 sheet: None (None), residues: 0 loop : -0.52 (0.48), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 604 TYR 0.020 0.002 TYR A 84 PHE 0.014 0.002 PHE A 409 TRP 0.014 0.001 TRP A 553 HIS 0.002 0.001 HIS A 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.15 ( 4459) covalent geometry : angle 0.52389 / 0.28 ( 6086) SS BOND : bond 0.00266 / 0.14 ( 1) SS BOND : angle 1.33581 / 0.76 ( 2) hydrogen bonds : bond 0.07406 / 4.80 ( 265) hydrogen bonds : angle 4.06839 / 2.72 ( 771) link_NAG-ASN : bond 0.00073 / 0.04 ( 1) link_NAG-ASN : angle 1.59872 / 0.92 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.194 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 46 average time/residue: 0.4149 time to fit residues: 20.0398 Evaluate side-chains 46 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 41 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 541 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 27 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 5 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.107530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.093939 restraints weight = 4681.714| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 0.94 r_work: 0.2798 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.2697 rms_B_bonded: 2.55 restraints_weight: 0.2500 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8962 moved from start: 0.0687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4461 Z= 0.141 Angle : 0.510 5.807 6091 Z= 0.276 Chirality : 0.041 0.141 681 Planarity : 0.005 0.035 738 Dihedral : 5.523 40.107 610 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 0.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.00 % Allowed : 15.08 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.90 (0.38), residues: 532 helix: 2.05 (0.28), residues: 363 sheet: None (None), residues: 0 loop : -0.49 (0.48), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 604 TYR 0.019 0.001 TYR A 84 PHE 0.013 0.001 PHE A 409 TRP 0.015 0.001 TRP A 553 HIS 0.002 0.001 HIS A 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.14 ( 4459) covalent geometry : angle 0.50823 / 0.28 ( 6086) SS BOND : bond 0.00253 / 0.13 ( 1) SS BOND : angle 1.27184 / 0.72 ( 2) hydrogen bonds : bond 0.07076 / 4.59 ( 265) hydrogen bonds : angle 4.02578 / 2.69 ( 771) link_NAG-ASN : bond 0.00096 / 0.05 ( 1) link_NAG-ASN : angle 1.54965 / 0.89 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 40 time to evaluate : 0.160 Fit side-chains outliers start: 9 outliers final: 6 residues processed: 46 average time/residue: 0.4762 time to fit residues: 22.9087 Evaluate side-chains 46 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 40 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 541 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 0 optimal weight: 7.9990 chunk 36 optimal weight: 0.9980 chunk 34 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 35 optimal weight: 0.5980 chunk 15 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.108393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.095879 restraints weight = 4765.880| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 0.93 r_work: 0.2806 rms_B_bonded: 1.37 restraints_weight: 0.5000 r_work: 0.2708 rms_B_bonded: 2.38 restraints_weight: 0.2500 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8970 moved from start: 0.0736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4461 Z= 0.144 Angle : 0.515 5.828 6091 Z= 0.279 Chirality : 0.041 0.142 681 Planarity : 0.005 0.035 738 Dihedral : 5.502 38.144 610 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 0.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.55 % Allowed : 15.52 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.87 (0.38), residues: 532 helix: 2.02 (0.28), residues: 364 sheet: None (None), residues: 0 loop : -0.50 (0.48), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 604 TYR 0.019 0.001 TYR A 84 PHE 0.014 0.001 PHE A 409 TRP 0.014 0.001 TRP A 553 HIS 0.002 0.001 HIS A 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 ( 4459) covalent geometry : angle 0.51299 / 0.28 ( 6086) SS BOND : bond 0.00259 / 0.14 ( 1) SS BOND : angle 1.28934 / 0.73 ( 2) hydrogen bonds : bond 0.07194 / 4.67 ( 265) hydrogen bonds : angle 4.03920 / 2.70 ( 771) link_NAG-ASN : bond 0.00133 / 0.07 ( 1) link_NAG-ASN : angle 1.58191 / 0.91 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.103 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 44 average time/residue: 0.4294 time to fit residues: 19.7490 Evaluate side-chains 46 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 40 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 541 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 1 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 0 optimal weight: 0.8980 chunk 37 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.106818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.093950 restraints weight = 4676.827| |-----------------------------------------------------------------------------| r_work (start): 0.2854 rms_B_bonded: 0.86 r_work: 0.2767 rms_B_bonded: 1.34 restraints_weight: 0.5000 r_work: 0.2669 rms_B_bonded: 2.33 restraints_weight: 0.2500 r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9005 moved from start: 0.0901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4461 Z= 0.186 Angle : 0.580 5.932 6091 Z= 0.314 Chirality : 0.044 0.156 681 Planarity : 0.005 0.036 738 Dihedral : 5.843 40.184 610 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 1.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.22 % Allowed : 14.41 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.60 (0.38), residues: 532 helix: 1.82 (0.28), residues: 364 sheet: None (None), residues: 0 loop : -0.60 (0.48), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 604 TYR 0.021 0.002 TYR A 84 PHE 0.018 0.002 PHE A 409 TRP 0.014 0.002 TRP A 553 HIS 0.003 0.001 HIS A 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.19 ( 4459) covalent geometry : angle 0.57863 / 0.31 ( 6086) SS BOND : bond 0.00325 / 0.17 ( 1) SS BOND : angle 1.45852 / 0.82 ( 2) hydrogen bonds : bond 0.08574 / 5.54 ( 265) hydrogen bonds : angle 4.22626 / 2.82 ( 771) link_NAG-ASN : bond 0.00274 / 0.14 ( 1) link_NAG-ASN : angle 1.73706 / 0.99 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 41 time to evaluate : 0.158 Fit side-chains outliers start: 10 outliers final: 6 residues processed: 48 average time/residue: 0.3804 time to fit residues: 19.2248 Evaluate side-chains 47 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 41 time to evaluate : 0.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 541 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 21 optimal weight: 4.9990 chunk 10 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.107581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.094743 restraints weight = 4637.398| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 0.86 r_work: 0.2781 rms_B_bonded: 1.35 restraints_weight: 0.5000 r_work: 0.2682 rms_B_bonded: 2.36 restraints_weight: 0.2500 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8998 moved from start: 0.0841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4461 Z= 0.170 Angle : 0.559 5.985 6091 Z= 0.303 Chirality : 0.043 0.150 681 Planarity : 0.005 0.036 738 Dihedral : 5.760 38.624 610 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 1.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.33 % Allowed : 15.74 % Favored : 82.93 % 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: 1.61 (0.38), residues: 532 helix: 1.84 (0.28), residues: 364 sheet: None (None), residues: 0 loop : -0.63 (0.48), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 604 TYR 0.020 0.002 TYR A 84 PHE 0.017 0.002 PHE A 409 TRP 0.014 0.002 TRP A 553 HIS 0.003 0.001 HIS A 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.17 ( 4459) covalent geometry : angle 0.55700 / 0.30 ( 6086) SS BOND : bond 0.00320 / 0.17 ( 1) SS BOND : angle 1.42270 / 0.80 ( 2) hydrogen bonds : bond 0.08084 / 5.23 ( 265) hydrogen bonds : angle 4.19635 / 2.81 ( 771) link_NAG-ASN : bond 0.00258 / 0.14 ( 1) link_NAG-ASN : angle 1.71038 / 0.98 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 40 time to evaluate : 0.161 Fit side-chains outliers start: 6 outliers final: 6 residues processed: 44 average time/residue: 0.4952 time to fit residues: 22.8218 Evaluate side-chains 46 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 40 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 541 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 42 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.105936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.091366 restraints weight = 4745.607| |-----------------------------------------------------------------------------| r_work (start): 0.2861 rms_B_bonded: 1.05 r_work: 0.2773 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.2669 rms_B_bonded: 2.63 restraints_weight: 0.2500 r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8938 moved from start: 0.0772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4461 Z= 0.154 Angle : 0.535 5.883 6091 Z= 0.290 Chirality : 0.042 0.145 681 Planarity : 0.005 0.036 738 Dihedral : 5.594 35.710 610 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 1.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.77 % Allowed : 15.30 % Favored : 82.93 % 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: 1.71 (0.38), residues: 532 helix: 1.91 (0.28), residues: 364 sheet: None (None), residues: 0 loop : -0.58 (0.48), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 604 TYR 0.019 0.002 TYR A 84 PHE 0.015 0.002 PHE A 409 TRP 0.015 0.001 TRP A 553 HIS 0.002 0.001 HIS A 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 ( 4459) covalent geometry : angle 0.53309 / 0.29 ( 6086) SS BOND : bond 0.00292 / 0.15 ( 1) SS BOND : angle 1.33737 / 0.75 ( 2) hydrogen bonds : bond 0.07563 / 4.90 ( 265) hydrogen bonds : angle 4.13258 / 2.77 ( 771) link_NAG-ASN : bond 0.00219 / 0.12 ( 1) link_NAG-ASN : angle 1.66838 / 0.96 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 40 time to evaluate : 0.167 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 45 average time/residue: 0.4360 time to fit residues: 20.5161 Evaluate side-chains 46 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 40 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 541 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 20 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 chunk 24 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 42 optimal weight: 0.5980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.108328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.095795 restraints weight = 4689.596| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 0.94 r_work: 0.2806 rms_B_bonded: 1.36 restraints_weight: 0.5000 r_work: 0.2707 rms_B_bonded: 2.38 restraints_weight: 0.2500 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8972 moved from start: 0.0727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4461 Z= 0.144 Angle : 0.517 5.838 6091 Z= 0.281 Chirality : 0.041 0.142 681 Planarity : 0.005 0.037 738 Dihedral : 5.436 33.355 610 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 1.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.55 % Allowed : 15.52 % Favored : 82.93 % 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: 1.80 (0.38), residues: 532 helix: 1.98 (0.28), residues: 364 sheet: None (None), residues: 0 loop : -0.54 (0.48), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 604 TYR 0.019 0.001 TYR A 84 PHE 0.014 0.001 PHE A 409 TRP 0.016 0.001 TRP A 553 HIS 0.002 0.001 HIS A 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 ( 4459) covalent geometry : angle 0.51581 / 0.28 ( 6086) SS BOND : bond 0.00271 / 0.14 ( 1) SS BOND : angle 1.29245 / 0.73 ( 2) hydrogen bonds : bond 0.07179 / 4.66 ( 265) hydrogen bonds : angle 4.08345 / 2.73 ( 771) link_NAG-ASN : bond 0.00169 / 0.09 ( 1) link_NAG-ASN : angle 1.58079 / 0.91 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 39 time to evaluate : 0.217 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 44 average time/residue: 0.4886 time to fit residues: 22.5011 Evaluate side-chains 45 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 39 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 541 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 2 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 chunk 39 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.107282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.092767 restraints weight = 4743.262| |-----------------------------------------------------------------------------| r_work (start): 0.2871 rms_B_bonded: 1.05 r_work: 0.2783 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.2680 rms_B_bonded: 2.62 restraints_weight: 0.2500 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8924 moved from start: 0.0730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4461 Z= 0.142 Angle : 0.513 5.753 6091 Z= 0.278 Chirality : 0.041 0.141 681 Planarity : 0.005 0.036 738 Dihedral : 5.380 33.216 610 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 1.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.55 % Allowed : 15.52 % Favored : 82.93 % 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: 1.80 (0.38), residues: 532 helix: 1.97 (0.28), residues: 365 sheet: None (None), residues: 0 loop : -0.56 (0.48), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 604 TYR 0.019 0.001 TYR A 84 PHE 0.013 0.001 PHE A 409 TRP 0.016 0.001 TRP A 553 HIS 0.002 0.001 HIS A 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.14 ( 4459) covalent geometry : angle 0.51186 / 0.28 ( 6086) SS BOND : bond 0.00257 / 0.14 ( 1) SS BOND : angle 1.26985 / 0.72 ( 2) hydrogen bonds : bond 0.07108 / 4.61 ( 265) hydrogen bonds : angle 4.07226 / 2.73 ( 771) link_NAG-ASN : bond 0.00156 / 0.08 ( 1) link_NAG-ASN : angle 1.54824 / 0.89 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1384.70 seconds wall clock time: 24 minutes 21.33 seconds (1461.33 seconds total)