Starting phenix.real_space_refine on Fri Aug 22 14:15:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tej_41188/08_2025/8tej_41188.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tej_41188/08_2025/8tej_41188.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tej_41188/08_2025/8tej_41188.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tej_41188/08_2025/8tej_41188.map" model { file = "/net/cci-nas-00/data/ceres_data/8tej_41188/08_2025/8tej_41188.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tej_41188/08_2025/8tej_41188.cif" } resolution = 2.55 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= 0.002 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 26 5.16 5 C 2555 2.51 5 N 645 2.21 5 O 698 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3925 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 3903 Classifications: {'peptide': 494} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 467} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'TPO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Time building chain proxies: 1.41, per 1000 atoms: 0.36 Number of scatterers: 3925 At special positions: 0 Unit cell: (64.74, 78.02, 93.79, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 26 16.00 P 1 15.00 O 698 8.00 N 645 7.00 C 2555 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.35 Conformation dependent library (CDL) restraints added in 159.2 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 912 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 1 sheets defined 77.9% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'A' and resid 8 through 19 Processing helix chain 'A' and resid 21 through 32 removed outlier: 3.671A pdb=" N ALA A 32 " --> pdb=" O GLY A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 35 No H-bonds generated for 'chain 'A' and resid 33 through 35' Processing helix chain 'A' and resid 36 through 62 Proline residue: A 50 - end of helix Processing helix chain 'A' and resid 67 through 86 Processing helix chain 'A' and resid 96 through 112 removed outlier: 3.633A pdb=" N ALA A 112 " --> pdb=" O ASN A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 142 Processing helix chain 'A' and resid 145 through 151 removed outlier: 4.172A pdb=" N ASN A 149 " --> pdb=" O CYS A 145 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ARG A 150 " --> pdb=" O SER A 146 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE A 151 " --> pdb=" O ILE A 147 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 145 through 151' Processing helix chain 'A' and resid 152 through 178 removed outlier: 3.681A pdb=" N GLY A 156 " --> pdb=" O THR A 152 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N PHE A 159 " --> pdb=" O ALA A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 192 Processing helix chain 'A' and resid 193 through 219 Processing helix chain 'A' and resid 220 through 224 Processing helix chain 'A' and resid 228 through 251 removed outlier: 6.277A pdb=" N VAL A 240 " --> pdb=" O ALA A 236 " (cutoff:3.500A) Proline residue: A 241 - end of helix Processing helix chain 'A' and resid 252 through 257 removed outlier: 4.447A pdb=" N GLY A 256 " --> pdb=" O ILE A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 287 removed outlier: 3.730A pdb=" N LEU A 287 " --> pdb=" O VAL A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 297 Processing helix chain 'A' and resid 297 through 319 removed outlier: 3.540A pdb=" N SER A 313 " --> pdb=" O TYR A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 325 Processing helix chain 'A' and resid 331 through 350 Processing helix chain 'A' and resid 359 through 391 removed outlier: 3.706A pdb=" N LYS A 389 " --> pdb=" O ARG A 385 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N THR A 390 " --> pdb=" O ARG A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 409 Processing helix chain 'A' and resid 424 through 431 removed outlier: 3.524A pdb=" N THR A 431 " --> pdb=" O THR A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 453 removed outlier: 4.379A pdb=" N ASP A 453 " --> pdb=" O GLU A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 456 No H-bonds generated for 'chain 'A' and resid 454 through 456' Processing helix chain 'A' and resid 464 through 477 Processing helix chain 'A' and resid 480 through 485 Processing helix chain 'A' and resid 488 through 503 removed outlier: 3.721A pdb=" N LEU A 492 " --> pdb=" O PRO A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 516 Processing sheet with id=AA1, first strand: chain 'A' and resid 93 through 94 259 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: 0.66 Time building geometry restraints manager: 0.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1209 1.34 - 1.46: 574 1.46 - 1.57: 2168 1.57 - 1.69: 3 1.69 - 1.81: 45 Bond restraints: 3999 Sorted by residual: bond pdb=" OG1 TPO A 410 " pdb=" P TPO A 410 " ideal model delta sigma weight residual 1.717 1.609 0.108 2.00e-02 2.50e+03 2.91e+01 bond pdb=" O3P TPO A 410 " pdb=" P TPO A 410 " ideal model delta sigma weight residual 1.528 1.609 -0.081 2.00e-02 2.50e+03 1.64e+01 bond pdb=" O2P TPO A 410 " pdb=" P TPO A 410 " ideal model delta sigma weight residual 1.528 1.607 -0.079 2.00e-02 2.50e+03 1.57e+01 bond pdb=" O1P TPO A 410 " pdb=" P TPO A 410 " ideal model delta sigma weight residual 1.525 1.479 0.046 2.00e-02 2.50e+03 5.35e+00 bond pdb=" N TPO A 410 " pdb=" CA TPO A 410 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.83e+00 ... (remaining 3994 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.30: 5374 2.30 - 4.60: 47 4.60 - 6.90: 3 6.90 - 9.20: 0 9.20 - 11.50: 2 Bond angle restraints: 5426 Sorted by residual: angle pdb=" CB TPO A 410 " pdb=" OG1 TPO A 410 " pdb=" P TPO A 410 " ideal model delta sigma weight residual 119.31 107.81 11.50 3.00e+00 1.11e-01 1.47e+01 angle pdb=" OG1 TPO A 410 " pdb=" P TPO A 410 " pdb=" O1P TPO A 410 " ideal model delta sigma weight residual 100.43 110.03 -9.60 3.00e+00 1.11e-01 1.02e+01 angle pdb=" C PRO A 7 " pdb=" N PHE A 8 " pdb=" CA PHE A 8 " ideal model delta sigma weight residual 121.54 125.90 -4.36 1.91e+00 2.74e-01 5.21e+00 angle pdb=" N GLY A 395 " pdb=" CA GLY A 395 " pdb=" C GLY A 395 " ideal model delta sigma weight residual 113.18 108.47 4.71 2.37e+00 1.78e-01 3.95e+00 angle pdb=" O1P TPO A 410 " pdb=" P TPO A 410 " pdb=" O3P TPO A 410 " ideal model delta sigma weight residual 115.11 109.22 5.89 3.00e+00 1.11e-01 3.85e+00 ... (remaining 5421 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.02: 1995 16.02 - 32.04: 245 32.04 - 48.06: 82 48.06 - 64.08: 36 64.08 - 80.10: 7 Dihedral angle restraints: 2365 sinusoidal: 946 harmonic: 1419 Sorted by residual: dihedral pdb=" CA ILE A 291 " pdb=" C ILE A 291 " pdb=" N VAL A 292 " pdb=" CA VAL A 292 " ideal model delta harmonic sigma weight residual 180.00 155.83 24.17 0 5.00e+00 4.00e-02 2.34e+01 dihedral pdb=" CA GLY A 395 " pdb=" C GLY A 395 " pdb=" N GLN A 396 " pdb=" CA GLN A 396 " ideal model delta harmonic sigma weight residual 180.00 161.07 18.93 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CA ILE A 295 " pdb=" CB ILE A 295 " pdb=" CG1 ILE A 295 " pdb=" CD1 ILE A 295 " ideal model delta sinusoidal sigma weight residual 60.00 119.76 -59.76 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 2362 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 396 0.026 - 0.052: 128 0.052 - 0.079: 62 0.079 - 0.105: 19 0.105 - 0.131: 11 Chirality restraints: 616 Sorted by residual: chirality pdb=" CA ILE A 181 " pdb=" N ILE A 181 " pdb=" C ILE A 181 " pdb=" CB ILE A 181 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.30e-01 chirality pdb=" CA VAL A 289 " pdb=" N VAL A 289 " pdb=" C VAL A 289 " pdb=" CB VAL A 289 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.13e-01 chirality pdb=" CA ILE A 92 " pdb=" N ILE A 92 " pdb=" C ILE A 92 " pdb=" CB ILE A 92 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.12e-01 ... (remaining 613 not shown) Planarity restraints: 674 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TRP A 247 " 0.005 2.00e-02 2.50e+03 9.47e-03 8.96e-01 pdb=" C TRP A 247 " -0.016 2.00e-02 2.50e+03 pdb=" O TRP A 247 " 0.006 2.00e-02 2.50e+03 pdb=" N THR A 248 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 258 " -0.015 5.00e-02 4.00e+02 2.22e-02 7.86e-01 pdb=" N PRO A 259 " 0.038 5.00e-02 4.00e+02 pdb=" CA PRO A 259 " -0.011 5.00e-02 4.00e+02 pdb=" CD PRO A 259 " -0.012 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 361 " -0.014 5.00e-02 4.00e+02 2.14e-02 7.30e-01 pdb=" N PRO A 362 " 0.037 5.00e-02 4.00e+02 pdb=" CA PRO A 362 " -0.011 5.00e-02 4.00e+02 pdb=" CD PRO A 362 " -0.012 5.00e-02 4.00e+02 ... (remaining 671 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 25 2.57 - 3.15: 3166 3.15 - 3.73: 6231 3.73 - 4.32: 8524 4.32 - 4.90: 14206 Nonbonded interactions: 32152 Sorted by model distance: nonbonded pdb=" OH TYR A 405 " pdb=" OE2 GLU A 459 " model vdw 1.984 3.040 nonbonded pdb=" OD2 ASP A 335 " pdb=" O HOH A 801 " model vdw 2.033 3.040 nonbonded pdb=" OH TYR A 22 " pdb=" O ILE A 84 " model vdw 2.042 3.040 nonbonded pdb=" O GLY A 261 " pdb=" O HOH A 802 " model vdw 2.085 3.040 nonbonded pdb=" O LYS A 424 " pdb=" OG1 THR A 427 " model vdw 2.171 3.040 ... (remaining 32147 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: 3.830 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: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.490 Find NCS groups from input model: 0.020 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:7.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 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 0.108 3999 Z= 0.188 Angle : 0.572 11.496 5426 Z= 0.276 Chirality : 0.036 0.131 616 Planarity : 0.003 0.027 674 Dihedral : 17.726 80.101 1453 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.87 % Allowed : 20.57 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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 aren not related in a simple way. whole: 2.14 (0.38), residues: 485 helix: 2.11 (0.28), residues: 336 sheet: None (None), residues: 0 loop : -0.15 (0.51), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 232 TYR 0.011 0.001 TYR A 495 PHE 0.006 0.001 PHE A 107 TRP 0.006 0.001 TRP A 247 HIS 0.003 0.001 HIS A 312 Details of bonding type rmsd covalent geometry : bond 0.00394 ( 3999) covalent geometry : angle 0.57239 ( 5426) hydrogen bonds : bond 0.11922 ( 259) hydrogen bonds : angle 5.03880 ( 753) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 44 time to evaluate : 0.166 Fit side-chains outliers start: 12 outliers final: 10 residues processed: 55 average time/residue: 0.5920 time to fit residues: 33.6188 Evaluate side-chains 54 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 44 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 230 TRP Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 490 SER Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 504 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 24 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 26 optimal weight: 0.0770 chunk 2 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 22 optimal weight: 0.4980 overall best weight: 0.5138 ------------------------------------------------------------------------------- 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 = 0.3690 r_free = 0.3690 target = 0.148889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.118704 restraints weight = 4364.831| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 1.54 r_work: 0.3164 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.0713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 3999 Z= 0.118 Angle : 0.483 5.517 5426 Z= 0.247 Chirality : 0.038 0.164 616 Planarity : 0.004 0.031 674 Dihedral : 6.020 41.204 547 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 1.91 % Allowed : 18.66 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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 aren not related in a simple way. whole: 2.31 (0.37), residues: 485 helix: 2.21 (0.27), residues: 339 sheet: None (None), residues: 0 loop : -0.06 (0.50), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 232 TYR 0.011 0.001 TYR A 495 PHE 0.008 0.001 PHE A 509 TRP 0.009 0.001 TRP A 131 HIS 0.002 0.001 HIS A 312 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 3999) covalent geometry : angle 0.48319 ( 5426) hydrogen bonds : bond 0.04575 ( 259) hydrogen bonds : angle 4.38391 ( 753) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 50 time to evaluate : 0.185 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 55 average time/residue: 0.5660 time to fit residues: 32.1436 Evaluate side-chains 48 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 44 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 504 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 7 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 3 optimal weight: 0.1980 chunk 15 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3676 r_free = 0.3676 target = 0.147953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.117833 restraints weight = 4295.841| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 1.54 r_work: 0.3170 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.0926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3999 Z= 0.116 Angle : 0.477 5.542 5426 Z= 0.241 Chirality : 0.038 0.159 616 Planarity : 0.004 0.032 674 Dihedral : 5.148 35.439 538 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.35 % Allowed : 17.94 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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 aren not related in a simple way. whole: 2.37 (0.37), residues: 485 helix: 2.25 (0.27), residues: 338 sheet: None (None), residues: 0 loop : -0.02 (0.50), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 232 TYR 0.011 0.001 TYR A 495 PHE 0.007 0.001 PHE A 509 TRP 0.008 0.001 TRP A 230 HIS 0.003 0.001 HIS A 312 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 3999) covalent geometry : angle 0.47716 ( 5426) hydrogen bonds : bond 0.04569 ( 259) hydrogen bonds : angle 4.27936 ( 753) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 47 time to evaluate : 0.155 Fit side-chains REVERT: A 35 ARG cc_start: 0.7399 (mtt180) cc_final: 0.6643 (mpp-170) REVERT: A 219 ARG cc_start: 0.8688 (OUTLIER) cc_final: 0.8422 (mmm160) REVERT: A 295 ILE cc_start: 0.8583 (OUTLIER) cc_final: 0.8074 (mp) outliers start: 14 outliers final: 6 residues processed: 59 average time/residue: 0.5586 time to fit residues: 33.9231 Evaluate side-chains 54 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 ARG Chi-restraints excluded: chain A residue 230 TRP Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 504 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 31 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 45 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 48 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.3651 r_free = 0.3651 target = 0.145840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.115518 restraints weight = 4308.003| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 1.53 r_work: 0.3171 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.0941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3999 Z= 0.147 Angle : 0.529 5.912 5426 Z= 0.268 Chirality : 0.040 0.168 616 Planarity : 0.004 0.033 674 Dihedral : 5.318 38.423 538 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 3.59 % Allowed : 19.14 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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 aren not related in a simple way. whole: 2.04 (0.37), residues: 485 helix: 2.01 (0.27), residues: 339 sheet: None (None), residues: 0 loop : -0.15 (0.49), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 232 TYR 0.014 0.002 TYR A 495 PHE 0.010 0.001 PHE A 509 TRP 0.008 0.001 TRP A 230 HIS 0.003 0.001 HIS A 312 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 3999) covalent geometry : angle 0.52882 ( 5426) hydrogen bonds : bond 0.05159 ( 259) hydrogen bonds : angle 4.40645 ( 753) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 46 time to evaluate : 0.157 Fit side-chains REVERT: A 219 ARG cc_start: 0.8718 (OUTLIER) cc_final: 0.8455 (mmm160) REVERT: A 295 ILE cc_start: 0.8630 (OUTLIER) cc_final: 0.8103 (mp) REVERT: A 463 GLN cc_start: 0.8962 (OUTLIER) cc_final: 0.7454 (pp30) outliers start: 15 outliers final: 7 residues processed: 58 average time/residue: 0.5692 time to fit residues: 34.0471 Evaluate side-chains 54 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 44 time to evaluate : 0.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 ARG Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 230 TRP Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 502 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 1 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 chunk 28 optimal weight: 0.2980 chunk 13 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 31 optimal weight: 0.0970 chunk 8 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- 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 = 0.3696 r_free = 0.3696 target = 0.149561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.119363 restraints weight = 4285.213| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 1.53 r_work: 0.3177 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.1130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3999 Z= 0.109 Angle : 0.473 6.749 5426 Z= 0.238 Chirality : 0.037 0.156 616 Planarity : 0.004 0.031 674 Dihedral : 4.666 33.997 536 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 3.35 % Allowed : 20.57 % Favored : 76.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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 aren not related in a simple way. whole: 2.30 (0.37), residues: 485 helix: 2.19 (0.27), residues: 339 sheet: None (None), residues: 0 loop : -0.03 (0.50), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 232 TYR 0.011 0.001 TYR A 495 PHE 0.006 0.001 PHE A 509 TRP 0.008 0.001 TRP A 247 HIS 0.002 0.001 HIS A 312 Details of bonding type rmsd covalent geometry : bond 0.00223 ( 3999) covalent geometry : angle 0.47270 ( 5426) hydrogen bonds : bond 0.04337 ( 259) hydrogen bonds : angle 4.22173 ( 753) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 48 time to evaluate : 0.162 Fit side-chains REVERT: A 16 LYS cc_start: 0.7300 (mtpp) cc_final: 0.6864 (pttp) REVERT: A 35 ARG cc_start: 0.7381 (OUTLIER) cc_final: 0.6624 (mpp-170) REVERT: A 219 ARG cc_start: 0.8666 (OUTLIER) cc_final: 0.8417 (mmm160) REVERT: A 295 ILE cc_start: 0.8553 (OUTLIER) cc_final: 0.8058 (mp) outliers start: 14 outliers final: 5 residues processed: 59 average time/residue: 0.5063 time to fit residues: 30.8941 Evaluate side-chains 56 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 48 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ARG Chi-restraints excluded: chain A residue 219 ARG Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 230 TRP Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 504 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 29 optimal weight: 0.6980 chunk 16 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 18 optimal weight: 10.0000 chunk 9 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 = 0.3656 r_free = 0.3656 target = 0.146383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.115924 restraints weight = 4365.690| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 1.54 r_work: 0.3146 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.1077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3999 Z= 0.138 Angle : 0.518 6.911 5426 Z= 0.260 Chirality : 0.039 0.162 616 Planarity : 0.004 0.031 674 Dihedral : 4.769 36.132 535 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 3.35 % Allowed : 19.86 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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 aren not related in a simple way. whole: 2.13 (0.37), residues: 485 helix: 2.09 (0.28), residues: 333 sheet: None (None), residues: 0 loop : -0.07 (0.49), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 232 TYR 0.013 0.002 TYR A 495 PHE 0.008 0.001 PHE A 509 TRP 0.008 0.001 TRP A 230 HIS 0.003 0.001 HIS A 312 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 3999) covalent geometry : angle 0.51771 ( 5426) hydrogen bonds : bond 0.04929 ( 259) hydrogen bonds : angle 4.31642 ( 753) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 46 time to evaluate : 0.155 Fit side-chains REVERT: A 219 ARG cc_start: 0.8690 (OUTLIER) cc_final: 0.8420 (mmm160) REVERT: A 295 ILE cc_start: 0.8601 (OUTLIER) cc_final: 0.8086 (mp) REVERT: A 448 ILE cc_start: 0.5966 (OUTLIER) cc_final: 0.5518 (mt) REVERT: A 463 GLN cc_start: 0.8952 (OUTLIER) cc_final: 0.7568 (pp30) outliers start: 14 outliers final: 6 residues processed: 56 average time/residue: 0.5472 time to fit residues: 31.6496 Evaluate side-chains 55 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 45 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 ARG Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 230 TRP Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain A residue 504 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 30 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.3677 r_free = 0.3677 target = 0.148116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.117692 restraints weight = 4408.867| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 1.55 r_work: 0.3205 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.1146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3999 Z= 0.129 Angle : 0.503 6.745 5426 Z= 0.253 Chirality : 0.039 0.159 616 Planarity : 0.004 0.032 674 Dihedral : 4.701 35.652 535 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 3.35 % Allowed : 19.86 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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 aren not related in a simple way. whole: 2.17 (0.37), residues: 485 helix: 2.11 (0.28), residues: 333 sheet: None (None), residues: 0 loop : -0.03 (0.49), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 232 TYR 0.012 0.001 TYR A 495 PHE 0.007 0.001 PHE A 509 TRP 0.008 0.001 TRP A 230 HIS 0.003 0.001 HIS A 312 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 3999) covalent geometry : angle 0.50303 ( 5426) hydrogen bonds : bond 0.04744 ( 259) hydrogen bonds : angle 4.28022 ( 753) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 46 time to evaluate : 0.090 Fit side-chains REVERT: A 16 LYS cc_start: 0.7363 (mtpp) cc_final: 0.6917 (pttp) REVERT: A 115 GLU cc_start: 0.6682 (OUTLIER) cc_final: 0.5689 (mp0) REVERT: A 219 ARG cc_start: 0.8707 (OUTLIER) cc_final: 0.8452 (mmm160) REVERT: A 295 ILE cc_start: 0.8601 (OUTLIER) cc_final: 0.8095 (mp) REVERT: A 463 GLN cc_start: 0.8952 (OUTLIER) cc_final: 0.7513 (pp30) outliers start: 14 outliers final: 6 residues processed: 56 average time/residue: 0.5187 time to fit residues: 29.8990 Evaluate side-chains 55 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 45 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 219 ARG Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 230 TRP Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain A residue 504 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 1 optimal weight: 0.9980 chunk 42 optimal weight: 8.9990 chunk 34 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3681 r_free = 0.3681 target = 0.148482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.118169 restraints weight = 4330.026| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 1.54 r_work: 0.3191 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.1164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3999 Z= 0.128 Angle : 0.504 6.810 5426 Z= 0.253 Chirality : 0.039 0.161 616 Planarity : 0.004 0.032 674 Dihedral : 4.723 35.548 535 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.87 % Allowed : 20.81 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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 aren not related in a simple way. whole: 2.18 (0.37), residues: 485 helix: 2.12 (0.28), residues: 333 sheet: None (None), residues: 0 loop : -0.03 (0.49), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 232 TYR 0.013 0.001 TYR A 495 PHE 0.008 0.001 PHE A 509 TRP 0.008 0.001 TRP A 230 HIS 0.003 0.001 HIS A 312 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 3999) covalent geometry : angle 0.50435 ( 5426) hydrogen bonds : bond 0.04752 ( 259) hydrogen bonds : angle 4.28803 ( 753) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 45 time to evaluate : 0.129 Fit side-chains REVERT: A 16 LYS cc_start: 0.7393 (mtpp) cc_final: 0.6993 (pttp) REVERT: A 35 ARG cc_start: 0.7498 (OUTLIER) cc_final: 0.7279 (mmt180) REVERT: A 219 ARG cc_start: 0.8709 (OUTLIER) cc_final: 0.8451 (mmm160) REVERT: A 295 ILE cc_start: 0.8582 (OUTLIER) cc_final: 0.8078 (mp) REVERT: A 463 GLN cc_start: 0.8958 (OUTLIER) cc_final: 0.7536 (pp30) outliers start: 12 outliers final: 5 residues processed: 54 average time/residue: 0.5910 time to fit residues: 32.8237 Evaluate side-chains 54 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 45 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ARG Chi-restraints excluded: chain A residue 219 ARG Chi-restraints excluded: chain A residue 230 TRP Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain A residue 504 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 9 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 25 optimal weight: 0.0000 chunk 47 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 11 optimal weight: 0.0270 chunk 21 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 overall best weight: 0.4642 ------------------------------------------------------------------------------- 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 = 0.3704 r_free = 0.3704 target = 0.150489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.120336 restraints weight = 4396.674| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 1.55 r_work: 0.3192 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.1339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3999 Z= 0.104 Angle : 0.458 6.043 5426 Z= 0.230 Chirality : 0.037 0.154 616 Planarity : 0.004 0.031 674 Dihedral : 4.456 31.147 535 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.39 % Allowed : 21.05 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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 aren not related in a simple way. whole: 2.47 (0.38), residues: 485 helix: 2.34 (0.28), residues: 332 sheet: None (None), residues: 0 loop : 0.10 (0.50), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 232 TYR 0.011 0.001 TYR A 495 PHE 0.005 0.001 PHE A 498 TRP 0.009 0.001 TRP A 131 HIS 0.002 0.001 HIS A 312 Details of bonding type rmsd covalent geometry : bond 0.00209 ( 3999) covalent geometry : angle 0.45784 ( 5426) hydrogen bonds : bond 0.04134 ( 259) hydrogen bonds : angle 4.12567 ( 753) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 49 time to evaluate : 0.147 Fit side-chains REVERT: A 16 LYS cc_start: 0.7375 (mtpp) cc_final: 0.6966 (pttp) REVERT: A 35 ARG cc_start: 0.7375 (OUTLIER) cc_final: 0.6565 (mpp-170) REVERT: A 113 ARG cc_start: 0.7932 (mmm160) cc_final: 0.7582 (mmt90) REVERT: A 219 ARG cc_start: 0.8673 (OUTLIER) cc_final: 0.8426 (mmm160) REVERT: A 295 ILE cc_start: 0.8574 (OUTLIER) cc_final: 0.8080 (mp) REVERT: A 394 LEU cc_start: 0.6733 (OUTLIER) cc_final: 0.6492 (tm) REVERT: A 396 GLN cc_start: 0.6777 (tt0) cc_final: 0.6533 (tt0) REVERT: A 463 GLN cc_start: 0.8932 (OUTLIER) cc_final: 0.7432 (pp30) outliers start: 10 outliers final: 3 residues processed: 57 average time/residue: 0.5818 time to fit residues: 34.1483 Evaluate side-chains 54 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ARG Chi-restraints excluded: chain A residue 219 ARG Chi-restraints excluded: chain A residue 230 TRP Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 504 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 42 optimal weight: 0.5980 chunk 12 optimal weight: 0.7980 chunk 48 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 3 optimal weight: 0.5980 chunk 45 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.149644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.119559 restraints weight = 4332.366| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 1.53 r_work: 0.3166 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3999 Z= 0.117 Angle : 0.487 6.556 5426 Z= 0.244 Chirality : 0.038 0.157 616 Planarity : 0.004 0.031 674 Dihedral : 4.538 30.664 535 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.15 % Allowed : 22.01 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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 aren not related in a simple way. whole: 2.38 (0.38), residues: 485 helix: 2.26 (0.28), residues: 333 sheet: None (None), residues: 0 loop : 0.08 (0.50), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 232 TYR 0.012 0.001 TYR A 495 PHE 0.006 0.001 PHE A 509 TRP 0.008 0.001 TRP A 230 HIS 0.003 0.001 HIS A 312 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 3999) covalent geometry : angle 0.48717 ( 5426) hydrogen bonds : bond 0.04471 ( 259) hydrogen bonds : angle 4.18795 ( 753) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 0.094 Fit side-chains REVERT: A 16 LYS cc_start: 0.7419 (mtpp) cc_final: 0.6979 (pttp) REVERT: A 35 ARG cc_start: 0.7413 (OUTLIER) cc_final: 0.6655 (mpp-170) REVERT: A 113 ARG cc_start: 0.7912 (mmm160) cc_final: 0.7625 (mmt90) REVERT: A 219 ARG cc_start: 0.8695 (OUTLIER) cc_final: 0.8442 (mmm160) REVERT: A 295 ILE cc_start: 0.8555 (OUTLIER) cc_final: 0.8063 (mp) REVERT: A 463 GLN cc_start: 0.8956 (OUTLIER) cc_final: 0.7515 (pp30) outliers start: 9 outliers final: 3 residues processed: 55 average time/residue: 0.6340 time to fit residues: 35.7891 Evaluate side-chains 53 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 46 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ARG Chi-restraints excluded: chain A residue 219 ARG Chi-restraints excluded: chain A residue 230 TRP Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 504 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 31 optimal weight: 0.5980 chunk 13 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 21 optimal weight: 0.1980 chunk 26 optimal weight: 1.9990 chunk 42 optimal weight: 0.0040 chunk 0 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 overall best weight: 0.4792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.150679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.120547 restraints weight = 4343.321| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 1.54 r_work: 0.3192 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3999 Z= 0.106 Angle : 0.473 6.177 5426 Z= 0.235 Chirality : 0.037 0.154 616 Planarity : 0.004 0.031 674 Dihedral : 4.062 27.962 533 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.91 % Allowed : 21.77 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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 aren not related in a simple way. whole: 2.48 (0.38), residues: 485 helix: 2.34 (0.28), residues: 333 sheet: None (None), residues: 0 loop : 0.11 (0.50), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 232 TYR 0.011 0.001 TYR A 495 PHE 0.008 0.001 PHE A 159 TRP 0.009 0.001 TRP A 131 HIS 0.002 0.001 HIS A 312 Details of bonding type rmsd covalent geometry : bond 0.00213 ( 3999) covalent geometry : angle 0.47345 ( 5426) hydrogen bonds : bond 0.04178 ( 259) hydrogen bonds : angle 4.11904 ( 753) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1485.41 seconds wall clock time: 26 minutes 10.14 seconds (1570.14 seconds total)