Starting phenix.real_space_refine on Fri May 9 19:11:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qta_18647/05_2025/8qta_18647.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qta_18647/05_2025/8qta_18647.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8qta_18647/05_2025/8qta_18647.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qta_18647/05_2025/8qta_18647.map" model { file = "/net/cci-nas-00/data/ceres_data/8qta_18647/05_2025/8qta_18647.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qta_18647/05_2025/8qta_18647.cif" } resolution = 2.64 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.099 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 Fe 2 7.16 5 P 5 5.49 5 S 11 5.16 5 C 2276 2.51 5 N 555 2.21 5 O 623 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 3472 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3258 Classifications: {'peptide': 399} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 385} Chain: "A" Number of atoms: 214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 214 Unusual residues: {'FAD': 1, 'HEM': 2, 'NDP': 1} Classifications: {'undetermined': 4, 'water': 27} Link IDs: {None: 30} Time building chain proxies: 2.96, per 1000 atoms: 0.85 Number of scatterers: 3472 At special positions: 0 Unit cell: (57.9384, 65.7378, 94.707, 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) Fe 2 26.01 S 11 16.00 P 5 15.00 O 623 8.00 N 555 7.00 C 2276 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.01 Conformation dependent library (CDL) restraints added in 369.1 milliseconds 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 740 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 2 sheets defined 53.1% alpha, 17.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 4 through 6 No H-bonds generated for 'chain 'A' and resid 4 through 6' Processing helix chain 'A' and resid 7 through 29 Processing helix chain 'A' and resid 32 through 48 Processing helix chain 'A' and resid 52 through 59 removed outlier: 3.587A pdb=" N GLU A 56 " --> pdb=" O LEU A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 88 Processing helix chain 'A' and resid 94 through 116 removed outlier: 3.690A pdb=" N GLY A 100 " --> pdb=" O ALA A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 130 Processing helix chain 'A' and resid 131 through 147 Processing helix chain 'A' and resid 155 through 178 Processing helix chain 'A' and resid 178 through 183 Processing helix chain 'A' and resid 255 through 263 removed outlier: 3.611A pdb=" N LEU A 263 " --> pdb=" O ILE A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 306 removed outlier: 3.780A pdb=" N TYR A 302 " --> pdb=" O PRO A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 325 removed outlier: 3.728A pdb=" N ALA A 325 " --> pdb=" O ASP A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 338 Processing helix chain 'A' and resid 372 through 387 removed outlier: 3.673A pdb=" N GLN A 386 " --> pdb=" O GLN A 382 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 233 through 236 removed outlier: 3.792A pdb=" N LYS A 268 " --> pdb=" O PHE A 224 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N TYR A 186 " --> pdb=" O PRO A 210 " (cutoff:3.500A) removed outlier: 8.472A pdb=" N GLY A 188 " --> pdb=" O SER A 208 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N SER A 208 " --> pdb=" O GLY A 188 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N ILE A 190 " --> pdb=" O HIS A 206 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N HIS A 206 " --> pdb=" O ILE A 190 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N HIS A 192 " --> pdb=" O GLN A 204 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N THR A 200 " --> pdb=" O LEU A 196 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N GLN A 243 " --> pdb=" O LEU A 207 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 341 through 347 removed outlier: 6.879A pdb=" N ASN A 286 " --> pdb=" O THR A 366 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N TYR A 368 " --> pdb=" O ASN A 286 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N VAL A 288 " --> pdb=" O TYR A 368 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N CYS A 370 " --> pdb=" O VAL A 288 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N ILE A 290 " --> pdb=" O CYS A 370 " (cutoff:3.500A) 187 hydrogen bonds defined for protein. 549 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: 0.95 Time building geometry restraints manager: 1.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.38: 1304 1.38 - 1.56: 2222 1.56 - 1.74: 8 1.74 - 1.93: 22 1.93 - 2.11: 7 Bond restraints: 3563 Sorted by residual: bond pdb=" O2B NDP A 501 " pdb=" P2B NDP A 501 " ideal model delta sigma weight residual 1.833 1.624 0.209 3.80e-02 6.93e+02 3.02e+01 bond pdb=" O5D NDP A 501 " pdb=" PN NDP A 501 " ideal model delta sigma weight residual 1.757 1.600 0.157 3.50e-02 8.16e+02 2.02e+01 bond pdb=" C3C HEM A 503 " pdb=" CAC HEM A 503 " ideal model delta sigma weight residual 1.544 1.467 0.077 2.00e-02 2.50e+03 1.50e+01 bond pdb=" C3B HEM A 503 " pdb=" CAB HEM A 503 " ideal model delta sigma weight residual 1.544 1.467 0.077 2.00e-02 2.50e+03 1.48e+01 bond pdb=" O5B FAD A 502 " pdb=" PA FAD A 502 " ideal model delta sigma weight residual 1.634 1.560 0.074 2.00e-02 2.50e+03 1.36e+01 ... (remaining 3558 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.67: 4831 4.67 - 9.33: 37 9.33 - 14.00: 1 14.00 - 18.67: 2 18.67 - 23.34: 1 Bond angle restraints: 4872 Sorted by residual: angle pdb=" PA NDP A 501 " pdb=" O3 NDP A 501 " pdb=" PN NDP A 501 " ideal model delta sigma weight residual 107.74 131.08 -23.34 1.95e+00 2.62e-01 1.43e+02 angle pdb=" C5B NDP A 501 " pdb=" O5B NDP A 501 " pdb=" PA NDP A 501 " ideal model delta sigma weight residual 103.84 118.26 -14.42 1.91e+00 2.73e-01 5.67e+01 angle pdb=" C5D NDP A 501 " pdb=" O5D NDP A 501 " pdb=" PN NDP A 501 " ideal model delta sigma weight residual 104.93 121.79 -16.86 2.66e+00 1.41e-01 4.02e+01 angle pdb=" N ASP A 254 " pdb=" CA ASP A 254 " pdb=" CB ASP A 254 " ideal model delta sigma weight residual 110.33 102.70 7.63 1.50e+00 4.44e-01 2.59e+01 angle pdb=" O2N NDP A 501 " pdb=" PN NDP A 501 " pdb=" O5D NDP A 501 " ideal model delta sigma weight residual 100.52 109.84 -9.32 1.91e+00 2.74e-01 2.38e+01 ... (remaining 4867 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.91: 1709 19.91 - 39.83: 211 39.83 - 59.74: 69 59.74 - 79.65: 14 79.65 - 99.56: 7 Dihedral angle restraints: 2010 sinusoidal: 848 harmonic: 1162 Sorted by residual: dihedral pdb=" C5B NDP A 501 " pdb=" O5B NDP A 501 " pdb=" PA NDP A 501 " pdb=" O3 NDP A 501 " ideal model delta sinusoidal sigma weight residual 175.04 75.48 99.56 1 3.00e+01 1.11e-03 1.24e+01 dihedral pdb=" C2D HEM A 503 " pdb=" C3D HEM A 503 " pdb=" CAD HEM A 503 " pdb=" CBD HEM A 503 " ideal model delta sinusoidal sigma weight residual -180.00 -99.38 -80.62 2 2.00e+01 2.50e-03 1.17e+01 dihedral pdb=" C1A HEM A 504 " pdb=" C2A HEM A 504 " pdb=" CAA HEM A 504 " pdb=" CBA HEM A 504 " ideal model delta sinusoidal sigma weight residual 180.00 101.87 78.13 2 2.00e+01 2.50e-03 1.15e+01 ... (remaining 2007 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 390 0.045 - 0.090: 83 0.090 - 0.134: 29 0.134 - 0.179: 4 0.179 - 0.224: 3 Chirality restraints: 509 Sorted by residual: chirality pdb=" C4D NDP A 501 " pdb=" C3D NDP A 501 " pdb=" C5D NDP A 501 " pdb=" O4D NDP A 501 " both_signs ideal model delta sigma weight residual False -2.71 -2.49 -0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" C3B NDP A 501 " pdb=" C2B NDP A 501 " pdb=" C4B NDP A 501 " pdb=" O3B NDP A 501 " both_signs ideal model delta sigma weight residual False -2.75 -2.54 -0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" C2D NDP A 501 " pdb=" C1D NDP A 501 " pdb=" C3D NDP A 501 " pdb=" O2D NDP A 501 " both_signs ideal model delta sigma weight residual False -2.71 -2.52 -0.19 2.00e-01 2.50e+01 8.59e-01 ... (remaining 506 not shown) Planarity restraints: 580 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2N NDP A 501 " -0.106 2.00e-02 2.50e+03 6.76e-02 5.71e+01 pdb=" C3N NDP A 501 " -0.025 2.00e-02 2.50e+03 pdb=" C4N NDP A 501 " -0.013 2.00e-02 2.50e+03 pdb=" C7N NDP A 501 " 0.061 2.00e-02 2.50e+03 pdb=" N1N NDP A 501 " 0.084 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C HEM A 503 " 0.003 2.00e-02 2.50e+03 1.58e-02 5.61e+00 pdb=" C2C HEM A 503 " -0.005 2.00e-02 2.50e+03 pdb=" C3C HEM A 503 " -0.002 2.00e-02 2.50e+03 pdb=" C4C HEM A 503 " -0.010 2.00e-02 2.50e+03 pdb=" CAC HEM A 503 " -0.002 2.00e-02 2.50e+03 pdb=" CHC HEM A 503 " 0.019 2.00e-02 2.50e+03 pdb=" CHD HEM A 503 " 0.027 2.00e-02 2.50e+03 pdb=" CMC HEM A 503 " 0.003 2.00e-02 2.50e+03 pdb=" NC HEM A 503 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1A HEM A 503 " 0.006 2.00e-02 2.50e+03 1.44e-02 4.64e+00 pdb=" C2A HEM A 503 " 0.004 2.00e-02 2.50e+03 pdb=" C3A HEM A 503 " 0.001 2.00e-02 2.50e+03 pdb=" C4A HEM A 503 " 0.001 2.00e-02 2.50e+03 pdb=" CAA HEM A 503 " 0.000 2.00e-02 2.50e+03 pdb=" CHA HEM A 503 " -0.023 2.00e-02 2.50e+03 pdb=" CHB HEM A 503 " -0.019 2.00e-02 2.50e+03 pdb=" CMA HEM A 503 " -0.000 2.00e-02 2.50e+03 pdb=" NA HEM A 503 " 0.030 2.00e-02 2.50e+03 ... (remaining 577 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 110 2.70 - 3.25: 3175 3.25 - 3.80: 5818 3.80 - 4.35: 8071 4.35 - 4.90: 12933 Nonbonded interactions: 30107 Sorted by model distance: nonbonded pdb=" NE2 HIS A 142 " pdb="FE HEM A 503 " model vdw 2.155 3.080 nonbonded pdb=" NE2 HIS A 129 " pdb="FE HEM A 504 " model vdw 2.212 3.080 nonbonded pdb=" O SER A 238 " pdb=" OG SER A 238 " model vdw 2.220 3.040 nonbonded pdb=" O HOH A 613 " pdb=" O HOH A 617 " model vdw 2.232 3.040 nonbonded pdb=" OD2 ASP A 254 " pdb=" O HOH A 601 " model vdw 2.242 3.040 ... (remaining 30102 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: 0.420 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: 0.140 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.630 Find NCS groups from input model: 0.030 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: 0.010 Load rotamer database and sin/cos tables:13.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 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 : 0.009 0.209 3565 Z= 0.365 Angle : 0.967 23.336 4872 Z= 0.430 Chirality : 0.045 0.224 509 Planarity : 0.004 0.068 580 Dihedral : 20.123 99.565 1270 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.16 % Allowed : 26.88 % Favored : 71.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.39), residues: 397 helix: -0.29 (0.34), residues: 200 sheet: 0.66 (0.54), residues: 87 loop : -1.06 (0.55), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 125 HIS 0.004 0.001 HIS A 69 PHE 0.009 0.001 PHE A 218 TYR 0.013 0.001 TYR A 275 ARG 0.002 0.000 ARG A 320 Details of bonding type rmsd hydrogen bonds : bond 0.22562 ( 187) hydrogen bonds : angle 7.63902 ( 549) covalent geometry : bond 0.00940 ( 3563) covalent geometry : angle 0.96657 ( 4872) Misc. bond : bond 0.02040 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 49 time to evaluate : 0.470 Fit side-chains revert: symmetry clash REVERT: A 394 TYR cc_start: 0.6008 (p90) cc_final: 0.5495 (p90) outliers start: 4 outliers final: 4 residues processed: 53 average time/residue: 1.4154 time to fit residues: 77.6218 Evaluate side-chains 52 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 254 ASP Chi-restraints excluded: chain A residue 353 TYR Chi-restraints excluded: chain A residue 370 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 4.9990 chunk 29 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 15 optimal weight: 4.9990 chunk 30 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 22 optimal weight: 0.0770 chunk 35 optimal weight: 3.9990 overall best weight: 0.6740 ------------------------------------------------------------------------------- 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 = 0.3692 r_free = 0.3692 target = 0.149360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.120058 restraints weight = 3367.536| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 1.58 r_work: 0.3251 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.1171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.183 3565 Z= 0.132 Angle : 0.633 13.461 4872 Z= 0.278 Chirality : 0.041 0.156 509 Planarity : 0.003 0.030 580 Dihedral : 11.554 84.317 516 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.31 % Allowed : 26.88 % Favored : 70.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.41), residues: 397 helix: 1.27 (0.35), residues: 201 sheet: 0.20 (0.54), residues: 93 loop : -0.85 (0.56), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 25 HIS 0.005 0.001 HIS A 69 PHE 0.009 0.001 PHE A 218 TYR 0.013 0.001 TYR A 275 ARG 0.002 0.000 ARG A 320 Details of bonding type rmsd hydrogen bonds : bond 0.04258 ( 187) hydrogen bonds : angle 4.71816 ( 549) covalent geometry : bond 0.00313 ( 3563) covalent geometry : angle 0.63278 ( 4872) Misc. bond : bond 0.15221 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.396 Fit side-chains revert: symmetry clash REVERT: A 254 ASP cc_start: 0.8097 (OUTLIER) cc_final: 0.7556 (p0) REVERT: A 320 ARG cc_start: 0.7365 (OUTLIER) cc_final: 0.6592 (mpt-90) outliers start: 8 outliers final: 4 residues processed: 53 average time/residue: 1.2807 time to fit residues: 70.0208 Evaluate side-chains 50 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 254 ASP Chi-restraints excluded: chain A residue 320 ARG Chi-restraints excluded: chain A residue 353 TYR Chi-restraints excluded: chain A residue 361 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 16 optimal weight: 0.9990 chunk 20 optimal weight: 0.0770 chunk 24 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 12 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 overall best weight: 0.6140 ------------------------------------------------------------------------------- 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 = 0.149883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.120813 restraints weight = 3377.062| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 1.58 r_work: 0.3260 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.159 3565 Z= 0.121 Angle : 0.610 13.015 4872 Z= 0.265 Chirality : 0.040 0.147 509 Planarity : 0.003 0.027 580 Dihedral : 10.811 77.371 515 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.89 % Allowed : 26.30 % Favored : 70.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.42), residues: 397 helix: 1.68 (0.36), residues: 201 sheet: 0.12 (0.54), residues: 93 loop : -0.83 (0.56), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 125 HIS 0.005 0.001 HIS A 69 PHE 0.010 0.001 PHE A 218 TYR 0.012 0.001 TYR A 275 ARG 0.002 0.000 ARG A 320 Details of bonding type rmsd hydrogen bonds : bond 0.03853 ( 187) hydrogen bonds : angle 4.38895 ( 549) covalent geometry : bond 0.00292 ( 3563) covalent geometry : angle 0.61038 ( 4872) Misc. bond : bond 0.13610 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 46 time to evaluate : 0.400 Fit side-chains revert: symmetry clash REVERT: A 254 ASP cc_start: 0.8022 (OUTLIER) cc_final: 0.7455 (p0) REVERT: A 320 ARG cc_start: 0.7167 (OUTLIER) cc_final: 0.6331 (mpt-90) outliers start: 10 outliers final: 4 residues processed: 55 average time/residue: 1.2394 time to fit residues: 70.3530 Evaluate side-chains 49 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 254 ASP Chi-restraints excluded: chain A residue 320 ARG Chi-restraints excluded: chain A residue 353 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 22 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 chunk 9 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 38 optimal weight: 0.0470 overall best weight: 0.6680 ------------------------------------------------------------------------------- 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 = 0.3687 r_free = 0.3687 target = 0.149125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.119947 restraints weight = 3441.447| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 1.60 r_work: 0.3254 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.154 3565 Z= 0.124 Angle : 0.614 12.937 4872 Z= 0.265 Chirality : 0.040 0.148 509 Planarity : 0.003 0.025 580 Dihedral : 10.762 77.145 513 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 3.18 % Allowed : 26.30 % Favored : 70.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.42), residues: 397 helix: 1.77 (0.36), residues: 201 sheet: 0.01 (0.54), residues: 93 loop : -0.87 (0.55), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 125 HIS 0.006 0.001 HIS A 69 PHE 0.010 0.001 PHE A 218 TYR 0.012 0.001 TYR A 275 ARG 0.002 0.000 ARG A 320 Details of bonding type rmsd hydrogen bonds : bond 0.03726 ( 187) hydrogen bonds : angle 4.30554 ( 549) covalent geometry : bond 0.00301 ( 3563) covalent geometry : angle 0.61378 ( 4872) Misc. bond : bond 0.13586 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 44 time to evaluate : 0.408 Fit side-chains revert: symmetry clash REVERT: A 254 ASP cc_start: 0.7938 (OUTLIER) cc_final: 0.7355 (p0) REVERT: A 320 ARG cc_start: 0.7163 (OUTLIER) cc_final: 0.6302 (mpt-90) outliers start: 11 outliers final: 5 residues processed: 53 average time/residue: 1.2047 time to fit residues: 65.9724 Evaluate side-chains 50 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 118 LYS Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 254 ASP Chi-restraints excluded: chain A residue 320 ARG Chi-restraints excluded: chain A residue 353 TYR Chi-restraints excluded: chain A residue 361 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 26 optimal weight: 0.7980 chunk 3 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 23 optimal weight: 4.9990 chunk 16 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 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 = 0.3679 r_free = 0.3679 target = 0.148286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.119067 restraints weight = 3458.051| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 1.60 r_work: 0.3239 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.157 3565 Z= 0.143 Angle : 0.641 13.238 4872 Z= 0.276 Chirality : 0.041 0.151 509 Planarity : 0.003 0.023 580 Dihedral : 10.864 77.112 513 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.18 % Allowed : 26.59 % Favored : 70.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.42), residues: 397 helix: 1.64 (0.36), residues: 201 sheet: 0.01 (0.53), residues: 93 loop : -0.91 (0.56), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 125 HIS 0.007 0.001 HIS A 69 PHE 0.010 0.001 PHE A 218 TYR 0.012 0.002 TYR A 275 ARG 0.003 0.000 ARG A 320 Details of bonding type rmsd hydrogen bonds : bond 0.03922 ( 187) hydrogen bonds : angle 4.34051 ( 549) covalent geometry : bond 0.00349 ( 3563) covalent geometry : angle 0.64073 ( 4872) Misc. bond : bond 0.15248 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 47 time to evaluate : 0.394 Fit side-chains revert: symmetry clash REVERT: A 254 ASP cc_start: 0.7962 (OUTLIER) cc_final: 0.7350 (p0) REVERT: A 318 SER cc_start: 0.7207 (OUTLIER) cc_final: 0.6875 (p) REVERT: A 320 ARG cc_start: 0.7224 (OUTLIER) cc_final: 0.6340 (mpt-90) REVERT: A 394 TYR cc_start: 0.6750 (p90) cc_final: 0.6225 (p90) outliers start: 11 outliers final: 5 residues processed: 55 average time/residue: 1.2458 time to fit residues: 70.7245 Evaluate side-chains 51 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 118 LYS Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 254 ASP Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 320 ARG Chi-restraints excluded: chain A residue 353 TYR Chi-restraints excluded: chain A residue 361 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 0 optimal weight: 7.9990 chunk 30 optimal weight: 3.9990 chunk 8 optimal weight: 0.0470 chunk 25 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 37 optimal weight: 0.0970 chunk 16 optimal weight: 1.9990 chunk 6 optimal weight: 8.9990 chunk 32 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- 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 = 0.3695 r_free = 0.3695 target = 0.149802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.120545 restraints weight = 3503.075| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 1.61 r_work: 0.3256 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.144 3565 Z= 0.118 Angle : 0.621 12.854 4872 Z= 0.265 Chirality : 0.040 0.144 509 Planarity : 0.003 0.022 580 Dihedral : 10.612 76.544 513 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.89 % Allowed : 26.88 % Favored : 70.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.42), residues: 397 helix: 1.77 (0.36), residues: 201 sheet: -0.06 (0.53), residues: 93 loop : -0.89 (0.56), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 125 HIS 0.006 0.001 HIS A 69 PHE 0.010 0.001 PHE A 218 TYR 0.012 0.001 TYR A 275 ARG 0.002 0.000 ARG A 320 Details of bonding type rmsd hydrogen bonds : bond 0.03554 ( 187) hydrogen bonds : angle 4.23676 ( 549) covalent geometry : bond 0.00286 ( 3563) covalent geometry : angle 0.62069 ( 4872) Misc. bond : bond 0.13048 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.399 Fit side-chains revert: symmetry clash REVERT: A 254 ASP cc_start: 0.7955 (OUTLIER) cc_final: 0.7321 (p0) REVERT: A 318 SER cc_start: 0.7182 (t) cc_final: 0.6918 (p) REVERT: A 320 ARG cc_start: 0.7161 (OUTLIER) cc_final: 0.6287 (mpt-90) REVERT: A 394 TYR cc_start: 0.6633 (p90) cc_final: 0.6144 (p90) outliers start: 10 outliers final: 4 residues processed: 54 average time/residue: 1.1840 time to fit residues: 66.0439 Evaluate side-chains 51 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 118 LYS Chi-restraints excluded: chain A residue 254 ASP Chi-restraints excluded: chain A residue 320 ARG Chi-restraints excluded: chain A residue 353 TYR Chi-restraints excluded: chain A residue 361 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 24 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 chunk 34 optimal weight: 5.9990 chunk 6 optimal weight: 0.0980 chunk 10 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 chunk 28 optimal weight: 0.5980 chunk 3 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.150688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.121568 restraints weight = 3423.993| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 1.59 r_work: 0.3269 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.136 3565 Z= 0.110 Angle : 0.613 12.567 4872 Z= 0.260 Chirality : 0.040 0.149 509 Planarity : 0.003 0.022 580 Dihedral : 10.300 76.710 513 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.18 % Allowed : 26.59 % Favored : 70.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.42), residues: 397 helix: 1.82 (0.36), residues: 202 sheet: -0.11 (0.53), residues: 93 loop : -0.83 (0.56), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 125 HIS 0.005 0.001 HIS A 69 PHE 0.010 0.001 PHE A 218 TYR 0.012 0.001 TYR A 275 ARG 0.002 0.000 ARG A 320 Details of bonding type rmsd hydrogen bonds : bond 0.03390 ( 187) hydrogen bonds : angle 4.16422 ( 549) covalent geometry : bond 0.00267 ( 3563) covalent geometry : angle 0.61322 ( 4872) Misc. bond : bond 0.11872 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 48 time to evaluate : 0.394 Fit side-chains revert: symmetry clash REVERT: A 254 ASP cc_start: 0.7882 (OUTLIER) cc_final: 0.7222 (p0) REVERT: A 318 SER cc_start: 0.7213 (OUTLIER) cc_final: 0.6980 (p) REVERT: A 320 ARG cc_start: 0.6995 (OUTLIER) cc_final: 0.6780 (tpp-160) REVERT: A 394 TYR cc_start: 0.6601 (p90) cc_final: 0.6075 (p90) outliers start: 11 outliers final: 5 residues processed: 56 average time/residue: 1.1929 time to fit residues: 69.0245 Evaluate side-chains 54 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 118 LYS Chi-restraints excluded: chain A residue 254 ASP Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 320 ARG Chi-restraints excluded: chain A residue 353 TYR Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 375 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 6 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 21 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 23 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 = 0.3673 r_free = 0.3673 target = 0.147682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.118269 restraints weight = 3438.536| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 1.59 r_work: 0.3231 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.1456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.184 3565 Z= 0.164 Angle : 0.678 13.623 4872 Z= 0.291 Chirality : 0.042 0.154 509 Planarity : 0.003 0.021 580 Dihedral : 10.826 76.988 513 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.47 % Allowed : 26.01 % Favored : 70.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.41), residues: 397 helix: 1.55 (0.36), residues: 202 sheet: -0.16 (0.52), residues: 93 loop : -0.97 (0.56), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 125 HIS 0.007 0.001 HIS A 69 PHE 0.010 0.001 PHE A 218 TYR 0.012 0.002 TYR A 275 ARG 0.003 0.000 ARG A 320 Details of bonding type rmsd hydrogen bonds : bond 0.04062 ( 187) hydrogen bonds : angle 4.34427 ( 549) covalent geometry : bond 0.00401 ( 3563) covalent geometry : angle 0.67824 ( 4872) Misc. bond : bond 0.17038 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 46 time to evaluate : 0.403 Fit side-chains revert: symmetry clash REVERT: A 254 ASP cc_start: 0.8024 (OUTLIER) cc_final: 0.7312 (p0) REVERT: A 320 ARG cc_start: 0.7140 (OUTLIER) cc_final: 0.6251 (mpt-90) REVERT: A 394 TYR cc_start: 0.6736 (p90) cc_final: 0.6159 (p90) outliers start: 12 outliers final: 5 residues processed: 55 average time/residue: 1.2749 time to fit residues: 72.2950 Evaluate side-chains 50 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 118 LYS Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 254 ASP Chi-restraints excluded: chain A residue 320 ARG Chi-restraints excluded: chain A residue 353 TYR Chi-restraints excluded: chain A residue 361 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 0.5980 chunk 2 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 34 optimal weight: 3.9990 chunk 12 optimal weight: 0.5980 chunk 18 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3689 r_free = 0.3689 target = 0.149082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.120046 restraints weight = 3369.537| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 1.56 r_work: 0.3256 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.145 3565 Z= 0.128 Angle : 0.659 13.045 4872 Z= 0.279 Chirality : 0.041 0.158 509 Planarity : 0.003 0.022 580 Dihedral : 10.594 76.262 513 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.31 % Allowed : 27.46 % Favored : 70.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.41), residues: 397 helix: 1.64 (0.36), residues: 202 sheet: -0.23 (0.52), residues: 93 loop : -0.93 (0.56), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 125 HIS 0.006 0.001 HIS A 69 PHE 0.010 0.001 PHE A 218 TYR 0.012 0.001 TYR A 275 ARG 0.002 0.000 ARG A 320 Details of bonding type rmsd hydrogen bonds : bond 0.03646 ( 187) hydrogen bonds : angle 4.25225 ( 549) covalent geometry : bond 0.00313 ( 3563) covalent geometry : angle 0.65867 ( 4872) Misc. bond : bond 0.14023 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.362 Fit side-chains revert: symmetry clash REVERT: A 254 ASP cc_start: 0.8058 (OUTLIER) cc_final: 0.7347 (p0) REVERT: A 320 ARG cc_start: 0.7059 (OUTLIER) cc_final: 0.6846 (tpp-160) REVERT: A 394 TYR cc_start: 0.6749 (p90) cc_final: 0.6128 (p90) outliers start: 8 outliers final: 5 residues processed: 52 average time/residue: 1.1793 time to fit residues: 63.3394 Evaluate side-chains 51 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 44 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 118 LYS Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 254 ASP Chi-restraints excluded: chain A residue 320 ARG Chi-restraints excluded: chain A residue 353 TYR Chi-restraints excluded: chain A residue 361 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 29 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 27 optimal weight: 0.0170 chunk 20 optimal weight: 0.8980 chunk 28 optimal weight: 0.0870 chunk 31 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 22 optimal weight: 0.1980 chunk 8 optimal weight: 0.0270 overall best weight: 0.2054 ------------------------------------------------------------------------------- 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 = 0.3763 r_free = 0.3763 target = 0.155107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.126946 restraints weight = 3570.142| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 1.59 r_work: 0.3389 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.124 3565 Z= 0.090 Angle : 0.599 13.212 4872 Z= 0.254 Chirality : 0.039 0.169 509 Planarity : 0.003 0.023 580 Dihedral : 9.486 76.235 513 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.73 % Allowed : 27.75 % Favored : 70.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.42), residues: 397 helix: 2.03 (0.37), residues: 202 sheet: -0.21 (0.53), residues: 92 loop : -0.79 (0.56), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 125 HIS 0.003 0.000 HIS A 69 PHE 0.010 0.001 PHE A 218 TYR 0.008 0.001 TYR A 275 ARG 0.002 0.000 ARG A 320 Details of bonding type rmsd hydrogen bonds : bond 0.02841 ( 187) hydrogen bonds : angle 4.03798 ( 549) covalent geometry : bond 0.00219 ( 3563) covalent geometry : angle 0.59905 ( 4872) Misc. bond : bond 0.08762 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 52 time to evaluate : 0.416 Fit side-chains revert: symmetry clash REVERT: A 254 ASP cc_start: 0.7941 (OUTLIER) cc_final: 0.7225 (p0) REVERT: A 312 GLN cc_start: 0.8013 (tp40) cc_final: 0.7655 (mm110) REVERT: A 320 ARG cc_start: 0.7007 (OUTLIER) cc_final: 0.6181 (mpt-90) REVERT: A 394 TYR cc_start: 0.6586 (p90) cc_final: 0.5979 (p90) outliers start: 6 outliers final: 4 residues processed: 57 average time/residue: 1.1802 time to fit residues: 69.5438 Evaluate side-chains 54 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 118 LYS Chi-restraints excluded: chain A residue 254 ASP Chi-restraints excluded: chain A residue 320 ARG Chi-restraints excluded: chain A residue 353 TYR Chi-restraints excluded: chain A residue 361 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 2 optimal weight: 0.8980 chunk 9 optimal weight: 0.5980 chunk 13 optimal weight: 0.9990 chunk 0 optimal weight: 8.9990 chunk 8 optimal weight: 0.0050 chunk 34 optimal weight: 5.9990 chunk 15 optimal weight: 0.0470 chunk 28 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 3 optimal weight: 3.9990 overall best weight: 0.4292 ------------------------------------------------------------------------------- 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 = 0.3733 r_free = 0.3733 target = 0.152327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.123710 restraints weight = 3573.246| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 1.59 r_work: 0.3346 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.128 3565 Z= 0.102 Angle : 0.592 11.781 4872 Z= 0.257 Chirality : 0.039 0.141 509 Planarity : 0.003 0.023 580 Dihedral : 9.602 77.636 513 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.02 % Allowed : 28.90 % Favored : 69.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.42), residues: 397 helix: 1.97 (0.37), residues: 201 sheet: -0.18 (0.52), residues: 93 loop : -0.83 (0.56), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 125 HIS 0.005 0.001 HIS A 69 PHE 0.010 0.001 PHE A 218 TYR 0.011 0.001 TYR A 275 ARG 0.002 0.000 ARG A 320 Details of bonding type rmsd hydrogen bonds : bond 0.03167 ( 187) hydrogen bonds : angle 4.08008 ( 549) covalent geometry : bond 0.00251 ( 3563) covalent geometry : angle 0.59178 ( 4872) Misc. bond : bond 0.10052 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2947.86 seconds wall clock time: 51 minutes 34.19 seconds (3094.19 seconds total)