Starting phenix.real_space_refine on Wed Feb 12 19:24:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ctl_26994/02_2025/8ctl_26994_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ctl_26994/02_2025/8ctl_26994.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ctl_26994/02_2025/8ctl_26994.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ctl_26994/02_2025/8ctl_26994.map" model { file = "/net/cci-nas-00/data/ceres_data/8ctl_26994/02_2025/8ctl_26994_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ctl_26994/02_2025/8ctl_26994_neut.cif" } resolution = 3.1 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= -0.001 sd= 0.028 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 233 5.49 5 S 21 5.16 5 C 4257 2.51 5 N 1486 2.21 5 O 2141 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 8138 Number of models: 1 Model: "" Number of chains: 4 Chain: "D" Number of atoms: 3209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3209 Classifications: {'peptide': 401} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 382} Chain breaks: 1 Chain: "C" Number of atoms: 3937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 3937 Classifications: {'RNA': 184} Modifications used: {'rna2p_pur': 15, 'rna2p_pyr': 11, 'rna3p_pur': 89, 'rna3p_pyr': 69} Link IDs: {'rna2p': 26, 'rna3p': 157} Chain breaks: 2 Chain: "A" Number of atoms: 579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 579 Classifications: {'DNA': 29} Link IDs: {'rna3p': 28} Chain: "B" Number of atoms: 413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 413 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Time building chain proxies: 5.41, per 1000 atoms: 0.66 Number of scatterers: 8138 At special positions: 0 Unit cell: (89.88, 103.79, 131.61, 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 21 16.00 P 233 15.00 O 2141 8.00 N 1486 7.00 C 4257 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: 2.22 Conformation dependent library (CDL) restraints added in 395.4 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: 752 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 6 sheets defined 29.9% alpha, 18.2% beta 75 base pairs and 130 stacking pairs defined. Time for finding SS restraints: 4.43 Creating SS restraints... Processing helix chain 'D' and resid 20 through 29 removed outlier: 3.755A pdb=" N LEU D 27 " --> pdb=" O VAL D 23 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 108 Processing helix chain 'D' and resid 109 through 121 Processing helix chain 'D' and resid 163 through 181 Processing helix chain 'D' and resid 297 through 313 Proline residue: D 304 - end of helix Processing helix chain 'D' and resid 323 through 333 Processing helix chain 'D' and resid 338 through 340 No H-bonds generated for 'chain 'D' and resid 338 through 340' Processing helix chain 'D' and resid 341 through 349 removed outlier: 3.658A pdb=" N CYS D 345 " --> pdb=" O LEU D 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 416 Processing helix chain 'D' and resid 417 through 422 Processing helix chain 'D' and resid 480 through 482 No H-bonds generated for 'chain 'D' and resid 480 through 482' Processing sheet with id=AA1, first strand: chain 'D' and resid 13 through 14 removed outlier: 4.626A pdb=" N VAL D 6 " --> pdb=" O LEU D 14 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N TYR D 5 " --> pdb=" O ILE D 42 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N LEU D 44 " --> pdb=" O TYR D 5 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ILE D 7 " --> pdb=" O LEU D 44 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N THR D 41 " --> pdb=" O VAL D 35 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 318 through 322 removed outlier: 6.256A pdb=" N VAL D 189 " --> pdb=" O CYS D 319 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N THR D 321 " --> pdb=" O VAL D 189 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N LEU D 191 " --> pdb=" O THR D 321 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N MET D 68 " --> pdb=" O ALA D 81 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N THR D 72 " --> pdb=" O SER D 77 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N SER D 77 " --> pdb=" O THR D 72 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL D 367 " --> pdb=" O GLN D 82 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N MET D 366 " --> pdb=" O TYR D 494 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 128 through 131 Processing sheet with id=AA4, first strand: chain 'D' and resid 378 through 380 Processing sheet with id=AA5, first strand: chain 'D' and resid 387 through 388 removed outlier: 6.045A pdb=" N TYR D 387 " --> pdb=" O VAL D 394 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 476 through 478 removed outlier: 6.535A pdb=" N TYR D 468 " --> pdb=" O SER D 458 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N SER D 458 " --> pdb=" O TYR D 468 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N VAL D 470 " --> pdb=" O SER D 456 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N VAL D 446 " --> pdb=" O TYR D 484 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N TYR D 484 " --> pdb=" O VAL D 446 " (cutoff:3.500A) 114 hydrogen bonds defined for protein. 324 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 190 hydrogen bonds 356 hydrogen bond angles 0 basepair planarities 75 basepair parallelities 130 stacking parallelities Total time for adding SS restraints: 3.37 Time building geometry restraints manager: 2.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 785 1.30 - 1.43: 3479 1.43 - 1.56: 4025 1.56 - 1.69: 460 1.69 - 1.81: 33 Bond restraints: 8782 Sorted by residual: bond pdb=" CA ARG D 131 " pdb=" C ARG D 131 " ideal model delta sigma weight residual 1.526 1.456 0.070 1.20e-02 6.94e+03 3.38e+01 bond pdb=" CA ALA D 381 " pdb=" C ALA D 381 " ideal model delta sigma weight residual 1.526 1.452 0.074 1.30e-02 5.92e+03 3.20e+01 bond pdb=" CA ARG D 371 " pdb=" C ARG D 371 " ideal model delta sigma weight residual 1.525 1.460 0.065 1.28e-02 6.10e+03 2.55e+01 bond pdb=" N GLN D 465 " pdb=" CA GLN D 465 " ideal model delta sigma weight residual 1.461 1.402 0.059 1.20e-02 6.94e+03 2.46e+01 bond pdb=" C ARG D 131 " pdb=" O ARG D 131 " ideal model delta sigma weight residual 1.235 1.178 0.056 1.14e-02 7.69e+03 2.45e+01 ... (remaining 8777 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 11629 2.17 - 4.35: 1182 4.35 - 6.52: 112 6.52 - 8.70: 21 8.70 - 10.87: 13 Bond angle restraints: 12957 Sorted by residual: angle pdb=" N THR D 352 " pdb=" CA THR D 352 " pdb=" C THR D 352 " ideal model delta sigma weight residual 111.03 121.20 -10.17 1.11e+00 8.12e-01 8.39e+01 angle pdb=" N ARG D 398 " pdb=" CA ARG D 398 " pdb=" C ARG D 398 " ideal model delta sigma weight residual 113.41 102.54 10.87 1.22e+00 6.72e-01 7.95e+01 angle pdb=" N ILE D 439 " pdb=" CA ILE D 439 " pdb=" C ILE D 439 " ideal model delta sigma weight residual 108.93 99.38 9.55 1.35e+00 5.49e-01 5.00e+01 angle pdb=" CA GLY D 460 " pdb=" C GLY D 460 " pdb=" O GLY D 460 " ideal model delta sigma weight residual 122.22 117.63 4.59 6.50e-01 2.37e+00 4.98e+01 angle pdb=" C THR D 352 " pdb=" CA THR D 352 " pdb=" CB THR D 352 " ideal model delta sigma weight residual 110.95 100.80 10.15 1.55e+00 4.16e-01 4.29e+01 ... (remaining 12952 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.28: 4525 35.28 - 70.56: 733 70.56 - 105.84: 69 105.84 - 141.12: 11 141.12 - 176.40: 13 Dihedral angle restraints: 5351 sinusoidal: 4183 harmonic: 1168 Sorted by residual: dihedral pdb=" C5' A C 93 " pdb=" C4' A C 93 " pdb=" C3' A C 93 " pdb=" O3' A C 93 " ideal model delta sinusoidal sigma weight residual 147.00 77.07 69.93 1 8.00e+00 1.56e-02 9.85e+01 dihedral pdb=" O4' C C 60 " pdb=" C1' C C 60 " pdb=" N1 C C 60 " pdb=" C2 C C 60 " ideal model delta sinusoidal sigma weight residual 200.00 31.04 168.96 1 1.50e+01 4.44e-03 8.45e+01 dihedral pdb=" C4' A C 93 " pdb=" C3' A C 93 " pdb=" C2' A C 93 " pdb=" C1' A C 93 " ideal model delta sinusoidal sigma weight residual -35.00 27.93 -62.93 1 8.00e+00 1.56e-02 8.17e+01 ... (remaining 5348 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 1037 0.081 - 0.163: 443 0.163 - 0.244: 102 0.244 - 0.325: 5 0.325 - 0.406: 5 Chirality restraints: 1592 Sorted by residual: chirality pdb=" CA LYS D 31 " pdb=" N LYS D 31 " pdb=" C LYS D 31 " pdb=" CB LYS D 31 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.13e+00 chirality pdb=" C3' DT B 113 " pdb=" C4' DT B 113 " pdb=" O3' DT B 113 " pdb=" C2' DT B 113 " both_signs ideal model delta sigma weight residual False -2.66 -2.27 -0.39 2.00e-01 2.50e+01 3.85e+00 chirality pdb=" CA ASN D 382 " pdb=" N ASN D 382 " pdb=" C ASN D 382 " pdb=" CB ASN D 382 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.75e+00 ... (remaining 1589 not shown) Planarity restraints: 798 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DC A 27 " 0.052 2.00e-02 2.50e+03 2.51e-02 1.42e+01 pdb=" N1 DC A 27 " -0.048 2.00e-02 2.50e+03 pdb=" C2 DC A 27 " -0.008 2.00e-02 2.50e+03 pdb=" O2 DC A 27 " -0.009 2.00e-02 2.50e+03 pdb=" N3 DC A 27 " 0.005 2.00e-02 2.50e+03 pdb=" C4 DC A 27 " 0.012 2.00e-02 2.50e+03 pdb=" N4 DC A 27 " 0.014 2.00e-02 2.50e+03 pdb=" C5 DC A 27 " -0.005 2.00e-02 2.50e+03 pdb=" C6 DC A 27 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A C 78 " 0.048 2.00e-02 2.50e+03 2.24e-02 1.38e+01 pdb=" N9 A C 78 " -0.053 2.00e-02 2.50e+03 pdb=" C8 A C 78 " -0.004 2.00e-02 2.50e+03 pdb=" N7 A C 78 " 0.005 2.00e-02 2.50e+03 pdb=" C5 A C 78 " 0.003 2.00e-02 2.50e+03 pdb=" C6 A C 78 " 0.009 2.00e-02 2.50e+03 pdb=" N6 A C 78 " 0.007 2.00e-02 2.50e+03 pdb=" N1 A C 78 " 0.003 2.00e-02 2.50e+03 pdb=" C2 A C 78 " -0.001 2.00e-02 2.50e+03 pdb=" N3 A C 78 " -0.008 2.00e-02 2.50e+03 pdb=" C4 A C 78 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG A 9 " 0.038 2.00e-02 2.50e+03 1.94e-02 1.13e+01 pdb=" N9 DG A 9 " -0.051 2.00e-02 2.50e+03 pdb=" C8 DG A 9 " 0.002 2.00e-02 2.50e+03 pdb=" N7 DG A 9 " 0.006 2.00e-02 2.50e+03 pdb=" C5 DG A 9 " 0.008 2.00e-02 2.50e+03 pdb=" C6 DG A 9 " 0.013 2.00e-02 2.50e+03 pdb=" O6 DG A 9 " -0.003 2.00e-02 2.50e+03 pdb=" N1 DG A 9 " 0.002 2.00e-02 2.50e+03 pdb=" C2 DG A 9 " 0.000 2.00e-02 2.50e+03 pdb=" N2 DG A 9 " 0.002 2.00e-02 2.50e+03 pdb=" N3 DG A 9 " -0.009 2.00e-02 2.50e+03 pdb=" C4 DG A 9 " -0.008 2.00e-02 2.50e+03 ... (remaining 795 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 2129 2.80 - 3.33: 7862 3.33 - 3.85: 17670 3.85 - 4.38: 20559 4.38 - 4.90: 26863 Nonbonded interactions: 75083 Sorted by model distance: nonbonded pdb=" OG SER D 8 " pdb=" OG SER D 10 " model vdw 2.280 3.040 nonbonded pdb=" O2' G C 95 " pdb=" N2 G C 131 " model vdw 2.309 3.120 nonbonded pdb=" OD1 ASN D 154 " pdb=" O2' U C 125 " model vdw 2.321 3.040 nonbonded pdb=" N3 C C 111 " pdb=" O6 G C 172 " model vdw 2.327 2.496 nonbonded pdb=" O ASN D 154 " pdb=" O2' C C 98 " model vdw 2.352 3.040 ... (remaining 75078 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.080 Set stop_for_unknowns flag: 0.010 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: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 25.320 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4489 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 0.074 8782 Z= 0.596 Angle : 1.320 10.875 12957 Z= 0.934 Chirality : 0.090 0.406 1592 Planarity : 0.005 0.071 798 Dihedral : 27.577 176.404 4599 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 32.18 Ramachandran Plot: Outliers : 0.50 % Allowed : 12.09 % Favored : 87.41 % Rotamer: Outliers : 7.20 % Allowed : 17.00 % Favored : 75.79 % Cbeta Deviations : 1.06 % Peptide Plane: Cis-proline : 5.56 % 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: -5.68 (0.29), residues: 397 helix: -4.32 (0.23), residues: 113 sheet: -3.35 (0.52), residues: 72 loop : -3.66 (0.30), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 161 HIS 0.008 0.002 HIS D 373 PHE 0.012 0.002 PHE D 196 TYR 0.011 0.002 TYR D 433 ARG 0.003 0.001 ARG D 86 *********************** 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 142 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 117 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 175 ASN cc_start: 0.6018 (m-40) cc_final: 0.5698 (m-40) REVERT: D 443 SER cc_start: 0.6737 (m) cc_final: 0.6077 (t) REVERT: D 470 VAL cc_start: 0.5463 (OUTLIER) cc_final: 0.5218 (t) outliers start: 25 outliers final: 3 residues processed: 129 average time/residue: 0.3210 time to fit residues: 50.6868 Evaluate side-chains 77 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 73 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 394 VAL Chi-restraints excluded: chain D residue 470 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 52 optimal weight: 4.9990 chunk 46 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 56 optimal weight: 10.0000 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 373 HIS D 376 GLN ** D 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 462 ASN D 465 GLN D 487 ASN D 492 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.129386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.095097 restraints weight = 13819.636| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 1.76 r_work: 0.3340 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6079 moved from start: 0.3820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 8782 Z= 0.298 Angle : 0.887 13.077 12957 Z= 0.456 Chirality : 0.046 0.365 1592 Planarity : 0.006 0.051 798 Dihedral : 27.186 179.845 3785 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 4.61 % Allowed : 17.00 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -3.05 (0.37), residues: 397 helix: -1.41 (0.44), residues: 117 sheet: -2.89 (0.54), residues: 68 loop : -2.05 (0.38), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 161 HIS 0.020 0.003 HIS D 22 PHE 0.023 0.003 PHE D 318 TYR 0.021 0.003 TYR D 388 ARG 0.007 0.001 ARG D 330 *********************** 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 89 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 73 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 148 LYS cc_start: 0.5433 (tttt) cc_final: 0.5180 (tptt) REVERT: D 436 MET cc_start: 0.7349 (mmm) cc_final: 0.7025 (mmm) REVERT: D 463 LYS cc_start: 0.8206 (mttm) cc_final: 0.7939 (mppt) outliers start: 16 outliers final: 6 residues processed: 84 average time/residue: 0.2659 time to fit residues: 28.4939 Evaluate side-chains 61 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 55 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain D residue 359 SER Chi-restraints excluded: chain D residue 449 GLU Chi-restraints excluded: chain D residue 494 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 51 optimal weight: 4.9990 chunk 4 optimal weight: 0.5980 chunk 3 optimal weight: 0.6980 chunk 28 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 35 optimal weight: 0.4980 chunk 7 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 53 GLN D 376 GLN ** D 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.128822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.094946 restraints weight = 14129.233| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 1.76 r_work: 0.3344 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6588 moved from start: 0.5889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.103 8782 Z= 0.247 Angle : 0.760 14.553 12957 Z= 0.394 Chirality : 0.042 0.417 1592 Planarity : 0.005 0.048 798 Dihedral : 26.450 178.251 3781 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 4.03 % Allowed : 17.00 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -2.32 (0.38), residues: 397 helix: -0.59 (0.45), residues: 118 sheet: -2.16 (0.53), residues: 78 loop : -1.82 (0.39), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 478 HIS 0.014 0.003 HIS D 333 PHE 0.028 0.002 PHE D 329 TYR 0.012 0.002 TYR D 387 ARG 0.012 0.001 ARG D 33 *********************** 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 84 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 70 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 33 ARG cc_start: 0.6095 (ttp80) cc_final: 0.5336 (ptm-80) REVERT: D 147 ASN cc_start: 0.6946 (p0) cc_final: 0.6724 (p0) REVERT: D 148 LYS cc_start: 0.5744 (tttt) cc_final: 0.5265 (tptt) REVERT: D 436 MET cc_start: 0.7655 (mmm) cc_final: 0.7225 (mmm) REVERT: D 461 ARG cc_start: 0.7845 (mmm160) cc_final: 0.7497 (mtp85) outliers start: 14 outliers final: 5 residues processed: 81 average time/residue: 0.2184 time to fit residues: 23.5114 Evaluate side-chains 56 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 51 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain D residue 359 SER Chi-restraints excluded: chain D residue 449 GLU Chi-restraints excluded: chain D residue 494 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 7 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 42 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 300 ASN D 376 GLN D 428 HIS ** D 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.127086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.092698 restraints weight = 14372.830| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 1.65 r_work: 0.3387 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3265 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.9459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.123 8782 Z= 0.399 Angle : 0.871 11.490 12957 Z= 0.448 Chirality : 0.047 0.310 1592 Planarity : 0.007 0.041 798 Dihedral : 26.395 174.513 3780 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 3.17 % Allowed : 17.29 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -2.11 (0.38), residues: 397 helix: -0.58 (0.42), residues: 118 sheet: -2.20 (0.67), residues: 55 loop : -1.64 (0.38), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP D 161 HIS 0.008 0.003 HIS D 333 PHE 0.018 0.003 PHE D 329 TYR 0.011 0.002 TYR D 365 ARG 0.019 0.001 ARG D 486 *********************** 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 61 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 50 time to evaluate : 0.530 Fit side-chains REVERT: D 445 LEU cc_start: 0.8291 (OUTLIER) cc_final: 0.8021 (mp) outliers start: 11 outliers final: 7 residues processed: 59 average time/residue: 0.1666 time to fit residues: 14.3048 Evaluate side-chains 46 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 38 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 89 ASP Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 303 ILE Chi-restraints excluded: chain D residue 430 SER Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 449 GLU Chi-restraints excluded: chain D residue 491 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 24 optimal weight: 7.9990 chunk 58 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 57 optimal weight: 10.0000 chunk 43 optimal weight: 5.9990 chunk 3 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 175 ASN D 376 GLN D 462 ASN D 492 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.128925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.094953 restraints weight = 14119.996| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 1.60 r_work: 0.3425 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 1.0318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8782 Z= 0.208 Angle : 0.676 9.666 12957 Z= 0.358 Chirality : 0.039 0.288 1592 Planarity : 0.005 0.034 798 Dihedral : 26.102 176.579 3780 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 3.17 % Allowed : 20.17 % Favored : 76.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -1.58 (0.39), residues: 397 helix: -0.11 (0.44), residues: 119 sheet: -1.49 (0.73), residues: 54 loop : -1.46 (0.38), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 161 HIS 0.005 0.001 HIS D 22 PHE 0.013 0.002 PHE D 198 TYR 0.024 0.002 TYR D 340 ARG 0.004 0.001 ARG D 461 *********************** 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 54 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 43 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 1 MET cc_start: 0.8345 (mmp) cc_final: 0.7935 (mmm) outliers start: 11 outliers final: 5 residues processed: 52 average time/residue: 0.2215 time to fit residues: 16.6071 Evaluate side-chains 47 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 42 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 309 GLN Chi-restraints excluded: chain D residue 371 ARG Chi-restraints excluded: chain D residue 449 GLU Chi-restraints excluded: chain D residue 494 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 37 optimal weight: 3.9990 chunk 14 optimal weight: 0.1980 chunk 22 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 47 optimal weight: 6.9990 chunk 11 optimal weight: 0.7980 chunk 6 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 chunk 56 optimal weight: 10.0000 chunk 10 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 333 HIS D 369 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.127254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.092792 restraints weight = 14151.479| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 1.66 r_work: 0.3389 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3266 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 1.1377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 8782 Z= 0.227 Angle : 0.684 9.491 12957 Z= 0.362 Chirality : 0.039 0.287 1592 Planarity : 0.005 0.079 798 Dihedral : 25.998 176.841 3780 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.46 % Allowed : 20.17 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -1.03 (0.41), residues: 397 helix: 0.46 (0.47), residues: 118 sheet: -1.48 (0.68), residues: 60 loop : -1.07 (0.41), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 478 HIS 0.013 0.002 HIS D 333 PHE 0.013 0.003 PHE D 329 TYR 0.008 0.001 TYR D 46 ARG 0.007 0.001 ARG D 330 *********************** 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 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 45 time to evaluate : 0.498 Fit side-chains REVERT: D 1 MET cc_start: 0.8463 (mmp) cc_final: 0.8104 (mmm) REVERT: D 199 MET cc_start: 0.4700 (tpp) cc_final: 0.4208 (mmp) REVERT: D 411 GLU cc_start: 0.7874 (mp0) cc_final: 0.7630 (mp0) REVERT: D 445 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7874 (mt) REVERT: D 492 GLN cc_start: 0.8430 (OUTLIER) cc_final: 0.6926 (mp10) outliers start: 12 outliers final: 5 residues processed: 53 average time/residue: 0.2045 time to fit residues: 14.9916 Evaluate side-chains 46 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 39 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 68 MET Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 425 THR Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 449 GLU Chi-restraints excluded: chain D residue 492 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 23 optimal weight: 4.9990 chunk 56 optimal weight: 10.0000 chunk 39 optimal weight: 3.9990 chunk 40 optimal weight: 7.9990 chunk 50 optimal weight: 3.9990 chunk 36 optimal weight: 0.6980 chunk 58 optimal weight: 4.9990 chunk 9 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 130 GLN ** D 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.122514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.087363 restraints weight = 14246.987| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 1.66 r_work: 0.3298 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 1.2717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 8782 Z= 0.316 Angle : 0.734 13.185 12957 Z= 0.385 Chirality : 0.041 0.310 1592 Planarity : 0.005 0.043 798 Dihedral : 25.982 176.127 3780 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.59 % Allowed : 21.61 % Favored : 75.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -1.06 (0.41), residues: 397 helix: 0.34 (0.47), residues: 118 sheet: -1.53 (0.59), residues: 73 loop : -0.94 (0.41), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 478 HIS 0.006 0.002 HIS D 333 PHE 0.015 0.002 PHE D 79 TYR 0.021 0.002 TYR D 340 ARG 0.007 0.001 ARG D 461 *********************** 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 50 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 41 time to evaluate : 0.551 Fit side-chains REVERT: D 1 MET cc_start: 0.8433 (mmp) cc_final: 0.8226 (mmm) REVERT: D 37 ARG cc_start: 0.7638 (ttp80) cc_final: 0.7172 (ttm110) REVERT: D 326 THR cc_start: 0.8821 (m) cc_final: 0.8591 (p) REVERT: D 393 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8454 (pt) REVERT: D 492 GLN cc_start: 0.8579 (OUTLIER) cc_final: 0.7100 (mp10) outliers start: 9 outliers final: 6 residues processed: 48 average time/residue: 0.1906 time to fit residues: 13.1879 Evaluate side-chains 44 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 36 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 68 MET Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 425 THR Chi-restraints excluded: chain D residue 449 GLU Chi-restraints excluded: chain D residue 492 GLN Chi-restraints excluded: chain D residue 493 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 6 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 47 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 333 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.121421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.086325 restraints weight = 14307.072| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 1.66 r_work: 0.3261 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 1.3744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 8782 Z= 0.303 Angle : 0.708 8.815 12957 Z= 0.375 Chirality : 0.042 0.318 1592 Planarity : 0.005 0.038 798 Dihedral : 25.938 176.864 3780 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.17 % Allowed : 21.33 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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 (0.40), residues: 397 helix: 0.34 (0.46), residues: 120 sheet: -1.04 (0.69), residues: 61 loop : -1.08 (0.39), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.002 TRP D 478 HIS 0.006 0.001 HIS D 339 PHE 0.016 0.002 PHE D 79 TYR 0.017 0.002 TYR D 340 ARG 0.004 0.001 ARG D 330 *********************** 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 49 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 38 time to evaluate : 0.510 Fit side-chains REVERT: D 37 ARG cc_start: 0.7657 (ttp80) cc_final: 0.7021 (ttm110) REVERT: D 106 ARG cc_start: 0.8010 (ttp80) cc_final: 0.7484 (ttt90) REVERT: D 326 THR cc_start: 0.8997 (m) cc_final: 0.8724 (p) REVERT: D 393 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8533 (pt) REVERT: D 403 ASP cc_start: 0.7799 (t0) cc_final: 0.7321 (t0) REVERT: D 492 GLN cc_start: 0.8631 (OUTLIER) cc_final: 0.7351 (mp10) outliers start: 11 outliers final: 6 residues processed: 47 average time/residue: 0.2319 time to fit residues: 14.8725 Evaluate side-chains 40 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 32 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 68 MET Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 425 THR Chi-restraints excluded: chain D residue 449 GLU Chi-restraints excluded: chain D residue 492 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 48 optimal weight: 4.9990 chunk 17 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 39 optimal weight: 0.0070 chunk 8 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 20 optimal weight: 0.0570 chunk 21 optimal weight: 0.7980 chunk 47 optimal weight: 5.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 333 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.125757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.091089 restraints weight = 14304.698| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 1.63 r_work: 0.3366 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 1.3869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8782 Z= 0.178 Angle : 0.633 9.868 12957 Z= 0.339 Chirality : 0.037 0.278 1592 Planarity : 0.004 0.041 798 Dihedral : 25.834 176.491 3780 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.73 % Allowed : 23.34 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.59 (0.41), residues: 397 helix: 0.97 (0.47), residues: 113 sheet: -1.10 (0.62), residues: 71 loop : -0.85 (0.41), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 161 HIS 0.004 0.001 HIS D 373 PHE 0.012 0.002 PHE D 329 TYR 0.016 0.001 TYR D 340 ARG 0.002 0.000 ARG D 110 *********************** 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 47 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 41 time to evaluate : 0.545 Fit side-chains REVERT: D 106 ARG cc_start: 0.8045 (ttp80) cc_final: 0.7516 (ttt90) REVERT: D 326 THR cc_start: 0.8910 (m) cc_final: 0.8555 (p) REVERT: D 403 ASP cc_start: 0.7777 (t0) cc_final: 0.7355 (t0) outliers start: 6 outliers final: 3 residues processed: 44 average time/residue: 0.2485 time to fit residues: 14.5950 Evaluate side-chains 36 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 33 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 68 MET Chi-restraints excluded: chain D residue 426 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 19 optimal weight: 0.0870 chunk 57 optimal weight: 10.0000 chunk 10 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 36 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 overall best weight: 1.1562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 333 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.123329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.088175 restraints weight = 14055.947| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 1.63 r_work: 0.3314 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 1.4126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8782 Z= 0.232 Angle : 0.666 12.987 12957 Z= 0.352 Chirality : 0.038 0.291 1592 Planarity : 0.005 0.042 798 Dihedral : 25.800 176.780 3780 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.44 % Allowed : 23.63 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.48 (0.42), residues: 397 helix: 0.84 (0.48), residues: 119 sheet: -0.63 (0.71), residues: 61 loop : -0.85 (0.41), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 478 HIS 0.003 0.001 HIS D 373 PHE 0.018 0.002 PHE D 318 TYR 0.016 0.001 TYR D 340 ARG 0.003 0.000 ARG D 385 ********************** 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 41 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 36 time to evaluate : 0.571 Fit side-chains REVERT: D 106 ARG cc_start: 0.8080 (ttp80) cc_final: 0.7549 (ttt90) REVERT: D 326 THR cc_start: 0.9008 (m) cc_final: 0.8692 (p) REVERT: D 403 ASP cc_start: 0.7864 (t0) cc_final: 0.7400 (t0) outliers start: 5 outliers final: 3 residues processed: 38 average time/residue: 0.2654 time to fit residues: 13.5084 Evaluate side-chains 37 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 34 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 68 MET Chi-restraints excluded: chain D residue 426 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 13 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 chunk 25 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 333 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.123701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.088599 restraints weight = 14189.984| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 1.63 r_work: 0.3323 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 1.4528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8782 Z= 0.229 Angle : 0.656 11.347 12957 Z= 0.347 Chirality : 0.038 0.297 1592 Planarity : 0.004 0.041 798 Dihedral : 25.722 177.604 3780 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.02 % Allowed : 23.05 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.49 (0.42), residues: 397 helix: 0.97 (0.48), residues: 118 sheet: -0.84 (0.69), residues: 61 loop : -0.88 (0.41), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP D 478 HIS 0.008 0.001 HIS D 333 PHE 0.014 0.002 PHE D 329 TYR 0.016 0.001 TYR D 340 ARG 0.003 0.000 ARG D 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5670.90 seconds wall clock time: 100 minutes 47.05 seconds (6047.05 seconds total)