Starting phenix.real_space_refine on Sat Sep 12 06:57:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7lys_23600/09_2026/7lys_23600.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lys_23600/09_2026/7lys_23600.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7lys_23600/09_2026/7lys_23600.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7lys_23600/09_2026/7lys_23600.cif" model { file = "/net/cci-nas-00/data/ceres_data/7lys_23600/09_2026/7lys_23600.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lys_23600/09_2026/7lys_23600.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7lys_23600/09_2026/7lys_23600.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lys_23600/09_2026/7lys_23600.map" } resolution = 3.05 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.171 sd= 1.109 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 899 atoms to isotropic. 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 P 88 5.49 5 S 14 5.16 5 C 4232 2.51 5 N 1313 2.21 5 O 1552 1.98 5 H 6374 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 58 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13573 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 10734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 669, 10734 Classifications: {'peptide': 669} Link IDs: {'PTRANS': 39, 'TRANS': 629} Chain breaks: 2 Chain: "B" Number of atoms: 1323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 1323 Classifications: {'RNAv2': 41} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 2, 'rna3p_pur': 20, 'rna3p_pyr': 16} Link IDs: {'rna2p': 5, 'rna3p': 35} Chain: "C" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 948 Classifications: {'DNA': 30} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 29} Chain: "D" Number of atoms: 568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 568 Classifications: {'DNA': 18} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 17} Time building chain proxies: 2.39, per 1000 atoms: 0.18 Number of scatterers: 13573 At special positions: 0 Unit cell: (84.74, 99.235, 125.995, 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) S 14 16.00 P 88 15.00 O 1552 8.00 N 1313 7.00 C 4232 6.00 H 6374 1.00 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: 1.21 Conformation dependent library (CDL) restraints added in 404.5 milliseconds 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1266 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 5 sheets defined 48.7% alpha, 9.4% beta 31 base pairs and 56 stacking pairs defined. Time for finding SS restraints: 2.70 Creating SS restraints... Processing helix chain 'A' and resid 8 through 18 Processing helix chain 'A' and resid 24 through 39 Processing helix chain 'A' and resid 40 through 48 removed outlier: 4.311A pdb=" N VAL A 44 " --> pdb=" O GLU A 40 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ALA A 45 " --> pdb=" O GLU A 41 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N TYR A 46 " --> pdb=" O ALA A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 75 Processing helix chain 'A' and resid 76 through 90 Processing helix chain 'A' and resid 93 through 99 Processing helix chain 'A' and resid 105 through 117 Processing helix chain 'A' and resid 125 through 169 removed outlier: 3.648A pdb=" N LEU A 144 " --> pdb=" O TYR A 140 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N VAL A 147 " --> pdb=" O VAL A 143 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER A 164 " --> pdb=" O SER A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 205 Processing helix chain 'A' and resid 252 through 256 Processing helix chain 'A' and resid 289 through 296 Processing helix chain 'A' and resid 313 through 323 removed outlier: 3.740A pdb=" N ARG A 323 " --> pdb=" O ASN A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 338 Processing helix chain 'A' and resid 373 through 384 removed outlier: 4.194A pdb=" N ALA A 377 " --> pdb=" O LYS A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 453 removed outlier: 3.838A pdb=" N GLU A 453 " --> pdb=" O ALA A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 483 removed outlier: 5.461A pdb=" N LYS A 471 " --> pdb=" O ASP A 467 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N GLU A 472 " --> pdb=" O GLY A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 509 Processing helix chain 'A' and resid 536 through 545 Processing helix chain 'A' and resid 549 through 566 Processing helix chain 'A' and resid 568 through 597 removed outlier: 3.531A pdb=" N LYS A 572 " --> pdb=" O PRO A 568 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N VAL A 588 " --> pdb=" O SER A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 613 Processing helix chain 'A' and resid 636 through 651 removed outlier: 4.347A pdb=" N THR A 649 " --> pdb=" O SER A 645 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG A 651 " --> pdb=" O LEU A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 708 Processing sheet with id=AA1, first strand: chain 'A' and resid 197 through 199 removed outlier: 5.741A pdb=" N VAL A 66 " --> pdb=" O ASP A 312 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N ASP A 312 " --> pdb=" O VAL A 66 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 259 through 262 Processing sheet with id=AA3, first strand: chain 'A' and resid 370 through 371 removed outlier: 6.313A pdb=" N LEU A 370 " --> pdb=" O GLU A 657 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL A 391 " --> pdb=" O ILE A 602 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLU A 606 " --> pdb=" O ILE A 393 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N LEU A 395 " --> pdb=" O GLU A 606 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N VAL A 388 " --> pdb=" O VAL A 408 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ARG A 407 " --> pdb=" O PRO A 419 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 410 through 411 Processing sheet with id=AA5, first strand: chain 'A' and resid 516 through 517 removed outlier: 3.562A pdb=" N VAL A 533 " --> pdb=" O PHE A 517 " (cutoff:3.500A) 265 hydrogen bonds defined for protein. 756 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 79 hydrogen bonds 154 hydrogen bond angles 0 basepair planarities 31 basepair parallelities 56 stacking parallelities Total time for adding SS restraints: 3.08 Time building geometry restraints manager: 1.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 6365 1.03 - 1.23: 51 1.23 - 1.42: 3348 1.42 - 1.62: 4126 1.62 - 1.81: 19 Bond restraints: 13909 Sorted by residual: bond pdb=" C1' DT D 1 " pdb=" N1 DT D 1 " ideal model delta sigma weight residual 1.468 1.509 -0.041 1.40e-02 5.10e+03 8.38e+00 bond pdb=" C1' DC D 6 " pdb=" N1 DC D 6 " ideal model delta sigma weight residual 1.468 1.504 -0.036 1.40e-02 5.10e+03 6.56e+00 bond pdb=" C1' DC D -9 " pdb=" N1 DC D -9 " ideal model delta sigma weight residual 1.468 1.504 -0.036 1.40e-02 5.10e+03 6.43e+00 bond pdb=" C3' DG D -8 " pdb=" C2' DG D -8 " ideal model delta sigma weight residual 1.516 1.534 -0.018 8.00e-03 1.56e+04 4.89e+00 bond pdb=" C1' DT C 0 " pdb=" N1 DT C 0 " ideal model delta sigma weight residual 1.468 1.499 -0.031 1.40e-02 5.10e+03 4.83e+00 ... (remaining 13904 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.07: 22874 1.07 - 2.15: 1880 2.15 - 3.22: 331 3.22 - 4.30: 57 4.30 - 5.37: 5 Bond angle restraints: 25147 Sorted by residual: angle pdb=" N3 DT C -14 " pdb=" C4 DT C -14 " pdb=" O4 DT C -14 " ideal model delta sigma weight residual 119.90 122.46 -2.56 6.00e-01 2.78e+00 1.81e+01 angle pdb=" N3 DT C 4 " pdb=" C4 DT C 4 " pdb=" O4 DT C 4 " ideal model delta sigma weight residual 119.90 122.40 -2.50 6.00e-01 2.78e+00 1.74e+01 angle pdb=" N3 DT C 0 " pdb=" C4 DT C 0 " pdb=" O4 DT C 0 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.72e+01 angle pdb=" N3 DT D -2 " pdb=" C4 DT D -2 " pdb=" O4 DT D -2 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.72e+01 angle pdb=" N3 DT C -9 " pdb=" C4 DT C -9 " pdb=" O4 DT C -9 " ideal model delta sigma weight residual 119.90 122.37 -2.47 6.00e-01 2.78e+00 1.70e+01 ... (remaining 25142 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.78: 5842 33.78 - 67.57: 387 67.57 - 101.35: 11 101.35 - 135.13: 0 135.13 - 168.92: 2 Dihedral angle restraints: 6242 sinusoidal: 3984 harmonic: 2258 Sorted by residual: dihedral pdb=" C4' A B 1 " pdb=" C3' A B 1 " pdb=" C2' A B 1 " pdb=" C1' A B 1 " ideal model delta sinusoidal sigma weight residual 36.34 -37.98 74.32 1 3.10e+00 1.04e-01 7.29e+02 dihedral pdb=" C4' A B -19 " pdb=" C3' A B -19 " pdb=" C2' A B -19 " pdb=" C1' A B -19 " ideal model delta sinusoidal sigma weight residual 36.34 -36.23 72.58 1 3.10e+00 1.04e-01 7.00e+02 dihedral pdb=" C4' U B -18 " pdb=" C3' U B -18 " pdb=" C2' U B -18 " pdb=" C1' U B -18 " ideal model delta sinusoidal sigma weight residual 36.34 -35.87 72.21 1 3.10e+00 1.04e-01 6.94e+02 ... (remaining 6239 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 988 0.061 - 0.122: 119 0.122 - 0.183: 47 0.183 - 0.244: 42 0.244 - 0.305: 11 Chirality restraints: 1207 Sorted by residual: chirality pdb=" C2' A B 1 " pdb=" C3' A B 1 " pdb=" O2' A B 1 " pdb=" C1' A B 1 " both_signs ideal model delta sigma weight residual False -2.79 -2.48 -0.30 2.00e-01 2.50e+01 2.32e+00 chirality pdb=" C2' U B -18 " pdb=" C3' U B -18 " pdb=" O2' U B -18 " pdb=" C1' U B -18 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" C2' C B -8 " pdb=" C3' C B -8 " pdb=" O2' C B -8 " pdb=" C1' C B -8 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 1.97e+00 ... (remaining 1204 not shown) Planarity restraints: 1746 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 620 " -0.021 5.00e-02 4.00e+02 3.23e-02 1.67e+00 pdb=" N PRO A 621 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO A 621 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 621 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 60 " 0.016 5.00e-02 4.00e+02 2.38e-02 9.09e-01 pdb=" N PRO A 61 " -0.041 5.00e-02 4.00e+02 pdb=" CA PRO A 61 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 61 " 0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 614 " 0.007 2.00e-02 2.50e+03 6.11e-03 8.39e-01 pdb=" CG HIS A 614 " -0.015 2.00e-02 2.50e+03 pdb=" ND1 HIS A 614 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 HIS A 614 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 HIS A 614 " 0.005 2.00e-02 2.50e+03 pdb=" NE2 HIS A 614 " 0.000 2.00e-02 2.50e+03 pdb=" HD1 HIS A 614 " -0.002 2.00e-02 2.50e+03 pdb=" HD2 HIS A 614 " 0.000 2.00e-02 2.50e+03 pdb=" HE1 HIS A 614 " -0.001 2.00e-02 2.50e+03 ... (remaining 1743 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 815 2.20 - 2.80: 25702 2.80 - 3.40: 35520 3.40 - 4.00: 47770 4.00 - 4.60: 71518 Nonbonded interactions: 181325 Sorted by model distance: nonbonded pdb=" OD1 ASN A 183 " pdb=" H GLU A 184 " model vdw 1.596 2.450 nonbonded pdb=" OE1 GLN A 386 " pdb=" H GLN A 386 " model vdw 1.625 2.450 nonbonded pdb="HH12 ARG A 582 " pdb=" OP2 G B 2 " model vdw 1.626 2.450 nonbonded pdb=" HZ1 LYS A 536 " pdb=" O5' DG C -18 " model vdw 1.636 2.450 nonbonded pdb=" HH TYR A 123 " pdb=" OH TYR A 201 " model vdw 1.679 2.450 ... (remaining 181320 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.080 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.780 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7535 Z= 0.296 Angle : 0.690 5.371 10601 Z= 0.451 Chirality : 0.067 0.305 1207 Planarity : 0.003 0.032 1048 Dihedral : 18.886 168.916 3094 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.17 % Allowed : 5.93 % Favored : 93.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.46 (0.30), residues: 663 helix: -0.22 (0.29), residues: 295 sheet: -1.50 (0.55), residues: 74 loop : -1.52 (0.33), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 538 TYR 0.010 0.001 TYR A 201 PHE 0.015 0.001 PHE A 613 TRP 0.006 0.001 TRP A 308 HIS 0.007 0.001 HIS A 614 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.30 ( 7535) covalent geometry : angle 0.69027 / 0.45 (10601) hydrogen bonds : bond 0.21570 / 14.33 ( 344) hydrogen bonds : angle 7.08980 / 5.15 ( 910) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 92 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 393 ILE cc_start: 0.9280 (mm) cc_final: 0.9040 (mt) REVERT: A 659 ARG cc_start: 0.8510 (mtt-85) cc_final: 0.8245 (mtt-85) outliers start: 1 outliers final: 0 residues processed: 93 average time/residue: 0.2244 time to fit residues: 26.7589 Evaluate side-chains 76 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.0670 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.0170 chunk 27 optimal weight: 0.6980 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 187 HIS A 650 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.076710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.066966 restraints weight = 43478.505| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 1.69 r_work: 0.2853 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2758 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.0996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7535 Z= 0.185 Angle : 0.927 24.330 10601 Z= 0.435 Chirality : 0.075 0.891 1207 Planarity : 0.005 0.038 1048 Dihedral : 19.189 172.069 1758 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.35 % Allowed : 10.12 % Favored : 89.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.32), residues: 663 helix: 0.75 (0.30), residues: 302 sheet: -1.37 (0.57), residues: 74 loop : -1.11 (0.35), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 575 TYR 0.009 0.001 TYR A 654 PHE 0.016 0.001 PHE A 613 TRP 0.006 0.001 TRP A 308 HIS 0.007 0.001 HIS A 614 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.18 ( 7535) covalent geometry : angle 0.92669 / 0.43 (10601) hydrogen bonds : bond 0.05795 / 3.86 ( 344) hydrogen bonds : angle 5.06612 / 3.65 ( 910) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 81 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 284 ARG cc_start: 0.8602 (ttm170) cc_final: 0.8392 (mtm-85) outliers start: 2 outliers final: 1 residues processed: 81 average time/residue: 0.2549 time to fit residues: 25.7898 Evaluate side-chains 75 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 74 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 467 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 69 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 54 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 3 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.077148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.067355 restraints weight = 43867.798| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 1.68 r_work: 0.2858 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.1372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7535 Z= 0.179 Angle : 0.749 12.196 10601 Z= 0.367 Chirality : 0.058 0.573 1207 Planarity : 0.004 0.044 1048 Dihedral : 19.469 174.115 1758 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.87 % Allowed : 10.30 % Favored : 88.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.33), residues: 663 helix: 1.18 (0.30), residues: 305 sheet: -1.62 (0.55), residues: 81 loop : -1.06 (0.36), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 512 TYR 0.008 0.001 TYR A 654 PHE 0.019 0.001 PHE A 354 TRP 0.006 0.001 TRP A 308 HIS 0.007 0.001 HIS A 614 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.18 ( 7535) covalent geometry : angle 0.74922 / 0.37 (10601) hydrogen bonds : bond 0.05364 / 3.62 ( 344) hydrogen bonds : angle 4.64522 / 3.36 ( 910) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 75 time to evaluate : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 GLU cc_start: 0.8039 (tm-30) cc_final: 0.7829 (tm-30) REVERT: A 284 ARG cc_start: 0.8609 (ttm170) cc_final: 0.8296 (mtt-85) outliers start: 5 outliers final: 5 residues processed: 78 average time/residue: 0.2516 time to fit residues: 24.3827 Evaluate side-chains 73 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 68 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain A residue 616 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 10 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 71 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 61 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 5 optimal weight: 0.2980 chunk 36 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.075787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.066076 restraints weight = 43913.586| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 1.67 r_work: 0.2834 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2740 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 7535 Z= 0.214 Angle : 0.731 11.467 10601 Z= 0.363 Chirality : 0.053 0.477 1207 Planarity : 0.005 0.046 1048 Dihedral : 19.422 174.060 1758 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.87 % Allowed : 11.69 % Favored : 87.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.33), residues: 663 helix: 1.42 (0.31), residues: 304 sheet: -1.86 (0.53), residues: 79 loop : -0.87 (0.36), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 512 TYR 0.010 0.001 TYR A 654 PHE 0.015 0.001 PHE A 613 TRP 0.005 0.001 TRP A 308 HIS 0.007 0.002 HIS A 614 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.21 ( 7535) covalent geometry : angle 0.73104 / 0.36 (10601) hydrogen bonds : bond 0.04801 / 3.27 ( 344) hydrogen bonds : angle 4.46519 / 3.25 ( 910) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 74 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 284 ARG cc_start: 0.8640 (ttm170) cc_final: 0.8320 (mtt-85) outliers start: 5 outliers final: 5 residues processed: 77 average time/residue: 0.2343 time to fit residues: 22.7342 Evaluate side-chains 75 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 70 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain A residue 616 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 59 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 73 optimal weight: 5.9990 chunk 10 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.077351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.067621 restraints weight = 43946.881| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 1.68 r_work: 0.2863 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7535 Z= 0.145 Angle : 0.671 9.209 10601 Z= 0.338 Chirality : 0.049 0.361 1207 Planarity : 0.004 0.036 1048 Dihedral : 19.410 173.588 1758 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.70 % Allowed : 13.09 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.34), residues: 663 helix: 1.60 (0.31), residues: 304 sheet: -1.74 (0.55), residues: 74 loop : -0.67 (0.37), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 512 TYR 0.010 0.001 TYR A 654 PHE 0.018 0.001 PHE A 354 TRP 0.006 0.001 TRP A 308 HIS 0.007 0.002 HIS A 614 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.15 ( 7535) covalent geometry : angle 0.67107 / 0.34 (10601) hydrogen bonds : bond 0.04597 / 3.16 ( 344) hydrogen bonds : angle 4.29679 / 3.13 ( 910) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 73 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 139 ARG cc_start: 0.8846 (mtm-85) cc_final: 0.8520 (mtm-85) REVERT: A 204 ILE cc_start: 0.8342 (mm) cc_final: 0.7858 (pt) REVERT: A 284 ARG cc_start: 0.8616 (ttm170) cc_final: 0.8314 (mtt-85) outliers start: 4 outliers final: 4 residues processed: 75 average time/residue: 0.2297 time to fit residues: 22.1236 Evaluate side-chains 75 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 71 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 241 CYS Chi-restraints excluded: chain A residue 325 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 41 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 27 optimal weight: 0.1980 chunk 61 optimal weight: 0.8980 chunk 50 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 73 optimal weight: 6.9990 chunk 63 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.076935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.067193 restraints weight = 43822.883| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 1.66 r_work: 0.2853 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2758 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7535 Z= 0.169 Angle : 0.669 7.410 10601 Z= 0.337 Chirality : 0.048 0.326 1207 Planarity : 0.004 0.038 1048 Dihedral : 19.329 173.399 1758 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.87 % Allowed : 13.26 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.34), residues: 663 helix: 1.77 (0.31), residues: 304 sheet: -1.85 (0.54), residues: 74 loop : -0.65 (0.37), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 155 TYR 0.009 0.001 TYR A 654 PHE 0.017 0.001 PHE A 354 TRP 0.005 0.001 TRP A 308 HIS 0.006 0.001 HIS A 614 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.17 ( 7535) covalent geometry : angle 0.66867 / 0.34 (10601) hydrogen bonds : bond 0.04442 / 3.04 ( 344) hydrogen bonds : angle 4.19254 / 3.05 ( 910) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 72 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 139 ARG cc_start: 0.8848 (mtm-85) cc_final: 0.8535 (mtm-85) REVERT: A 204 ILE cc_start: 0.8351 (mm) cc_final: 0.7883 (pt) REVERT: A 284 ARG cc_start: 0.8616 (ttm170) cc_final: 0.8312 (mtt-85) outliers start: 5 outliers final: 5 residues processed: 75 average time/residue: 0.2222 time to fit residues: 21.1406 Evaluate side-chains 75 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 70 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 241 CYS Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 616 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 63 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 70 optimal weight: 7.9990 chunk 28 optimal weight: 0.6980 chunk 7 optimal weight: 0.6980 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 295 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.076500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.066765 restraints weight = 43647.074| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 1.66 r_work: 0.2845 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2751 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7535 Z= 0.178 Angle : 0.655 7.505 10601 Z= 0.332 Chirality : 0.047 0.283 1207 Planarity : 0.005 0.070 1048 Dihedral : 19.412 172.937 1758 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.05 % Allowed : 14.31 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.34), residues: 663 helix: 1.81 (0.31), residues: 305 sheet: -1.87 (0.53), residues: 74 loop : -0.66 (0.37), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 422 TYR 0.010 0.001 TYR A 654 PHE 0.013 0.001 PHE A 613 TRP 0.005 0.001 TRP A 308 HIS 0.006 0.001 HIS A 614 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.18 ( 7535) covalent geometry : angle 0.65495 / 0.33 (10601) hydrogen bonds : bond 0.04440 / 3.05 ( 344) hydrogen bonds : angle 4.15794 / 3.03 ( 910) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 74 time to evaluate : 0.306 Fit side-chains revert: symmetry clash REVERT: A 35 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8294 (tp) REVERT: A 139 ARG cc_start: 0.8847 (mtm-85) cc_final: 0.8538 (mtm-85) REVERT: A 204 ILE cc_start: 0.8386 (mm) cc_final: 0.7941 (pt) REVERT: A 284 ARG cc_start: 0.8633 (ttm170) cc_final: 0.8329 (mtt-85) outliers start: 6 outliers final: 5 residues processed: 78 average time/residue: 0.2063 time to fit residues: 20.8972 Evaluate side-chains 78 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 72 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 241 CYS Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 325 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 60 optimal weight: 1.9990 chunk 70 optimal weight: 7.9990 chunk 44 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 58 optimal weight: 0.5980 chunk 64 optimal weight: 0.4980 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.075937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.066170 restraints weight = 43828.255| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 1.66 r_work: 0.2835 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2741 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7535 Z= 0.194 Angle : 0.660 7.308 10601 Z= 0.334 Chirality : 0.048 0.302 1207 Planarity : 0.004 0.037 1048 Dihedral : 19.476 172.669 1758 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.22 % Allowed : 14.14 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.34), residues: 663 helix: 1.83 (0.31), residues: 305 sheet: -1.91 (0.53), residues: 74 loop : -0.67 (0.37), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 155 TYR 0.011 0.001 TYR A 654 PHE 0.013 0.001 PHE A 613 TRP 0.005 0.001 TRP A 308 HIS 0.006 0.001 HIS A 614 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.19 ( 7535) covalent geometry : angle 0.66000 / 0.33 (10601) hydrogen bonds : bond 0.04442 / 3.04 ( 344) hydrogen bonds : angle 4.12930 / 3.01 ( 910) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 71 time to evaluate : 0.319 Fit side-chains revert: symmetry clash REVERT: A 35 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8298 (tp) REVERT: A 204 ILE cc_start: 0.8399 (mm) cc_final: 0.7985 (pt) REVERT: A 284 ARG cc_start: 0.8654 (ttm170) cc_final: 0.8348 (mtt-85) outliers start: 7 outliers final: 6 residues processed: 76 average time/residue: 0.2195 time to fit residues: 21.1195 Evaluate side-chains 75 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 68 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 241 CYS Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 616 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 52 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 295 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.076516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.066815 restraints weight = 44155.262| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 1.67 r_work: 0.2844 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7535 Z= 0.162 Angle : 0.647 7.272 10601 Z= 0.327 Chirality : 0.047 0.273 1207 Planarity : 0.004 0.040 1048 Dihedral : 19.475 172.525 1758 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.22 % Allowed : 14.14 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.34), residues: 663 helix: 1.88 (0.31), residues: 305 sheet: -1.79 (0.53), residues: 74 loop : -0.58 (0.38), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 155 TYR 0.011 0.001 TYR A 654 PHE 0.011 0.001 PHE A 613 TRP 0.006 0.001 TRP A 308 HIS 0.006 0.001 HIS A 614 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.16 ( 7535) covalent geometry : angle 0.64707 / 0.33 (10601) hydrogen bonds : bond 0.04312 / 2.95 ( 344) hydrogen bonds : angle 4.08975 / 2.98 ( 910) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 72 time to evaluate : 0.320 Fit side-chains revert: symmetry clash REVERT: A 35 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8261 (tp) REVERT: A 139 ARG cc_start: 0.8835 (mtm-85) cc_final: 0.8533 (mtm-85) REVERT: A 204 ILE cc_start: 0.8391 (mm) cc_final: 0.7986 (pt) REVERT: A 284 ARG cc_start: 0.8661 (ttm170) cc_final: 0.8363 (mtt-85) outliers start: 7 outliers final: 6 residues processed: 77 average time/residue: 0.2069 time to fit residues: 20.4864 Evaluate side-chains 77 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 241 CYS Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 616 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 18 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 47 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 25 optimal weight: 0.0570 chunk 31 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 overall best weight: 1.3504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 702 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.075903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.066173 restraints weight = 44071.969| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 1.65 r_work: 0.2834 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2742 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7535 Z= 0.189 Angle : 0.663 7.241 10601 Z= 0.334 Chirality : 0.047 0.281 1207 Planarity : 0.004 0.038 1048 Dihedral : 19.453 172.302 1758 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.22 % Allowed : 14.49 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.34), residues: 663 helix: 1.88 (0.31), residues: 305 sheet: -1.78 (0.53), residues: 74 loop : -0.64 (0.38), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 155 TYR 0.011 0.001 TYR A 654 PHE 0.013 0.001 PHE A 613 TRP 0.005 0.001 TRP A 308 HIS 0.006 0.001 HIS A 614 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.19 ( 7535) covalent geometry : angle 0.66308 / 0.33 (10601) hydrogen bonds : bond 0.04388 / 3.00 ( 344) hydrogen bonds : angle 4.07398 / 2.97 ( 910) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 67 time to evaluate : 0.253 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 139 ARG cc_start: 0.8839 (mtm-85) cc_final: 0.8538 (mtm-85) REVERT: A 204 ILE cc_start: 0.8403 (mm) cc_final: 0.8012 (pt) REVERT: A 284 ARG cc_start: 0.8663 (ttm170) cc_final: 0.8348 (mtt-85) outliers start: 7 outliers final: 7 residues processed: 72 average time/residue: 0.2294 time to fit residues: 21.0407 Evaluate side-chains 75 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 68 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 241 CYS Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 616 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 44 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 14 optimal weight: 0.5980 chunk 66 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 54 optimal weight: 0.6980 chunk 29 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 295 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.077052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.067338 restraints weight = 44361.980| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 1.67 r_work: 0.2856 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7535 Z= 0.141 Angle : 0.637 7.077 10601 Z= 0.322 Chirality : 0.047 0.260 1207 Planarity : 0.004 0.040 1048 Dihedral : 19.402 172.292 1758 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.22 % Allowed : 14.49 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.34), residues: 663 helix: 1.95 (0.31), residues: 305 sheet: -1.72 (0.53), residues: 74 loop : -0.58 (0.38), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 155 TYR 0.011 0.001 TYR A 654 PHE 0.011 0.001 PHE A 613 TRP 0.007 0.001 TRP A 308 HIS 0.005 0.001 HIS A 614 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.14 ( 7535) covalent geometry : angle 0.63737 / 0.32 (10601) hydrogen bonds : bond 0.04182 / 2.85 ( 344) hydrogen bonds : angle 4.03448 / 2.94 ( 910) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2948.43 seconds wall clock time: 50 minutes 44.44 seconds (3044.44 seconds total)