Starting phenix.real_space_refine on Thu Jul 2 04:30:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9z2q_73775/07_2026/9z2q_73775.cif Found real_map, /net/cci-nas-00/data/ceres_data/9z2q_73775/07_2026/9z2q_73775.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9z2q_73775/07_2026/9z2q_73775.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9z2q_73775/07_2026/9z2q_73775.map" model { file = "/net/cci-nas-00/data/ceres_data/9z2q_73775/07_2026/9z2q_73775.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9z2q_73775/07_2026/9z2q_73775.cif" } resolution = 2.88 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 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 75 5.49 5 S 31 5.16 5 C 3816 2.51 5 N 1123 2.21 5 O 1406 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6451 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4851 Classifications: {'peptide': 600} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 558} Chain breaks: 1 Chain: "B" Number of atoms: 1600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1600 Classifications: {'RNA': 75} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 5, 'rna3p_pur': 30, 'rna3p_pyr': 33} Link IDs: {'rna2p': 12, 'rna3p': 62} Time building chain proxies: 1.42, per 1000 atoms: 0.22 Number of scatterers: 6451 At special positions: 0 Unit cell: (71.832, 91.512, 106.272, 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 31 16.00 P 75 15.00 O 1406 8.00 N 1123 7.00 C 3816 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.53 Conformation dependent library (CDL) restraints added in 256.2 milliseconds 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1140 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 8 sheets defined 41.3% alpha, 17.5% beta 23 base pairs and 37 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'A' and resid 45 through 55 Processing helix chain 'A' and resid 62 through 71 Processing helix chain 'A' and resid 86 through 97 Processing helix chain 'A' and resid 98 through 103 removed outlier: 3.630A pdb=" N GLU A 103 " --> pdb=" O LYS A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 124 removed outlier: 3.706A pdb=" N GLU A 124 " --> pdb=" O TYR A 121 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 121 through 124' Processing helix chain 'A' and resid 133 through 139 Processing helix chain 'A' and resid 142 through 156 Processing helix chain 'A' and resid 163 through 165 No H-bonds generated for 'chain 'A' and resid 163 through 165' Processing helix chain 'A' and resid 166 through 173 removed outlier: 3.870A pdb=" N LEU A 170 " --> pdb=" O MET A 166 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASN A 173 " --> pdb=" O PRO A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 199 Processing helix chain 'A' and resid 217 through 229 Processing helix chain 'A' and resid 242 through 246 removed outlier: 3.663A pdb=" N ILE A 246 " --> pdb=" O ALA A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 277 removed outlier: 4.002A pdb=" N MET A 277 " --> pdb=" O ASP A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 287 Processing helix chain 'A' and resid 289 through 309 removed outlier: 4.641A pdb=" N GLY A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N LEU A 298 " --> pdb=" O GLN A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 340 removed outlier: 4.227A pdb=" N ALA A 330 " --> pdb=" O ILE A 326 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N VAL A 331 " --> pdb=" O GLU A 327 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ILE A 332 " --> pdb=" O ASP A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 385 Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 397 through 405 removed outlier: 3.779A pdb=" N HIS A 405 " --> pdb=" O LEU A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 408 No H-bonds generated for 'chain 'A' and resid 406 through 408' Processing helix chain 'A' and resid 529 through 538 removed outlier: 3.833A pdb=" N ILE A 533 " --> pdb=" O LEU A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 546 No H-bonds generated for 'chain 'A' and resid 544 through 546' Processing helix chain 'A' and resid 564 through 574 Processing helix chain 'A' and resid 607 through 612 Processing helix chain 'A' and resid 613 through 615 No H-bonds generated for 'chain 'A' and resid 613 through 615' Processing helix chain 'A' and resid 623 through 633 Processing helix chain 'A' and resid 637 through 641 Processing helix chain 'A' and resid 642 through 651 removed outlier: 3.811A pdb=" N ASP A 651 " --> pdb=" O SER A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 691 through 702 Processing sheet with id=AA1, first strand: chain 'A' and resid 116 through 117 Processing sheet with id=AA2, first strand: chain 'A' and resid 106 through 107 Processing sheet with id=AA3, first strand: chain 'A' and resid 343 through 345 Processing sheet with id=AA4, first strand: chain 'A' and resid 343 through 345 removed outlier: 3.502A pdb=" N LYS A 429 " --> pdb=" O GLY A 314 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N GLY A 314 " --> pdb=" O LYS A 429 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N TYR A 262 " --> pdb=" O ALA A 311 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N GLY A 313 " --> pdb=" O TYR A 262 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N ARG A 264 " --> pdb=" O GLY A 313 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ARG A 315 " --> pdb=" O ARG A 264 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N LEU A 266 " --> pdb=" O ARG A 315 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N VAL A 317 " --> pdb=" O LEU A 266 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N LYS A 179 " --> pdb=" O ARG A 264 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N LEU A 266 " --> pdb=" O LYS A 179 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LEU A 181 " --> pdb=" O LEU A 266 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ILE A 180 " --> pdb=" O ILE A 212 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N ASN A 214 " --> pdb=" O ILE A 180 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ASP A 182 " --> pdb=" O ASN A 214 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N VAL A 211 " --> pdb=" O MET A 237 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N VAL A 239 " --> pdb=" O VAL A 211 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ALA A 213 " --> pdb=" O VAL A 239 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N ASN A 240 " --> pdb=" O VAL A 580 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N VAL A 580 " --> pdb=" O ASN A 240 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 250 through 253 Processing sheet with id=AA6, first strand: chain 'A' and resid 366 through 367 Processing sheet with id=AA7, first strand: chain 'A' and resid 521 through 522 removed outlier: 6.737A pdb=" N LEU A 560 " --> pdb=" O VAL A 587 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 619 through 622 removed outlier: 3.595A pdb=" N ILE A 675 " --> pdb=" O TYR A 661 " (cutoff:3.500A) 184 hydrogen bonds defined for protein. 492 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 61 hydrogen bonds 106 hydrogen bond angles 0 basepair planarities 23 basepair parallelities 37 stacking parallelities Total time for adding SS restraints: 1.03 Time building geometry restraints manager: 0.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1735 1.34 - 1.45: 1486 1.45 - 1.57: 3338 1.57 - 1.69: 149 1.69 - 1.81: 50 Bond restraints: 6758 Sorted by residual: bond pdb=" N1 C B 48 " pdb=" C2 C B 48 " ideal model delta sigma weight residual 1.397 1.414 -0.017 1.00e-02 1.00e+04 2.84e+00 bond pdb=" N3 C B 48 " pdb=" C4 C B 48 " ideal model delta sigma weight residual 1.335 1.326 0.009 7.00e-03 2.04e+04 1.64e+00 bond pdb=" C8 G B 49 " pdb=" N7 G B 49 " ideal model delta sigma weight residual 1.305 1.298 0.007 6.00e-03 2.78e+04 1.42e+00 bond pdb=" N3 C B 65 " pdb=" C4 C B 65 " ideal model delta sigma weight residual 1.335 1.327 0.008 7.00e-03 2.04e+04 1.23e+00 bond pdb=" N9 A B 64 " pdb=" C4 A B 64 " ideal model delta sigma weight residual 1.374 1.380 -0.006 6.00e-03 2.78e+04 1.03e+00 ... (remaining 6753 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.26: 9336 1.26 - 2.51: 128 2.51 - 3.77: 44 3.77 - 5.02: 2 5.02 - 6.28: 4 Bond angle restraints: 9514 Sorted by residual: angle pdb=" N1 C B 48 " pdb=" C2 C B 48 " pdb=" O2 C B 48 " ideal model delta sigma weight residual 118.90 122.46 -3.56 6.00e-01 2.78e+00 3.52e+01 angle pdb=" O2 C B 48 " pdb=" C2 C B 48 " pdb=" N3 C B 48 " ideal model delta sigma weight residual 121.90 118.37 3.53 7.00e-01 2.04e+00 2.55e+01 angle pdb=" C1' C B 48 " pdb=" N1 C B 48 " pdb=" C2 C B 48 " ideal model delta sigma weight residual 118.80 124.27 -5.47 1.10e+00 8.26e-01 2.47e+01 angle pdb=" C2 C B 48 " pdb=" N1 C B 48 " pdb=" C6 C B 48 " ideal model delta sigma weight residual 120.30 118.35 1.95 4.00e-01 6.25e+00 2.37e+01 angle pdb=" N1 C B 48 " pdb=" C6 C B 48 " pdb=" C5 C B 48 " ideal model delta sigma weight residual 121.00 122.65 -1.65 5.00e-01 4.00e+00 1.10e+01 ... (remaining 9509 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.74: 4037 33.74 - 67.49: 181 67.49 - 101.23: 27 101.23 - 134.98: 1 134.98 - 168.72: 2 Dihedral angle restraints: 4248 sinusoidal: 2494 harmonic: 1754 Sorted by residual: dihedral pdb=" O4' C B 60 " pdb=" C1' C B 60 " pdb=" N1 C B 60 " pdb=" C2 C B 60 " ideal model delta sinusoidal sigma weight residual -128.00 40.72 -168.72 1 1.70e+01 3.46e-03 6.58e+01 dihedral pdb=" O4' C B 48 " pdb=" C1' C B 48 " pdb=" N1 C B 48 " pdb=" C2 C B 48 " ideal model delta sinusoidal sigma weight residual 232.00 79.18 152.82 1 1.70e+01 3.46e-03 6.28e+01 dihedral pdb=" O4' G B 15 " pdb=" C1' G B 15 " pdb=" N9 G B 15 " pdb=" C4 G B 15 " ideal model delta sinusoidal sigma weight residual -90.00 -15.18 -74.82 1 2.00e+01 2.50e-03 1.77e+01 ... (remaining 4245 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 754 0.026 - 0.053: 223 0.053 - 0.079: 66 0.079 - 0.105: 41 0.105 - 0.131: 23 Chirality restraints: 1107 Sorted by residual: chirality pdb=" CA VAL A 58 " pdb=" N VAL A 58 " pdb=" C VAL A 58 " pdb=" CB VAL A 58 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.30e-01 chirality pdb=" CA VAL A 114 " pdb=" N VAL A 114 " pdb=" C VAL A 114 " pdb=" CB VAL A 114 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.29e-01 chirality pdb=" CA VAL A 424 " pdb=" N VAL A 424 " pdb=" C VAL A 424 " pdb=" CB VAL A 424 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.73e-01 ... (remaining 1104 not shown) Planarity restraints: 941 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C B 65 " -0.024 2.00e-02 2.50e+03 1.22e-02 3.35e+00 pdb=" N1 C B 65 " 0.026 2.00e-02 2.50e+03 pdb=" C2 C B 65 " 0.002 2.00e-02 2.50e+03 pdb=" O2 C B 65 " 0.003 2.00e-02 2.50e+03 pdb=" N3 C B 65 " -0.002 2.00e-02 2.50e+03 pdb=" C4 C B 65 " -0.003 2.00e-02 2.50e+03 pdb=" N4 C B 65 " -0.007 2.00e-02 2.50e+03 pdb=" C5 C B 65 " 0.001 2.00e-02 2.50e+03 pdb=" C6 C B 65 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 531 " 0.023 5.00e-02 4.00e+02 3.41e-02 1.86e+00 pdb=" N PRO A 532 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 532 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 532 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 148 " 0.007 2.00e-02 2.50e+03 1.34e-02 1.80e+00 pdb=" C PHE A 148 " -0.023 2.00e-02 2.50e+03 pdb=" O PHE A 148 " 0.009 2.00e-02 2.50e+03 pdb=" N LEU A 149 " 0.008 2.00e-02 2.50e+03 ... (remaining 938 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 605 2.74 - 3.28: 5868 3.28 - 3.82: 11259 3.82 - 4.36: 13523 4.36 - 4.90: 21211 Nonbonded interactions: 52466 Sorted by model distance: nonbonded pdb=" O2' U B 47 " pdb=" OP1 C B 48 " model vdw 2.204 3.040 nonbonded pdb=" OP2 U B 50 " pdb=" N2 G B 59 " model vdw 2.217 3.120 nonbonded pdb=" NH2 ARG A 438 " pdb=" OP2 U B 33 " model vdw 2.281 3.120 nonbonded pdb=" OH TYR A 52 " pdb=" OD2 ASP A 274 " model vdw 2.291 3.040 nonbonded pdb=" O2 C B 17 " pdb=" N2 G B 18 " model vdw 2.321 3.120 ... (remaining 52461 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: 1.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.720 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 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 : 0.002 0.026 6758 Z= 0.126 Angle : 0.429 6.280 9514 Z= 0.309 Chirality : 0.035 0.131 1107 Planarity : 0.004 0.034 941 Dihedral : 17.584 168.723 3108 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 1.91 (0.36), residues: 596 helix: 1.70 (0.41), residues: 193 sheet: 0.38 (0.50), residues: 110 loop : 1.59 (0.37), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 700 TYR 0.012 0.001 TYR A 121 PHE 0.011 0.001 PHE A 66 TRP 0.010 0.001 TRP A 287 HIS 0.002 0.000 HIS A 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.13 ( 6758) covalent geometry : angle 0.42944 / 0.31 ( 9514) hydrogen bonds : bond 0.13962 / 8.87 ( 243) hydrogen bonds : angle 5.66214 / 4.12 ( 598) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.157 Fit side-chains REVERT: A 88 LYS cc_start: 0.8977 (mttt) cc_final: 0.8568 (tptt) REVERT: A 104 ASP cc_start: 0.9011 (m-30) cc_final: 0.8737 (p0) REVERT: A 268 ASP cc_start: 0.8161 (t70) cc_final: 0.7798 (t0) REVERT: A 606 GLU cc_start: 0.8753 (tt0) cc_final: 0.8524 (mp0) outliers start: 0 outliers final: 1 residues processed: 60 average time/residue: 0.7725 time to fit residues: 47.9975 Evaluate side-chains 38 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 37 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 49 optimal weight: 0.0770 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 20.0000 chunk 51 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 30.0000 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 overall best weight: 2.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 417 GLN A 436 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.117538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.065522 restraints weight = 11248.197| |-----------------------------------------------------------------------------| r_work (start): 0.2844 rms_B_bonded: 2.87 r_work: 0.2648 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.1446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 6758 Z= 0.282 Angle : 0.578 6.887 9514 Z= 0.300 Chirality : 0.041 0.135 1107 Planarity : 0.005 0.041 941 Dihedral : 20.558 167.639 1854 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.29 % Allowed : 6.47 % Favored : 92.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 1.88 (0.36), residues: 596 helix: 1.91 (0.40), residues: 187 sheet: 0.11 (0.50), residues: 110 loop : 1.52 (0.38), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 639 TYR 0.013 0.002 TYR A 51 PHE 0.017 0.002 PHE A 66 TRP 0.008 0.001 TRP A 120 HIS 0.004 0.001 HIS A 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00683 / 0.28 ( 6758) covalent geometry : angle 0.57803 / 0.30 ( 9514) hydrogen bonds : bond 0.05492 / 3.78 ( 243) hydrogen bonds : angle 4.58464 / 3.39 ( 598) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 35 time to evaluate : 0.208 Fit side-chains revert: symmetry clash REVERT: A 88 LYS cc_start: 0.8967 (mttt) cc_final: 0.8524 (tptt) REVERT: A 104 ASP cc_start: 0.9213 (m-30) cc_final: 0.8772 (p0) REVERT: A 154 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.8326 (mp0) REVERT: A 268 ASP cc_start: 0.8417 (t70) cc_final: 0.8203 (t0) REVERT: A 606 GLU cc_start: 0.8807 (tt0) cc_final: 0.8520 (mp0) outliers start: 7 outliers final: 1 residues processed: 39 average time/residue: 0.7026 time to fit residues: 28.6180 Evaluate side-chains 33 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 31 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 211 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 54 optimal weight: 8.9990 chunk 17 optimal weight: 0.9980 chunk 64 optimal weight: 10.0000 chunk 37 optimal weight: 0.9990 chunk 62 optimal weight: 20.0000 chunk 31 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 18 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 417 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.118682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.067132 restraints weight = 11104.280| |-----------------------------------------------------------------------------| r_work (start): 0.2869 rms_B_bonded: 2.84 r_work: 0.2672 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6758 Z= 0.137 Angle : 0.466 6.786 9514 Z= 0.243 Chirality : 0.037 0.132 1107 Planarity : 0.005 0.076 941 Dihedral : 20.609 168.574 1851 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 0.74 % Allowed : 8.13 % Favored : 91.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 1.85 (0.36), residues: 596 helix: 1.92 (0.40), residues: 188 sheet: 0.02 (0.50), residues: 110 loop : 1.51 (0.38), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 256 TYR 0.015 0.002 TYR A 646 PHE 0.014 0.001 PHE A 48 TRP 0.008 0.001 TRP A 287 HIS 0.003 0.001 HIS A 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 ( 6758) covalent geometry : angle 0.46628 / 0.24 ( 9514) hydrogen bonds : bond 0.04349 / 3.02 ( 243) hydrogen bonds : angle 4.25921 / 3.18 ( 598) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 29 time to evaluate : 0.207 Fit side-chains revert: symmetry clash REVERT: A 88 LYS cc_start: 0.8943 (mttt) cc_final: 0.8553 (tptt) REVERT: A 154 GLU cc_start: 0.8524 (mp0) cc_final: 0.8308 (mp0) REVERT: A 606 GLU cc_start: 0.8773 (tt0) cc_final: 0.8517 (mp0) outliers start: 4 outliers final: 0 residues processed: 32 average time/residue: 0.7240 time to fit residues: 24.2427 Evaluate side-chains 29 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 61 optimal weight: 20.0000 chunk 41 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 1 optimal weight: 0.2980 chunk 60 optimal weight: 10.0000 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 417 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.117764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.066552 restraints weight = 11333.742| |-----------------------------------------------------------------------------| r_work (start): 0.2853 rms_B_bonded: 2.85 r_work: 0.2657 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6758 Z= 0.161 Angle : 0.469 6.753 9514 Z= 0.243 Chirality : 0.038 0.132 1107 Planarity : 0.004 0.043 941 Dihedral : 20.596 168.375 1851 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.11 % Allowed : 9.43 % Favored : 89.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 1.81 (0.36), residues: 596 helix: 1.93 (0.40), residues: 188 sheet: -0.05 (0.49), residues: 110 loop : 1.47 (0.38), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 256 TYR 0.011 0.001 TYR A 51 PHE 0.013 0.001 PHE A 48 TRP 0.007 0.001 TRP A 287 HIS 0.002 0.001 HIS A 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.16 ( 6758) covalent geometry : angle 0.46892 / 0.24 ( 9514) hydrogen bonds : bond 0.04122 / 2.81 ( 243) hydrogen bonds : angle 4.15590 / 3.10 ( 598) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 31 time to evaluate : 0.205 Fit side-chains revert: symmetry clash REVERT: A 88 LYS cc_start: 0.8948 (mttt) cc_final: 0.8565 (tptt) REVERT: A 104 ASP cc_start: 0.9195 (m-30) cc_final: 0.8779 (p0) REVERT: A 154 GLU cc_start: 0.8605 (OUTLIER) cc_final: 0.8305 (mp0) REVERT: A 606 GLU cc_start: 0.8800 (tt0) cc_final: 0.8538 (mp0) outliers start: 6 outliers final: 1 residues processed: 35 average time/residue: 0.7376 time to fit residues: 26.9595 Evaluate side-chains 31 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 29 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 211 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 32 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 35 optimal weight: 0.0870 chunk 20 optimal weight: 0.9980 chunk 17 optimal weight: 0.2980 chunk 47 optimal weight: 0.0870 chunk 49 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 46 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 overall best weight: 0.3536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 417 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.119466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.069130 restraints weight = 11392.044| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 2.74 r_work: 0.2714 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6758 Z= 0.087 Angle : 0.438 6.700 9514 Z= 0.227 Chirality : 0.036 0.131 1107 Planarity : 0.005 0.097 941 Dihedral : 20.617 170.481 1851 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 1.29 % Allowed : 9.98 % Favored : 88.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.90 (0.36), residues: 596 helix: 1.97 (0.39), residues: 188 sheet: 0.05 (0.50), residues: 110 loop : 1.52 (0.38), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 248 TYR 0.016 0.001 TYR A 646 PHE 0.013 0.001 PHE A 48 TRP 0.007 0.001 TRP A 284 HIS 0.002 0.000 HIS A 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00191 / 0.09 ( 6758) covalent geometry : angle 0.43787 / 0.23 ( 9514) hydrogen bonds : bond 0.03490 / 2.36 ( 243) hydrogen bonds : angle 3.97364 / 2.96 ( 598) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 32 time to evaluate : 0.197 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 88 LYS cc_start: 0.8934 (mttt) cc_final: 0.8570 (tptt) REVERT: A 104 ASP cc_start: 0.9151 (m-30) cc_final: 0.8755 (p0) REVERT: A 154 GLU cc_start: 0.8585 (OUTLIER) cc_final: 0.8282 (mp0) REVERT: A 624 MET cc_start: 0.8602 (mmm) cc_final: 0.8390 (mmm) outliers start: 7 outliers final: 0 residues processed: 36 average time/residue: 0.6637 time to fit residues: 25.0238 Evaluate side-chains 31 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 30 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 56 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 63 optimal weight: 30.0000 chunk 8 optimal weight: 0.7980 chunk 34 optimal weight: 5.9990 chunk 61 optimal weight: 30.0000 chunk 51 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 417 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.118428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.067332 restraints weight = 11257.883| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 2.77 r_work: 0.2682 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6758 Z= 0.140 Angle : 0.453 6.779 9514 Z= 0.235 Chirality : 0.037 0.131 1107 Planarity : 0.004 0.042 941 Dihedral : 20.562 169.506 1851 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 0.92 % Allowed : 10.72 % Favored : 88.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 1.93 (0.36), residues: 596 helix: 2.04 (0.40), residues: 188 sheet: 0.04 (0.50), residues: 110 loop : 1.52 (0.38), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 248 TYR 0.011 0.001 TYR A 52 PHE 0.013 0.001 PHE A 48 TRP 0.007 0.001 TRP A 287 HIS 0.002 0.000 HIS A 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.14 ( 6758) covalent geometry : angle 0.45319 / 0.23 ( 9514) hydrogen bonds : bond 0.03684 / 2.47 ( 243) hydrogen bonds : angle 3.95435 / 2.94 ( 598) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 29 time to evaluate : 0.215 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 88 LYS cc_start: 0.8926 (mttt) cc_final: 0.8564 (tptt) REVERT: A 104 ASP cc_start: 0.9158 (m-30) cc_final: 0.8765 (p0) REVERT: A 154 GLU cc_start: 0.8609 (OUTLIER) cc_final: 0.8296 (mp0) outliers start: 5 outliers final: 2 residues processed: 33 average time/residue: 0.7349 time to fit residues: 25.3687 Evaluate side-chains 32 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 29 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 GLN Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 211 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 21 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 chunk 46 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 58 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 417 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.118940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.067528 restraints weight = 11411.202| |-----------------------------------------------------------------------------| r_work (start): 0.2884 rms_B_bonded: 2.79 r_work: 0.2688 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6758 Z= 0.115 Angle : 0.441 6.724 9514 Z= 0.227 Chirality : 0.036 0.132 1107 Planarity : 0.005 0.086 941 Dihedral : 20.573 170.103 1851 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 0.92 % Allowed : 10.91 % Favored : 88.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 1.92 (0.36), residues: 596 helix: 2.01 (0.40), residues: 188 sheet: 0.05 (0.50), residues: 110 loop : 1.53 (0.38), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG A 256 TYR 0.010 0.001 TYR A 52 PHE 0.013 0.001 PHE A 48 TRP 0.007 0.001 TRP A 287 HIS 0.002 0.000 HIS A 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.11 ( 6758) covalent geometry : angle 0.44065 / 0.23 ( 9514) hydrogen bonds : bond 0.03470 / 2.32 ( 243) hydrogen bonds : angle 3.91269 / 2.91 ( 598) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 31 time to evaluate : 0.189 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 88 LYS cc_start: 0.8877 (mttt) cc_final: 0.8527 (tptt) REVERT: A 104 ASP cc_start: 0.9147 (m-30) cc_final: 0.8761 (p0) REVERT: A 154 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.8267 (mp0) REVERT: A 606 GLU cc_start: 0.8807 (mp0) cc_final: 0.8475 (mp0) outliers start: 5 outliers final: 3 residues processed: 35 average time/residue: 0.7247 time to fit residues: 26.5282 Evaluate side-chains 34 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 30 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 147 GLN Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 211 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 0 optimal weight: 6.9990 chunk 14 optimal weight: 0.6980 chunk 15 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 chunk 47 optimal weight: 0.4980 chunk 45 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 63 optimal weight: 20.0000 chunk 60 optimal weight: 10.0000 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 417 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.119003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.067979 restraints weight = 11315.642| |-----------------------------------------------------------------------------| r_work (start): 0.2894 rms_B_bonded: 2.75 r_work: 0.2699 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6758 Z= 0.107 Angle : 0.433 6.707 9514 Z= 0.223 Chirality : 0.036 0.131 1107 Planarity : 0.004 0.059 941 Dihedral : 20.555 170.480 1851 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.11 % Allowed : 10.72 % Favored : 88.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 1.93 (0.36), residues: 596 helix: 1.98 (0.40), residues: 188 sheet: 0.09 (0.50), residues: 110 loop : 1.54 (0.38), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 256 TYR 0.011 0.001 TYR A 661 PHE 0.013 0.001 PHE A 48 TRP 0.006 0.001 TRP A 287 HIS 0.002 0.000 HIS A 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 ( 6758) covalent geometry : angle 0.43326 / 0.22 ( 9514) hydrogen bonds : bond 0.03354 / 2.23 ( 243) hydrogen bonds : angle 3.85575 / 2.87 ( 598) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 30 time to evaluate : 0.215 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 88 LYS cc_start: 0.8863 (mttt) cc_final: 0.8514 (tptt) REVERT: A 104 ASP cc_start: 0.9139 (m-30) cc_final: 0.8761 (p0) REVERT: A 154 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.8246 (mp0) REVERT: A 606 GLU cc_start: 0.8806 (mp0) cc_final: 0.8459 (mp0) outliers start: 6 outliers final: 3 residues processed: 35 average time/residue: 0.7147 time to fit residues: 26.1921 Evaluate side-chains 33 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 29 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 GLN Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 424 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 53 optimal weight: 1.9990 chunk 62 optimal weight: 20.0000 chunk 39 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 66 optimal weight: 10.0000 chunk 65 optimal weight: 10.0000 chunk 35 optimal weight: 0.9980 chunk 49 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 417 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.117733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.066192 restraints weight = 11545.398| |-----------------------------------------------------------------------------| r_work (start): 0.2856 rms_B_bonded: 2.76 r_work: 0.2659 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6758 Z= 0.169 Angle : 0.473 7.723 9514 Z= 0.242 Chirality : 0.037 0.134 1107 Planarity : 0.005 0.064 941 Dihedral : 20.533 169.139 1851 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.11 % Allowed : 11.09 % Favored : 87.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 1.83 (0.36), residues: 596 helix: 1.93 (0.40), residues: 188 sheet: -0.02 (0.49), residues: 110 loop : 1.49 (0.38), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 256 TYR 0.011 0.002 TYR A 52 PHE 0.013 0.001 PHE A 48 TRP 0.008 0.001 TRP A 287 HIS 0.002 0.001 HIS A 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.17 ( 6758) covalent geometry : angle 0.47256 / 0.24 ( 9514) hydrogen bonds : bond 0.03745 / 2.47 ( 243) hydrogen bonds : angle 3.97116 / 2.95 ( 598) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 27 time to evaluate : 0.217 Fit side-chains revert: symmetry clash REVERT: A 88 LYS cc_start: 0.8884 (mttt) cc_final: 0.8534 (tptt) REVERT: A 104 ASP cc_start: 0.9147 (m-30) cc_final: 0.8771 (p0) REVERT: A 154 GLU cc_start: 0.8604 (mp0) cc_final: 0.8307 (mp0) REVERT: A 546 MET cc_start: 0.8916 (mmm) cc_final: 0.8674 (mmt) outliers start: 6 outliers final: 3 residues processed: 32 average time/residue: 0.8044 time to fit residues: 26.8897 Evaluate side-chains 30 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 27 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 GLN Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 424 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 47 optimal weight: 0.0370 chunk 45 optimal weight: 0.5980 chunk 24 optimal weight: 0.0870 chunk 16 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 35 optimal weight: 0.0980 chunk 25 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 8 optimal weight: 0.4980 overall best weight: 0.2636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 417 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.119706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.069005 restraints weight = 11186.596| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 2.76 r_work: 0.2714 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6758 Z= 0.083 Angle : 0.454 10.707 9514 Z= 0.230 Chirality : 0.036 0.131 1107 Planarity : 0.004 0.045 941 Dihedral : 20.562 171.367 1851 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 0.74 % Allowed : 11.28 % Favored : 87.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.90 (0.36), residues: 596 helix: 1.91 (0.40), residues: 189 sheet: 0.11 (0.50), residues: 110 loop : 1.54 (0.38), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 256 TYR 0.011 0.001 TYR A 52 PHE 0.013 0.001 PHE A 48 TRP 0.009 0.001 TRP A 284 HIS 0.002 0.000 HIS A 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00180 / 0.08 ( 6758) covalent geometry : angle 0.45437 / 0.23 ( 9514) hydrogen bonds : bond 0.03176 / 2.09 ( 243) hydrogen bonds : angle 3.82420 / 2.85 ( 598) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 31 time to evaluate : 0.222 Fit side-chains revert: symmetry clash REVERT: A 88 LYS cc_start: 0.8849 (mttt) cc_final: 0.8482 (tptt) REVERT: A 154 GLU cc_start: 0.8514 (mp0) cc_final: 0.8226 (mp0) outliers start: 4 outliers final: 2 residues processed: 35 average time/residue: 0.6986 time to fit residues: 25.6016 Evaluate side-chains 29 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 27 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 GLN Chi-restraints excluded: chain A residue 211 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 45 optimal weight: 1.9990 chunk 64 optimal weight: 10.0000 chunk 23 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 49 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 1 optimal weight: 0.0870 chunk 47 optimal weight: 0.0010 chunk 13 optimal weight: 0.9980 overall best weight: 0.4764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 417 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.119630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.068699 restraints weight = 11226.287| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 2.78 r_work: 0.2710 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 6758 Z= 0.092 Angle : 0.455 8.020 9514 Z= 0.233 Chirality : 0.036 0.145 1107 Planarity : 0.005 0.059 941 Dihedral : 20.530 171.261 1851 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.11 % Allowed : 11.28 % Favored : 87.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 1.91 (0.36), residues: 596 helix: 1.88 (0.40), residues: 190 sheet: 0.19 (0.51), residues: 110 loop : 1.53 (0.38), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 256 TYR 0.010 0.001 TYR A 52 PHE 0.012 0.001 PHE A 48 TRP 0.007 0.001 TRP A 284 HIS 0.002 0.000 HIS A 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00210 / 0.09 ( 6758) covalent geometry : angle 0.45546 / 0.23 ( 9514) hydrogen bonds : bond 0.03169 / 2.08 ( 243) hydrogen bonds : angle 3.77752 / 2.81 ( 598) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1906.76 seconds wall clock time: 33 minutes 23.54 seconds (2003.54 seconds total)