Starting phenix.real_space_refine on Tue Aug 4 13:05:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/21nq_67847/08_2026/21nq_67847_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/21nq_67847/08_2026/21nq_67847.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/21nq_67847/08_2026/21nq_67847.map" default_real_map = "/net/cci-nas-00/data/ceres_data/21nq_67847/08_2026/21nq_67847.map" model { file = "/net/cci-nas-00/data/ceres_data/21nq_67847/08_2026/21nq_67847_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/21nq_67847/08_2026/21nq_67847_neut.cif" } resolution = 2.8 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= 0.000 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: 4 Type Number sf(0) Gaussians S 19 5.16 5 C 2078 2.51 5 N 505 2.21 5 O 557 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3159 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3159 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 16, 'TRANS': 397} Chain breaks: 1 Time building chain proxies: 0.93, per 1000 atoms: 0.29 Number of scatterers: 3159 At special positions: 0 Unit cell: (74.562, 54.91, 72.828, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 19 16.00 O 557 8.00 N 505 7.00 C 2078 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: 0.26 Conformation dependent library (CDL) restraints added in 121.4 milliseconds 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 746 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 0 sheets defined 88.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.08 Creating SS restraints... Processing helix chain 'A' and resid 5 through 29 removed outlier: 3.594A pdb=" N TYR A 9 " --> pdb=" O GLY A 5 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 42 Proline residue: A 36 - end of helix Processing helix chain 'A' and resid 45 through 74 Processing helix chain 'A' and resid 75 through 97 removed outlier: 3.605A pdb=" N LEU A 79 " --> pdb=" O SER A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 115 removed outlier: 3.679A pdb=" N GLY A 115 " --> pdb=" O GLY A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 129 removed outlier: 3.804A pdb=" N CYS A 121 " --> pdb=" O GLY A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 132 No H-bonds generated for 'chain 'A' and resid 130 through 132' Processing helix chain 'A' and resid 133 through 164 removed outlier: 3.591A pdb=" N TRP A 137 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N SER A 144 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N MET A 145 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ASN A 146 " --> pdb=" O SER A 142 " (cutoff:3.500A) Proline residue: A 153 - end of helix removed outlier: 3.530A pdb=" N SER A 164 " --> pdb=" O ALA A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 187 Processing helix chain 'A' and resid 190 through 195 Processing helix chain 'A' and resid 216 through 222 Processing helix chain 'A' and resid 223 through 254 removed outlier: 3.802A pdb=" N TRP A 227 " --> pdb=" O SER A 223 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N GLN A 248 " --> pdb=" O THR A 244 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N PHE A 249 " --> pdb=" O ASP A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 290 Processing helix chain 'A' and resid 300 through 321 Processing helix chain 'A' and resid 327 through 357 Proline residue: A 345 - end of helix removed outlier: 3.508A pdb=" N GLY A 350 " --> pdb=" O ILE A 346 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA A 357 " --> pdb=" O ALA A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 380 Processing helix chain 'A' and resid 381 through 391 Processing helix chain 'A' and resid 392 through 414 272 hydrogen bonds defined for protein. 807 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.54 Time building geometry restraints manager: 0.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 540 1.33 - 1.45: 922 1.45 - 1.57: 1754 1.57 - 1.70: 0 1.70 - 1.82: 31 Bond restraints: 3247 Sorted by residual: bond pdb=" CA THR A 143 " pdb=" C THR A 143 " ideal model delta sigma weight residual 1.522 1.479 0.043 1.37e-02 5.33e+03 9.85e+00 bond pdb=" C THR A 143 " pdb=" O THR A 143 " ideal model delta sigma weight residual 1.236 1.205 0.031 1.31e-02 5.83e+03 5.64e+00 bond pdb=" C LEU A 151 " pdb=" N GLY A 152 " ideal model delta sigma weight residual 1.340 1.331 0.009 6.60e-03 2.30e+04 2.02e+00 bond pdb=" C THR A 143 " pdb=" N SER A 144 " ideal model delta sigma weight residual 1.335 1.317 0.018 1.31e-02 5.83e+03 1.86e+00 bond pdb=" CB GLU A 41 " pdb=" CG GLU A 41 " ideal model delta sigma weight residual 1.520 1.560 -0.040 3.00e-02 1.11e+03 1.74e+00 ... (remaining 3242 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.51: 4361 2.51 - 5.03: 46 5.03 - 7.54: 9 7.54 - 10.05: 1 10.05 - 12.56: 2 Bond angle restraints: 4419 Sorted by residual: angle pdb=" CB MET A 372 " pdb=" CG MET A 372 " pdb=" SD MET A 372 " ideal model delta sigma weight residual 112.70 125.26 -12.56 3.00e+00 1.11e-01 1.75e+01 angle pdb=" CB MET A 35 " pdb=" CG MET A 35 " pdb=" SD MET A 35 " ideal model delta sigma weight residual 112.70 123.38 -10.68 3.00e+00 1.11e-01 1.27e+01 angle pdb=" CB GLU A 41 " pdb=" CG GLU A 41 " pdb=" CD GLU A 41 " ideal model delta sigma weight residual 112.60 117.67 -5.07 1.70e+00 3.46e-01 8.91e+00 angle pdb=" CA GLU A 41 " pdb=" CB GLU A 41 " pdb=" CG GLU A 41 " ideal model delta sigma weight residual 114.10 119.93 -5.83 2.00e+00 2.50e-01 8.50e+00 angle pdb=" CG ARG A 197 " pdb=" CD ARG A 197 " pdb=" NE ARG A 197 " ideal model delta sigma weight residual 112.00 118.12 -6.12 2.20e+00 2.07e-01 7.73e+00 ... (remaining 4414 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.13: 1574 16.13 - 32.26: 192 32.26 - 48.39: 65 48.39 - 64.53: 13 64.53 - 80.66: 1 Dihedral angle restraints: 1845 sinusoidal: 671 harmonic: 1174 Sorted by residual: dihedral pdb=" CA SER A 75 " pdb=" C SER A 75 " pdb=" N ALA A 76 " pdb=" CA ALA A 76 " ideal model delta harmonic sigma weight residual 180.00 -161.39 -18.61 0 5.00e+00 4.00e-02 1.39e+01 dihedral pdb=" CA GLN A 248 " pdb=" CB GLN A 248 " pdb=" CG GLN A 248 " pdb=" CD GLN A 248 " ideal model delta sinusoidal sigma weight residual -180.00 -124.35 -55.65 3 1.50e+01 4.44e-03 9.36e+00 dihedral pdb=" N LEU A 70 " pdb=" CA LEU A 70 " pdb=" CB LEU A 70 " pdb=" CG LEU A 70 " ideal model delta sinusoidal sigma weight residual -180.00 -129.12 -50.88 3 1.50e+01 4.44e-03 8.95e+00 ... (remaining 1842 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 371 0.043 - 0.086: 105 0.086 - 0.129: 22 0.129 - 0.172: 0 0.172 - 0.214: 1 Chirality restraints: 499 Sorted by residual: chirality pdb=" CB THR A 143 " pdb=" CA THR A 143 " pdb=" OG1 THR A 143 " pdb=" CG2 THR A 143 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CA ILE A 42 " pdb=" N ILE A 42 " pdb=" C ILE A 42 " pdb=" CB ILE A 42 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.98e-01 chirality pdb=" CB THR A 30 " pdb=" CA THR A 30 " pdb=" OG1 THR A 30 " pdb=" CG2 THR A 30 " both_signs ideal model delta sigma weight residual False 2.55 2.43 0.12 2.00e-01 2.50e+01 3.49e-01 ... (remaining 496 not shown) Planarity restraints: 543 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 384 " 0.025 2.00e-02 2.50e+03 2.36e-02 9.74e+00 pdb=" CG PHE A 384 " -0.054 2.00e-02 2.50e+03 pdb=" CD1 PHE A 384 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE A 384 " 0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE A 384 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 PHE A 384 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 384 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 8 " -0.010 2.00e-02 2.50e+03 1.39e-02 3.89e+00 pdb=" CG TYR A 8 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR A 8 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR A 8 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 TYR A 8 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR A 8 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 8 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 8 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A 298 " -0.030 5.00e-02 4.00e+02 4.50e-02 3.24e+00 pdb=" N PRO A 299 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 299 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 299 " -0.025 5.00e-02 4.00e+02 ... (remaining 540 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 808 2.79 - 3.32: 3184 3.32 - 3.85: 5461 3.85 - 4.37: 5978 4.37 - 4.90: 10570 Nonbonded interactions: 26001 Sorted by model distance: nonbonded pdb=" OG SER A 284 " pdb=" NH1 ARG A 300 " model vdw 2.268 3.120 nonbonded pdb=" O TRP A 78 " pdb=" OG SER A 82 " model vdw 2.270 3.040 nonbonded pdb=" OG SER A 63 " pdb=" O LEU A 112 " model vdw 2.326 3.040 nonbonded pdb=" O PHE A 338 " pdb=" OG SER A 342 " model vdw 2.393 3.040 nonbonded pdb=" OD2 ASP A 72 " pdb=" OG1 THR A 364 " model vdw 2.409 3.040 ... (remaining 25996 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.040 Find NCS groups from input model: 0.010 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:6.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 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 0.043 3247 Z= 0.179 Angle : 0.682 12.563 4419 Z= 0.343 Chirality : 0.039 0.214 499 Planarity : 0.006 0.058 543 Dihedral : 15.907 80.656 1099 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.50 % Allowed : 23.72 % Favored : 74.77 % 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: 3.21 (0.41), residues: 410 helix: 2.31 (0.27), residues: 344 sheet: None (None), residues: 0 loop : 1.31 (0.78), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 197 TYR 0.034 0.002 TYR A 8 PHE 0.054 0.002 PHE A 384 TRP 0.012 0.001 TRP A 138 HIS 0.004 0.001 HIS A 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.18 ( 3247) covalent geometry : angle 0.68221 / 0.34 ( 4419) hydrogen bonds : bond 0.10418 / 6.96 ( 272) hydrogen bonds : angle 4.49333 / 3.29 ( 807) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 63 time to evaluate : 0.072 Fit side-chains REVERT: A 97 SER cc_start: 0.8388 (m) cc_final: 0.8035 (p) REVERT: A 216 THR cc_start: 0.8179 (OUTLIER) cc_final: 0.7944 (p) outliers start: 5 outliers final: 2 residues processed: 68 average time/residue: 0.5332 time to fit residues: 37.2510 Evaluate side-chains 63 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 60 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 407 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 24 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.3980 chunk 25 optimal weight: 2.9990 chunk 19 optimal weight: 0.0870 chunk 30 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 chunk 37 optimal weight: 0.9980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 27 ASN ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.101668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.085390 restraints weight = 5487.768| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 2.65 r_work: 0.3033 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.0998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3247 Z= 0.141 Angle : 0.558 6.903 4419 Z= 0.289 Chirality : 0.038 0.145 499 Planarity : 0.005 0.043 543 Dihedral : 4.139 20.136 443 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.70 % Allowed : 22.82 % Favored : 74.47 % 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: 3.29 (0.41), residues: 410 helix: 2.34 (0.27), residues: 348 sheet: None (None), residues: 0 loop : 1.42 (0.84), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 197 TYR 0.020 0.001 TYR A 8 PHE 0.021 0.001 PHE A 384 TRP 0.011 0.001 TRP A 165 HIS 0.002 0.001 HIS A 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.14 ( 3247) covalent geometry : angle 0.55824 / 0.29 ( 4419) hydrogen bonds : bond 0.05311 / 3.49 ( 272) hydrogen bonds : angle 3.97451 / 2.89 ( 807) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 61 time to evaluate : 0.122 Fit side-chains REVERT: A 77 ARG cc_start: 0.8067 (OUTLIER) cc_final: 0.7089 (ttm170) REVERT: A 97 SER cc_start: 0.8529 (m) cc_final: 0.8209 (p) REVERT: A 130 GLU cc_start: 0.7343 (mp0) cc_final: 0.7132 (mp0) REVERT: A 161 GLN cc_start: 0.8857 (OUTLIER) cc_final: 0.8375 (pp30) REVERT: A 219 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7762 (pt0) outliers start: 9 outliers final: 3 residues processed: 68 average time/residue: 0.4793 time to fit residues: 33.6343 Evaluate side-chains 67 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 62 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 TYR Chi-restraints excluded: chain A residue 77 ARG Chi-restraints excluded: chain A residue 161 GLN Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 260 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 4 optimal weight: 0.4980 chunk 14 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 chunk 25 optimal weight: 5.9990 chunk 32 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 27 ASN ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.101484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.085015 restraints weight = 5428.357| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 2.63 r_work: 0.3026 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.1213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3247 Z= 0.141 Angle : 0.551 9.524 4419 Z= 0.282 Chirality : 0.037 0.135 499 Planarity : 0.005 0.041 543 Dihedral : 3.743 15.831 440 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.30 % Allowed : 21.62 % Favored : 75.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 3.32 (0.41), residues: 410 helix: 2.35 (0.27), residues: 348 sheet: None (None), residues: 0 loop : 1.45 (0.84), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 197 TYR 0.018 0.001 TYR A 8 PHE 0.024 0.001 PHE A 384 TRP 0.010 0.001 TRP A 138 HIS 0.001 0.001 HIS A 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.14 ( 3247) covalent geometry : angle 0.55125 / 0.28 ( 4419) hydrogen bonds : bond 0.05150 / 3.41 ( 272) hydrogen bonds : angle 3.91615 / 2.85 ( 807) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.122 Fit side-chains REVERT: A 4 GLN cc_start: 0.7687 (mt0) cc_final: 0.7410 (tt0) REVERT: A 77 ARG cc_start: 0.8041 (OUTLIER) cc_final: 0.7050 (ttm170) REVERT: A 97 SER cc_start: 0.8546 (m) cc_final: 0.8244 (p) REVERT: A 130 GLU cc_start: 0.7431 (mp0) cc_final: 0.7206 (mp0) REVERT: A 161 GLN cc_start: 0.8878 (OUTLIER) cc_final: 0.8411 (pp30) REVERT: A 216 THR cc_start: 0.8301 (m) cc_final: 0.7781 (p) REVERT: A 219 GLU cc_start: 0.8144 (mt-10) cc_final: 0.7716 (pt0) REVERT: A 421 MET cc_start: 0.8674 (OUTLIER) cc_final: 0.7584 (mmm) outliers start: 11 outliers final: 4 residues processed: 71 average time/residue: 0.5274 time to fit residues: 38.5323 Evaluate side-chains 67 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 60 time to evaluate : 0.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 TYR Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 77 ARG Chi-restraints excluded: chain A residue 161 GLN Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 421 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 14 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 15 optimal weight: 0.0020 chunk 7 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 overall best weight: 0.9590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 114 GLN ** 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 = 0.3420 r_free = 0.3420 target = 0.099684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.083268 restraints weight = 5564.741| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 2.70 r_work: 0.2998 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3247 Z= 0.151 Angle : 0.557 10.222 4419 Z= 0.281 Chirality : 0.037 0.135 499 Planarity : 0.005 0.041 543 Dihedral : 3.641 12.219 440 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 4.80 % Allowed : 19.52 % Favored : 75.68 % 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: 3.31 (0.41), residues: 410 helix: 2.35 (0.27), residues: 349 sheet: None (None), residues: 0 loop : 1.41 (0.84), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 197 TYR 0.013 0.001 TYR A 24 PHE 0.021 0.001 PHE A 384 TRP 0.010 0.001 TRP A 138 HIS 0.002 0.001 HIS A 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.15 ( 3247) covalent geometry : angle 0.55674 / 0.28 ( 4419) hydrogen bonds : bond 0.05185 / 3.43 ( 272) hydrogen bonds : angle 3.90671 / 2.84 ( 807) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 61 time to evaluate : 0.118 Fit side-chains REVERT: A 77 ARG cc_start: 0.7992 (OUTLIER) cc_final: 0.6984 (ttm170) REVERT: A 97 SER cc_start: 0.8590 (m) cc_final: 0.8280 (p) REVERT: A 130 GLU cc_start: 0.7462 (mp0) cc_final: 0.7147 (mp0) REVERT: A 161 GLN cc_start: 0.8893 (pt0) cc_final: 0.8455 (pp30) REVERT: A 216 THR cc_start: 0.8312 (m) cc_final: 0.7914 (p) REVERT: A 219 GLU cc_start: 0.8177 (mt-10) cc_final: 0.7897 (mt-10) outliers start: 16 outliers final: 6 residues processed: 73 average time/residue: 0.4457 time to fit residues: 33.6382 Evaluate side-chains 71 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 64 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 TYR Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 77 ARG Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 421 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 2 optimal weight: 0.6980 chunk 25 optimal weight: 5.9990 chunk 22 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 30 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 chunk 15 optimal weight: 0.0870 chunk 32 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 114 GLN ** 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 = 0.3441 r_free = 0.3441 target = 0.100437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.083754 restraints weight = 5559.813| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 2.73 r_work: 0.3018 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3247 Z= 0.134 Angle : 0.562 9.218 4419 Z= 0.282 Chirality : 0.037 0.129 499 Planarity : 0.005 0.045 543 Dihedral : 3.645 12.569 440 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.60 % Allowed : 19.52 % Favored : 76.88 % 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: 3.24 (0.41), residues: 410 helix: 2.32 (0.27), residues: 348 sheet: None (None), residues: 0 loop : 1.23 (0.81), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 197 TYR 0.017 0.001 TYR A 8 PHE 0.026 0.001 PHE A 384 TRP 0.009 0.001 TRP A 138 HIS 0.001 0.001 HIS A 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.13 ( 3247) covalent geometry : angle 0.56224 / 0.28 ( 4419) hydrogen bonds : bond 0.04978 / 3.30 ( 272) hydrogen bonds : angle 3.89631 / 2.84 ( 807) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 0.119 Fit side-chains revert: symmetry clash REVERT: A 77 ARG cc_start: 0.7957 (OUTLIER) cc_final: 0.6971 (ttm170) REVERT: A 97 SER cc_start: 0.8596 (m) cc_final: 0.8276 (p) REVERT: A 130 GLU cc_start: 0.7442 (mp0) cc_final: 0.7183 (mp0) REVERT: A 161 GLN cc_start: 0.8865 (OUTLIER) cc_final: 0.8431 (pp30) REVERT: A 216 THR cc_start: 0.8285 (m) cc_final: 0.7886 (p) REVERT: A 219 GLU cc_start: 0.8168 (mt-10) cc_final: 0.7886 (mt-10) outliers start: 12 outliers final: 4 residues processed: 74 average time/residue: 0.4502 time to fit residues: 34.3519 Evaluate side-chains 67 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 61 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 TYR Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 77 ARG Chi-restraints excluded: chain A residue 161 GLN Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 304 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 3 optimal weight: 0.0870 chunk 21 optimal weight: 0.0980 chunk 2 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 37 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 24 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 114 GLN ** 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 = 0.3454 r_free = 0.3454 target = 0.101403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.084803 restraints weight = 5586.543| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 2.74 r_work: 0.3027 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3247 Z= 0.131 Angle : 0.570 11.672 4419 Z= 0.283 Chirality : 0.037 0.132 499 Planarity : 0.005 0.049 543 Dihedral : 3.622 12.779 440 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.60 % Allowed : 21.02 % Favored : 75.38 % 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: 3.27 (0.41), residues: 410 helix: 2.34 (0.27), residues: 348 sheet: None (None), residues: 0 loop : 1.25 (0.82), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 197 TYR 0.011 0.001 TYR A 24 PHE 0.023 0.001 PHE A 384 TRP 0.009 0.001 TRP A 138 HIS 0.002 0.001 HIS A 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.13 ( 3247) covalent geometry : angle 0.57016 / 0.28 ( 4419) hydrogen bonds : bond 0.04870 / 3.22 ( 272) hydrogen bonds : angle 3.84694 / 2.80 ( 807) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 0.125 Fit side-chains REVERT: A 35 MET cc_start: 0.8626 (OUTLIER) cc_final: 0.8419 (tpt) REVERT: A 77 ARG cc_start: 0.7988 (OUTLIER) cc_final: 0.7014 (ttm170) REVERT: A 97 SER cc_start: 0.8604 (m) cc_final: 0.8308 (p) REVERT: A 130 GLU cc_start: 0.7517 (mp0) cc_final: 0.7231 (mp0) REVERT: A 161 GLN cc_start: 0.8874 (OUTLIER) cc_final: 0.8465 (pp30) REVERT: A 216 THR cc_start: 0.8317 (m) cc_final: 0.7908 (p) REVERT: A 219 GLU cc_start: 0.8158 (mt-10) cc_final: 0.7868 (mt-10) outliers start: 12 outliers final: 3 residues processed: 72 average time/residue: 0.4265 time to fit residues: 31.6902 Evaluate side-chains 68 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 62 time to evaluate : 0.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 TYR Chi-restraints excluded: chain A residue 35 MET Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 77 ARG Chi-restraints excluded: chain A residue 161 GLN Chi-restraints excluded: chain A residue 260 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 37 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 31 optimal weight: 0.0670 chunk 26 optimal weight: 2.9990 chunk 11 optimal weight: 0.0770 chunk 35 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 overall best weight: 0.6080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 114 GLN ** 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 = 0.3456 r_free = 0.3456 target = 0.101886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.085291 restraints weight = 5684.073| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 2.78 r_work: 0.3034 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3247 Z= 0.136 Angle : 0.584 12.891 4419 Z= 0.295 Chirality : 0.037 0.139 499 Planarity : 0.005 0.057 543 Dihedral : 3.727 16.550 440 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.90 % Allowed : 20.72 % Favored : 75.38 % 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: 3.21 (0.41), residues: 410 helix: 2.32 (0.27), residues: 348 sheet: None (None), residues: 0 loop : 1.16 (0.82), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 197 TYR 0.013 0.001 TYR A 233 PHE 0.023 0.001 PHE A 384 TRP 0.008 0.001 TRP A 138 HIS 0.001 0.000 HIS A 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.14 ( 3247) covalent geometry : angle 0.58404 / 0.29 ( 4419) hydrogen bonds : bond 0.04877 / 3.23 ( 272) hydrogen bonds : angle 3.86820 / 2.82 ( 807) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 65 time to evaluate : 0.123 Fit side-chains revert: symmetry clash REVERT: A 77 ARG cc_start: 0.7976 (OUTLIER) cc_final: 0.7035 (ttm170) REVERT: A 97 SER cc_start: 0.8576 (m) cc_final: 0.8276 (p) REVERT: A 130 GLU cc_start: 0.7512 (mp0) cc_final: 0.7205 (mp0) REVERT: A 161 GLN cc_start: 0.8868 (OUTLIER) cc_final: 0.8470 (pp30) REVERT: A 216 THR cc_start: 0.8333 (m) cc_final: 0.7907 (p) REVERT: A 219 GLU cc_start: 0.8185 (mt-10) cc_final: 0.7877 (mt-10) outliers start: 13 outliers final: 4 residues processed: 75 average time/residue: 0.4900 time to fit residues: 37.9054 Evaluate side-chains 66 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 60 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 TYR Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 77 ARG Chi-restraints excluded: chain A residue 161 GLN Chi-restraints excluded: chain A residue 260 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 33 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 14 optimal weight: 0.0370 chunk 36 optimal weight: 0.1980 chunk 28 optimal weight: 1.9990 overall best weight: 0.6262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 114 GLN ** 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 = 0.3455 r_free = 0.3455 target = 0.101818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.085362 restraints weight = 5663.076| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 2.75 r_work: 0.3036 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3247 Z= 0.140 Angle : 0.609 11.654 4419 Z= 0.305 Chirality : 0.038 0.136 499 Planarity : 0.005 0.059 543 Dihedral : 3.854 16.196 440 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.70 % Allowed : 22.52 % Favored : 74.77 % 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: 3.15 (0.41), residues: 410 helix: 2.27 (0.27), residues: 348 sheet: None (None), residues: 0 loop : 1.15 (0.81), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 197 TYR 0.022 0.001 TYR A 8 PHE 0.019 0.001 PHE A 384 TRP 0.009 0.001 TRP A 138 HIS 0.001 0.000 HIS A 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.14 ( 3247) covalent geometry : angle 0.60861 / 0.31 ( 4419) hydrogen bonds : bond 0.04891 / 3.24 ( 272) hydrogen bonds : angle 3.92766 / 2.87 ( 807) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 0.116 Fit side-chains revert: symmetry clash REVERT: A 77 ARG cc_start: 0.8002 (OUTLIER) cc_final: 0.7041 (ttm170) REVERT: A 97 SER cc_start: 0.8605 (m) cc_final: 0.8321 (p) REVERT: A 130 GLU cc_start: 0.7525 (mp0) cc_final: 0.7226 (mp0) REVERT: A 161 GLN cc_start: 0.8858 (OUTLIER) cc_final: 0.8464 (pp30) REVERT: A 216 THR cc_start: 0.8355 (m) cc_final: 0.7946 (p) REVERT: A 219 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7926 (mt-10) outliers start: 9 outliers final: 4 residues processed: 70 average time/residue: 0.4933 time to fit residues: 35.6355 Evaluate side-chains 70 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 64 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 TYR Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 77 ARG Chi-restraints excluded: chain A residue 161 GLN Chi-restraints excluded: chain A residue 260 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 15 optimal weight: 1.9990 chunk 20 optimal weight: 0.1980 chunk 25 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 = 0.3376 r_free = 0.3376 target = 0.097489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.080734 restraints weight = 5575.865| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 2.70 r_work: 0.2943 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3247 Z= 0.178 Angle : 0.657 11.099 4419 Z= 0.326 Chirality : 0.040 0.152 499 Planarity : 0.006 0.067 543 Dihedral : 3.906 16.229 440 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.00 % Allowed : 23.12 % Favored : 73.87 % 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: 3.02 (0.41), residues: 410 helix: 2.20 (0.27), residues: 348 sheet: None (None), residues: 0 loop : 1.01 (0.79), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 197 TYR 0.018 0.002 TYR A 8 PHE 0.021 0.001 PHE A 384 TRP 0.009 0.001 TRP A 138 HIS 0.001 0.000 HIS A 390 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.18 ( 3247) covalent geometry : angle 0.65723 / 0.33 ( 4419) hydrogen bonds : bond 0.05259 / 3.49 ( 272) hydrogen bonds : angle 4.06214 / 2.99 ( 807) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.126 Fit side-chains revert: symmetry clash REVERT: A 77 ARG cc_start: 0.8005 (OUTLIER) cc_final: 0.7011 (ttm170) REVERT: A 97 SER cc_start: 0.8640 (m) cc_final: 0.8357 (p) REVERT: A 130 GLU cc_start: 0.7544 (mp0) cc_final: 0.7219 (mp0) REVERT: A 161 GLN cc_start: 0.8879 (OUTLIER) cc_final: 0.8491 (pp30) REVERT: A 216 THR cc_start: 0.8331 (m) cc_final: 0.7811 (p) REVERT: A 219 GLU cc_start: 0.8239 (mt-10) cc_final: 0.7941 (mt-10) outliers start: 10 outliers final: 5 residues processed: 70 average time/residue: 0.5319 time to fit residues: 38.3145 Evaluate side-chains 67 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 60 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 TYR Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 77 ARG Chi-restraints excluded: chain A residue 107 TRP Chi-restraints excluded: chain A residue 161 GLN Chi-restraints excluded: chain A residue 260 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 8 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 3 optimal weight: 0.3980 chunk 18 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 114 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.100726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 20)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.084459 restraints weight = 5499.689| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 2.67 r_work: 0.2985 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3247 Z= 0.148 Angle : 0.634 10.772 4419 Z= 0.317 Chirality : 0.039 0.133 499 Planarity : 0.006 0.077 543 Dihedral : 3.965 15.386 440 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.10 % Allowed : 24.02 % Favored : 73.87 % 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: 2.98 (0.41), residues: 410 helix: 2.16 (0.27), residues: 348 sheet: None (None), residues: 0 loop : 1.08 (0.83), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 197 TYR 0.016 0.001 TYR A 8 PHE 0.015 0.001 PHE A 384 TRP 0.008 0.001 TRP A 138 HIS 0.001 0.000 HIS A 390 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.15 ( 3247) covalent geometry : angle 0.63450 / 0.32 ( 4419) hydrogen bonds : bond 0.04975 / 3.31 ( 272) hydrogen bonds : angle 4.06431 / 3.00 ( 807) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 64 time to evaluate : 0.138 Fit side-chains revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8724 (pmtt) cc_final: 0.8399 (tptt) REVERT: A 77 ARG cc_start: 0.7942 (OUTLIER) cc_final: 0.6925 (ttm170) REVERT: A 97 SER cc_start: 0.8633 (m) cc_final: 0.8339 (p) REVERT: A 130 GLU cc_start: 0.7581 (mp0) cc_final: 0.7297 (mp0) REVERT: A 161 GLN cc_start: 0.8858 (OUTLIER) cc_final: 0.8495 (pp30) REVERT: A 216 THR cc_start: 0.8326 (m) cc_final: 0.7797 (p) REVERT: A 219 GLU cc_start: 0.8258 (mt-10) cc_final: 0.7952 (mt-10) outliers start: 7 outliers final: 4 residues processed: 69 average time/residue: 0.4739 time to fit residues: 33.7296 Evaluate side-chains 72 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 66 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 TYR Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 77 ARG Chi-restraints excluded: chain A residue 107 TRP Chi-restraints excluded: chain A residue 161 GLN Chi-restraints excluded: chain A residue 260 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 39 optimal weight: 0.6980 chunk 1 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 28 optimal weight: 0.0020 chunk 3 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 8 optimal weight: 0.8980 chunk 29 optimal weight: 0.6980 chunk 35 optimal weight: 0.7980 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 114 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.101463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.084786 restraints weight = 5539.827| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 2.73 r_work: 0.2993 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3247 Z= 0.141 Angle : 0.653 11.680 4419 Z= 0.320 Chirality : 0.040 0.223 499 Planarity : 0.006 0.069 543 Dihedral : 3.890 15.868 440 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.40 % Allowed : 23.42 % Favored : 74.17 % 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: 3.09 (0.41), residues: 410 helix: 2.21 (0.27), residues: 347 sheet: None (None), residues: 0 loop : 1.29 (0.85), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 197 TYR 0.015 0.001 TYR A 8 PHE 0.015 0.001 PHE A 340 TRP 0.008 0.001 TRP A 107 HIS 0.001 0.000 HIS A 390 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.14 ( 3247) covalent geometry : angle 0.65257 / 0.32 ( 4419) hydrogen bonds : bond 0.04865 / 3.23 ( 272) hydrogen bonds : angle 3.95269 / 2.88 ( 807) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1225.55 seconds wall clock time: 21 minutes 36.99 seconds (1296.99 seconds total)