Starting phenix.real_space_refine on Fri Aug 22 13:19:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qcy_18337/08_2025/8qcy_18337.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qcy_18337/08_2025/8qcy_18337.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8qcy_18337/08_2025/8qcy_18337.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qcy_18337/08_2025/8qcy_18337.map" model { file = "/net/cci-nas-00/data/ceres_data/8qcy_18337/08_2025/8qcy_18337.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qcy_18337/08_2025/8qcy_18337.cif" } resolution = 2.9 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= 0.008 sd= 0.189 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 2176 2.51 5 N 520 2.21 5 O 558 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3273 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3273 Classifications: {'peptide': 421} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 405} Chain breaks: 1 Time building chain proxies: 0.86, per 1000 atoms: 0.26 Number of scatterers: 3273 At special positions: 0 Unit cell: (82.512, 53.862, 64.176, 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 558 8.00 N 520 7.00 C 2176 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: 0.23 Conformation dependent library (CDL) restraints added in 128.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 770 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 0 sheets defined 91.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.06 Creating SS restraints... Processing helix chain 'A' and resid 82 through 108 removed outlier: 4.462A pdb=" N ALA A 86 " --> pdb=" O ARG A 82 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N TYR A 105 " --> pdb=" O GLN A 101 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N GLY A 106 " --> pdb=" O TRP A 102 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE A 108 " --> pdb=" O GLN A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 117 removed outlier: 3.663A pdb=" N HIS A 114 " --> pdb=" O ASN A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 149 removed outlier: 3.605A pdb=" N ILE A 123 " --> pdb=" O SER A 119 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N SER A 127 " --> pdb=" O ILE A 123 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N TYR A 130 " --> pdb=" O LEU A 126 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N MET A 131 " --> pdb=" O SER A 127 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU A 132 " --> pdb=" O MET A 128 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ILE A 135 " --> pdb=" O MET A 131 " (cutoff:3.500A) Proline residue: A 136 - end of helix removed outlier: 4.848A pdb=" N LEU A 139 " --> pdb=" O ILE A 135 " (cutoff:3.500A) Proline residue: A 140 - end of helix removed outlier: 4.380A pdb=" N GLU A 146 " --> pdb=" O ALA A 142 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS A 147 " --> pdb=" O TRP A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 167 removed outlier: 3.905A pdb=" N ILE A 153 " --> pdb=" O GLY A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 171 Processing helix chain 'A' and resid 176 through 193 removed outlier: 3.745A pdb=" N THR A 180 " --> pdb=" O LEU A 176 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL A 192 " --> pdb=" O SER A 188 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N PHE A 193 " --> pdb=" O VAL A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 206 Processing helix chain 'A' and resid 210 through 232 removed outlier: 3.578A pdb=" N CYS A 215 " --> pdb=" O VAL A 211 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE A 226 " --> pdb=" O ASN A 222 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU A 231 " --> pdb=" O ALA A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 237 Processing helix chain 'A' and resid 242 through 271 removed outlier: 3.545A pdb=" N TYR A 248 " --> pdb=" O ASP A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 291 removed outlier: 3.546A pdb=" N ALA A 289 " --> pdb=" O SER A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 307 Processing helix chain 'A' and resid 307 through 339 removed outlier: 4.859A pdb=" N ASN A 332 " --> pdb=" O SER A 328 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N ARG A 333 " --> pdb=" O THR A 329 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N HIS A 338 " --> pdb=" O MET A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 372 removed outlier: 3.670A pdb=" N VAL A 354 " --> pdb=" O GLY A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 396 Processing helix chain 'A' and resid 397 through 399 No H-bonds generated for 'chain 'A' and resid 397 through 399' Processing helix chain 'A' and resid 400 through 430 removed outlier: 3.852A pdb=" N VAL A 404 " --> pdb=" O HIS A 400 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N PHE A 405 " --> pdb=" O LEU A 401 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ILE A 406 " --> pdb=" O TRP A 402 " (cutoff:3.500A) Proline residue: A 420 - end of helix Processing helix chain 'A' and resid 434 through 465 Processing helix chain 'A' and resid 465 through 486 removed outlier: 3.539A pdb=" N GLY A 469 " --> pdb=" O GLY A 465 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE A 486 " --> pdb=" O ALA A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 500 removed outlier: 3.748A pdb=" N LYS A 495 " --> pdb=" O LEU A 491 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N THR A 500 " --> pdb=" O ALA A 496 " (cutoff:3.500A) 266 hydrogen bonds defined for protein. 795 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: 0.42 Time building geometry restraints manager: 0.29 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: 975 1.34 - 1.46: 521 1.46 - 1.57: 1828 1.57 - 1.69: 0 1.69 - 1.81: 31 Bond restraints: 3355 Sorted by residual: bond pdb=" N ASN A 307 " pdb=" CA ASN A 307 " ideal model delta sigma weight residual 1.460 1.488 -0.028 1.28e-02 6.10e+03 4.80e+00 bond pdb=" C ASN A 307 " pdb=" O ASN A 307 " ideal model delta sigma weight residual 1.235 1.245 -0.010 1.15e-02 7.56e+03 7.37e-01 bond pdb=" CG LEU A 169 " pdb=" CD1 LEU A 169 " ideal model delta sigma weight residual 1.521 1.493 0.028 3.30e-02 9.18e+02 7.30e-01 bond pdb=" CG LEU A 169 " pdb=" CD2 LEU A 169 " ideal model delta sigma weight residual 1.521 1.493 0.028 3.30e-02 9.18e+02 6.95e-01 bond pdb=" C MET A 197 " pdb=" N PRO A 198 " ideal model delta sigma weight residual 1.334 1.347 -0.013 1.51e-02 4.39e+03 6.91e-01 ... (remaining 3350 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.47: 4443 1.47 - 2.93: 103 2.93 - 4.40: 14 4.40 - 5.87: 6 5.87 - 7.34: 3 Bond angle restraints: 4569 Sorted by residual: angle pdb=" N MET A 197 " pdb=" CA MET A 197 " pdb=" C MET A 197 " ideal model delta sigma weight residual 109.81 117.15 -7.34 2.21e+00 2.05e-01 1.10e+01 angle pdb=" N ILE A 103 " pdb=" CA ILE A 103 " pdb=" CB ILE A 103 " ideal model delta sigma weight residual 112.26 108.57 3.69 1.29e+00 6.01e-01 8.19e+00 angle pdb=" C TYR A 134 " pdb=" N ILE A 135 " pdb=" CA ILE A 135 " ideal model delta sigma weight residual 120.33 122.52 -2.19 8.00e-01 1.56e+00 7.48e+00 angle pdb=" CG1 ILE A 108 " pdb=" CB ILE A 108 " pdb=" CG2 ILE A 108 " ideal model delta sigma weight residual 110.70 103.41 7.29 3.00e+00 1.11e-01 5.90e+00 angle pdb=" N PRO A 233 " pdb=" CA PRO A 233 " pdb=" C PRO A 233 " ideal model delta sigma weight residual 110.70 113.63 -2.93 1.22e+00 6.72e-01 5.75e+00 ... (remaining 4564 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.61: 1803 17.61 - 35.22: 102 35.22 - 52.83: 22 52.83 - 70.44: 1 70.44 - 88.05: 2 Dihedral angle restraints: 1930 sinusoidal: 722 harmonic: 1208 Sorted by residual: dihedral pdb=" CA LEU A 169 " pdb=" C LEU A 169 " pdb=" N GLY A 170 " pdb=" CA GLY A 170 " ideal model delta harmonic sigma weight residual 180.00 161.96 18.04 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CA TYR A 94 " pdb=" C TYR A 94 " pdb=" N SER A 95 " pdb=" CA SER A 95 " ideal model delta harmonic sigma weight residual 180.00 162.58 17.42 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" CA ILE A 270 " pdb=" C ILE A 270 " pdb=" N VAL A 271 " pdb=" CA VAL A 271 " ideal model delta harmonic sigma weight residual -180.00 -163.74 -16.26 0 5.00e+00 4.00e-02 1.06e+01 ... (remaining 1927 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 336 0.031 - 0.062: 145 0.062 - 0.093: 44 0.093 - 0.124: 15 0.124 - 0.155: 2 Chirality restraints: 542 Sorted by residual: chirality pdb=" CB ILE A 108 " pdb=" CA ILE A 108 " pdb=" CG1 ILE A 108 " pdb=" CG2 ILE A 108 " both_signs ideal model delta sigma weight residual False 2.64 2.80 -0.15 2.00e-01 2.50e+01 5.97e-01 chirality pdb=" CA MET A 197 " pdb=" N MET A 197 " pdb=" C MET A 197 " pdb=" CB MET A 197 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.97e-01 chirality pdb=" CA LEU A 169 " pdb=" N LEU A 169 " pdb=" C LEU A 169 " pdb=" CB LEU A 169 " both_signs ideal model delta sigma weight residual False 2.51 2.40 0.11 2.00e-01 2.50e+01 3.25e-01 ... (remaining 539 not shown) Planarity restraints: 553 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 130 " 0.016 2.00e-02 2.50e+03 1.72e-02 5.94e+00 pdb=" CG TYR A 130 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TYR A 130 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR A 130 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR A 130 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR A 130 " 0.010 2.00e-02 2.50e+03 pdb=" CZ TYR A 130 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 130 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 232 " -0.023 5.00e-02 4.00e+02 3.43e-02 1.88e+00 pdb=" N PRO A 233 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 233 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 233 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 431 " 0.021 5.00e-02 4.00e+02 3.18e-02 1.62e+00 pdb=" N PRO A 432 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO A 432 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 432 " 0.016 5.00e-02 4.00e+02 ... (remaining 550 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.78: 758 2.78 - 3.31: 3431 3.31 - 3.84: 5463 3.84 - 4.37: 6729 4.37 - 4.90: 11431 Nonbonded interactions: 27812 Sorted by model distance: nonbonded pdb=" O LEU A 429 " pdb=" NH2 ARG A 492 " model vdw 2.245 3.120 nonbonded pdb=" OG SER A 203 " pdb=" NE2 GLN A 284 " model vdw 2.256 3.120 nonbonded pdb=" OG SER A 107 " pdb=" O GLY A 229 " model vdw 2.300 3.040 nonbonded pdb=" O GLU A 435 " pdb=" OG SER A 439 " model vdw 2.309 3.040 nonbonded pdb=" O GLY A 450 " pdb=" OG1 THR A 454 " model vdw 2.327 3.040 ... (remaining 27807 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.220 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: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 4.080 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:5.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 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 0.036 3355 Z= 0.151 Angle : 0.582 7.336 4569 Z= 0.316 Chirality : 0.040 0.155 542 Planarity : 0.004 0.034 553 Dihedral : 11.881 88.055 1160 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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 aren not related in a simple way. whole: 0.40 (0.40), residues: 417 helix: 0.61 (0.27), residues: 341 sheet: None (None), residues: 0 loop : -0.88 (0.71), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 84 TYR 0.041 0.002 TYR A 130 PHE 0.016 0.002 PHE A 272 TRP 0.018 0.001 TRP A 125 HIS 0.001 0.000 HIS A 338 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 3355) covalent geometry : angle 0.58219 ( 4569) hydrogen bonds : bond 0.23434 ( 266) hydrogen bonds : angle 8.77599 ( 795) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.071 Fit side-chains REVERT: A 245 GLU cc_start: 0.6516 (tp30) cc_final: 0.5974 (mm-30) REVERT: A 332 ASN cc_start: 0.7568 (m-40) cc_final: 0.7212 (t0) REVERT: A 342 GLU cc_start: 0.8014 (mm-30) cc_final: 0.7492 (mm-30) outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.4415 time to fit residues: 25.9440 Evaluate side-chains 38 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 22 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 284 GLN A 459 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.125775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.105954 restraints weight = 4296.695| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 2.32 r_work: 0.3126 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7126 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 3355 Z= 0.187 Angle : 0.660 9.130 4569 Z= 0.336 Chirality : 0.044 0.190 542 Planarity : 0.005 0.031 553 Dihedral : 4.428 17.863 451 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.56 % Allowed : 9.38 % Favored : 88.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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 aren not related in a simple way. whole: 1.30 (0.40), residues: 417 helix: 1.26 (0.26), residues: 349 sheet: None (None), residues: 0 loop : -0.96 (0.75), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 84 TYR 0.026 0.002 TYR A 94 PHE 0.020 0.002 PHE A 472 TRP 0.015 0.001 TRP A 125 HIS 0.001 0.000 HIS A 338 Details of bonding type rmsd covalent geometry : bond 0.00433 ( 3355) covalent geometry : angle 0.65953 ( 4569) hydrogen bonds : bond 0.05269 ( 266) hydrogen bonds : angle 5.22655 ( 795) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 44 time to evaluate : 0.131 Fit side-chains revert: symmetry clash REVERT: A 96 MET cc_start: 0.7595 (OUTLIER) cc_final: 0.7149 (ptp) REVERT: A 108 ILE cc_start: 0.6778 (OUTLIER) cc_final: 0.6558 (mt) REVERT: A 255 TYR cc_start: 0.8102 (m-80) cc_final: 0.7839 (m-80) REVERT: A 376 GLU cc_start: 0.7696 (mp0) cc_final: 0.7439 (mp0) outliers start: 9 outliers final: 3 residues processed: 48 average time/residue: 0.3711 time to fit residues: 18.6851 Evaluate side-chains 45 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 40 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 290 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 9 optimal weight: 0.8980 chunk 32 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 15 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.126545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.106460 restraints weight = 4251.598| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.30 r_work: 0.3133 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3355 Z= 0.148 Angle : 0.596 8.397 4569 Z= 0.297 Chirality : 0.041 0.173 542 Planarity : 0.004 0.036 553 Dihedral : 4.314 17.716 451 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.12 % Allowed : 11.36 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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 aren not related in a simple way. whole: 1.62 (0.40), residues: 417 helix: 1.52 (0.26), residues: 351 sheet: None (None), residues: 0 loop : -1.16 (0.77), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 84 TYR 0.023 0.001 TYR A 94 PHE 0.020 0.002 PHE A 472 TRP 0.013 0.001 TRP A 125 HIS 0.001 0.000 HIS A 338 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 3355) covalent geometry : angle 0.59623 ( 4569) hydrogen bonds : bond 0.04586 ( 266) hydrogen bonds : angle 4.72193 ( 795) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 45 time to evaluate : 0.125 Fit side-chains REVERT: A 96 MET cc_start: 0.7590 (OUTLIER) cc_final: 0.7160 (ptp) REVERT: A 255 TYR cc_start: 0.8317 (m-80) cc_final: 0.7996 (m-80) REVERT: A 376 GLU cc_start: 0.7721 (mp0) cc_final: 0.7437 (mp0) REVERT: A 476 PHE cc_start: 0.7824 (m-80) cc_final: 0.7565 (m-80) outliers start: 11 outliers final: 4 residues processed: 52 average time/residue: 0.4081 time to fit residues: 22.1218 Evaluate side-chains 41 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 36 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 290 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 16 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 39 optimal weight: 0.3980 chunk 18 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.125723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.105862 restraints weight = 4231.376| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 2.28 r_work: 0.3072 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6978 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3355 Z= 0.141 Angle : 0.597 9.144 4569 Z= 0.295 Chirality : 0.042 0.191 542 Planarity : 0.004 0.039 553 Dihedral : 4.302 18.490 451 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.84 % Allowed : 14.20 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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 aren not related in a simple way. whole: 1.81 (0.40), residues: 417 helix: 1.62 (0.26), residues: 353 sheet: None (None), residues: 0 loop : -1.05 (0.76), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 84 TYR 0.024 0.001 TYR A 94 PHE 0.020 0.002 PHE A 472 TRP 0.008 0.001 TRP A 125 HIS 0.001 0.000 HIS A 338 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 3355) covalent geometry : angle 0.59739 ( 4569) hydrogen bonds : bond 0.04329 ( 266) hydrogen bonds : angle 4.57960 ( 795) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 44 time to evaluate : 0.122 Fit side-chains REVERT: A 82 ARG cc_start: 0.7397 (OUTLIER) cc_final: 0.7141 (mtp85) REVERT: A 96 MET cc_start: 0.7437 (OUTLIER) cc_final: 0.7034 (ptp) REVERT: A 113 MET cc_start: 0.5587 (mtm) cc_final: 0.5034 (mmm) REVERT: A 255 TYR cc_start: 0.8226 (m-80) cc_final: 0.7929 (m-80) REVERT: A 332 ASN cc_start: 0.7038 (m-40) cc_final: 0.6737 (t0) REVERT: A 476 PHE cc_start: 0.7595 (m-80) cc_final: 0.7366 (m-80) outliers start: 10 outliers final: 4 residues processed: 48 average time/residue: 0.4091 time to fit residues: 20.4501 Evaluate side-chains 46 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 40 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ARG Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 290 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 32 optimal weight: 0.5980 chunk 2 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.128052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.108252 restraints weight = 4182.820| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 2.26 r_work: 0.3130 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7088 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3355 Z= 0.145 Angle : 0.583 9.036 4569 Z= 0.290 Chirality : 0.041 0.168 542 Planarity : 0.004 0.039 553 Dihedral : 4.267 18.317 451 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.69 % Allowed : 15.34 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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 aren not related in a simple way. whole: 1.93 (0.40), residues: 417 helix: 1.73 (0.26), residues: 353 sheet: None (None), residues: 0 loop : -1.17 (0.75), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 282 TYR 0.024 0.001 TYR A 94 PHE 0.021 0.002 PHE A 472 TRP 0.007 0.001 TRP A 125 HIS 0.001 0.000 HIS A 338 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 3355) covalent geometry : angle 0.58295 ( 4569) hydrogen bonds : bond 0.04230 ( 266) hydrogen bonds : angle 4.50305 ( 795) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 41 time to evaluate : 0.130 Fit side-chains REVERT: A 82 ARG cc_start: 0.7545 (OUTLIER) cc_final: 0.7281 (mtp85) REVERT: A 96 MET cc_start: 0.7582 (OUTLIER) cc_final: 0.7162 (ptp) REVERT: A 376 GLU cc_start: 0.7760 (mp0) cc_final: 0.7492 (mp0) REVERT: A 382 TYR cc_start: 0.8514 (t80) cc_final: 0.8287 (t80) REVERT: A 433 GLU cc_start: 0.7329 (OUTLIER) cc_final: 0.6170 (mp0) REVERT: A 476 PHE cc_start: 0.7718 (m-80) cc_final: 0.7503 (m-80) outliers start: 13 outliers final: 5 residues processed: 49 average time/residue: 0.3528 time to fit residues: 18.0365 Evaluate side-chains 45 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 37 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ARG Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain A residue 471 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 37 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 39 optimal weight: 0.8980 chunk 26 optimal weight: 5.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.128258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.108653 restraints weight = 4218.439| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.26 r_work: 0.3133 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7100 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3355 Z= 0.141 Angle : 0.609 10.198 4569 Z= 0.293 Chirality : 0.042 0.177 542 Planarity : 0.004 0.040 553 Dihedral : 4.267 17.987 451 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.84 % Allowed : 16.19 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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 aren not related in a simple way. whole: 2.02 (0.40), residues: 417 helix: 1.80 (0.26), residues: 354 sheet: None (None), residues: 0 loop : -1.23 (0.76), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 84 TYR 0.024 0.001 TYR A 94 PHE 0.020 0.002 PHE A 472 TRP 0.007 0.001 TRP A 125 HIS 0.001 0.000 HIS A 338 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 3355) covalent geometry : angle 0.60905 ( 4569) hydrogen bonds : bond 0.04155 ( 266) hydrogen bonds : angle 4.44926 ( 795) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 41 time to evaluate : 0.079 Fit side-chains REVERT: A 82 ARG cc_start: 0.7549 (OUTLIER) cc_final: 0.7287 (mtp85) REVERT: A 96 MET cc_start: 0.7605 (OUTLIER) cc_final: 0.7188 (ptp) REVERT: A 113 MET cc_start: 0.5825 (mtm) cc_final: 0.5195 (mmm) REVERT: A 376 GLU cc_start: 0.7784 (mp0) cc_final: 0.7475 (mp0) REVERT: A 382 TYR cc_start: 0.8575 (t80) cc_final: 0.8374 (t80) REVERT: A 433 GLU cc_start: 0.7282 (OUTLIER) cc_final: 0.6109 (mp0) outliers start: 10 outliers final: 5 residues processed: 47 average time/residue: 0.4233 time to fit residues: 20.6446 Evaluate side-chains 45 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 37 time to evaluate : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ARG Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain A residue 471 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 32 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 497 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.127713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.108058 restraints weight = 4333.732| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.30 r_work: 0.3128 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7118 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3355 Z= 0.146 Angle : 0.594 9.001 4569 Z= 0.288 Chirality : 0.042 0.165 542 Planarity : 0.004 0.039 553 Dihedral : 4.256 17.784 451 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.69 % Allowed : 16.76 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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 aren not related in a simple way. whole: 2.07 (0.40), residues: 417 helix: 1.81 (0.26), residues: 356 sheet: None (None), residues: 0 loop : -1.19 (0.79), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 243 TYR 0.025 0.001 TYR A 94 PHE 0.021 0.002 PHE A 472 TRP 0.007 0.001 TRP A 125 HIS 0.001 0.000 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 3355) covalent geometry : angle 0.59445 ( 4569) hydrogen bonds : bond 0.04145 ( 266) hydrogen bonds : angle 4.43943 ( 795) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 39 time to evaluate : 0.082 Fit side-chains REVERT: A 82 ARG cc_start: 0.7592 (OUTLIER) cc_final: 0.7337 (mtp85) REVERT: A 113 MET cc_start: 0.5868 (mtm) cc_final: 0.5336 (mmm) REVERT: A 376 GLU cc_start: 0.7797 (mp0) cc_final: 0.7477 (mp0) REVERT: A 382 TYR cc_start: 0.8580 (t80) cc_final: 0.8364 (t80) outliers start: 13 outliers final: 5 residues processed: 49 average time/residue: 0.3488 time to fit residues: 17.8345 Evaluate side-chains 46 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 40 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ARG Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 471 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 27 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 chunk 12 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.128175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.108481 restraints weight = 4345.659| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 2.30 r_work: 0.3109 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6996 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3355 Z= 0.141 Angle : 0.621 10.769 4569 Z= 0.295 Chirality : 0.041 0.158 542 Planarity : 0.004 0.039 553 Dihedral : 4.242 18.604 451 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.27 % Allowed : 18.75 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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 aren not related in a simple way. whole: 2.15 (0.40), residues: 417 helix: 1.86 (0.26), residues: 356 sheet: None (None), residues: 0 loop : -1.17 (0.79), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 348 TYR 0.023 0.001 TYR A 94 PHE 0.019 0.002 PHE A 472 TRP 0.006 0.001 TRP A 125 HIS 0.002 0.000 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 3355) covalent geometry : angle 0.62141 ( 4569) hydrogen bonds : bond 0.04068 ( 266) hydrogen bonds : angle 4.39406 ( 795) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.142 Fit side-chains REVERT: A 82 ARG cc_start: 0.7481 (OUTLIER) cc_final: 0.7201 (mtp85) REVERT: A 96 MET cc_start: 0.7477 (OUTLIER) cc_final: 0.7076 (ptp) REVERT: A 113 MET cc_start: 0.5707 (mtm) cc_final: 0.5160 (mmm) REVERT: A 376 GLU cc_start: 0.7850 (mp0) cc_final: 0.7520 (mp0) outliers start: 8 outliers final: 5 residues processed: 48 average time/residue: 0.3770 time to fit residues: 18.9055 Evaluate side-chains 45 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 38 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ARG Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 471 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.127991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.108497 restraints weight = 4270.489| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 2.27 r_work: 0.3138 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7079 moved from start: 0.2931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3355 Z= 0.147 Angle : 0.605 9.604 4569 Z= 0.293 Chirality : 0.041 0.160 542 Planarity : 0.004 0.037 553 Dihedral : 4.247 18.419 451 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.69 % Allowed : 18.18 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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 aren not related in a simple way. whole: 2.09 (0.40), residues: 417 helix: 1.83 (0.26), residues: 356 sheet: None (None), residues: 0 loop : -1.19 (0.79), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 348 TYR 0.025 0.001 TYR A 94 PHE 0.019 0.002 PHE A 472 TRP 0.006 0.001 TRP A 125 HIS 0.001 0.000 HIS A 338 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 3355) covalent geometry : angle 0.60471 ( 4569) hydrogen bonds : bond 0.04151 ( 266) hydrogen bonds : angle 4.40610 ( 795) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 39 time to evaluate : 0.077 Fit side-chains REVERT: A 82 ARG cc_start: 0.7519 (OUTLIER) cc_final: 0.7260 (mtp85) REVERT: A 96 MET cc_start: 0.7600 (OUTLIER) cc_final: 0.7190 (ptp) REVERT: A 113 MET cc_start: 0.5793 (mtm) cc_final: 0.5229 (mmm) REVERT: A 376 GLU cc_start: 0.7908 (mp0) cc_final: 0.7573 (mp0) outliers start: 13 outliers final: 5 residues processed: 47 average time/residue: 0.3525 time to fit residues: 17.2642 Evaluate side-chains 44 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 37 time to evaluate : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ARG Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 471 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 21 optimal weight: 0.6980 chunk 20 optimal weight: 0.0060 chunk 29 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 26 optimal weight: 4.9990 chunk 28 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.128425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.108887 restraints weight = 4250.611| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 2.26 r_work: 0.3198 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7048 moved from start: 0.3046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3355 Z= 0.132 Angle : 0.607 11.226 4569 Z= 0.292 Chirality : 0.041 0.187 542 Planarity : 0.004 0.038 553 Dihedral : 4.242 18.086 451 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.99 % Allowed : 18.75 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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 aren not related in a simple way. whole: 2.16 (0.40), residues: 417 helix: 1.85 (0.26), residues: 357 sheet: None (None), residues: 0 loop : -1.07 (0.79), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 493 TYR 0.022 0.001 TYR A 94 PHE 0.017 0.001 PHE A 472 TRP 0.006 0.001 TRP A 125 HIS 0.001 0.000 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 3355) covalent geometry : angle 0.60724 ( 4569) hydrogen bonds : bond 0.04041 ( 266) hydrogen bonds : angle 4.32802 ( 795) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 39 time to evaluate : 0.131 Fit side-chains REVERT: A 82 ARG cc_start: 0.7502 (OUTLIER) cc_final: 0.7244 (mtp85) REVERT: A 96 MET cc_start: 0.7612 (OUTLIER) cc_final: 0.7234 (ptp) REVERT: A 255 TYR cc_start: 0.8182 (m-80) cc_final: 0.7906 (m-80) REVERT: A 305 PHE cc_start: 0.7452 (m-80) cc_final: 0.7145 (m-80) REVERT: A 376 GLU cc_start: 0.7879 (mp0) cc_final: 0.7583 (mp0) outliers start: 7 outliers final: 5 residues processed: 43 average time/residue: 0.4452 time to fit residues: 19.9098 Evaluate side-chains 44 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 37 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ARG Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 471 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 25 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 32 optimal weight: 0.1980 chunk 29 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 7 optimal weight: 0.3980 chunk 36 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.130334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.110728 restraints weight = 4329.049| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 2.30 r_work: 0.3190 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7070 moved from start: 0.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3355 Z= 0.134 Angle : 0.617 11.865 4569 Z= 0.295 Chirality : 0.042 0.203 542 Planarity : 0.004 0.038 553 Dihedral : 4.215 18.512 451 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.99 % Allowed : 19.32 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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 aren not related in a simple way. whole: 2.16 (0.40), residues: 417 helix: 1.86 (0.26), residues: 358 sheet: None (None), residues: 0 loop : -1.18 (0.79), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 348 TYR 0.023 0.001 TYR A 94 PHE 0.017 0.001 PHE A 472 TRP 0.006 0.001 TRP A 125 HIS 0.001 0.000 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 3355) covalent geometry : angle 0.61698 ( 4569) hydrogen bonds : bond 0.04021 ( 266) hydrogen bonds : angle 4.32496 ( 795) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1072.29 seconds wall clock time: 19 minutes 3.34 seconds (1143.34 seconds total)