Starting phenix.real_space_refine on Fri Aug 22 14:33:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bh1_44529/08_2025/9bh1_44529.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bh1_44529/08_2025/9bh1_44529.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bh1_44529/08_2025/9bh1_44529.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bh1_44529/08_2025/9bh1_44529.map" model { file = "/net/cci-nas-00/data/ceres_data/9bh1_44529/08_2025/9bh1_44529.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bh1_44529/08_2025/9bh1_44529.cif" } resolution = 3.1 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= 0.001 sd= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1504 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 17 5.16 5 C 1943 2.51 5 N 471 2.21 5 O 511 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 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: 2942 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 2942 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 17, 'TRANS': 377} Chain breaks: 1 Time building chain proxies: 0.93, per 1000 atoms: 0.32 Number of scatterers: 2942 At special positions: 0 Unit cell: (66.834, 65.142, 76.986, 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 17 16.00 O 511 8.00 N 471 7.00 C 1943 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: 0.19 Conformation dependent library (CDL) restraints added in 88.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 714 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 0 sheets defined 89.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.10 Creating SS restraints... Processing helix chain 'A' and resid 2 through 10 Processing helix chain 'A' and resid 11 through 34 Processing helix chain 'A' and resid 35 through 43 Processing helix chain 'A' and resid 43 through 72 removed outlier: 3.644A pdb=" N GLY A 47 " --> pdb=" O VAL A 43 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL A 58 " --> pdb=" O LEU A 54 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N MET A 59 " --> pdb=" O LYS A 55 " (cutoff:3.500A) Proline residue: A 60 - end of helix removed outlier: 3.692A pdb=" N LEU A 66 " --> pdb=" O VAL A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 108 removed outlier: 3.545A pdb=" N THR A 98 " --> pdb=" O ALA A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 136 removed outlier: 3.699A pdb=" N ILE A 133 " --> pdb=" O PRO A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 148 Processing helix chain 'A' and resid 150 through 170 Processing helix chain 'A' and resid 173 through 220 removed outlier: 3.537A pdb=" N TYR A 204 " --> pdb=" O GLY A 200 " (cutoff:3.500A) Proline residue: A 206 - end of helix removed outlier: 4.153A pdb=" N VAL A 216 " --> pdb=" O LEU A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 246 Processing helix chain 'A' and resid 246 through 254 Processing helix chain 'A' and resid 257 through 265 Processing helix chain 'A' and resid 265 through 275 Processing helix chain 'A' and resid 281 through 292 Processing helix chain 'A' and resid 298 through 310 Proline residue: A 304 - end of helix removed outlier: 3.957A pdb=" N THR A 308 " --> pdb=" O PRO A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 329 removed outlier: 3.820A pdb=" N PHE A 323 " --> pdb=" O GLY A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 349 Processing helix chain 'A' and resid 357 through 370 removed outlier: 3.791A pdb=" N MET A 365 " --> pdb=" O ILE A 361 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL A 366 " --> pdb=" O MET A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 414 removed outlier: 4.325A pdb=" N ALA A 391 " --> pdb=" O LEU A 387 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N ILE A 392 " --> pdb=" O GLY A 388 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N MET A 399 " --> pdb=" O MET A 395 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU A 406 " --> pdb=" O VAL A 402 " (cutoff:3.500A) 254 hydrogen bonds defined for protein. 762 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: 0.47 Time building geometry restraints manager: 0.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 907 1.34 - 1.46: 504 1.46 - 1.57: 1553 1.57 - 1.69: 1 1.69 - 1.81: 33 Bond restraints: 2998 Sorted by residual: bond pdb=" CB PRO A 128 " pdb=" CG PRO A 128 " ideal model delta sigma weight residual 1.492 1.599 -0.107 5.00e-02 4.00e+02 4.59e+00 bond pdb=" N PRO A 128 " pdb=" CA PRO A 128 " ideal model delta sigma weight residual 1.466 1.449 0.017 1.50e-02 4.44e+03 1.27e+00 bond pdb=" C VAL A 225 " pdb=" O VAL A 225 " ideal model delta sigma weight residual 1.236 1.226 0.011 1.19e-02 7.06e+03 8.08e-01 bond pdb=" CB GLU A 219 " pdb=" CG GLU A 219 " ideal model delta sigma weight residual 1.520 1.543 -0.023 3.00e-02 1.11e+03 5.91e-01 bond pdb=" CA GLU A 219 " pdb=" CB GLU A 219 " ideal model delta sigma weight residual 1.532 1.546 -0.014 1.78e-02 3.16e+03 5.86e-01 ... (remaining 2993 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.44: 4019 1.44 - 2.88: 45 2.88 - 4.32: 19 4.32 - 5.76: 1 5.76 - 7.20: 2 Bond angle restraints: 4086 Sorted by residual: angle pdb=" CA PRO A 128 " pdb=" N PRO A 128 " pdb=" CD PRO A 128 " ideal model delta sigma weight residual 112.00 104.80 7.20 1.40e+00 5.10e-01 2.65e+01 angle pdb=" CA GLU A 219 " pdb=" CB GLU A 219 " pdb=" CG GLU A 219 " ideal model delta sigma weight residual 114.10 120.52 -6.42 2.00e+00 2.50e-01 1.03e+01 angle pdb=" N PRO A 128 " pdb=" CD PRO A 128 " pdb=" CG PRO A 128 " ideal model delta sigma weight residual 103.20 99.20 4.00 1.50e+00 4.44e-01 7.11e+00 angle pdb=" C GLU A 219 " pdb=" CA GLU A 219 " pdb=" CB GLU A 219 " ideal model delta sigma weight residual 110.01 114.14 -4.13 1.80e+00 3.09e-01 5.26e+00 angle pdb=" CB GLU A 219 " pdb=" CG GLU A 219 " pdb=" CD GLU A 219 " ideal model delta sigma weight residual 112.60 116.40 -3.80 1.70e+00 3.46e-01 5.00e+00 ... (remaining 4081 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.24: 1518 13.24 - 26.48: 171 26.48 - 39.71: 56 39.71 - 52.95: 17 52.95 - 66.19: 4 Dihedral angle restraints: 1766 sinusoidal: 641 harmonic: 1125 Sorted by residual: dihedral pdb=" CA GLU A 219 " pdb=" C GLU A 219 " pdb=" N GLN A 220 " pdb=" CA GLN A 220 " ideal model delta harmonic sigma weight residual 180.00 160.55 19.45 0 5.00e+00 4.00e-02 1.51e+01 dihedral pdb=" CA ARG A 287 " pdb=" CB ARG A 287 " pdb=" CG ARG A 287 " pdb=" CD ARG A 287 " ideal model delta sinusoidal sigma weight residual -60.00 -114.93 54.93 3 1.50e+01 4.44e-03 9.32e+00 dihedral pdb=" CA ARG A 276 " pdb=" CB ARG A 276 " pdb=" CG ARG A 276 " pdb=" CD ARG A 276 " ideal model delta sinusoidal sigma weight residual -60.00 -112.48 52.48 3 1.50e+01 4.44e-03 9.12e+00 ... (remaining 1763 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 327 0.026 - 0.052: 100 0.052 - 0.078: 65 0.078 - 0.104: 18 0.104 - 0.130: 7 Chirality restraints: 517 Sorted by residual: chirality pdb=" CA GLU A 219 " pdb=" N GLU A 219 " pdb=" C GLU A 219 " pdb=" CB GLU A 219 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.23e-01 chirality pdb=" CA VAL A 138 " pdb=" N VAL A 138 " pdb=" C VAL A 138 " pdb=" CB VAL A 138 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.22e-01 chirality pdb=" CA ILE A 256 " pdb=" N ILE A 256 " pdb=" C ILE A 256 " pdb=" CB ILE A 256 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.11 2.00e-01 2.50e+01 3.12e-01 ... (remaining 514 not shown) Planarity restraints: 497 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU A 219 " -0.006 2.00e-02 2.50e+03 1.29e-02 1.66e+00 pdb=" CD GLU A 219 " 0.022 2.00e-02 2.50e+03 pdb=" OE1 GLU A 219 " -0.008 2.00e-02 2.50e+03 pdb=" OE2 GLU A 219 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 219 " 0.005 2.00e-02 2.50e+03 9.27e-03 8.59e-01 pdb=" C GLU A 219 " -0.016 2.00e-02 2.50e+03 pdb=" O GLU A 219 " 0.006 2.00e-02 2.50e+03 pdb=" N GLN A 220 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 74 " 0.011 5.00e-02 4.00e+02 1.60e-02 4.11e-01 pdb=" N PRO A 75 " -0.028 5.00e-02 4.00e+02 pdb=" CA PRO A 75 " 0.008 5.00e-02 4.00e+02 pdb=" CD PRO A 75 " 0.009 5.00e-02 4.00e+02 ... (remaining 494 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 750 2.80 - 3.32: 3428 3.32 - 3.85: 5059 3.85 - 4.37: 5900 4.37 - 4.90: 9879 Nonbonded interactions: 25016 Sorted by model distance: nonbonded pdb=" NH2 ARG A 105 " pdb=" O LEU A 333 " model vdw 2.269 3.120 nonbonded pdb=" O SER A 171 " pdb=" NH1 ARG A 177 " model vdw 2.281 3.120 nonbonded pdb=" O MET A 399 " pdb=" OG1 THR A 403 " model vdw 2.287 3.040 nonbonded pdb=" OG1 THR A 92 " pdb=" OD1 ASP A 312 " model vdw 2.300 3.040 nonbonded pdb=" O ALA A 229 " pdb=" OG1 THR A 232 " model vdw 2.351 3.040 ... (remaining 25011 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: 3.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.480 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 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:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 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 : 0.003 0.107 2998 Z= 0.121 Angle : 0.483 7.203 4086 Z= 0.254 Chirality : 0.037 0.130 517 Planarity : 0.002 0.016 497 Dihedral : 13.562 66.189 1052 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Rotamer: Outliers : 0.00 % Allowed : 12.54 % Favored : 87.46 % 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 aren not related in a simple way. whole: 2.41 (0.43), residues: 391 helix: 1.91 (0.28), residues: 342 sheet: None (None), residues: 0 loop : -0.50 (0.88), residues: 49 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 105 TYR 0.006 0.001 TYR A 299 PHE 0.009 0.001 PHE A 248 HIS 0.001 0.000 HIS A 40 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 2998) covalent geometry : angle 0.48252 ( 4086) hydrogen bonds : bond 0.21659 ( 254) hydrogen bonds : angle 7.61978 ( 762) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.075 Fit side-chains REVERT: A 41 THR cc_start: 0.8191 (m) cc_final: 0.7803 (p) REVERT: A 174 GLU cc_start: 0.8262 (tt0) cc_final: 0.7998 (mt-10) REVERT: A 196 LYS cc_start: 0.7781 (mmtm) cc_final: 0.5531 (pttt) REVERT: A 202 MET cc_start: 0.8755 (mmp) cc_final: 0.8461 (mmm) REVERT: A 203 GLN cc_start: 0.8734 (mm-40) cc_final: 0.8409 (mm-40) REVERT: A 335 VAL cc_start: 0.7850 (p) cc_final: 0.7588 (t) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.0728 time to fit residues: 7.3623 Evaluate side-chains 71 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 24 optimal weight: 0.9980 chunk 26 optimal weight: 0.3980 chunk 2 optimal weight: 0.5980 chunk 16 optimal weight: 0.6980 chunk 32 optimal weight: 0.5980 chunk 31 optimal weight: 0.1980 chunk 25 optimal weight: 0.5980 chunk 19 optimal weight: 0.2980 chunk 30 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 chunk 37 optimal weight: 0.6980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 HIS ** A 318 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 = 0.3303 r_free = 0.3303 target = 0.092538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.084706 restraints weight = 5179.917| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 1.66 r_work: 0.3079 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 2998 Z= 0.206 Angle : 0.656 8.498 4086 Z= 0.340 Chirality : 0.045 0.134 517 Planarity : 0.005 0.045 497 Dihedral : 4.280 15.766 420 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 2.57 % Allowed : 17.36 % Favored : 80.06 % 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 aren not related in a simple way. whole: 2.00 (0.42), residues: 391 helix: 1.49 (0.27), residues: 352 sheet: None (None), residues: 0 loop : 0.32 (1.06), residues: 39 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 52 TYR 0.012 0.002 TYR A 299 PHE 0.009 0.001 PHE A 323 HIS 0.002 0.001 HIS A 264 Details of bonding type rmsd covalent geometry : bond 0.00491 ( 2998) covalent geometry : angle 0.65584 ( 4086) hydrogen bonds : bond 0.05431 ( 254) hydrogen bonds : angle 5.01563 ( 762) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 80 time to evaluate : 0.113 Fit side-chains REVERT: A 33 TYR cc_start: 0.7698 (OUTLIER) cc_final: 0.7187 (t80) REVERT: A 41 THR cc_start: 0.8556 (m) cc_final: 0.8202 (p) REVERT: A 169 MET cc_start: 0.8751 (mtp) cc_final: 0.8531 (mtp) REVERT: A 174 GLU cc_start: 0.8748 (tt0) cc_final: 0.8351 (mt-10) REVERT: A 196 LYS cc_start: 0.8401 (mmtm) cc_final: 0.5934 (pttt) REVERT: A 202 MET cc_start: 0.9000 (mmp) cc_final: 0.8780 (mmm) REVERT: A 203 GLN cc_start: 0.8996 (mm-40) cc_final: 0.8614 (mm-40) REVERT: A 309 ILE cc_start: 0.8751 (mm) cc_final: 0.8488 (tt) outliers start: 8 outliers final: 7 residues processed: 85 average time/residue: 0.0704 time to fit residues: 7.1994 Evaluate side-chains 82 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 33 TYR Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 393 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 16 optimal weight: 0.7980 chunk 0 optimal weight: 0.9990 chunk 13 optimal weight: 0.0870 chunk 11 optimal weight: 0.9980 chunk 23 optimal weight: 0.3980 chunk 17 optimal weight: 0.0020 chunk 1 optimal weight: 0.8980 chunk 38 optimal weight: 0.4980 chunk 10 optimal weight: 0.2980 chunk 19 optimal weight: 0.5980 chunk 15 optimal weight: 0.9980 overall best weight: 0.2566 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 338 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.094107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.086327 restraints weight = 5298.876| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 1.72 r_work: 0.3106 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 2998 Z= 0.155 Angle : 0.565 7.117 4086 Z= 0.294 Chirality : 0.042 0.156 517 Planarity : 0.005 0.046 497 Dihedral : 4.116 14.784 420 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 4.50 % Allowed : 19.94 % Favored : 75.56 % 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 aren not related in a simple way. whole: 1.91 (0.42), residues: 391 helix: 1.45 (0.27), residues: 353 sheet: None (None), residues: 0 loop : 0.06 (1.05), residues: 38 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 52 TYR 0.011 0.001 TYR A 317 PHE 0.008 0.001 PHE A 261 HIS 0.001 0.000 HIS A 264 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 2998) covalent geometry : angle 0.56533 ( 4086) hydrogen bonds : bond 0.04634 ( 254) hydrogen bonds : angle 4.62575 ( 762) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 0.114 Fit side-chains REVERT: A 33 TYR cc_start: 0.7720 (OUTLIER) cc_final: 0.7298 (t80) REVERT: A 41 THR cc_start: 0.8592 (m) cc_final: 0.8309 (p) REVERT: A 103 MET cc_start: 0.7882 (tpp) cc_final: 0.7552 (mpp) REVERT: A 133 ILE cc_start: 0.8695 (mm) cc_final: 0.8406 (mt) REVERT: A 174 GLU cc_start: 0.8654 (tt0) cc_final: 0.8288 (mt-10) REVERT: A 196 LYS cc_start: 0.8417 (mmtm) cc_final: 0.5888 (pttt) REVERT: A 219 GLU cc_start: 0.8406 (pp20) cc_final: 0.8111 (pp20) REVERT: A 290 LYS cc_start: 0.9006 (ttpt) cc_final: 0.8749 (ttpp) outliers start: 14 outliers final: 10 residues processed: 83 average time/residue: 0.0577 time to fit residues: 5.8186 Evaluate side-chains 81 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 70 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 33 TYR Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 365 MET Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 407 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 23 optimal weight: 0.8980 chunk 17 optimal weight: 0.0980 chunk 22 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 13 optimal weight: 0.0970 chunk 12 optimal weight: 0.4980 chunk 10 optimal weight: 0.0370 chunk 37 optimal weight: 0.5980 chunk 29 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 overall best weight: 0.2656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.094546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.086700 restraints weight = 5308.121| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 1.71 r_work: 0.3114 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.2815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 2998 Z= 0.153 Angle : 0.579 7.742 4086 Z= 0.296 Chirality : 0.042 0.164 517 Planarity : 0.005 0.051 497 Dihedral : 4.166 15.132 420 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 4.50 % Allowed : 22.51 % Favored : 72.99 % 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 aren not related in a simple way. whole: 1.81 (0.42), residues: 391 helix: 1.41 (0.27), residues: 353 sheet: None (None), residues: 0 loop : -0.24 (1.04), residues: 38 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 52 TYR 0.010 0.001 TYR A 299 PHE 0.007 0.001 PHE A 261 HIS 0.002 0.000 HIS A 223 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 2998) covalent geometry : angle 0.57919 ( 4086) hydrogen bonds : bond 0.04376 ( 254) hydrogen bonds : angle 4.47870 ( 762) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 0.087 Fit side-chains REVERT: A 33 TYR cc_start: 0.7700 (OUTLIER) cc_final: 0.7252 (t80) REVERT: A 41 THR cc_start: 0.8653 (m) cc_final: 0.8412 (p) REVERT: A 103 MET cc_start: 0.7865 (tpp) cc_final: 0.7549 (mpp) REVERT: A 133 ILE cc_start: 0.8664 (mm) cc_final: 0.8374 (mt) REVERT: A 174 GLU cc_start: 0.8641 (tt0) cc_final: 0.8307 (mt-10) REVERT: A 196 LYS cc_start: 0.8407 (mmtm) cc_final: 0.5779 (pttt) REVERT: A 203 GLN cc_start: 0.8941 (mm-40) cc_final: 0.8711 (mm-40) REVERT: A 219 GLU cc_start: 0.8447 (pp20) cc_final: 0.8042 (pp20) REVERT: A 290 LYS cc_start: 0.9023 (ttpt) cc_final: 0.8814 (ttmm) outliers start: 14 outliers final: 11 residues processed: 82 average time/residue: 0.0498 time to fit residues: 4.9567 Evaluate side-chains 87 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 75 time to evaluate : 0.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 33 TYR Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 365 MET Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 407 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 0.6980 chunk 26 optimal weight: 0.0870 chunk 7 optimal weight: 0.3980 chunk 21 optimal weight: 0.3980 chunk 14 optimal weight: 0.3980 chunk 22 optimal weight: 0.7980 chunk 23 optimal weight: 0.3980 chunk 9 optimal weight: 0.5980 chunk 20 optimal weight: 0.0970 chunk 5 optimal weight: 0.4980 chunk 16 optimal weight: 0.9990 overall best weight: 0.2756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 318 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 = 0.3346 r_free = 0.3346 target = 0.094601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.086829 restraints weight = 5275.925| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 1.65 r_work: 0.3119 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 2998 Z= 0.152 Angle : 0.575 7.633 4086 Z= 0.290 Chirality : 0.042 0.136 517 Planarity : 0.005 0.051 497 Dihedral : 4.111 15.538 420 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 5.79 % Allowed : 20.58 % Favored : 73.63 % 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 aren not related in a simple way. whole: 1.80 (0.42), residues: 391 helix: 1.41 (0.27), residues: 353 sheet: None (None), residues: 0 loop : -0.36 (1.03), residues: 38 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 52 TYR 0.010 0.001 TYR A 299 PHE 0.007 0.001 PHE A 261 HIS 0.001 0.000 HIS A 264 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 2998) covalent geometry : angle 0.57513 ( 4086) hydrogen bonds : bond 0.04209 ( 254) hydrogen bonds : angle 4.40607 ( 762) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 73 time to evaluate : 0.116 Fit side-chains REVERT: A 33 TYR cc_start: 0.7660 (OUTLIER) cc_final: 0.7225 (t80) REVERT: A 41 THR cc_start: 0.8637 (m) cc_final: 0.8427 (p) REVERT: A 103 MET cc_start: 0.7818 (tpp) cc_final: 0.7496 (mpp) REVERT: A 133 ILE cc_start: 0.8640 (mm) cc_final: 0.8350 (mt) REVERT: A 174 GLU cc_start: 0.8609 (tt0) cc_final: 0.8287 (mt-10) REVERT: A 219 GLU cc_start: 0.8469 (pp20) cc_final: 0.8090 (pp20) REVERT: A 362 MET cc_start: 0.7395 (ptm) cc_final: 0.7125 (ptm) outliers start: 18 outliers final: 11 residues processed: 83 average time/residue: 0.0567 time to fit residues: 5.8688 Evaluate side-chains 87 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 75 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LEU Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 33 TYR Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 365 MET Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 407 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 31 optimal weight: 1.9990 chunk 19 optimal weight: 0.0970 chunk 33 optimal weight: 0.0470 chunk 7 optimal weight: 0.6980 chunk 4 optimal weight: 0.6980 chunk 28 optimal weight: 0.0980 chunk 27 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 overall best weight: 0.3076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 318 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 = 0.3366 r_free = 0.3366 target = 0.095410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.087556 restraints weight = 5226.076| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 1.69 r_work: 0.3114 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 2998 Z= 0.159 Angle : 0.585 7.407 4086 Z= 0.293 Chirality : 0.042 0.159 517 Planarity : 0.005 0.051 497 Dihedral : 4.122 16.199 420 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 5.47 % Allowed : 21.22 % Favored : 73.31 % 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 aren not related in a simple way. whole: 1.77 (0.42), residues: 391 helix: 1.39 (0.27), residues: 353 sheet: None (None), residues: 0 loop : -0.35 (1.06), residues: 38 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 52 TYR 0.011 0.001 TYR A 299 PHE 0.007 0.001 PHE A 261 HIS 0.001 0.000 HIS A 264 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 2998) covalent geometry : angle 0.58471 ( 4086) hydrogen bonds : bond 0.04188 ( 254) hydrogen bonds : angle 4.40269 ( 762) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 77 time to evaluate : 0.110 Fit side-chains REVERT: A 33 TYR cc_start: 0.7633 (OUTLIER) cc_final: 0.7210 (t80) REVERT: A 103 MET cc_start: 0.7800 (tpp) cc_final: 0.7471 (mpp) REVERT: A 133 ILE cc_start: 0.8615 (mm) cc_final: 0.8325 (mt) REVERT: A 174 GLU cc_start: 0.8637 (tt0) cc_final: 0.8314 (mt-10) REVERT: A 196 LYS cc_start: 0.8409 (mmmt) cc_final: 0.5655 (pttt) REVERT: A 219 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.8078 (pp20) outliers start: 17 outliers final: 11 residues processed: 85 average time/residue: 0.0566 time to fit residues: 5.7852 Evaluate side-chains 87 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 0.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LEU Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 33 TYR Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 365 MET Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 407 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 19 optimal weight: 0.5980 chunk 11 optimal weight: 0.0010 chunk 12 optimal weight: 0.0470 chunk 22 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 chunk 29 optimal weight: 0.2980 chunk 32 optimal weight: 0.3980 chunk 3 optimal weight: 0.6980 chunk 0 optimal weight: 0.9980 overall best weight: 0.2684 ------------------------------------------------------------------------------- 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 = 0.3377 r_free = 0.3377 target = 0.096060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.088127 restraints weight = 5280.597| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 1.70 r_work: 0.3148 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.3230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 2998 Z= 0.157 Angle : 0.598 7.652 4086 Z= 0.300 Chirality : 0.043 0.173 517 Planarity : 0.005 0.051 497 Dihedral : 4.188 18.153 420 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 5.79 % Allowed : 22.51 % Favored : 71.70 % 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 aren not related in a simple way. whole: 1.72 (0.42), residues: 391 helix: 1.36 (0.27), residues: 353 sheet: None (None), residues: 0 loop : -0.42 (1.05), residues: 38 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 52 TYR 0.011 0.001 TYR A 299 PHE 0.007 0.001 PHE A 261 HIS 0.004 0.001 HIS A 37 Details of bonding type rmsd covalent geometry : bond 0.00380 ( 2998) covalent geometry : angle 0.59801 ( 4086) hydrogen bonds : bond 0.04185 ( 254) hydrogen bonds : angle 4.43992 ( 762) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 74 time to evaluate : 0.086 Fit side-chains revert: symmetry clash REVERT: A 33 TYR cc_start: 0.7619 (OUTLIER) cc_final: 0.7204 (t80) REVERT: A 103 MET cc_start: 0.7728 (tpp) cc_final: 0.7412 (mpp) REVERT: A 133 ILE cc_start: 0.8589 (mm) cc_final: 0.8310 (mt) REVERT: A 174 GLU cc_start: 0.8596 (tt0) cc_final: 0.8308 (mt-10) REVERT: A 196 LYS cc_start: 0.8493 (mmmt) cc_final: 0.5722 (pttt) REVERT: A 219 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.8103 (pp20) outliers start: 18 outliers final: 14 residues processed: 83 average time/residue: 0.0558 time to fit residues: 5.6879 Evaluate side-chains 90 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 74 time to evaluate : 0.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LEU Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 33 TYR Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain A residue 220 GLN Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 365 MET Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 407 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 4 optimal weight: 0.6980 chunk 20 optimal weight: 0.0050 chunk 30 optimal weight: 0.5980 chunk 33 optimal weight: 0.5980 chunk 15 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 17 optimal weight: 0.2980 chunk 12 optimal weight: 0.5980 chunk 1 optimal weight: 0.6980 chunk 2 optimal weight: 0.5980 overall best weight: 0.4194 ------------------------------------------------------------------------------- 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 = 0.3352 r_free = 0.3352 target = 0.094443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.086470 restraints weight = 5327.061| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 1.71 r_work: 0.3114 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.3225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 2998 Z= 0.193 Angle : 0.622 7.947 4086 Z= 0.310 Chirality : 0.044 0.171 517 Planarity : 0.005 0.051 497 Dihedral : 4.274 20.228 420 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 6.43 % Allowed : 22.51 % Favored : 71.06 % 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 aren not related in a simple way. whole: 1.57 (0.42), residues: 391 helix: 1.26 (0.27), residues: 353 sheet: None (None), residues: 0 loop : -0.50 (1.04), residues: 38 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 52 TYR 0.012 0.001 TYR A 299 PHE 0.008 0.001 PHE A 324 HIS 0.003 0.001 HIS A 37 Details of bonding type rmsd covalent geometry : bond 0.00467 ( 2998) covalent geometry : angle 0.62173 ( 4086) hydrogen bonds : bond 0.04335 ( 254) hydrogen bonds : angle 4.49291 ( 762) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 76 time to evaluate : 0.068 Fit side-chains REVERT: A 33 TYR cc_start: 0.7626 (OUTLIER) cc_final: 0.7195 (t80) REVERT: A 103 MET cc_start: 0.7803 (tpp) cc_final: 0.7474 (mpp) REVERT: A 174 GLU cc_start: 0.8651 (tt0) cc_final: 0.8357 (mt-10) REVERT: A 196 LYS cc_start: 0.8545 (mmmt) cc_final: 0.5783 (pttt) REVERT: A 219 GLU cc_start: 0.8466 (OUTLIER) cc_final: 0.8080 (pp20) outliers start: 20 outliers final: 14 residues processed: 86 average time/residue: 0.0625 time to fit residues: 6.5256 Evaluate side-chains 86 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 70 time to evaluate : 0.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LEU Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 33 TYR Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 365 MET Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 407 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 18 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 31 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 33 optimal weight: 0.0980 chunk 29 optimal weight: 0.6980 chunk 19 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3314 r_free = 0.3314 target = 0.092483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.084329 restraints weight = 5366.013| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 1.71 r_work: 0.3095 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 2998 Z= 0.228 Angle : 0.652 8.196 4086 Z= 0.323 Chirality : 0.045 0.203 517 Planarity : 0.005 0.050 497 Dihedral : 4.395 20.776 420 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 5.47 % Allowed : 24.44 % Favored : 70.10 % 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 aren not related in a simple way. whole: 1.42 (0.42), residues: 391 helix: 1.17 (0.27), residues: 353 sheet: None (None), residues: 0 loop : -0.62 (1.05), residues: 38 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 52 TYR 0.014 0.002 TYR A 299 PHE 0.009 0.001 PHE A 324 HIS 0.003 0.001 HIS A 37 Details of bonding type rmsd covalent geometry : bond 0.00556 ( 2998) covalent geometry : angle 0.65169 ( 4086) hydrogen bonds : bond 0.04441 ( 254) hydrogen bonds : angle 4.56843 ( 762) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 69 time to evaluate : 0.069 Fit side-chains revert: symmetry clash REVERT: A 33 TYR cc_start: 0.7639 (OUTLIER) cc_final: 0.7215 (t80) REVERT: A 103 MET cc_start: 0.7845 (tpp) cc_final: 0.7505 (mpp) REVERT: A 174 GLU cc_start: 0.8657 (tt0) cc_final: 0.8363 (mt-10) REVERT: A 219 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.8036 (pp20) outliers start: 17 outliers final: 14 residues processed: 78 average time/residue: 0.0419 time to fit residues: 4.1456 Evaluate side-chains 85 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 69 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LEU Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 33 TYR Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 365 MET Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 407 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 24 optimal weight: 0.5980 chunk 9 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 6 optimal weight: 0.3980 chunk 31 optimal weight: 0.0170 chunk 4 optimal weight: 0.5980 chunk 32 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 33 optimal weight: 0.0060 chunk 10 optimal weight: 0.0070 overall best weight: 0.2052 ------------------------------------------------------------------------------- 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 = 0.3380 r_free = 0.3380 target = 0.096461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.088390 restraints weight = 5280.649| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 1.73 r_work: 0.3146 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.3413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 2998 Z= 0.146 Angle : 0.614 7.675 4086 Z= 0.302 Chirality : 0.043 0.181 517 Planarity : 0.005 0.051 497 Dihedral : 4.214 19.510 420 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 4.82 % Allowed : 25.08 % Favored : 70.10 % 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 aren not related in a simple way. whole: 1.63 (0.42), residues: 391 helix: 1.32 (0.27), residues: 353 sheet: None (None), residues: 0 loop : -0.69 (1.03), residues: 38 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 52 TYR 0.010 0.001 TYR A 299 PHE 0.007 0.001 PHE A 261 HIS 0.004 0.001 HIS A 37 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 2998) covalent geometry : angle 0.61433 ( 4086) hydrogen bonds : bond 0.04090 ( 254) hydrogen bonds : angle 4.42390 ( 762) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 73 time to evaluate : 0.111 Fit side-chains revert: symmetry clash REVERT: A 33 TYR cc_start: 0.7558 (OUTLIER) cc_final: 0.7172 (t80) REVERT: A 103 MET cc_start: 0.7731 (tpp) cc_final: 0.7418 (mpp) REVERT: A 174 GLU cc_start: 0.8612 (tt0) cc_final: 0.8317 (mt-10) REVERT: A 219 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.8039 (pp20) outliers start: 15 outliers final: 13 residues processed: 81 average time/residue: 0.0524 time to fit residues: 5.2946 Evaluate side-chains 86 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 71 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LEU Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 33 TYR Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 365 MET Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 407 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 20 optimal weight: 1.9990 chunk 6 optimal weight: 0.0980 chunk 23 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 8 optimal weight: 0.0970 chunk 28 optimal weight: 0.6980 chunk 26 optimal weight: 0.0670 chunk 13 optimal weight: 0.0980 chunk 2 optimal weight: 0.6980 chunk 29 optimal weight: 0.2980 chunk 21 optimal weight: 0.8980 overall best weight: 0.1316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 338 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 = 0.3397 r_free = 0.3397 target = 0.097658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.089757 restraints weight = 5222.455| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 1.69 r_work: 0.3170 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.3549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 2998 Z= 0.133 Angle : 0.604 7.485 4086 Z= 0.297 Chirality : 0.043 0.176 517 Planarity : 0.005 0.051 497 Dihedral : 4.102 19.026 420 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 4.50 % Allowed : 25.40 % Favored : 70.10 % 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 aren not related in a simple way. whole: 1.72 (0.42), residues: 391 helix: 1.38 (0.27), residues: 354 sheet: None (None), residues: 0 loop : -0.74 (1.04), residues: 37 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 52 TYR 0.009 0.001 TYR A 215 PHE 0.006 0.001 PHE A 210 HIS 0.004 0.001 HIS A 37 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 2998) covalent geometry : angle 0.60365 ( 4086) hydrogen bonds : bond 0.03966 ( 254) hydrogen bonds : angle 4.30261 ( 762) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 899.38 seconds wall clock time: 15 minutes 59.39 seconds (959.39 seconds total)