Starting phenix.real_space_refine on Fri May 9 23:21:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bh1_44529/05_2025/9bh1_44529.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bh1_44529/05_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_44529/05_2025/9bh1_44529.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bh1_44529/05_2025/9bh1_44529.map" model { file = "/net/cci-nas-00/data/ceres_data/9bh1_44529/05_2025/9bh1_44529.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bh1_44529/05_2025/9bh1_44529.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 3.03, per 1000 atoms: 1.03 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: 0.89 Conformation dependent library (CDL) restraints added in 520.9 milliseconds 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: 0.34 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: 0.79 Time building geometry restraints manager: 0.93 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: 5.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.600 Find NCS groups from input model: 0.040 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.280 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 HIS 0.001 0.000 HIS A 40 PHE 0.009 0.001 PHE A 248 TYR 0.006 0.001 TYR A 299 ARG 0.002 0.000 ARG A 105 Details of bonding type rmsd hydrogen bonds : bond 0.21659 ( 254) hydrogen bonds : angle 7.61978 ( 762) covalent geometry : bond 0.00321 ( 2998) covalent geometry : angle 0.48252 ( 4086) *********************** 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 : 0.293 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: 0.1564 time to fit residues: 15.6731 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 : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 0.5980 chunk 29 optimal weight: 0.0470 chunk 16 optimal weight: 0.6980 chunk 10 optimal weight: 0.0980 chunk 19 optimal weight: 0.5980 chunk 15 optimal weight: 0.3980 chunk 30 optimal weight: 0.5980 chunk 11 optimal weight: 0.0470 chunk 18 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 35 optimal weight: 0.7980 overall best weight: 0.2376 ------------------------------------------------------------------------------- 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 = 0.3323 r_free = 0.3323 target = 0.093670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.085766 restraints weight = 5167.735| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 1.67 r_work: 0.3095 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 2998 Z= 0.171 Angle : 0.622 7.806 4086 Z= 0.324 Chirality : 0.044 0.133 517 Planarity : 0.004 0.044 497 Dihedral : 4.148 15.087 420 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 2.25 % Allowed : 17.68 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.24 (0.42), residues: 391 helix: 1.64 (0.27), residues: 352 sheet: None (None), residues: 0 loop : 0.49 (1.08), residues: 39 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 32 PHE 0.008 0.001 PHE A 261 TYR 0.011 0.001 TYR A 299 ARG 0.006 0.001 ARG A 52 Details of bonding type rmsd hydrogen bonds : bond 0.05656 ( 254) hydrogen bonds : angle 5.05233 ( 762) covalent geometry : bond 0.00389 ( 2998) covalent geometry : angle 0.62228 ( 4086) *********************** 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 86 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 79 time to evaluate : 0.292 Fit side-chains REVERT: A 33 TYR cc_start: 0.7684 (OUTLIER) cc_final: 0.7135 (t80) REVERT: A 41 THR cc_start: 0.8534 (m) cc_final: 0.8189 (p) REVERT: A 169 MET cc_start: 0.8716 (mtp) cc_final: 0.8428 (mtp) REVERT: A 174 GLU cc_start: 0.8765 (tt0) cc_final: 0.8356 (mt-10) REVERT: A 196 LYS cc_start: 0.8386 (mmtm) cc_final: 0.5933 (pttt) REVERT: A 202 MET cc_start: 0.8994 (mmp) cc_final: 0.8762 (mmm) REVERT: A 290 LYS cc_start: 0.8938 (ttpt) cc_final: 0.8654 (ttpp) REVERT: A 309 ILE cc_start: 0.8744 (mm) cc_final: 0.8479 (tt) outliers start: 7 outliers final: 5 residues processed: 82 average time/residue: 0.1467 time to fit residues: 14.3769 Evaluate side-chains 80 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 74 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 35 optimal weight: 0.2980 chunk 0 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 10 optimal weight: 0.4980 chunk 16 optimal weight: 0.5980 chunk 21 optimal weight: 0.3980 chunk 18 optimal weight: 0.4980 chunk 9 optimal weight: 0.5980 chunk 12 optimal weight: 0.7980 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 = 0.3312 r_free = 0.3312 target = 0.092682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.085027 restraints weight = 5169.902| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 1.67 r_work: 0.3081 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 2998 Z= 0.203 Angle : 0.597 7.844 4086 Z= 0.311 Chirality : 0.044 0.160 517 Planarity : 0.005 0.044 497 Dihedral : 4.196 15.745 420 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 5.14 % Allowed : 19.29 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.42), residues: 391 helix: 1.39 (0.27), residues: 353 sheet: None (None), residues: 0 loop : -0.03 (1.06), residues: 38 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 264 PHE 0.008 0.001 PHE A 248 TYR 0.014 0.001 TYR A 317 ARG 0.004 0.001 ARG A 52 Details of bonding type rmsd hydrogen bonds : bond 0.04839 ( 254) hydrogen bonds : angle 4.69141 ( 762) covalent geometry : bond 0.00485 ( 2998) covalent geometry : angle 0.59707 ( 4086) *********************** 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 94 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 78 time to evaluate : 0.333 Fit side-chains REVERT: A 33 TYR cc_start: 0.7728 (OUTLIER) cc_final: 0.7289 (t80) REVERT: A 41 THR cc_start: 0.8604 (m) cc_final: 0.8327 (p) REVERT: A 85 ILE cc_start: 0.8469 (OUTLIER) cc_final: 0.8268 (tp) REVERT: A 133 ILE cc_start: 0.8699 (mm) cc_final: 0.8399 (mt) REVERT: A 174 GLU cc_start: 0.8669 (tt0) cc_final: 0.8294 (mt-10) REVERT: A 196 LYS cc_start: 0.8420 (mmtm) cc_final: 0.5851 (pttt) REVERT: A 203 GLN cc_start: 0.8994 (mm-40) cc_final: 0.8706 (mm-40) REVERT: A 219 GLU cc_start: 0.8379 (pp20) cc_final: 0.8084 (pp20) REVERT: A 290 LYS cc_start: 0.9028 (ttpt) cc_final: 0.8779 (ttpp) outliers start: 16 outliers final: 10 residues processed: 87 average time/residue: 0.1335 time to fit residues: 14.2175 Evaluate side-chains 86 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 74 time to evaluate : 0.307 ------------------------------------------------------------------------------- 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 85 ILE Chi-restraints excluded: chain A residue 266 LYS 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 393 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 0 optimal weight: 0.9990 chunk 23 optimal weight: 0.0570 chunk 20 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 14 optimal weight: 0.6980 chunk 32 optimal weight: 0.1980 chunk 12 optimal weight: 0.4980 chunk 35 optimal weight: 0.0270 chunk 2 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 overall best weight: 0.2956 ------------------------------------------------------------------------------- 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 = 0.3339 r_free = 0.3339 target = 0.094053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.086289 restraints weight = 5229.691| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 1.67 r_work: 0.3108 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.2779 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= 0.160 Angle : 0.593 7.914 4086 Z= 0.301 Chirality : 0.042 0.131 517 Planarity : 0.005 0.051 497 Dihedral : 4.210 15.653 420 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 4.50 % Allowed : 22.19 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.42), residues: 391 helix: 1.39 (0.27), residues: 353 sheet: None (None), residues: 0 loop : -0.26 (1.05), residues: 38 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 264 PHE 0.007 0.001 PHE A 261 TYR 0.011 0.001 TYR A 299 ARG 0.003 0.001 ARG A 52 Details of bonding type rmsd hydrogen bonds : bond 0.04462 ( 254) hydrogen bonds : angle 4.50709 ( 762) covalent geometry : bond 0.00380 ( 2998) covalent geometry : angle 0.59300 ( 4086) *********************** 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 : 0.289 Fit side-chains REVERT: A 33 TYR cc_start: 0.7708 (OUTLIER) cc_final: 0.7255 (t80) REVERT: A 41 THR cc_start: 0.8653 (m) cc_final: 0.8384 (p) REVERT: A 85 ILE cc_start: 0.8462 (OUTLIER) cc_final: 0.8261 (tp) REVERT: A 103 MET cc_start: 0.7840 (mpp) cc_final: 0.7597 (mpp) REVERT: A 133 ILE cc_start: 0.8643 (mm) cc_final: 0.8353 (mt) REVERT: A 174 GLU cc_start: 0.8634 (tt0) cc_final: 0.8304 (mt-10) REVERT: A 196 LYS cc_start: 0.8432 (mmtm) cc_final: 0.5834 (pttt) REVERT: A 203 GLN cc_start: 0.8956 (mm-40) cc_final: 0.8682 (mm-40) REVERT: A 219 GLU cc_start: 0.8431 (pp20) cc_final: 0.8021 (pp20) REVERT: A 290 LYS cc_start: 0.9042 (ttpt) cc_final: 0.8779 (ttpp) outliers start: 14 outliers final: 11 residues processed: 83 average time/residue: 0.1366 time to fit residues: 13.7901 Evaluate side-chains 88 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 75 time to evaluate : 0.286 ------------------------------------------------------------------------------- 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 85 ILE Chi-restraints excluded: chain A residue 130 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 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 24 optimal weight: 0.8980 chunk 7 optimal weight: 0.5980 chunk 8 optimal weight: 0.2980 chunk 25 optimal weight: 0.5980 chunk 36 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 0 optimal weight: 0.9990 chunk 33 optimal weight: 0.0980 chunk 35 optimal weight: 0.0770 chunk 5 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 overall best weight: 0.3338 ------------------------------------------------------------------------------- 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 = 0.3333 r_free = 0.3333 target = 0.093791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.086060 restraints weight = 5222.375| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 1.65 r_work: 0.3102 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 2998 Z= 0.166 Angle : 0.584 7.999 4086 Z= 0.295 Chirality : 0.042 0.140 517 Planarity : 0.005 0.051 497 Dihedral : 4.175 16.613 420 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 6.11 % Allowed : 20.26 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.42), residues: 391 helix: 1.37 (0.27), residues: 353 sheet: None (None), residues: 0 loop : -0.43 (1.05), residues: 38 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 264 PHE 0.007 0.001 PHE A 261 TYR 0.011 0.001 TYR A 299 ARG 0.002 0.000 ARG A 52 Details of bonding type rmsd hydrogen bonds : bond 0.04303 ( 254) hydrogen bonds : angle 4.44995 ( 762) covalent geometry : bond 0.00398 ( 2998) covalent geometry : angle 0.58401 ( 4086) *********************** 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 92 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 73 time to evaluate : 0.300 Fit side-chains revert: symmetry clash REVERT: A 33 TYR cc_start: 0.7686 (OUTLIER) cc_final: 0.7270 (t80) REVERT: A 41 THR cc_start: 0.8629 (m) cc_final: 0.8411 (p) REVERT: A 85 ILE cc_start: 0.8473 (OUTLIER) cc_final: 0.8267 (tp) REVERT: A 103 MET cc_start: 0.7822 (mpp) cc_final: 0.7603 (mpp) REVERT: A 133 ILE cc_start: 0.8629 (mm) cc_final: 0.8346 (mt) REVERT: A 174 GLU cc_start: 0.8623 (tt0) cc_final: 0.8300 (mt-10) REVERT: A 362 MET cc_start: 0.7425 (ptm) cc_final: 0.7133 (ptm) outliers start: 19 outliers final: 11 residues processed: 83 average time/residue: 0.1212 time to fit residues: 12.4707 Evaluate side-chains 89 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 76 time to evaluate : 0.282 ------------------------------------------------------------------------------- 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 85 ILE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 4 optimal weight: 0.6980 chunk 11 optimal weight: 0.0670 chunk 38 optimal weight: 0.9980 chunk 21 optimal weight: 0.3980 chunk 29 optimal weight: 0.7980 chunk 12 optimal weight: 0.2980 chunk 3 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 chunk 23 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 chunk 32 optimal weight: 0.0980 overall best weight: 0.2918 ------------------------------------------------------------------------------- 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 = 0.3370 r_free = 0.3370 target = 0.095552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.087684 restraints weight = 5283.208| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 1.70 r_work: 0.3118 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.3084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 2998 Z= 0.155 Angle : 0.587 7.455 4086 Z= 0.293 Chirality : 0.042 0.152 517 Planarity : 0.005 0.050 497 Dihedral : 4.151 15.873 420 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 6.75 % Allowed : 19.61 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.42), residues: 391 helix: 1.38 (0.27), residues: 353 sheet: None (None), residues: 0 loop : -0.48 (1.06), residues: 38 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 264 PHE 0.007 0.001 PHE A 261 TYR 0.011 0.001 TYR A 299 ARG 0.002 0.000 ARG A 52 Details of bonding type rmsd hydrogen bonds : bond 0.04202 ( 254) hydrogen bonds : angle 4.41281 ( 762) covalent geometry : bond 0.00370 ( 2998) covalent geometry : angle 0.58706 ( 4086) *********************** 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 97 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 76 time to evaluate : 0.327 Fit side-chains revert: symmetry clash REVERT: A 33 TYR cc_start: 0.7644 (OUTLIER) cc_final: 0.7224 (t80) REVERT: A 85 ILE cc_start: 0.8489 (OUTLIER) cc_final: 0.8284 (tp) REVERT: A 103 MET cc_start: 0.7777 (mpp) cc_final: 0.7559 (mpp) REVERT: A 133 ILE cc_start: 0.8591 (mm) cc_final: 0.8315 (mt) REVERT: A 174 GLU cc_start: 0.8616 (tt0) cc_final: 0.8323 (mt-10) REVERT: A 196 LYS cc_start: 0.8494 (mmmt) cc_final: 0.5785 (pttt) outliers start: 21 outliers final: 13 residues processed: 84 average time/residue: 0.1519 time to fit residues: 15.4222 Evaluate side-chains 89 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 74 time to evaluate : 0.312 ------------------------------------------------------------------------------- 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 30 LEU Chi-restraints excluded: chain A residue 33 TYR Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 219 GLU 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 347 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 1 optimal weight: 0.5980 chunk 7 optimal weight: 0.0970 chunk 30 optimal weight: 0.9990 chunk 28 optimal weight: 0.0370 chunk 15 optimal weight: 0.3980 chunk 26 optimal weight: 0.0980 chunk 29 optimal weight: 0.5980 chunk 12 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 37 optimal weight: 0.5980 chunk 33 optimal weight: 0.0070 overall best weight: 0.1274 ------------------------------------------------------------------------------- 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 = 0.3407 r_free = 0.3407 target = 0.097881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.089903 restraints weight = 5285.330| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 1.73 r_work: 0.3156 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.3307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2998 Z= 0.128 Angle : 0.589 7.426 4086 Z= 0.294 Chirality : 0.042 0.150 517 Planarity : 0.005 0.049 497 Dihedral : 4.154 18.642 420 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 5.79 % Allowed : 22.19 % Favored : 72.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.42), residues: 391 helix: 1.41 (0.27), residues: 354 sheet: None (None), residues: 0 loop : -0.50 (1.10), residues: 37 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 37 PHE 0.008 0.001 PHE A 261 TYR 0.009 0.001 TYR A 299 ARG 0.002 0.000 ARG A 52 Details of bonding type rmsd hydrogen bonds : bond 0.04060 ( 254) hydrogen bonds : angle 4.41634 ( 762) covalent geometry : bond 0.00294 ( 2998) covalent geometry : angle 0.58863 ( 4086) *********************** 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 95 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 77 time to evaluate : 0.322 Fit side-chains REVERT: A 33 TYR cc_start: 0.7636 (OUTLIER) cc_final: 0.7199 (t80) REVERT: A 85 ILE cc_start: 0.8474 (OUTLIER) cc_final: 0.8260 (tp) REVERT: A 103 MET cc_start: 0.7711 (OUTLIER) cc_final: 0.7472 (mpp) REVERT: A 133 ILE cc_start: 0.8564 (mm) cc_final: 0.8285 (mt) REVERT: A 174 GLU cc_start: 0.8586 (tt0) cc_final: 0.8301 (mt-10) REVERT: A 219 GLU cc_start: 0.8505 (pp20) cc_final: 0.7959 (pp20) outliers start: 18 outliers final: 10 residues processed: 82 average time/residue: 0.1445 time to fit residues: 14.3640 Evaluate side-chains 88 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 75 time to evaluate : 0.318 ------------------------------------------------------------------------------- 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 85 ILE Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 130 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 374 LEU Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 393 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 4 optimal weight: 0.5980 chunk 6 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 13 optimal weight: 0.0970 chunk 8 optimal weight: 0.1980 chunk 25 optimal weight: 0.0770 chunk 36 optimal weight: 0.5980 chunk 28 optimal weight: 0.0980 chunk 37 optimal weight: 0.6980 overall best weight: 0.2136 ------------------------------------------------------------------------------- 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 = 0.3396 r_free = 0.3396 target = 0.097325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.089389 restraints weight = 5225.767| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 1.70 r_work: 0.3143 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.3418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 2998 Z= 0.143 Angle : 0.587 7.265 4086 Z= 0.295 Chirality : 0.044 0.188 517 Planarity : 0.005 0.051 497 Dihedral : 4.100 19.080 420 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 5.14 % Allowed : 23.15 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.43), residues: 391 helix: 1.46 (0.27), residues: 353 sheet: None (None), residues: 0 loop : -0.46 (1.05), residues: 38 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 37 PHE 0.006 0.001 PHE A 261 TYR 0.010 0.001 TYR A 299 ARG 0.002 0.000 ARG A 52 Details of bonding type rmsd hydrogen bonds : bond 0.04085 ( 254) hydrogen bonds : angle 4.36417 ( 762) covalent geometry : bond 0.00344 ( 2998) covalent geometry : angle 0.58686 ( 4086) *********************** 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 88 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 72 time to evaluate : 0.336 Fit side-chains revert: symmetry clash REVERT: A 33 TYR cc_start: 0.7585 (OUTLIER) cc_final: 0.7144 (t80) REVERT: A 99 LEU cc_start: 0.8076 (tp) cc_final: 0.7802 (tp) REVERT: A 103 MET cc_start: 0.7686 (OUTLIER) cc_final: 0.7437 (mpp) REVERT: A 133 ILE cc_start: 0.8560 (mm) cc_final: 0.8269 (mt) REVERT: A 174 GLU cc_start: 0.8607 (tt0) cc_final: 0.8309 (mt-10) outliers start: 16 outliers final: 10 residues processed: 77 average time/residue: 0.1241 time to fit residues: 12.0271 Evaluate side-chains 81 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 69 time to evaluate : 0.312 ------------------------------------------------------------------------------- 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 103 MET Chi-restraints excluded: chain A residue 219 GLU 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 347 LEU Chi-restraints excluded: chain A residue 365 MET Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 393 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 12 optimal weight: 0.1980 chunk 33 optimal weight: 0.0770 chunk 20 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 6 optimal weight: 0.7980 chunk 38 optimal weight: 0.5980 chunk 4 optimal weight: 0.7980 chunk 28 optimal weight: 0.0970 chunk 32 optimal weight: 0.5980 chunk 30 optimal weight: 0.3980 chunk 2 optimal weight: 0.7980 overall best weight: 0.2736 ------------------------------------------------------------------------------- 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 = 0.3389 r_free = 0.3389 target = 0.096799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.088760 restraints weight = 5269.145| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 1.72 r_work: 0.3157 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.3436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 2998 Z= 0.155 Angle : 0.619 9.578 4086 Z= 0.303 Chirality : 0.044 0.180 517 Planarity : 0.005 0.051 497 Dihedral : 4.129 19.720 420 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 4.18 % Allowed : 25.72 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.42), residues: 391 helix: 1.44 (0.27), residues: 353 sheet: None (None), residues: 0 loop : -0.63 (1.04), residues: 38 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 37 PHE 0.007 0.001 PHE A 261 TYR 0.010 0.001 TYR A 299 ARG 0.001 0.000 ARG A 52 Details of bonding type rmsd hydrogen bonds : bond 0.04093 ( 254) hydrogen bonds : angle 4.35608 ( 762) covalent geometry : bond 0.00375 ( 2998) covalent geometry : angle 0.61901 ( 4086) *********************** 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 82 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 69 time to evaluate : 0.319 Fit side-chains revert: symmetry clash REVERT: A 33 TYR cc_start: 0.7585 (OUTLIER) cc_final: 0.7198 (t80) REVERT: A 103 MET cc_start: 0.7707 (OUTLIER) cc_final: 0.7482 (mpp) REVERT: A 133 ILE cc_start: 0.8563 (mm) cc_final: 0.8276 (mt) REVERT: A 174 GLU cc_start: 0.8612 (tt0) cc_final: 0.8313 (mt-10) outliers start: 13 outliers final: 9 residues processed: 74 average time/residue: 0.1206 time to fit residues: 11.1028 Evaluate side-chains 80 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 69 time to evaluate : 0.287 ------------------------------------------------------------------------------- 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 103 MET 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 347 LEU Chi-restraints excluded: chain A residue 365 MET Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 393 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 4 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 38 optimal weight: 0.0370 chunk 35 optimal weight: 0.0000 chunk 20 optimal weight: 0.0170 chunk 17 optimal weight: 0.3980 chunk 15 optimal weight: 0.3980 chunk 24 optimal weight: 0.9990 chunk 3 optimal weight: 0.6980 chunk 26 optimal weight: 0.0570 chunk 31 optimal weight: 0.8980 overall best weight: 0.1018 ------------------------------------------------------------------------------- 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 = 0.3427 r_free = 0.3427 target = 0.099296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.091332 restraints weight = 5259.656| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 1.72 r_work: 0.3194 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.3640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2998 Z= 0.127 Angle : 0.611 9.382 4086 Z= 0.296 Chirality : 0.043 0.176 517 Planarity : 0.005 0.051 497 Dihedral : 4.024 17.085 420 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 3.54 % Allowed : 26.69 % Favored : 69.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.42), residues: 391 helix: 1.52 (0.27), residues: 353 sheet: None (None), residues: 0 loop : -0.51 (1.03), residues: 38 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 37 PHE 0.009 0.001 PHE A 261 TYR 0.007 0.001 TYR A 299 ARG 0.002 0.000 ARG A 105 Details of bonding type rmsd hydrogen bonds : bond 0.03913 ( 254) hydrogen bonds : angle 4.27605 ( 762) covalent geometry : bond 0.00295 ( 2998) covalent geometry : angle 0.61116 ( 4086) ********************** 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 83 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 72 time to evaluate : 0.288 Fit side-chains revert: symmetry clash REVERT: A 33 TYR cc_start: 0.7474 (OUTLIER) cc_final: 0.7176 (t80) REVERT: A 133 ILE cc_start: 0.8536 (mm) cc_final: 0.8245 (mt) REVERT: A 174 GLU cc_start: 0.8602 (tt0) cc_final: 0.8310 (mt-10) outliers start: 11 outliers final: 9 residues processed: 77 average time/residue: 0.1252 time to fit residues: 12.0082 Evaluate side-chains 82 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 72 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 374 LEU Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 393 LEU 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 23 optimal weight: 0.7980 chunk 27 optimal weight: 0.0980 chunk 4 optimal weight: 0.4980 chunk 5 optimal weight: 0.0980 chunk 25 optimal weight: 0.6980 chunk 32 optimal weight: 0.2980 chunk 9 optimal weight: 0.9990 chunk 6 optimal weight: 0.4980 chunk 1 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 overall best weight: 0.2980 ------------------------------------------------------------------------------- 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 = 0.3394 r_free = 0.3394 target = 0.097166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.089151 restraints weight = 5222.805| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 1.71 r_work: 0.3164 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.3544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 2998 Z= 0.161 Angle : 0.632 9.990 4086 Z= 0.305 Chirality : 0.044 0.179 517 Planarity : 0.005 0.051 497 Dihedral : 4.047 17.176 420 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 3.86 % Allowed : 26.05 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.42), residues: 391 helix: 1.46 (0.27), residues: 353 sheet: None (None), residues: 0 loop : -0.58 (1.02), residues: 38 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 37 PHE 0.007 0.001 PHE A 261 TYR 0.011 0.001 TYR A 299 ARG 0.001 0.000 ARG A 52 Details of bonding type rmsd hydrogen bonds : bond 0.04019 ( 254) hydrogen bonds : angle 4.28981 ( 762) covalent geometry : bond 0.00398 ( 2998) covalent geometry : angle 0.63195 ( 4086) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1848.93 seconds wall clock time: 32 minutes 48.36 seconds (1968.36 seconds total)