Starting phenix.real_space_refine on Sun Apr 27 02:37:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bh1_44529/04_2025/9bh1_44529.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bh1_44529/04_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_44529/04_2025/9bh1_44529.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bh1_44529/04_2025/9bh1_44529.map" model { file = "/net/cci-nas-00/data/ceres_data/9bh1_44529/04_2025/9bh1_44529.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bh1_44529/04_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-5669/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: 3.18, per 1000 atoms: 1.08 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: 0.99 Conformation dependent library (CDL) restraints added in 386.6 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: 0.28 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: 0.78 Time building geometry restraints manager: 0.99 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: 6.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.600 Find NCS groups from input model: 0.030 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:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.110 ------------------------------------------------------------------------------- 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 : 0.406 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: 0.1661 time to fit residues: 16.7089 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 : 0.321 ------------------------------------------------------------------------------- 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: 0.0870 chunk 19 optimal weight: 0.5980 chunk 15 optimal weight: 0.3980 chunk 30 optimal weight: 0.5980 chunk 11 optimal weight: 0.3980 chunk 18 optimal weight: 0.7980 chunk 22 optimal weight: 0.4980 chunk 35 optimal weight: 0.7980 overall best weight: 0.2856 ------------------------------------------------------------------------------- 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 = 0.3321 r_free = 0.3321 target = 0.093497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.085594 restraints weight = 5161.944| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 1.66 r_work: 0.3094 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 2998 Z= 0.178 Angle : 0.627 7.832 4086 Z= 0.326 Chirality : 0.044 0.134 517 Planarity : 0.004 0.042 497 Dihedral : 4.174 15.357 420 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 1.93 % Allowed : 18.65 % Favored : 79.42 % 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: 2.25 (0.42), residues: 391 helix: 1.65 (0.27), residues: 352 sheet: None (None), residues: 0 loop : 0.47 (1.08), residues: 39 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 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 0.05598 ( 254) hydrogen bonds : angle 5.02020 ( 762) covalent geometry : bond 0.00409 ( 2998) covalent geometry : angle 0.62698 ( 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: 6 poor density : 80 time to evaluate : 0.486 Fit side-chains REVERT: A 33 TYR cc_start: 0.7680 (OUTLIER) cc_final: 0.7130 (t80) REVERT: A 41 THR cc_start: 0.8541 (m) cc_final: 0.8197 (p) REVERT: A 169 MET cc_start: 0.8732 (mtp) cc_final: 0.8466 (mtp) REVERT: A 174 GLU cc_start: 0.8766 (tt0) cc_final: 0.8361 (mt-10) REVERT: A 196 LYS cc_start: 0.8390 (mmtm) cc_final: 0.5920 (pttt) REVERT: A 202 MET cc_start: 0.9000 (mmp) cc_final: 0.8775 (mmm) REVERT: A 290 LYS cc_start: 0.8948 (ttpt) cc_final: 0.8666 (ttpp) REVERT: A 309 ILE cc_start: 0.8746 (mm) cc_final: 0.8481 (tt) outliers start: 6 outliers final: 4 residues processed: 83 average time/residue: 0.1721 time to fit residues: 17.1044 Evaluate side-chains 79 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 74 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 TYR 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: 0.0040 chunk 0 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 10 optimal weight: 0.2980 chunk 16 optimal weight: 0.4980 chunk 21 optimal weight: 0.2980 chunk 18 optimal weight: 0.2980 chunk 9 optimal weight: 0.5980 chunk 12 optimal weight: 0.4980 overall best weight: 0.2792 ------------------------------------------------------------------------------- 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 = 0.3336 r_free = 0.3336 target = 0.093899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.086103 restraints weight = 5176.681| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 1.69 r_work: 0.3107 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 2998 Z= 0.159 Angle : 0.578 7.136 4086 Z= 0.298 Chirality : 0.042 0.157 517 Planarity : 0.005 0.044 497 Dihedral : 4.101 14.894 420 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 : 5.47 % Allowed : 19.29 % Favored : 75.24 % 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: 2.00 (0.42), residues: 391 helix: 1.51 (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 0.012 0.001 TYR A 317 ARG 0.003 0.001 ARG A 52 Details of bonding type rmsd hydrogen bonds : bond 0.04698 ( 254) hydrogen bonds : angle 4.64013 ( 762) covalent geometry : bond 0.00373 ( 2998) covalent geometry : angle 0.57758 ( 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 91 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 74 time to evaluate : 0.336 Fit side-chains revert: symmetry clash REVERT: A 33 TYR cc_start: 0.7723 (OUTLIER) cc_final: 0.7290 (t80) REVERT: A 41 THR cc_start: 0.8580 (m) cc_final: 0.8305 (p) REVERT: A 103 MET cc_start: 0.7892 (tpp) cc_final: 0.7557 (mpp) REVERT: A 133 ILE cc_start: 0.8692 (mm) cc_final: 0.8403 (mt) REVERT: A 174 GLU cc_start: 0.8676 (tt0) cc_final: 0.8298 (mt-10) REVERT: A 196 LYS cc_start: 0.8382 (mmtm) cc_final: 0.5886 (pttt) REVERT: A 203 GLN cc_start: 0.8953 (mm-40) cc_final: 0.8737 (mm-40) REVERT: A 219 GLU cc_start: 0.8424 (pp20) cc_final: 0.8146 (pp20) REVERT: A 290 LYS cc_start: 0.8995 (ttpt) cc_final: 0.8711 (ttpp) outliers start: 17 outliers final: 12 residues processed: 84 average time/residue: 0.1467 time to fit residues: 14.9598 Evaluate side-chains 83 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 70 time to evaluate : 0.333 ------------------------------------------------------------------------------- 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 237 VAL 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: 0.9980 chunk 20 optimal weight: 0.0770 chunk 3 optimal weight: 1.9990 chunk 28 optimal weight: 0.3980 chunk 14 optimal weight: 0.5980 chunk 32 optimal weight: 0.2980 chunk 12 optimal weight: 0.5980 chunk 35 optimal weight: 0.0870 chunk 2 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 overall best weight: 0.2916 ------------------------------------------------------------------------------- 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 = 0.3343 r_free = 0.3343 target = 0.094375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.086553 restraints weight = 5259.568| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 1.69 r_work: 0.3113 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.2787 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= 0.157 Angle : 0.575 7.612 4086 Z= 0.294 Chirality : 0.042 0.160 517 Planarity : 0.005 0.049 497 Dihedral : 4.109 16.366 420 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 3.86 % Allowed : 22.19 % Favored : 73.95 % 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: 1.84 (0.42), residues: 391 helix: 1.43 (0.27), residues: 353 sheet: None (None), residues: 0 loop : -0.29 (1.05), residues: 38 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 223 PHE 0.006 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 0.04369 ( 254) hydrogen bonds : angle 4.47595 ( 762) covalent geometry : bond 0.00372 ( 2998) covalent geometry : angle 0.57452 ( 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 87 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 75 time to evaluate : 0.294 Fit side-chains REVERT: A 33 TYR cc_start: 0.7698 (OUTLIER) cc_final: 0.7248 (t80) REVERT: A 41 THR cc_start: 0.8657 (m) cc_final: 0.8411 (p) REVERT: A 103 MET cc_start: 0.7844 (tpp) cc_final: 0.7526 (mpp) REVERT: A 133 ILE cc_start: 0.8659 (mm) cc_final: 0.8366 (mt) REVERT: A 174 GLU cc_start: 0.8645 (tt0) cc_final: 0.8304 (mt-10) REVERT: A 196 LYS cc_start: 0.8385 (mmtm) cc_final: 0.5728 (pttt) REVERT: A 203 GLN cc_start: 0.8956 (mm-40) cc_final: 0.8696 (mm-40) REVERT: A 219 GLU cc_start: 0.8421 (pp20) cc_final: 0.8003 (pp20) REVERT: A 290 LYS cc_start: 0.9031 (ttpt) cc_final: 0.8773 (ttpp) outliers start: 12 outliers final: 9 residues processed: 83 average time/residue: 0.1404 time to fit residues: 14.0979 Evaluate side-chains 84 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 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 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 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: 0.7980 chunk 7 optimal weight: 0.3980 chunk 8 optimal weight: 0.4980 chunk 25 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 chunk 20 optimal weight: 0.0270 chunk 0 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 35 optimal weight: 0.0370 chunk 5 optimal weight: 0.5980 chunk 15 optimal weight: 0.0870 overall best weight: 0.2094 ------------------------------------------------------------------------------- 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 = 0.3363 r_free = 0.3363 target = 0.095665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.087771 restraints weight = 5214.951| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 1.70 r_work: 0.3134 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.2966 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= 0.139 Angle : 0.563 6.755 4086 Z= 0.285 Chirality : 0.042 0.147 517 Planarity : 0.005 0.050 497 Dihedral : 4.099 15.271 420 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % 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 (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: 1.86 (0.42), residues: 391 helix: 1.45 (0.27), residues: 353 sheet: None (None), residues: 0 loop : -0.40 (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 0.010 0.001 TYR A 317 ARG 0.002 0.000 ARG A 52 Details of bonding type rmsd hydrogen bonds : bond 0.04181 ( 254) hydrogen bonds : angle 4.38380 ( 762) covalent geometry : bond 0.00325 ( 2998) covalent geometry : angle 0.56314 ( 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 89 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 72 time to evaluate : 0.330 Fit side-chains revert: symmetry clash REVERT: A 33 TYR cc_start: 0.7676 (OUTLIER) cc_final: 0.7236 (t80) REVERT: A 41 THR cc_start: 0.8617 (m) cc_final: 0.8410 (p) REVERT: A 103 MET cc_start: 0.7842 (tpp) cc_final: 0.7525 (mpp) REVERT: A 133 ILE cc_start: 0.8627 (mm) cc_final: 0.8338 (mt) REVERT: A 174 GLU cc_start: 0.8597 (tt0) cc_final: 0.8279 (mt-10) outliers start: 17 outliers final: 10 residues processed: 81 average time/residue: 0.1296 time to fit residues: 12.9835 Evaluate side-chains 87 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 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 130 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 4 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 38 optimal weight: 0.3980 chunk 21 optimal weight: 0.3980 chunk 29 optimal weight: 0.8980 chunk 12 optimal weight: 0.0870 chunk 3 optimal weight: 0.6980 chunk 19 optimal weight: 0.6980 chunk 23 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 32 optimal weight: 0.2980 overall best weight: 0.3558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 318 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.095277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.087241 restraints weight = 5278.331| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 1.74 r_work: 0.3129 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.3080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 2998 Z= 0.171 Angle : 0.586 7.687 4086 Z= 0.296 Chirality : 0.043 0.170 517 Planarity : 0.005 0.050 497 Dihedral : 4.129 16.057 420 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 4.82 % Allowed : 21.22 % Favored : 73.95 % 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: 1.40 (0.27), residues: 353 sheet: None (None), residues: 0 loop : -0.38 (1.07), residues: 38 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 264 PHE 0.006 0.001 PHE A 324 TYR 0.012 0.001 TYR A 299 ARG 0.002 0.000 ARG A 52 Details of bonding type rmsd hydrogen bonds : bond 0.04222 ( 254) hydrogen bonds : angle 4.41369 ( 762) covalent geometry : bond 0.00413 ( 2998) covalent geometry : angle 0.58608 ( 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 90 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 75 time to evaluate : 0.605 Fit side-chains revert: symmetry clash REVERT: A 33 TYR cc_start: 0.7651 (OUTLIER) cc_final: 0.7210 (t80) REVERT: A 103 MET cc_start: 0.7863 (tpp) cc_final: 0.7530 (mpp) REVERT: A 133 ILE cc_start: 0.8600 (mm) cc_final: 0.8315 (mt) REVERT: A 174 GLU cc_start: 0.8599 (tt0) cc_final: 0.8274 (mt-10) REVERT: A 196 LYS cc_start: 0.8436 (mmmt) cc_final: 0.5738 (pttt) outliers start: 15 outliers final: 10 residues processed: 82 average time/residue: 0.2057 time to fit residues: 20.2260 Evaluate side-chains 82 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 71 time to evaluate : 0.365 ------------------------------------------------------------------------------- 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 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 1 optimal weight: 0.5980 chunk 7 optimal weight: 0.0030 chunk 30 optimal weight: 0.2980 chunk 28 optimal weight: 0.0980 chunk 15 optimal weight: 0.3980 chunk 26 optimal weight: 0.0980 chunk 29 optimal weight: 0.2980 chunk 12 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 37 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 overall best weight: 0.1590 ------------------------------------------------------------------------------- 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 = 0.3396 r_free = 0.3396 target = 0.097113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.089151 restraints weight = 5312.335| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 1.71 r_work: 0.3144 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.3265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 2998 Z= 0.135 Angle : 0.580 7.253 4086 Z= 0.289 Chirality : 0.042 0.160 517 Planarity : 0.005 0.050 497 Dihedral : 4.061 14.283 420 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 4.18 % Allowed : 23.15 % Favored : 72.67 % 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 (0.43), residues: 391 helix: 1.41 (0.27), residues: 353 sheet: None (None), residues: 0 loop : -0.41 (1.07), residues: 38 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 37 PHE 0.007 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 0.04081 ( 254) hydrogen bonds : angle 4.39062 ( 762) covalent geometry : bond 0.00316 ( 2998) covalent geometry : angle 0.57975 ( 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 87 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 0.342 Fit side-chains revert: symmetry clash REVERT: A 33 TYR cc_start: 0.7622 (OUTLIER) cc_final: 0.7191 (t80) REVERT: A 103 MET cc_start: 0.7749 (tpp) cc_final: 0.7425 (mpp) REVERT: A 133 ILE cc_start: 0.8577 (mm) cc_final: 0.8287 (mt) REVERT: A 174 GLU cc_start: 0.8600 (tt0) cc_final: 0.8287 (mt-10) REVERT: A 196 LYS cc_start: 0.8432 (mmmt) cc_final: 0.5678 (pttt) REVERT: A 262 ILE cc_start: 0.8964 (tt) cc_final: 0.8760 (mm) outliers start: 13 outliers final: 10 residues processed: 79 average time/residue: 0.1725 time to fit residues: 16.3143 Evaluate side-chains 84 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 73 time to evaluate : 0.359 ------------------------------------------------------------------------------- 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 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 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: 0.1980 chunk 6 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 38 optimal weight: 0.5980 chunk 29 optimal weight: 0.8980 chunk 13 optimal weight: 0.5980 chunk 8 optimal weight: 0.0870 chunk 25 optimal weight: 0.0570 chunk 36 optimal weight: 0.9980 chunk 28 optimal weight: 0.0980 chunk 37 optimal weight: 0.6980 overall best weight: 0.2076 ------------------------------------------------------------------------------- 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 = 0.3401 r_free = 0.3401 target = 0.097525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.089555 restraints weight = 5253.338| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 1.71 r_work: 0.3170 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.3356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 2998 Z= 0.140 Angle : 0.592 7.714 4086 Z= 0.295 Chirality : 0.042 0.174 517 Planarity : 0.005 0.051 497 Dihedral : 4.106 17.838 420 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 5.47 % Allowed : 23.47 % 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 (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 (0.43), residues: 391 helix: 1.40 (0.28), residues: 353 sheet: None (None), residues: 0 loop : -0.45 (1.07), 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 0.009 0.001 TYR A 299 ARG 0.002 0.000 ARG A 52 Details of bonding type rmsd hydrogen bonds : bond 0.03999 ( 254) hydrogen bonds : angle 4.38498 ( 762) covalent geometry : bond 0.00332 ( 2998) covalent geometry : angle 0.59155 ( 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 91 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 74 time to evaluate : 0.598 Fit side-chains revert: symmetry clash REVERT: A 33 TYR cc_start: 0.7580 (OUTLIER) cc_final: 0.7157 (t80) REVERT: A 59 MET cc_start: 0.8857 (tpp) cc_final: 0.8521 (tpp) REVERT: A 103 MET cc_start: 0.7689 (tpp) cc_final: 0.7410 (mpp) REVERT: A 133 ILE cc_start: 0.8564 (mm) cc_final: 0.8280 (mt) REVERT: A 174 GLU cc_start: 0.8592 (tt0) cc_final: 0.8290 (mt-10) outliers start: 17 outliers final: 12 residues processed: 82 average time/residue: 0.1731 time to fit residues: 18.0928 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 : 0.371 ------------------------------------------------------------------------------- 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 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 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 12 optimal weight: 0.4980 chunk 33 optimal weight: 0.3980 chunk 20 optimal weight: 1.9990 chunk 23 optimal weight: 0.0370 chunk 6 optimal weight: 0.7980 chunk 38 optimal weight: 0.5980 chunk 4 optimal weight: 0.7980 chunk 28 optimal weight: 0.0980 chunk 32 optimal weight: 0.4980 chunk 30 optimal weight: 0.5980 chunk 2 optimal weight: 0.5980 overall best weight: 0.3058 ------------------------------------------------------------------------------- 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 = 0.3382 r_free = 0.3382 target = 0.096262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.088349 restraints weight = 5287.295| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 1.71 r_work: 0.3148 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.3345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 2998 Z= 0.163 Angle : 0.619 9.698 4086 Z= 0.304 Chirality : 0.044 0.184 517 Planarity : 0.005 0.050 497 Dihedral : 4.148 20.121 420 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 4.18 % Allowed : 24.44 % Favored : 71.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.39 (0.27), residues: 353 sheet: None (None), residues: 0 loop : -0.53 (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 324 TYR 0.011 0.001 TYR A 299 ARG 0.002 0.000 ARG A 52 Details of bonding type rmsd hydrogen bonds : bond 0.04131 ( 254) hydrogen bonds : angle 4.39067 ( 762) covalent geometry : bond 0.00397 ( 2998) covalent geometry : angle 0.61878 ( 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 86 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 73 time to evaluate : 0.307 Fit side-chains revert: symmetry clash REVERT: A 33 TYR cc_start: 0.7597 (OUTLIER) cc_final: 0.7164 (t80) REVERT: A 103 MET cc_start: 0.7731 (tpp) cc_final: 0.7449 (mpp) REVERT: A 133 ILE cc_start: 0.8565 (mm) cc_final: 0.8277 (mt) REVERT: A 174 GLU cc_start: 0.8603 (tt0) cc_final: 0.8306 (mt-10) REVERT: A 196 LYS cc_start: 0.8445 (mmmt) cc_final: 0.5688 (pttt) outliers start: 13 outliers final: 11 residues processed: 80 average time/residue: 0.1507 time to fit residues: 14.5715 Evaluate side-chains 84 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 0.342 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 4 optimal weight: 0.4980 chunk 22 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 chunk 35 optimal weight: 0.0980 chunk 20 optimal weight: 0.0370 chunk 17 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 24 optimal weight: 0.0980 chunk 3 optimal weight: 0.3980 chunk 26 optimal weight: 0.1980 chunk 31 optimal weight: 0.2980 overall best weight: 0.1458 ------------------------------------------------------------------------------- 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 = 0.3418 r_free = 0.3418 target = 0.098745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.090752 restraints weight = 5235.601| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 1.74 r_work: 0.3185 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.3542 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= 0.132 Angle : 0.608 9.545 4086 Z= 0.295 Chirality : 0.042 0.172 517 Planarity : 0.005 0.051 497 Dihedral : 4.079 18.997 420 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 3.22 % Allowed : 25.08 % 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: 1.95 (0.42), residues: 391 helix: 1.56 (0.28), residues: 350 sheet: None (None), residues: 0 loop : -0.65 (0.98), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 37 PHE 0.008 0.001 PHE A 261 TYR 0.008 0.001 TYR A 317 ARG 0.002 0.000 ARG A 52 Details of bonding type rmsd hydrogen bonds : bond 0.03930 ( 254) hydrogen bonds : angle 4.28828 ( 762) covalent geometry : bond 0.00309 ( 2998) covalent geometry : angle 0.60844 ( 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 84 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 74 time to evaluate : 0.328 Fit side-chains revert: symmetry clash REVERT: A 33 TYR cc_start: 0.7520 (OUTLIER) cc_final: 0.7174 (t80) REVERT: A 103 MET cc_start: 0.7647 (tpp) cc_final: 0.7376 (mpp) REVERT: A 133 ILE cc_start: 0.8529 (mm) cc_final: 0.8238 (mt) REVERT: A 174 GLU cc_start: 0.8585 (tt0) cc_final: 0.8294 (mt-10) outliers start: 10 outliers final: 9 residues processed: 79 average time/residue: 0.1605 time to fit residues: 15.1952 Evaluate side-chains 84 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 74 time to evaluate : 0.353 ------------------------------------------------------------------------------- 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 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: 0.0980 chunk 23 optimal weight: 0.0060 chunk 27 optimal weight: 0.7980 chunk 4 optimal weight: 0.5980 chunk 5 optimal weight: 0.0770 chunk 25 optimal weight: 0.6980 chunk 32 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 6 optimal weight: 0.1980 chunk 1 optimal weight: 0.3980 chunk 21 optimal weight: 0.5980 overall best weight: 0.1554 ------------------------------------------------------------------------------- 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 = 0.3423 r_free = 0.3423 target = 0.098874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.090939 restraints weight = 5181.918| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 1.71 r_work: 0.3193 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.3604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 2998 Z= 0.132 Angle : 0.609 9.848 4086 Z= 0.295 Chirality : 0.042 0.175 517 Planarity : 0.005 0.050 497 Dihedral : 4.013 18.497 420 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 4.18 % Allowed : 24.44 % Favored : 71.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.99 (0.42), residues: 391 helix: 1.58 (0.27), residues: 349 sheet: None (None), residues: 0 loop : -0.60 (0.95), residues: 42 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 37 PHE 0.008 0.001 PHE A 261 TYR 0.008 0.001 TYR A 299 ARG 0.002 0.000 ARG A 52 Details of bonding type rmsd hydrogen bonds : bond 0.03911 ( 254) hydrogen bonds : angle 4.24655 ( 762) covalent geometry : bond 0.00314 ( 2998) covalent geometry : angle 0.60880 ( 4086) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2124.29 seconds wall clock time: 37 minutes 55.18 seconds (2275.18 seconds total)