Starting phenix.real_space_refine on Fri Aug 22 13:46:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f6t_28890/08_2025/8f6t_28890.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f6t_28890/08_2025/8f6t_28890.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8f6t_28890/08_2025/8f6t_28890.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f6t_28890/08_2025/8f6t_28890.map" model { file = "/net/cci-nas-00/data/ceres_data/8f6t_28890/08_2025/8f6t_28890.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f6t_28890/08_2025/8f6t_28890.cif" } resolution = 2.76 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 sd= 0.114 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Fe 3 7.16 5 S 11 5.16 5 C 2261 2.51 5 N 604 2.21 5 O 594 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3473 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3458 Classifications: {'peptide': 428} Link IDs: {'PTRANS': 30, 'TRANS': 397} Chain breaks: 1 Chain: "A" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 15 Unusual residues: {' FE': 3, 'D12': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3074 SG CYS A 418 40.499 23.954 46.620 1.00125.12 S ATOM 3095 SG CYS A 421 40.898 27.411 46.825 1.00127.79 S ATOM 3331 SG CYS A 451 38.727 26.710 49.011 1.00124.73 S ATOM 3352 SG CYS A 454 37.613 26.470 45.458 1.00120.95 S Time building chain proxies: 0.93, per 1000 atoms: 0.27 Number of scatterers: 3473 At special positions: 0 Unit cell: (65.268, 81.252, 75.924, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 3 26.01 S 11 16.00 O 594 8.00 N 604 7.00 C 2261 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.19 Conformation dependent library (CDL) restraints added in 93.3 milliseconds Enol-peptide restraints added in 0.0 nanoseconds 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 796 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 1 sheets defined 65.2% alpha, 0.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'A' and resid 18 through 25 removed outlier: 3.558A pdb=" N TRP A 21 " --> pdb=" O ARG A 18 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU A 23 " --> pdb=" O LEU A 20 " (cutoff:3.500A) Proline residue: A 25 - end of helix Processing helix chain 'A' and resid 26 through 42 Processing helix chain 'A' and resid 43 through 48 Processing helix chain 'A' and resid 50 through 56 Processing helix chain 'A' and resid 57 through 65 removed outlier: 4.890A pdb=" N TRP A 63 " --> pdb=" O PRO A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 81 removed outlier: 4.258A pdb=" N ALA A 78 " --> pdb=" O GLU A 74 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N GLN A 79 " --> pdb=" O ALA A 75 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLU A 81 " --> pdb=" O VAL A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 92 removed outlier: 4.041A pdb=" N VAL A 90 " --> pdb=" O TYR A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 111 removed outlier: 3.672A pdb=" N GLN A 97 " --> pdb=" O TYR A 93 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N TYR A 98 " --> pdb=" O LEU A 94 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N ALA A 99 " --> pdb=" O PRO A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 141 removed outlier: 3.917A pdb=" N HIS A 141 " --> pdb=" O HIS A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 155 removed outlier: 3.595A pdb=" N ARG A 148 " --> pdb=" O GLU A 144 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TRP A 149 " --> pdb=" O ASN A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 170 removed outlier: 4.004A pdb=" N ASN A 168 " --> pdb=" O PHE A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 192 Processing helix chain 'A' and resid 193 through 216 Processing helix chain 'A' and resid 225 through 245 removed outlier: 3.910A pdb=" N MET A 233 " --> pdb=" O GLN A 229 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N THR A 234 " --> pdb=" O ALA A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 272 removed outlier: 3.595A pdb=" N LEU A 250 " --> pdb=" O GLY A 246 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE A 267 " --> pdb=" O LEU A 263 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N HIS A 272 " --> pdb=" O ASN A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 293 removed outlier: 3.866A pdb=" N SER A 293 " --> pdb=" O PRO A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 305 Processing helix chain 'A' and resid 312 through 317 Processing helix chain 'A' and resid 321 through 325 removed outlier: 3.754A pdb=" N LEU A 325 " --> pdb=" O PHE A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 347 removed outlier: 3.547A pdb=" N VAL A 347 " --> pdb=" O ILE A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 363 Proline residue: A 357 - end of helix Processing helix chain 'A' and resid 373 through 375 No H-bonds generated for 'chain 'A' and resid 373 through 375' Processing helix chain 'A' and resid 376 through 385 Processing helix chain 'A' and resid 441 through 445 Processing helix chain 'A' and resid 458 through 462 Processing sheet with id=AA1, first strand: chain 'A' and resid 424 through 425 165 hydrogen bonds defined for protein. 453 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: 0.48 Time building geometry restraints manager: 0.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1104 1.34 - 1.46: 717 1.46 - 1.57: 1749 1.57 - 1.69: 0 1.69 - 1.81: 15 Bond restraints: 3585 Sorted by residual: bond pdb=" CA HIS A 314 " pdb=" C HIS A 314 " ideal model delta sigma weight residual 1.523 1.512 0.011 1.30e-02 5.92e+03 7.03e-01 bond pdb=" CG PRO A 25 " pdb=" CD PRO A 25 " ideal model delta sigma weight residual 1.503 1.478 0.025 3.40e-02 8.65e+02 5.39e-01 bond pdb=" CG1 ILE A 131 " pdb=" CD1 ILE A 131 " ideal model delta sigma weight residual 1.513 1.485 0.028 3.90e-02 6.57e+02 5.31e-01 bond pdb=" N GLU A 271 " pdb=" CA GLU A 271 " ideal model delta sigma weight residual 1.459 1.468 -0.009 1.19e-02 7.06e+03 5.20e-01 bond pdb=" C ILE A 343 " pdb=" N PRO A 344 " ideal model delta sigma weight residual 1.334 1.350 -0.017 2.34e-02 1.83e+03 5.02e-01 ... (remaining 3580 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.21: 4637 1.21 - 2.41: 203 2.41 - 3.62: 36 3.62 - 4.82: 15 4.82 - 6.03: 7 Bond angle restraints: 4898 Sorted by residual: angle pdb=" N ASP A 453 " pdb=" CA ASP A 453 " pdb=" C ASP A 453 " ideal model delta sigma weight residual 114.56 110.05 4.51 1.27e+00 6.20e-01 1.26e+01 angle pdb=" CA ASP A 453 " pdb=" C ASP A 453 " pdb=" N CYS A 454 " ideal model delta sigma weight residual 119.26 116.45 2.81 1.14e+00 7.69e-01 6.09e+00 angle pdb=" C ASN A 168 " pdb=" N ARG A 169 " pdb=" CA ARG A 169 " ideal model delta sigma weight residual 121.99 118.70 3.29 1.56e+00 4.11e-01 4.46e+00 angle pdb=" CA ASP A 453 " pdb=" C ASP A 453 " pdb=" O ASP A 453 " ideal model delta sigma weight residual 118.55 120.78 -2.23 1.14e+00 7.69e-01 3.83e+00 angle pdb=" N PRO A 374 " pdb=" CA PRO A 374 " pdb=" C PRO A 374 " ideal model delta sigma weight residual 110.70 112.87 -2.17 1.22e+00 6.72e-01 3.17e+00 ... (remaining 4893 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.14: 1849 16.14 - 32.29: 184 32.29 - 48.43: 38 48.43 - 64.57: 2 64.57 - 80.71: 1 Dihedral angle restraints: 2074 sinusoidal: 830 harmonic: 1244 Sorted by residual: dihedral pdb=" CA LEU A 367 " pdb=" C LEU A 367 " pdb=" N THR A 368 " pdb=" CA THR A 368 " ideal model delta harmonic sigma weight residual 180.00 161.77 18.23 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA PRO A 59 " pdb=" C PRO A 59 " pdb=" N LEU A 60 " pdb=" CA LEU A 60 " ideal model delta harmonic sigma weight residual 180.00 162.65 17.35 0 5.00e+00 4.00e-02 1.20e+01 dihedral pdb=" CA TYR A 160 " pdb=" C TYR A 160 " pdb=" N GLY A 161 " pdb=" CA GLY A 161 " ideal model delta harmonic sigma weight residual 180.00 -163.69 -16.31 0 5.00e+00 4.00e-02 1.06e+01 ... (remaining 2071 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 267 0.027 - 0.053: 151 0.053 - 0.080: 64 0.080 - 0.107: 27 0.107 - 0.134: 7 Chirality restraints: 516 Sorted by residual: chirality pdb=" CA ARG A 169 " pdb=" N ARG A 169 " pdb=" C ARG A 169 " pdb=" CB ARG A 169 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.46e-01 chirality pdb=" CA VAL A 347 " pdb=" N VAL A 347 " pdb=" C VAL A 347 " pdb=" CB VAL A 347 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.14e-01 chirality pdb=" CA ILE A 445 " pdb=" N ILE A 445 " pdb=" C ILE A 445 " pdb=" CB ILE A 445 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.89e-01 ... (remaining 513 not shown) Planarity restraints: 624 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 373 " -0.032 5.00e-02 4.00e+02 4.88e-02 3.81e+00 pdb=" N PRO A 374 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 374 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 374 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 180 " -0.024 5.00e-02 4.00e+02 3.61e-02 2.08e+00 pdb=" N PRO A 181 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO A 181 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 181 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 440 " 0.023 5.00e-02 4.00e+02 3.41e-02 1.86e+00 pdb=" N PRO A 441 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 441 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 441 " 0.019 5.00e-02 4.00e+02 ... (remaining 621 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 52 2.68 - 3.23: 3346 3.23 - 3.79: 5315 3.79 - 4.34: 7139 4.34 - 4.90: 11788 Nonbonded interactions: 27640 Sorted by model distance: nonbonded pdb=" NE2 HIS A 167 " pdb="FE FE A 502 " model vdw 2.119 2.340 nonbonded pdb=" NE2 HIS A 272 " pdb="FE FE A 501 " model vdw 2.163 2.340 nonbonded pdb=" NE2 HIS A 314 " pdb="FE FE A 502 " model vdw 2.167 2.340 nonbonded pdb=" NE2 HIS A 141 " pdb="FE FE A 502 " model vdw 2.198 2.340 nonbonded pdb=" ND2 ASN A 129 " pdb=" OE1 GLN A 256 " model vdw 2.215 3.120 ... (remaining 27635 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.180 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3585 Z= 0.181 Angle : 0.629 6.030 4898 Z= 0.344 Chirality : 0.041 0.134 516 Planarity : 0.005 0.049 624 Dihedral : 12.871 80.711 1278 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.80 (0.42), residues: 424 helix: 1.16 (0.36), residues: 239 sheet: None (None), residues: 0 loop : -0.22 (0.45), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 361 TYR 0.010 0.001 TYR A 423 PHE 0.010 0.001 PHE A 26 TRP 0.008 0.001 TRP A 106 HIS 0.007 0.001 HIS A 315 Details of bonding type rmsd covalent geometry : bond 0.00416 ( 3585) covalent geometry : angle 0.62911 ( 4898) hydrogen bonds : bond 0.13718 ( 165) hydrogen bonds : angle 5.59803 ( 453) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.134 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.4463 time to fit residues: 13.9664 Evaluate side-chains 21 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 37 optimal weight: 8.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 309 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 = 0.3023 r_free = 0.3023 target = 0.075849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.060924 restraints weight = 7122.752| |-----------------------------------------------------------------------------| r_work (start): 0.2750 rms_B_bonded: 2.62 r_work: 0.2627 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.0785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3585 Z= 0.189 Angle : 0.606 7.800 4898 Z= 0.309 Chirality : 0.042 0.124 516 Planarity : 0.005 0.048 624 Dihedral : 5.785 59.747 485 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 1.40 % Allowed : 5.59 % Favored : 93.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.10 (0.43), residues: 424 helix: 1.35 (0.37), residues: 239 sheet: None (None), residues: 0 loop : 0.00 (0.47), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 361 TYR 0.012 0.001 TYR A 160 PHE 0.010 0.001 PHE A 193 TRP 0.012 0.001 TRP A 442 HIS 0.007 0.001 HIS A 315 Details of bonding type rmsd covalent geometry : bond 0.00449 ( 3585) covalent geometry : angle 0.60603 ( 4898) hydrogen bonds : bond 0.05583 ( 165) hydrogen bonds : angle 4.87108 ( 453) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 23 time to evaluate : 0.137 Fit side-chains REVERT: A 42 ASP cc_start: 0.8832 (t0) cc_final: 0.8627 (OUTLIER) REVERT: A 226 GLU cc_start: 0.8786 (OUTLIER) cc_final: 0.8330 (mp0) REVERT: A 271 GLU cc_start: 0.8526 (mt-10) cc_final: 0.8196 (mt-10) outliers start: 5 outliers final: 2 residues processed: 24 average time/residue: 0.4398 time to fit residues: 11.0603 Evaluate side-chains 25 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 23 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 226 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 4 optimal weight: 0.0770 chunk 11 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- 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 = 0.3083 r_free = 0.3083 target = 0.079464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.064953 restraints weight = 7005.371| |-----------------------------------------------------------------------------| r_work (start): 0.2817 rms_B_bonded: 2.60 r_work: 0.2696 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.1178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 3585 Z= 0.108 Angle : 0.531 5.613 4898 Z= 0.268 Chirality : 0.038 0.116 516 Planarity : 0.005 0.047 624 Dihedral : 5.353 55.978 485 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 1.12 % Allowed : 8.38 % Favored : 90.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.35 (0.43), residues: 424 helix: 1.62 (0.37), residues: 233 sheet: None (None), residues: 0 loop : 0.08 (0.47), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 433 TYR 0.008 0.001 TYR A 85 PHE 0.008 0.001 PHE A 193 TRP 0.008 0.001 TRP A 442 HIS 0.005 0.001 HIS A 315 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 3585) covalent geometry : angle 0.53146 ( 4898) hydrogen bonds : bond 0.04132 ( 165) hydrogen bonds : angle 4.51784 ( 453) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 28 time to evaluate : 0.149 Fit side-chains REVERT: A 42 ASP cc_start: 0.8887 (t0) cc_final: 0.8636 (OUTLIER) REVERT: A 226 GLU cc_start: 0.8749 (OUTLIER) cc_final: 0.8309 (mp0) outliers start: 4 outliers final: 2 residues processed: 29 average time/residue: 0.3634 time to fit residues: 11.1621 Evaluate side-chains 25 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 23 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 226 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 15 optimal weight: 1.9990 chunk 1 optimal weight: 0.1980 chunk 3 optimal weight: 0.0060 chunk 2 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 40 optimal weight: 0.0020 chunk 41 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 chunk 18 optimal weight: 4.9990 overall best weight: 0.3404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.081796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.067374 restraints weight = 6964.881| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 2.66 r_work: 0.2748 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 3585 Z= 0.098 Angle : 0.509 5.594 4898 Z= 0.255 Chirality : 0.037 0.121 516 Planarity : 0.005 0.045 624 Dihedral : 5.134 57.234 485 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 1.68 % Allowed : 9.78 % Favored : 88.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.23 (0.43), residues: 424 helix: 1.40 (0.37), residues: 241 sheet: None (None), residues: 0 loop : 0.13 (0.48), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 433 TYR 0.007 0.001 TYR A 85 PHE 0.007 0.001 PHE A 193 TRP 0.007 0.001 TRP A 116 HIS 0.005 0.001 HIS A 315 Details of bonding type rmsd covalent geometry : bond 0.00224 ( 3585) covalent geometry : angle 0.50883 ( 4898) hydrogen bonds : bond 0.03493 ( 165) hydrogen bonds : angle 4.31227 ( 453) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 27 time to evaluate : 0.085 Fit side-chains REVERT: A 42 ASP cc_start: 0.8863 (t0) cc_final: 0.8577 (OUTLIER) REVERT: A 63 TRP cc_start: 0.9040 (t60) cc_final: 0.8564 (t60) REVERT: A 226 GLU cc_start: 0.8719 (OUTLIER) cc_final: 0.8308 (mp0) outliers start: 6 outliers final: 3 residues processed: 30 average time/residue: 0.3977 time to fit residues: 12.4682 Evaluate side-chains 28 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 25 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 226 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 40 optimal weight: 0.7980 chunk 3 optimal weight: 0.0870 chunk 1 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 8 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 overall best weight: 0.7758 ------------------------------------------------------------------------------- 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 = 0.3105 r_free = 0.3105 target = 0.080517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.065996 restraints weight = 7138.832| |-----------------------------------------------------------------------------| r_work (start): 0.2842 rms_B_bonded: 2.66 r_work: 0.2721 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3585 Z= 0.106 Angle : 0.505 5.577 4898 Z= 0.255 Chirality : 0.037 0.121 516 Planarity : 0.005 0.045 624 Dihedral : 5.055 55.459 485 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 1.12 % Allowed : 11.45 % Favored : 87.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.24 (0.43), residues: 424 helix: 1.40 (0.37), residues: 241 sheet: None (None), residues: 0 loop : 0.18 (0.48), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 433 TYR 0.007 0.001 TYR A 85 PHE 0.008 0.001 PHE A 193 TRP 0.006 0.001 TRP A 116 HIS 0.004 0.001 HIS A 311 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 3585) covalent geometry : angle 0.50546 ( 4898) hydrogen bonds : bond 0.03668 ( 165) hydrogen bonds : angle 4.26144 ( 453) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 25 time to evaluate : 0.134 Fit side-chains REVERT: A 42 ASP cc_start: 0.8871 (t0) cc_final: 0.8578 (OUTLIER) REVERT: A 63 TRP cc_start: 0.9001 (t60) cc_final: 0.8541 (t60) REVERT: A 226 GLU cc_start: 0.8715 (OUTLIER) cc_final: 0.8306 (mp0) outliers start: 4 outliers final: 2 residues processed: 26 average time/residue: 0.4000 time to fit residues: 10.8916 Evaluate side-chains 27 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 25 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 226 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 13 optimal weight: 0.4980 chunk 8 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 16 optimal weight: 0.5980 chunk 6 optimal weight: 0.0870 chunk 30 optimal weight: 0.8980 chunk 27 optimal weight: 0.0370 chunk 38 optimal weight: 6.9990 chunk 37 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 overall best weight: 0.4036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 309 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 = 0.3133 r_free = 0.3133 target = 0.082117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.067638 restraints weight = 7044.165| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 2.67 r_work: 0.2760 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 3585 Z= 0.098 Angle : 0.498 5.536 4898 Z= 0.251 Chirality : 0.037 0.122 516 Planarity : 0.005 0.044 624 Dihedral : 4.882 53.286 485 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 1.68 % Allowed : 11.17 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.19 (0.43), residues: 424 helix: 1.45 (0.37), residues: 241 sheet: 0.21 (1.77), residues: 9 loop : -0.01 (0.48), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 433 TYR 0.006 0.001 TYR A 85 PHE 0.010 0.001 PHE A 193 TRP 0.007 0.001 TRP A 116 HIS 0.003 0.000 HIS A 315 Details of bonding type rmsd covalent geometry : bond 0.00230 ( 3585) covalent geometry : angle 0.49780 ( 4898) hydrogen bonds : bond 0.03295 ( 165) hydrogen bonds : angle 4.19434 ( 453) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 28 time to evaluate : 0.136 Fit side-chains REVERT: A 42 ASP cc_start: 0.8852 (t0) cc_final: 0.8562 (OUTLIER) REVERT: A 63 TRP cc_start: 0.8994 (t60) cc_final: 0.8506 (t60) REVERT: A 226 GLU cc_start: 0.8696 (OUTLIER) cc_final: 0.8299 (mp0) REVERT: A 271 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.7693 (tt0) outliers start: 6 outliers final: 4 residues processed: 31 average time/residue: 0.3213 time to fit residues: 10.4933 Evaluate side-chains 32 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 27 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 271 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 6.9990 chunk 40 optimal weight: 0.9990 chunk 1 optimal weight: 0.0070 chunk 15 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 14 optimal weight: 0.9990 overall best weight: 0.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 309 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 = 0.3111 r_free = 0.3111 target = 0.080984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.066667 restraints weight = 7189.995| |-----------------------------------------------------------------------------| r_work (start): 0.2855 rms_B_bonded: 2.66 r_work: 0.2734 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3585 Z= 0.105 Angle : 0.510 6.200 4898 Z= 0.256 Chirality : 0.037 0.122 516 Planarity : 0.004 0.043 624 Dihedral : 4.822 51.008 485 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.84 % Allowed : 12.57 % Favored : 86.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.18 (0.43), residues: 424 helix: 1.44 (0.36), residues: 241 sheet: 0.34 (1.79), residues: 9 loop : -0.02 (0.48), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 433 TYR 0.006 0.001 TYR A 85 PHE 0.009 0.001 PHE A 193 TRP 0.006 0.001 TRP A 116 HIS 0.003 0.001 HIS A 315 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 3585) covalent geometry : angle 0.50986 ( 4898) hydrogen bonds : bond 0.03535 ( 165) hydrogen bonds : angle 4.18891 ( 453) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 23 time to evaluate : 0.142 Fit side-chains REVERT: A 42 ASP cc_start: 0.8851 (t0) cc_final: 0.8522 (OUTLIER) REVERT: A 63 TRP cc_start: 0.8998 (t60) cc_final: 0.8508 (t60) REVERT: A 226 GLU cc_start: 0.8655 (OUTLIER) cc_final: 0.8279 (mp0) REVERT: A 271 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.7741 (tt0) outliers start: 3 outliers final: 2 residues processed: 24 average time/residue: 0.4509 time to fit residues: 11.2847 Evaluate side-chains 26 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 23 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 271 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 0.0070 chunk 15 optimal weight: 4.9990 chunk 2 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 35 optimal weight: 6.9990 chunk 33 optimal weight: 0.0040 chunk 25 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 overall best weight: 0.9614 ------------------------------------------------------------------------------- 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 = 0.3090 r_free = 0.3090 target = 0.079686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.065168 restraints weight = 7207.675| |-----------------------------------------------------------------------------| r_work (start): 0.2831 rms_B_bonded: 2.66 r_work: 0.2709 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3585 Z= 0.115 Angle : 0.524 5.613 4898 Z= 0.265 Chirality : 0.038 0.122 516 Planarity : 0.005 0.044 624 Dihedral : 4.740 45.694 485 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 1.68 % Allowed : 12.01 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.25 (0.43), residues: 424 helix: 1.63 (0.37), residues: 235 sheet: 0.44 (1.81), residues: 9 loop : -0.17 (0.47), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 433 TYR 0.006 0.001 TYR A 259 PHE 0.008 0.001 PHE A 193 TRP 0.005 0.001 TRP A 21 HIS 0.004 0.001 HIS A 315 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 3585) covalent geometry : angle 0.52364 ( 4898) hydrogen bonds : bond 0.03809 ( 165) hydrogen bonds : angle 4.19972 ( 453) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 24 time to evaluate : 0.090 Fit side-chains REVERT: A 42 ASP cc_start: 0.8847 (t0) cc_final: 0.8522 (OUTLIER) REVERT: A 63 TRP cc_start: 0.8998 (t60) cc_final: 0.8507 (t60) REVERT: A 186 MET cc_start: 0.8574 (OUTLIER) cc_final: 0.8264 (ttp) REVERT: A 226 GLU cc_start: 0.8672 (OUTLIER) cc_final: 0.8294 (mp0) outliers start: 6 outliers final: 3 residues processed: 26 average time/residue: 0.4146 time to fit residues: 11.3169 Evaluate side-chains 27 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 23 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 186 MET Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 367 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 2 optimal weight: 0.9980 chunk 12 optimal weight: 9.9990 chunk 16 optimal weight: 0.0370 chunk 6 optimal weight: 0.0370 chunk 23 optimal weight: 0.9980 chunk 5 optimal weight: 5.9990 chunk 21 optimal weight: 0.9990 chunk 10 optimal weight: 0.0970 chunk 13 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 overall best weight: 0.4334 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 309 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 = 0.3126 r_free = 0.3126 target = 0.081935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.067538 restraints weight = 7046.719| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 2.68 r_work: 0.2755 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 3585 Z= 0.099 Angle : 0.499 5.642 4898 Z= 0.252 Chirality : 0.037 0.123 516 Planarity : 0.004 0.043 624 Dihedral : 4.507 36.858 485 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 1.12 % Allowed : 12.57 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.31 (0.43), residues: 424 helix: 1.53 (0.37), residues: 241 sheet: 0.42 (1.82), residues: 9 loop : 0.05 (0.48), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 433 TYR 0.006 0.001 TYR A 85 PHE 0.008 0.001 PHE A 193 TRP 0.006 0.001 TRP A 116 HIS 0.003 0.001 HIS A 315 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 3585) covalent geometry : angle 0.49943 ( 4898) hydrogen bonds : bond 0.03315 ( 165) hydrogen bonds : angle 4.13906 ( 453) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 27 time to evaluate : 0.109 Fit side-chains REVERT: A 42 ASP cc_start: 0.8839 (t0) cc_final: 0.8547 (OUTLIER) REVERT: A 63 TRP cc_start: 0.8980 (t60) cc_final: 0.8485 (t60) REVERT: A 142 LYS cc_start: 0.8405 (mptt) cc_final: 0.7995 (mmtp) REVERT: A 226 GLU cc_start: 0.8635 (OUTLIER) cc_final: 0.8272 (mp0) outliers start: 4 outliers final: 4 residues processed: 29 average time/residue: 0.3917 time to fit residues: 11.9062 Evaluate side-chains 29 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 25 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 367 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 21 optimal weight: 0.7980 chunk 38 optimal weight: 7.9990 chunk 7 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 41 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 6 optimal weight: 0.0000 chunk 34 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 overall best weight: 0.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 309 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 = 0.3117 r_free = 0.3117 target = 0.081368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.067047 restraints weight = 7144.340| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 2.67 r_work: 0.2745 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3585 Z= 0.106 Angle : 0.531 6.808 4898 Z= 0.262 Chirality : 0.037 0.122 516 Planarity : 0.004 0.044 624 Dihedral : 4.512 33.139 485 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 1.40 % Allowed : 12.85 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.32 (0.43), residues: 424 helix: 1.54 (0.37), residues: 241 sheet: 0.45 (1.81), residues: 9 loop : 0.06 (0.48), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 433 TYR 0.006 0.001 TYR A 259 PHE 0.010 0.001 PHE A 193 TRP 0.006 0.001 TRP A 116 HIS 0.003 0.001 HIS A 315 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 3585) covalent geometry : angle 0.53107 ( 4898) hydrogen bonds : bond 0.03473 ( 165) hydrogen bonds : angle 4.20962 ( 453) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 26 time to evaluate : 0.114 Fit side-chains REVERT: A 42 ASP cc_start: 0.8801 (t0) cc_final: 0.8512 (OUTLIER) REVERT: A 63 TRP cc_start: 0.8994 (t60) cc_final: 0.8494 (t60) REVERT: A 142 LYS cc_start: 0.8421 (mptt) cc_final: 0.8010 (mmtp) REVERT: A 226 GLU cc_start: 0.8625 (OUTLIER) cc_final: 0.8236 (mp0) REVERT: A 271 GLU cc_start: 0.8458 (OUTLIER) cc_final: 0.7818 (tt0) outliers start: 5 outliers final: 4 residues processed: 29 average time/residue: 0.3784 time to fit residues: 11.4852 Evaluate side-chains 30 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 25 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain A residue 367 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 16 optimal weight: 0.0970 chunk 34 optimal weight: 0.7980 chunk 11 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 39 optimal weight: 0.3980 chunk 29 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 35 optimal weight: 0.0870 overall best weight: 0.4556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 309 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 = 0.3134 r_free = 0.3134 target = 0.082374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.068006 restraints weight = 7065.667| |-----------------------------------------------------------------------------| r_work (start): 0.2881 rms_B_bonded: 2.69 r_work: 0.2762 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 3585 Z= 0.101 Angle : 0.520 6.084 4898 Z= 0.258 Chirality : 0.037 0.123 516 Planarity : 0.004 0.043 624 Dihedral : 4.462 26.999 485 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 1.40 % Allowed : 12.85 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.34 (0.43), residues: 424 helix: 1.53 (0.37), residues: 241 sheet: 0.46 (1.82), residues: 9 loop : 0.11 (0.49), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 433 TYR 0.005 0.001 TYR A 259 PHE 0.011 0.001 PHE A 193 TRP 0.006 0.001 TRP A 116 HIS 0.003 0.000 HIS A 315 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 3585) covalent geometry : angle 0.51965 ( 4898) hydrogen bonds : bond 0.03301 ( 165) hydrogen bonds : angle 4.18838 ( 453) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 906.44 seconds wall clock time: 16 minutes 11.21 seconds (971.21 seconds total)