Starting phenix.real_space_refine on Tue Feb 3 14:35:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9okf_70562/02_2026/9okf_70562.cif Found real_map, /net/cci-nas-00/data/ceres_data/9okf_70562/02_2026/9okf_70562.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9okf_70562/02_2026/9okf_70562.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9okf_70562/02_2026/9okf_70562.map" model { file = "/net/cci-nas-00/data/ceres_data/9okf_70562/02_2026/9okf_70562.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9okf_70562/02_2026/9okf_70562.cif" } resolution = 2.8 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= 0.000 sd= 0.048 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 32 5.16 5 C 2464 2.51 5 N 620 2.21 5 O 637 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3753 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 479, 3753 Classifications: {'peptide': 479} Link IDs: {'PTRANS': 13, 'TRANS': 465} Chain breaks: 2 Time building chain proxies: 0.90, per 1000 atoms: 0.24 Number of scatterers: 3753 At special positions: 0 Unit cell: (77.88, 72.688, 83.721, 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 32 16.00 O 637 8.00 N 620 7.00 C 2464 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: 0.28 Conformation dependent library (CDL) restraints added in 87.1 milliseconds 946 Ramachandran restraints generated. 473 Oldfield, 0 Emsley, 473 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 868 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 1 sheets defined 86.4% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.07 Creating SS restraints... Processing helix chain 'A' and resid 139 through 160 Processing helix chain 'A' and resid 162 through 198 removed outlier: 3.749A pdb=" N LEU A 174 " --> pdb=" O PHE A 170 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ALA A 175 " --> pdb=" O VAL A 171 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL A 183 " --> pdb=" O ASP A 179 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N PHE A 184 " --> pdb=" O GLY A 180 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N VAL A 186 " --> pdb=" O GLU A 182 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N GLY A 187 " --> pdb=" O VAL A 183 " (cutoff:3.500A) Proline residue: A 191 - end of helix removed outlier: 4.586A pdb=" N LYS A 195 " --> pdb=" O PRO A 191 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASP A 196 " --> pdb=" O SER A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 230 removed outlier: 4.447A pdb=" N VAL A 211 " --> pdb=" O LEU A 207 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N TYR A 212 " --> pdb=" O GLY A 208 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ASP A 227 " --> pdb=" O GLY A 223 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ARG A 228 " --> pdb=" O GLY A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 252 removed outlier: 3.569A pdb=" N SER A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N PHE A 251 " --> pdb=" O PHE A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 270 Processing helix chain 'A' and resid 271 through 282 removed outlier: 3.524A pdb=" N SER A 278 " --> pdb=" O PRO A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 295 Processing helix chain 'A' and resid 297 through 315 removed outlier: 3.976A pdb=" N MET A 301 " --> pdb=" O CYS A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 321 Processing helix chain 'A' and resid 331 through 340 removed outlier: 3.665A pdb=" N VAL A 335 " --> pdb=" O HIS A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 352 Processing helix chain 'A' and resid 357 through 364 removed outlier: 3.528A pdb=" N PHE A 361 " --> pdb=" O SER A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 385 removed outlier: 3.565A pdb=" N ALA A 370 " --> pdb=" O LYS A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 438 Processing helix chain 'A' and resid 443 through 481 Proline residue: A 469 - end of helix Processing helix chain 'A' and resid 596 through 607 Processing helix chain 'A' and resid 608 through 623 removed outlier: 5.208A pdb=" N ASP A 620 " --> pdb=" O ALA A 616 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N LYS A 621 " --> pdb=" O LEU A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 641 removed outlier: 3.544A pdb=" N MET A 627 " --> pdb=" O GLY A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 645 Processing helix chain 'A' and resid 647 through 676 removed outlier: 4.383A pdb=" N ALA A 664 " --> pdb=" O GLY A 660 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N SER A 665 " --> pdb=" O VAL A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 708 removed outlier: 3.512A pdb=" N PHE A 707 " --> pdb=" O ILE A 703 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N VAL A 708 " --> pdb=" O PHE A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 731 removed outlier: 3.661A pdb=" N LEU A 731 " --> pdb=" O SER A 727 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 322 through 323 297 hydrogen bonds defined for protein. 879 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: 0.35 Time building geometry restraints manager: 0.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 839 1.33 - 1.45: 930 1.45 - 1.57: 2034 1.57 - 1.69: 0 1.69 - 1.81: 53 Bond restraints: 3856 Sorted by residual: bond pdb=" C ILE A 273 " pdb=" O ILE A 273 " ideal model delta sigma weight residual 1.240 1.216 0.024 1.26e-02 6.30e+03 3.50e+00 bond pdb=" N TYR A 279 " pdb=" CA TYR A 279 " ideal model delta sigma weight residual 1.459 1.480 -0.021 1.20e-02 6.94e+03 3.13e+00 bond pdb=" N ALA A 139 " pdb=" CA ALA A 139 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.93e+00 bond pdb=" C MET A 298 " pdb=" O MET A 298 " ideal model delta sigma weight residual 1.236 1.214 0.022 1.31e-02 5.83e+03 2.77e+00 bond pdb=" CA HIS A 317 " pdb=" C HIS A 317 " ideal model delta sigma weight residual 1.523 1.509 0.015 1.34e-02 5.57e+03 1.18e+00 ... (remaining 3851 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.44: 5142 1.44 - 2.88: 62 2.88 - 4.32: 12 4.32 - 5.75: 2 5.75 - 7.19: 1 Bond angle restraints: 5219 Sorted by residual: angle pdb=" CA TYR A 279 " pdb=" C TYR A 279 " pdb=" O TYR A 279 " ideal model delta sigma weight residual 120.90 117.32 3.58 1.07e+00 8.73e-01 1.12e+01 angle pdb=" N ILE A 273 " pdb=" CA ILE A 273 " pdb=" C ILE A 273 " ideal model delta sigma weight residual 108.88 116.07 -7.19 2.16e+00 2.14e-01 1.11e+01 angle pdb=" CA TYR A 279 " pdb=" CB TYR A 279 " pdb=" CG TYR A 279 " ideal model delta sigma weight residual 113.90 117.84 -3.94 1.80e+00 3.09e-01 4.79e+00 angle pdb=" C PHE A 468 " pdb=" CA PHE A 468 " pdb=" CB PHE A 468 " ideal model delta sigma weight residual 113.49 110.02 3.47 1.82e+00 3.02e-01 3.63e+00 angle pdb=" CA TYR A 279 " pdb=" C TYR A 279 " pdb=" N PHE A 280 " ideal model delta sigma weight residual 116.97 119.14 -2.17 1.20e+00 6.94e-01 3.26e+00 ... (remaining 5214 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.69: 2006 14.69 - 29.38: 152 29.38 - 44.07: 29 44.07 - 58.76: 8 58.76 - 73.45: 3 Dihedral angle restraints: 2198 sinusoidal: 838 harmonic: 1360 Sorted by residual: dihedral pdb=" CA LEU A 199 " pdb=" C LEU A 199 " pdb=" N SER A 200 " pdb=" CA SER A 200 " ideal model delta harmonic sigma weight residual 180.00 158.33 21.67 0 5.00e+00 4.00e-02 1.88e+01 dihedral pdb=" CB MET A 301 " pdb=" CG MET A 301 " pdb=" SD MET A 301 " pdb=" CE MET A 301 " ideal model delta sinusoidal sigma weight residual 60.00 119.78 -59.78 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CB MET A 215 " pdb=" CG MET A 215 " pdb=" SD MET A 215 " pdb=" CE MET A 215 " ideal model delta sinusoidal sigma weight residual 60.00 113.97 -53.97 3 1.50e+01 4.44e-03 9.25e+00 ... (remaining 2195 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 376 0.026 - 0.052: 116 0.052 - 0.079: 54 0.079 - 0.105: 21 0.105 - 0.131: 4 Chirality restraints: 571 Sorted by residual: chirality pdb=" CA ILE A 397 " pdb=" N ILE A 397 " pdb=" C ILE A 397 " pdb=" CB ILE A 397 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.30e-01 chirality pdb=" CA MET A 298 " pdb=" N MET A 298 " pdb=" C MET A 298 " pdb=" CB MET A 298 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.39e-01 chirality pdb=" CA VAL A 391 " pdb=" N VAL A 391 " pdb=" C VAL A 391 " pdb=" CB VAL A 391 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 2.92e-01 ... (remaining 568 not shown) Planarity restraints: 645 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 278 " -0.009 2.00e-02 2.50e+03 1.86e-02 3.44e+00 pdb=" C SER A 278 " 0.032 2.00e-02 2.50e+03 pdb=" O SER A 278 " -0.012 2.00e-02 2.50e+03 pdb=" N TYR A 279 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 181 " 0.004 2.00e-02 2.50e+03 8.20e-03 6.72e-01 pdb=" C VAL A 181 " -0.014 2.00e-02 2.50e+03 pdb=" O VAL A 181 " 0.005 2.00e-02 2.50e+03 pdb=" N GLU A 182 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 219 " 0.004 2.00e-02 2.50e+03 7.72e-03 5.96e-01 pdb=" C ALA A 219 " -0.013 2.00e-02 2.50e+03 pdb=" O ALA A 219 " 0.005 2.00e-02 2.50e+03 pdb=" N PHE A 220 " 0.004 2.00e-02 2.50e+03 ... (remaining 642 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 672 2.76 - 3.30: 3724 3.30 - 3.83: 6496 3.83 - 4.37: 7400 4.37 - 4.90: 13128 Nonbonded interactions: 31420 Sorted by model distance: nonbonded pdb=" OH TYR A 279 " pdb=" O PRO A 355 " model vdw 2.226 3.040 nonbonded pdb=" OD1 ASP A 227 " pdb=" OG1 THR A 683 " model vdw 2.264 3.040 nonbonded pdb=" OE1 GLU A 675 " pdb=" OG1 THR A 736 " model vdw 2.322 3.040 nonbonded pdb=" OD2 ASP A 179 " pdb=" OG SER A 272 " model vdw 2.364 3.040 nonbonded pdb=" OE1 GLU A 282 " pdb=" OG SER A 357 " model vdw 2.368 3.040 ... (remaining 31415 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: 10.040 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 4.070 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 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 : 0.002 0.032 3856 Z= 0.144 Angle : 0.486 7.192 5219 Z= 0.278 Chirality : 0.034 0.131 571 Planarity : 0.003 0.031 645 Dihedral : 11.583 73.454 1330 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % 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 are not related in a simple way. whole: 2.52 (0.38), residues: 473 helix: 2.17 (0.26), residues: 374 sheet: None (None), residues: 0 loop : -0.26 (0.61), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 383 TYR 0.009 0.001 TYR A 169 PHE 0.010 0.001 PHE A 245 TRP 0.005 0.001 TRP A 416 HIS 0.001 0.001 HIS A 292 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 3856) covalent geometry : angle 0.48580 ( 5219) hydrogen bonds : bond 0.10175 ( 297) hydrogen bonds : angle 5.41989 ( 879) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 946 Ramachandran restraints generated. 473 Oldfield, 0 Emsley, 473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 946 Ramachandran restraints generated. 473 Oldfield, 0 Emsley, 473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.138 Fit side-chains outliers start: 0 outliers final: 1 residues processed: 62 average time/residue: 0.3606 time to fit residues: 23.2067 Evaluate side-chains 52 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 51 time to evaluate : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 464 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 24 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 30 optimal weight: 0.5980 chunk 22 optimal weight: 0.0870 chunk 37 optimal weight: 0.8980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 GLN A 331 HIS A 434 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.151525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.107002 restraints weight = 3974.276| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 1.74 r_work: 0.3050 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.1188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3856 Z= 0.152 Angle : 0.505 5.406 5219 Z= 0.265 Chirality : 0.038 0.123 571 Planarity : 0.004 0.033 645 Dihedral : 4.379 48.765 517 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 1.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Rotamer: Outliers : 2.04 % Allowed : 7.14 % Favored : 90.82 % 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 are not related in a simple way. whole: 2.96 (0.38), residues: 473 helix: 2.50 (0.26), residues: 375 sheet: None (None), residues: 0 loop : -0.19 (0.63), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 141 TYR 0.013 0.001 TYR A 169 PHE 0.015 0.001 PHE A 245 TRP 0.007 0.001 TRP A 300 HIS 0.001 0.000 HIS A 317 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 3856) covalent geometry : angle 0.50516 ( 5219) hydrogen bonds : bond 0.05148 ( 297) hydrogen bonds : angle 4.26708 ( 879) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 946 Ramachandran restraints generated. 473 Oldfield, 0 Emsley, 473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 946 Ramachandran restraints generated. 473 Oldfield, 0 Emsley, 473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 0.091 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 55 average time/residue: 0.3459 time to fit residues: 19.7282 Evaluate side-chains 54 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 50 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 MET Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 606 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 26 optimal weight: 0.6980 chunk 24 optimal weight: 0.4980 chunk 1 optimal weight: 0.5980 chunk 18 optimal weight: 0.9980 chunk 41 optimal weight: 0.0980 chunk 15 optimal weight: 1.9990 chunk 13 optimal weight: 0.0970 chunk 5 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 chunk 46 optimal weight: 0.5980 chunk 9 optimal weight: 0.3980 overall best weight: 0.3378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 430 GLN A 434 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.153353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.109049 restraints weight = 3890.322| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 1.73 r_work: 0.3086 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3856 Z= 0.119 Angle : 0.470 6.901 5219 Z= 0.240 Chirality : 0.036 0.116 571 Planarity : 0.003 0.028 645 Dihedral : 3.578 13.636 515 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Rotamer: Outliers : 2.04 % Allowed : 8.93 % Favored : 89.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.10 (0.38), residues: 473 helix: 2.54 (0.26), residues: 386 sheet: None (None), residues: 0 loop : -0.29 (0.64), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 141 TYR 0.012 0.001 TYR A 169 PHE 0.012 0.001 PHE A 245 TRP 0.007 0.001 TRP A 300 HIS 0.001 0.000 HIS A 317 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 3856) covalent geometry : angle 0.46999 ( 5219) hydrogen bonds : bond 0.04364 ( 297) hydrogen bonds : angle 3.99163 ( 879) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 946 Ramachandran restraints generated. 473 Oldfield, 0 Emsley, 473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 946 Ramachandran restraints generated. 473 Oldfield, 0 Emsley, 473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 0.139 Fit side-chains REVERT: A 206 MET cc_start: 0.8232 (tpp) cc_final: 0.7942 (tpp) outliers start: 8 outliers final: 3 residues processed: 56 average time/residue: 0.4658 time to fit residues: 26.9973 Evaluate side-chains 54 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 51 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 606 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 34 optimal weight: 2.9990 chunk 9 optimal weight: 0.0470 chunk 43 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 chunk 4 optimal weight: 0.5980 chunk 5 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 chunk 2 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.157927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.114980 restraints weight = 4137.252| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 1.81 r_work: 0.3317 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3856 Z= 0.138 Angle : 0.475 5.895 5219 Z= 0.244 Chirality : 0.037 0.116 571 Planarity : 0.004 0.041 645 Dihedral : 3.559 11.911 515 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 1.79 % Allowed : 10.71 % Favored : 87.50 % 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 are not related in a simple way. whole: 3.14 (0.38), residues: 473 helix: 2.57 (0.26), residues: 384 sheet: None (None), residues: 0 loop : -0.21 (0.63), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 141 TYR 0.011 0.001 TYR A 462 PHE 0.013 0.001 PHE A 245 TRP 0.007 0.001 TRP A 166 HIS 0.001 0.000 HIS A 378 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 3856) covalent geometry : angle 0.47512 ( 5219) hydrogen bonds : bond 0.04733 ( 297) hydrogen bonds : angle 3.93198 ( 879) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 946 Ramachandran restraints generated. 473 Oldfield, 0 Emsley, 473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 946 Ramachandran restraints generated. 473 Oldfield, 0 Emsley, 473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 56 time to evaluate : 0.088 Fit side-chains REVERT: A 206 MET cc_start: 0.7959 (tpp) cc_final: 0.7643 (tpp) REVERT: A 467 TRP cc_start: 0.5901 (t60) cc_final: 0.5642 (t60) REVERT: A 718 PHE cc_start: 0.6897 (OUTLIER) cc_final: 0.6167 (t80) outliers start: 7 outliers final: 2 residues processed: 59 average time/residue: 0.4880 time to fit residues: 29.7289 Evaluate side-chains 56 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 53 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 718 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 28 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.156031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.112940 restraints weight = 4131.644| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 1.81 r_work: 0.3290 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3856 Z= 0.172 Angle : 0.501 5.515 5219 Z= 0.258 Chirality : 0.038 0.116 571 Planarity : 0.004 0.054 645 Dihedral : 3.627 11.951 515 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 2.55 % Allowed : 10.71 % Favored : 86.73 % 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 are not related in a simple way. whole: 2.91 (0.38), residues: 473 helix: 2.45 (0.26), residues: 383 sheet: None (None), residues: 0 loop : -0.43 (0.62), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 141 TYR 0.011 0.001 TYR A 462 PHE 0.015 0.001 PHE A 245 TRP 0.006 0.001 TRP A 166 HIS 0.001 0.000 HIS A 378 Details of bonding type rmsd covalent geometry : bond 0.00408 ( 3856) covalent geometry : angle 0.50094 ( 5219) hydrogen bonds : bond 0.05286 ( 297) hydrogen bonds : angle 4.01628 ( 879) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 946 Ramachandran restraints generated. 473 Oldfield, 0 Emsley, 473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 946 Ramachandran restraints generated. 473 Oldfield, 0 Emsley, 473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 55 time to evaluate : 0.084 Fit side-chains REVERT: A 206 MET cc_start: 0.8024 (tpp) cc_final: 0.7721 (tpp) REVERT: A 465 THR cc_start: 0.6869 (m) cc_final: 0.6226 (p) REVERT: A 718 PHE cc_start: 0.6911 (OUTLIER) cc_final: 0.6293 (t80) outliers start: 10 outliers final: 2 residues processed: 59 average time/residue: 0.3943 time to fit residues: 24.0809 Evaluate side-chains 56 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 53 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 718 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 10 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 chunk 40 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 chunk 5 optimal weight: 0.1980 chunk 45 optimal weight: 0.8980 chunk 1 optimal weight: 0.6980 chunk 24 optimal weight: 0.3980 chunk 31 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 430 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.157653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.114403 restraints weight = 4209.864| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 1.84 r_work: 0.3307 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3856 Z= 0.140 Angle : 0.470 5.446 5219 Z= 0.243 Chirality : 0.037 0.114 571 Planarity : 0.004 0.044 645 Dihedral : 3.547 11.895 515 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 1.79 % Allowed : 12.76 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.97 (0.38), residues: 473 helix: 2.52 (0.26), residues: 382 sheet: None (None), residues: 0 loop : -0.49 (0.60), residues: 91 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 141 TYR 0.012 0.001 TYR A 462 PHE 0.013 0.001 PHE A 245 TRP 0.009 0.001 TRP A 467 HIS 0.001 0.000 HIS A 378 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 3856) covalent geometry : angle 0.46999 ( 5219) hydrogen bonds : bond 0.04765 ( 297) hydrogen bonds : angle 3.94940 ( 879) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 946 Ramachandran restraints generated. 473 Oldfield, 0 Emsley, 473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 946 Ramachandran restraints generated. 473 Oldfield, 0 Emsley, 473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 54 time to evaluate : 0.085 Fit side-chains REVERT: A 206 MET cc_start: 0.7996 (tpp) cc_final: 0.7652 (tpp) REVERT: A 465 THR cc_start: 0.6748 (m) cc_final: 0.6207 (p) outliers start: 7 outliers final: 3 residues processed: 58 average time/residue: 0.3858 time to fit residues: 23.2105 Evaluate side-chains 56 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 53 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 468 PHE Chi-restraints excluded: chain A residue 597 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 3 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 21 optimal weight: 0.0870 chunk 12 optimal weight: 0.5980 chunk 15 optimal weight: 0.5980 chunk 9 optimal weight: 0.3980 chunk 17 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 overall best weight: 0.4558 ------------------------------------------------------------------------------- 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 = 0.3886 r_free = 0.3886 target = 0.158291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.114921 restraints weight = 4291.183| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 1.86 r_work: 0.3317 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3856 Z= 0.129 Angle : 0.459 5.431 5219 Z= 0.236 Chirality : 0.036 0.113 571 Planarity : 0.004 0.042 645 Dihedral : 3.486 12.072 515 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 1.79 % Allowed : 13.52 % Favored : 84.69 % 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 are not related in a simple way. whole: 3.07 (0.38), residues: 473 helix: 2.59 (0.26), residues: 383 sheet: None (None), residues: 0 loop : -0.53 (0.60), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 141 TYR 0.012 0.001 TYR A 462 PHE 0.013 0.001 PHE A 245 TRP 0.008 0.001 TRP A 467 HIS 0.001 0.000 HIS A 378 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 3856) covalent geometry : angle 0.45894 ( 5219) hydrogen bonds : bond 0.04543 ( 297) hydrogen bonds : angle 3.88557 ( 879) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 946 Ramachandran restraints generated. 473 Oldfield, 0 Emsley, 473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 946 Ramachandran restraints generated. 473 Oldfield, 0 Emsley, 473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 53 time to evaluate : 0.140 Fit side-chains REVERT: A 206 MET cc_start: 0.7992 (tpp) cc_final: 0.7651 (tpp) REVERT: A 430 GLN cc_start: 0.7950 (mt0) cc_final: 0.7734 (mt0) REVERT: A 465 THR cc_start: 0.6738 (m) cc_final: 0.6173 (p) outliers start: 7 outliers final: 3 residues processed: 57 average time/residue: 0.4322 time to fit residues: 25.5061 Evaluate side-chains 56 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 53 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 468 PHE Chi-restraints excluded: chain A residue 597 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 46 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 6 optimal weight: 0.3980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3861 r_free = 0.3861 target = 0.156097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.113088 restraints weight = 4189.797| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 1.82 r_work: 0.3293 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3856 Z= 0.174 Angle : 0.501 5.510 5219 Z= 0.257 Chirality : 0.038 0.117 571 Planarity : 0.004 0.051 645 Dihedral : 3.595 12.416 515 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 1.53 % Allowed : 14.54 % Favored : 83.93 % 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 are not related in a simple way. whole: 2.84 (0.38), residues: 473 helix: 2.45 (0.26), residues: 382 sheet: None (None), residues: 0 loop : -0.67 (0.61), residues: 91 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 141 TYR 0.013 0.001 TYR A 462 PHE 0.015 0.001 PHE A 245 TRP 0.006 0.001 TRP A 166 HIS 0.001 0.000 HIS A 378 Details of bonding type rmsd covalent geometry : bond 0.00415 ( 3856) covalent geometry : angle 0.50146 ( 5219) hydrogen bonds : bond 0.05256 ( 297) hydrogen bonds : angle 3.98900 ( 879) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 946 Ramachandran restraints generated. 473 Oldfield, 0 Emsley, 473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 946 Ramachandran restraints generated. 473 Oldfield, 0 Emsley, 473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 53 time to evaluate : 0.096 Fit side-chains REVERT: A 206 MET cc_start: 0.8031 (tpp) cc_final: 0.7690 (tpp) REVERT: A 465 THR cc_start: 0.6770 (m) cc_final: 0.6201 (p) REVERT: A 665 SER cc_start: 0.8424 (OUTLIER) cc_final: 0.8095 (p) outliers start: 6 outliers final: 4 residues processed: 57 average time/residue: 0.4333 time to fit residues: 25.6658 Evaluate side-chains 58 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 53 time to evaluate : 0.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 468 PHE Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 665 SER Chi-restraints excluded: chain A residue 674 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 12 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 chunk 45 optimal weight: 0.1980 chunk 44 optimal weight: 0.0070 chunk 43 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 overall best weight: 0.4198 ------------------------------------------------------------------------------- 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 = 0.3886 r_free = 0.3886 target = 0.158321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.115268 restraints weight = 4155.828| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 1.82 r_work: 0.3320 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3856 Z= 0.125 Angle : 0.455 5.433 5219 Z= 0.235 Chirality : 0.036 0.112 571 Planarity : 0.004 0.043 645 Dihedral : 3.471 12.174 515 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 2.55 % Allowed : 13.78 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.06 (0.39), residues: 473 helix: 2.59 (0.26), residues: 383 sheet: None (None), residues: 0 loop : -0.58 (0.61), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 141 TYR 0.013 0.001 TYR A 462 PHE 0.012 0.001 PHE A 245 TRP 0.009 0.001 TRP A 467 HIS 0.001 0.000 HIS A 378 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 3856) covalent geometry : angle 0.45460 ( 5219) hydrogen bonds : bond 0.04443 ( 297) hydrogen bonds : angle 3.87096 ( 879) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 946 Ramachandran restraints generated. 473 Oldfield, 0 Emsley, 473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 946 Ramachandran restraints generated. 473 Oldfield, 0 Emsley, 473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 52 time to evaluate : 0.133 Fit side-chains REVERT: A 141 ARG cc_start: 0.7153 (ttt-90) cc_final: 0.6945 (tpt90) REVERT: A 206 MET cc_start: 0.7982 (tpp) cc_final: 0.7642 (tpp) REVERT: A 665 SER cc_start: 0.8394 (OUTLIER) cc_final: 0.8050 (p) outliers start: 10 outliers final: 3 residues processed: 60 average time/residue: 0.4360 time to fit residues: 27.2260 Evaluate side-chains 55 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 51 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 665 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 34 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 1 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 21 optimal weight: 0.2980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 430 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.157534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.114332 restraints weight = 4217.350| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 1.84 r_work: 0.3309 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3856 Z= 0.148 Angle : 0.478 5.480 5219 Z= 0.245 Chirality : 0.037 0.114 571 Planarity : 0.004 0.047 645 Dihedral : 3.497 12.473 515 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 1.28 % Allowed : 15.31 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.96 (0.38), residues: 473 helix: 2.50 (0.26), residues: 385 sheet: None (None), residues: 0 loop : -0.54 (0.62), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 141 TYR 0.012 0.001 TYR A 462 PHE 0.014 0.001 PHE A 245 TRP 0.006 0.001 TRP A 467 HIS 0.001 0.000 HIS A 378 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 3856) covalent geometry : angle 0.47816 ( 5219) hydrogen bonds : bond 0.04832 ( 297) hydrogen bonds : angle 3.92513 ( 879) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 946 Ramachandran restraints generated. 473 Oldfield, 0 Emsley, 473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 946 Ramachandran restraints generated. 473 Oldfield, 0 Emsley, 473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 51 time to evaluate : 0.140 Fit side-chains REVERT: A 206 MET cc_start: 0.8015 (tpp) cc_final: 0.7673 (tpp) REVERT: A 665 SER cc_start: 0.8405 (OUTLIER) cc_final: 0.8061 (p) outliers start: 5 outliers final: 3 residues processed: 55 average time/residue: 0.4760 time to fit residues: 27.0514 Evaluate side-chains 55 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 51 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 665 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 8 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 12 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 16 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.156960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.114042 restraints weight = 4101.948| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 1.81 r_work: 0.3305 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3856 Z= 0.153 Angle : 0.482 5.488 5219 Z= 0.247 Chirality : 0.037 0.115 571 Planarity : 0.004 0.047 645 Dihedral : 3.508 12.164 515 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 1.79 % Allowed : 14.54 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.93 (0.38), residues: 473 helix: 2.49 (0.26), residues: 383 sheet: None (None), residues: 0 loop : -0.57 (0.61), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 141 TYR 0.012 0.001 TYR A 462 PHE 0.014 0.001 PHE A 245 TRP 0.007 0.001 TRP A 295 HIS 0.001 0.000 HIS A 378 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 3856) covalent geometry : angle 0.48172 ( 5219) hydrogen bonds : bond 0.04962 ( 297) hydrogen bonds : angle 3.94852 ( 879) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1391.95 seconds wall clock time: 24 minutes 25.34 seconds (1465.34 seconds total)