Starting phenix.real_space_refine on Thu Jul 2 00:06:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9r1h_53509/07_2026/9r1h_53509.cif Found real_map, /net/cci-nas-00/data/ceres_data/9r1h_53509/07_2026/9r1h_53509.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9r1h_53509/07_2026/9r1h_53509.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9r1h_53509/07_2026/9r1h_53509.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9r1h_53509/07_2026/9r1h_53509.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9r1h_53509/07_2026/9r1h_53509.map" } resolution = 3.02 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= 0.009 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: 6 Type Number sf(0) Gaussians S 33 5.16 5 Cl 1 4.86 5 Na 1 4.78 5 C 2931 2.51 5 N 663 2.21 5 O 732 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4361 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 547, 4352 Classifications: {'peptide': 547} Link IDs: {'PTRANS': 30, 'TRANS': 516} Chain breaks: 2 Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 7 Ad-hoc single atom residues: {' NA': 1, ' CL': 1} Inner-chain residues flagged as termini: ['pdbres="GLY A 803 "'] Classifications: {'peptide': 1, 'water': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Chain breaks: 2 Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N MET A 773 " occ=0.00 ... (6 atoms not shown) pdb=" CE MET A 773 " occ=0.00 residue: pdb=" N LEU A 777 " occ=0.00 ... (6 atoms not shown) pdb=" CD2 LEU A 777 " occ=0.00 residue: pdb=" N GLY A 778 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY A 778 " occ=0.00 residue: pdb=" N THR A 779 " occ=0.00 ... (5 atoms not shown) pdb=" CG2 THR A 779 " occ=0.00 Time building chain proxies: 1.23, per 1000 atoms: 0.28 Number of scatterers: 4361 At special positions: 0 Unit cell: (84.448, 66.248, 86.632, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 1 17.00 S 33 16.00 Na 1 11.00 O 732 8.00 N 663 7.00 C 2931 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: 0.39 Conformation dependent library (CDL) restraints added in 158.5 milliseconds 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1012 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 2 sheets defined 79.2% alpha, 0.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'A' and resid 195 through 209 removed outlier: 4.013A pdb=" N ASP A 199 " --> pdb=" O SER A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 215 Processing helix chain 'A' and resid 215 through 225 Processing helix chain 'A' and resid 229 through 240 removed outlier: 3.523A pdb=" N ALA A 238 " --> pdb=" O LEU A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 256 Processing helix chain 'A' and resid 261 through 268 removed outlier: 3.989A pdb=" N ALA A 265 " --> pdb=" O VAL A 262 " (cutoff:3.500A) Proline residue: A 267 - end of helix Processing helix chain 'A' and resid 269 through 302 removed outlier: 4.035A pdb=" N GLY A 273 " --> pdb=" O LEU A 269 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ASN A 288 " --> pdb=" O ALA A 284 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N VAL A 289 " --> pdb=" O ILE A 285 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE A 290 " --> pdb=" O TYR A 286 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE A 291 " --> pdb=" O TYR A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 310 removed outlier: 4.060A pdb=" N SER A 310 " --> pdb=" O PRO A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 378 removed outlier: 3.629A pdb=" N PHE A 375 " --> pdb=" O SER A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 413 removed outlier: 3.576A pdb=" N LYS A 413 " --> pdb=" O ALA A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 426 Processing helix chain 'A' and resid 427 through 442 Processing helix chain 'A' and resid 445 through 455 removed outlier: 3.804A pdb=" N GLY A 449 " --> pdb=" O GLY A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 462 removed outlier: 3.599A pdb=" N THR A 462 " --> pdb=" O GLU A 459 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 459 through 462' Processing helix chain 'A' and resid 463 through 479 removed outlier: 3.715A pdb=" N TRP A 467 " --> pdb=" O ASP A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 491 removed outlier: 3.839A pdb=" N TYR A 491 " --> pdb=" O THR A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 532 removed outlier: 3.612A pdb=" N VAL A 523 " --> pdb=" O VAL A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 538 removed outlier: 3.756A pdb=" N VAL A 538 " --> pdb=" O ILE A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 555 Proline residue: A 551 - end of helix Processing helix chain 'A' and resid 559 through 592 removed outlier: 3.570A pdb=" N TRP A 563 " --> pdb=" O LEU A 559 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASP A 577 " --> pdb=" O THR A 573 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N THR A 578 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA A 581 " --> pdb=" O ASP A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 599 Processing helix chain 'A' and resid 601 through 617 Processing helix chain 'A' and resid 618 through 621 Processing helix chain 'A' and resid 624 through 637 removed outlier: 4.304A pdb=" N MET A 628 " --> pdb=" O GLY A 624 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ALA A 637 " --> pdb=" O ASP A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 655 removed outlier: 3.550A pdb=" N VAL A 642 " --> pdb=" O SER A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 657 through 670 Processing helix chain 'A' and resid 674 through 683 Processing helix chain 'A' and resid 683 through 699 Processing helix chain 'A' and resid 711 through 727 removed outlier: 4.053A pdb=" N SER A 725 " --> pdb=" O MET A 721 " (cutoff:3.500A) Processing helix chain 'A' and resid 727 through 740 Processing helix chain 'A' and resid 743 through 751 Processing helix chain 'A' and resid 762 through 767 removed outlier: 3.728A pdb=" N ARG A 766 " --> pdb=" O ALA A 763 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLY A 767 " --> pdb=" O GLN A 764 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 320 through 321 Processing sheet with id=AA2, first strand: chain 'A' and resid 704 through 705 283 hydrogen bonds defined for protein. 828 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: 0.69 Time building geometry restraints manager: 0.52 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: 1250 1.34 - 1.46: 990 1.46 - 1.58: 2206 1.58 - 1.69: 0 1.69 - 1.81: 51 Bond restraints: 4497 Sorted by residual: bond pdb=" N ALA A 481 " pdb=" CA ALA A 481 " ideal model delta sigma weight residual 1.459 1.484 -0.025 1.15e-02 7.56e+03 4.88e+00 bond pdb=" N TRP A 482 " pdb=" CA TRP A 482 " ideal model delta sigma weight residual 1.458 1.485 -0.027 1.27e-02 6.20e+03 4.51e+00 bond pdb=" N ALA A 480 " pdb=" CA ALA A 480 " ideal model delta sigma weight residual 1.455 1.481 -0.026 1.30e-02 5.92e+03 3.89e+00 bond pdb=" N GLY A 483 " pdb=" CA GLY A 483 " ideal model delta sigma weight residual 1.451 1.475 -0.024 1.29e-02 6.01e+03 3.50e+00 bond pdb=" CA ALA A 481 " pdb=" CB ALA A 481 " ideal model delta sigma weight residual 1.533 1.510 0.024 1.66e-02 3.63e+03 2.06e+00 ... (remaining 4492 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 5956 1.85 - 3.70: 141 3.70 - 5.54: 27 5.54 - 7.39: 4 7.39 - 9.24: 3 Bond angle restraints: 6131 Sorted by residual: angle pdb=" N ALA A 481 " pdb=" CA ALA A 481 " pdb=" C ALA A 481 " ideal model delta sigma weight residual 113.38 108.98 4.40 1.17e+00 7.31e-01 1.42e+01 angle pdb=" N GLY A 483 " pdb=" CA GLY A 483 " pdb=" C GLY A 483 " ideal model delta sigma weight residual 114.48 110.01 4.47 1.19e+00 7.06e-01 1.41e+01 angle pdb=" CA MET A 773 " pdb=" CB MET A 773 " pdb=" CG MET A 773 " ideal model delta sigma weight residual 114.10 121.59 -7.49 2.00e+00 2.50e-01 1.40e+01 angle pdb=" CA ALA A 480 " pdb=" C ALA A 480 " pdb=" O ALA A 480 " ideal model delta sigma weight residual 121.05 117.36 3.69 1.14e+00 7.69e-01 1.05e+01 angle pdb=" CA LYS A 323 " pdb=" CB LYS A 323 " pdb=" CG LYS A 323 " ideal model delta sigma weight residual 114.10 120.40 -6.30 2.00e+00 2.50e-01 9.91e+00 ... (remaining 6126 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 2310 17.78 - 35.56: 184 35.56 - 53.34: 51 53.34 - 71.12: 10 71.12 - 88.90: 3 Dihedral angle restraints: 2558 sinusoidal: 974 harmonic: 1584 Sorted by residual: dihedral pdb=" CD ARG A 769 " pdb=" NE ARG A 769 " pdb=" CZ ARG A 769 " pdb=" NH1 ARG A 769 " ideal model delta sinusoidal sigma weight residual 0.00 68.12 -68.12 1 1.00e+01 1.00e-02 6.02e+01 dihedral pdb=" CA GLU A 530 " pdb=" C GLU A 530 " pdb=" N ARG A 531 " pdb=" CA ARG A 531 " ideal model delta harmonic sigma weight residual 180.00 -153.55 -26.45 0 5.00e+00 4.00e-02 2.80e+01 dihedral pdb=" CA CYS A 752 " pdb=" C CYS A 752 " pdb=" N SER A 753 " pdb=" CA SER A 753 " ideal model delta harmonic sigma weight residual 180.00 154.61 25.39 0 5.00e+00 4.00e-02 2.58e+01 ... (remaining 2555 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 458 0.041 - 0.083: 170 0.083 - 0.124: 49 0.124 - 0.165: 9 0.165 - 0.206: 1 Chirality restraints: 687 Sorted by residual: chirality pdb=" CA TRP A 482 " pdb=" N TRP A 482 " pdb=" C TRP A 482 " pdb=" CB TRP A 482 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CA TYR A 635 " pdb=" N TYR A 635 " pdb=" C TYR A 635 " pdb=" CB TYR A 635 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.46e-01 chirality pdb=" CA TYR A 286 " pdb=" N TYR A 286 " pdb=" C TYR A 286 " pdb=" CB TYR A 286 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.32e-01 ... (remaining 684 not shown) Planarity restraints: 743 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 769 " 0.838 9.50e-02 1.11e+02 3.77e-01 1.00e+02 pdb=" NE ARG A 769 " -0.075 2.00e-02 2.50e+03 pdb=" CZ ARG A 769 " 0.056 2.00e-02 2.50e+03 pdb=" NH1 ARG A 769 " -0.019 2.00e-02 2.50e+03 pdb=" NH2 ARG A 769 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 660 " 0.234 9.50e-02 1.11e+02 1.06e-01 8.90e+00 pdb=" NE ARG A 660 " -0.022 2.00e-02 2.50e+03 pdb=" CZ ARG A 660 " 0.023 2.00e-02 2.50e+03 pdb=" NH1 ARG A 660 " -0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG A 660 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 272 " -0.014 2.00e-02 2.50e+03 2.82e-02 7.95e+00 pdb=" C CYS A 272 " 0.049 2.00e-02 2.50e+03 pdb=" O CYS A 272 " -0.018 2.00e-02 2.50e+03 pdb=" N GLY A 273 " -0.016 2.00e-02 2.50e+03 ... (remaining 740 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 1342 2.83 - 3.35: 4478 3.35 - 3.86: 7566 3.86 - 4.38: 8909 4.38 - 4.90: 15101 Nonbonded interactions: 37396 Sorted by model distance: nonbonded pdb=" NZ LYS A 376 " pdb=" OH TYR A 705 " model vdw 2.310 3.120 nonbonded pdb=" OD1 ASP A 577 " pdb="NA NA A 801 " model vdw 2.311 3.210 nonbonded pdb=" O GLY A 206 " pdb="NA NA A 801 " model vdw 2.323 3.210 nonbonded pdb=" O LEU A 649 " pdb=" OG SER A 653 " model vdw 2.324 3.040 nonbonded pdb=" O VAL A 209 " pdb="NA NA A 801 " model vdw 2.339 3.210 ... (remaining 37391 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=0.00 max=1.00 mean=0.99 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: 2.050 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: 0.010 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.250 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:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4497 Z= 0.173 Angle : 0.739 9.242 6131 Z= 0.430 Chirality : 0.047 0.206 687 Planarity : 0.016 0.377 743 Dihedral : 14.654 88.898 1546 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.50 % Allowed : 14.38 % Favored : 84.12 % 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: -1.72 (0.30), residues: 541 helix: -0.93 (0.22), residues: 374 sheet: None (None), residues: 0 loop : -1.26 (0.41), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.066 0.005 ARG A 769 TYR 0.027 0.004 TYR A 207 PHE 0.042 0.002 PHE A 580 TRP 0.021 0.001 TRP A 713 HIS 0.001 0.000 HIS A 738 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.17 ( 4497) covalent geometry : angle 0.73898 / 0.43 ( 6131) hydrogen bonds : bond 0.13474 / 9.21 ( 283) hydrogen bonds : angle 7.10984 / 5.05 ( 828) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 60 time to evaluate : 0.159 Fit side-chains REVERT: A 373 GLU cc_start: 0.8146 (mm-30) cc_final: 0.7910 (mt-10) REVERT: A 735 ILE cc_start: 0.7534 (mt) cc_final: 0.7307 (mt) outliers start: 7 outliers final: 4 residues processed: 67 average time/residue: 0.0686 time to fit residues: 5.9268 Evaluate side-chains 62 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 58 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 TYR Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 482 TRP Chi-restraints excluded: chain A residue 757 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 24 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 0.0770 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 50 optimal weight: 7.9990 chunk 53 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 overall best weight: 0.6340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.148936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.124999 restraints weight = 5132.075| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 1.84 r_work: 0.3325 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.1373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4497 Z= 0.140 Angle : 0.578 8.397 6131 Z= 0.308 Chirality : 0.043 0.145 687 Planarity : 0.005 0.034 743 Dihedral : 5.548 52.941 594 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 2.15 % Allowed : 13.09 % Favored : 84.76 % 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: 0.57 (0.34), residues: 541 helix: 0.91 (0.26), residues: 385 sheet: None (None), residues: 0 loop : -0.83 (0.44), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 766 TYR 0.019 0.002 TYR A 219 PHE 0.011 0.001 PHE A 521 TRP 0.015 0.001 TRP A 713 HIS 0.001 0.000 HIS A 601 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 ( 4497) covalent geometry : angle 0.57818 / 0.31 ( 6131) hydrogen bonds : bond 0.04367 / 2.96 ( 283) hydrogen bonds : angle 4.87515 / 3.46 ( 828) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.163 Fit side-chains REVERT: A 438 ILE cc_start: 0.7148 (mm) cc_final: 0.6941 (mt) REVERT: A 735 ILE cc_start: 0.7326 (mt) cc_final: 0.7067 (mt) outliers start: 10 outliers final: 5 residues processed: 69 average time/residue: 0.0568 time to fit residues: 5.3716 Evaluate side-chains 58 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 53 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 TYR Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 775 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 37 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 52 optimal weight: 0.0970 chunk 12 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 48 optimal weight: 0.5980 chunk 29 optimal weight: 5.9990 chunk 42 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 529 ASN A 601 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.151445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.128600 restraints weight = 5059.170| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 1.73 r_work: 0.3247 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4497 Z= 0.132 Angle : 0.555 8.701 6131 Z= 0.290 Chirality : 0.042 0.137 687 Planarity : 0.004 0.033 743 Dihedral : 5.024 58.035 590 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 2.58 % Allowed : 13.09 % Favored : 84.33 % 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: 1.18 (0.36), residues: 541 helix: 1.31 (0.26), residues: 386 sheet: None (None), residues: 0 loop : -0.40 (0.48), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 599 TYR 0.020 0.002 TYR A 219 PHE 0.011 0.001 PHE A 580 TRP 0.012 0.001 TRP A 713 HIS 0.001 0.000 HIS A 765 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 ( 4497) covalent geometry : angle 0.55531 / 0.29 ( 6131) hydrogen bonds : bond 0.04035 / 2.70 ( 283) hydrogen bonds : angle 4.57359 / 3.23 ( 828) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 0.158 Fit side-chains REVERT: A 204 MET cc_start: 0.6753 (OUTLIER) cc_final: 0.6394 (mtt) REVERT: A 735 ILE cc_start: 0.7167 (mt) cc_final: 0.6930 (mt) outliers start: 12 outliers final: 8 residues processed: 68 average time/residue: 0.0626 time to fit residues: 5.6910 Evaluate side-chains 65 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 219 TYR Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 529 ASN Chi-restraints excluded: chain A residue 545 ILE Chi-restraints excluded: chain A residue 556 ARG Chi-restraints excluded: chain A residue 775 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 27 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 38 optimal weight: 0.0170 chunk 34 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 12 optimal weight: 5.9990 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.149609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.125680 restraints weight = 5073.753| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 1.83 r_work: 0.3243 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4497 Z= 0.127 Angle : 0.543 7.531 6131 Z= 0.282 Chirality : 0.042 0.138 687 Planarity : 0.004 0.031 743 Dihedral : 4.988 59.987 590 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.79 % Allowed : 12.88 % Favored : 84.33 % 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: 1.34 (0.36), residues: 541 helix: 1.42 (0.26), residues: 387 sheet: None (None), residues: 0 loop : -0.35 (0.49), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 531 TYR 0.019 0.002 TYR A 219 PHE 0.010 0.001 PHE A 580 TRP 0.011 0.001 TRP A 713 HIS 0.001 0.000 HIS A 601 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 ( 4497) covalent geometry : angle 0.54312 / 0.28 ( 6131) hydrogen bonds : bond 0.03909 / 2.62 ( 283) hydrogen bonds : angle 4.45876 / 3.15 ( 828) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 57 time to evaluate : 0.096 Fit side-chains REVERT: A 204 MET cc_start: 0.6691 (OUTLIER) cc_final: 0.6351 (mtt) REVERT: A 323 LYS cc_start: 0.7956 (mmtm) cc_final: 0.7630 (pttt) REVERT: A 391 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7382 (pm20) REVERT: A 408 TYR cc_start: 0.8057 (t80) cc_final: 0.7736 (t80) REVERT: A 422 VAL cc_start: 0.6861 (m) cc_final: 0.6653 (p) REVERT: A 735 ILE cc_start: 0.7289 (mt) cc_final: 0.7051 (mt) REVERT: A 746 GLU cc_start: 0.7123 (mt-10) cc_final: 0.6865 (mt-10) REVERT: A 748 LEU cc_start: 0.6877 (tp) cc_final: 0.6658 (tp) outliers start: 13 outliers final: 8 residues processed: 69 average time/residue: 0.0617 time to fit residues: 5.4977 Evaluate side-chains 66 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 219 TYR Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 391 GLU Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 545 ILE Chi-restraints excluded: chain A residue 556 ARG Chi-restraints excluded: chain A residue 775 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 8 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 7 optimal weight: 0.4980 chunk 3 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 45 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 529 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.145262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.121106 restraints weight = 5208.058| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 1.87 r_work: 0.3221 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4497 Z= 0.138 Angle : 0.554 8.296 6131 Z= 0.286 Chirality : 0.042 0.137 687 Planarity : 0.004 0.031 743 Dihedral : 4.939 57.040 590 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.79 % Allowed : 12.45 % Favored : 84.76 % 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: 1.45 (0.36), residues: 541 helix: 1.52 (0.26), residues: 387 sheet: None (None), residues: 0 loop : -0.35 (0.49), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 766 TYR 0.021 0.002 TYR A 219 PHE 0.010 0.001 PHE A 580 TRP 0.010 0.001 TRP A 713 HIS 0.001 0.000 HIS A 601 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 ( 4497) covalent geometry : angle 0.55373 / 0.29 ( 6131) hydrogen bonds : bond 0.03980 / 2.68 ( 283) hydrogen bonds : angle 4.42968 / 3.12 ( 828) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 0.098 Fit side-chains REVERT: A 204 MET cc_start: 0.6694 (OUTLIER) cc_final: 0.6347 (mtt) REVERT: A 215 TRP cc_start: 0.7659 (OUTLIER) cc_final: 0.7016 (t60) REVERT: A 323 LYS cc_start: 0.7976 (mmtm) cc_final: 0.7614 (pttt) REVERT: A 391 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7395 (pm20) REVERT: A 532 LYS cc_start: 0.7699 (mmtt) cc_final: 0.7487 (mmtm) REVERT: A 735 ILE cc_start: 0.7300 (mt) cc_final: 0.7065 (mt) outliers start: 13 outliers final: 8 residues processed: 73 average time/residue: 0.0611 time to fit residues: 5.9364 Evaluate side-chains 69 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 215 TRP Chi-restraints excluded: chain A residue 219 TYR Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 391 GLU Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 529 ASN Chi-restraints excluded: chain A residue 556 ARG Chi-restraints excluded: chain A residue 726 VAL Chi-restraints excluded: chain A residue 775 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 2 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 50 optimal weight: 0.2980 chunk 29 optimal weight: 0.0060 chunk 20 optimal weight: 0.0870 chunk 9 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 32 optimal weight: 0.3980 chunk 27 optimal weight: 0.6980 overall best weight: 0.2974 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.150053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.126046 restraints weight = 5139.287| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 1.86 r_work: 0.3305 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 4497 Z= 0.106 Angle : 0.519 9.115 6131 Z= 0.266 Chirality : 0.040 0.140 687 Planarity : 0.004 0.029 743 Dihedral : 4.688 55.937 590 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 2.15 % Allowed : 14.16 % Favored : 83.69 % 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: 1.69 (0.36), residues: 541 helix: 1.67 (0.26), residues: 386 sheet: None (None), residues: 0 loop : -0.18 (0.49), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 531 TYR 0.014 0.001 TYR A 219 PHE 0.011 0.001 PHE A 580 TRP 0.011 0.001 TRP A 713 HIS 0.001 0.000 HIS A 601 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 ( 4497) covalent geometry : angle 0.51923 / 0.27 ( 6131) hydrogen bonds : bond 0.03451 / 2.29 ( 283) hydrogen bonds : angle 4.23802 / 3.00 ( 828) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.137 Fit side-chains REVERT: A 323 LYS cc_start: 0.8002 (mmtm) cc_final: 0.7606 (pttt) REVERT: A 373 GLU cc_start: 0.7917 (mm-30) cc_final: 0.7395 (mt-10) REVERT: A 391 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7350 (pm20) REVERT: A 746 GLU cc_start: 0.7120 (mt-10) cc_final: 0.6861 (mt-10) outliers start: 10 outliers final: 4 residues processed: 73 average time/residue: 0.0499 time to fit residues: 4.8889 Evaluate side-chains 65 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 60 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 TRP Chi-restraints excluded: chain A residue 219 TYR Chi-restraints excluded: chain A residue 391 GLU Chi-restraints excluded: chain A residue 556 ARG Chi-restraints excluded: chain A residue 775 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 53 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 49 optimal weight: 0.6980 chunk 32 optimal weight: 0.0470 chunk 47 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 25 optimal weight: 0.5980 chunk 50 optimal weight: 7.9990 chunk 42 optimal weight: 0.7980 overall best weight: 0.8280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 529 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.150439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.127509 restraints weight = 5067.549| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 1.74 r_work: 0.3254 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4497 Z= 0.143 Angle : 0.564 9.548 6131 Z= 0.287 Chirality : 0.043 0.151 687 Planarity : 0.004 0.030 743 Dihedral : 4.653 52.927 588 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.36 % Allowed : 15.02 % Favored : 82.62 % 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: 1.59 (0.36), residues: 541 helix: 1.58 (0.26), residues: 387 sheet: None (None), residues: 0 loop : -0.19 (0.49), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 531 TYR 0.022 0.002 TYR A 219 PHE 0.012 0.001 PHE A 580 TRP 0.013 0.001 TRP A 482 HIS 0.001 0.000 HIS A 738 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.14 ( 4497) covalent geometry : angle 0.56405 / 0.29 ( 6131) hydrogen bonds : bond 0.03982 / 2.69 ( 283) hydrogen bonds : angle 4.39026 / 3.10 ( 828) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 time to evaluate : 0.155 Fit side-chains REVERT: A 204 MET cc_start: 0.6809 (OUTLIER) cc_final: 0.6510 (mtt) REVERT: A 215 TRP cc_start: 0.7919 (OUTLIER) cc_final: 0.7315 (t60) REVERT: A 323 LYS cc_start: 0.8118 (mmtm) cc_final: 0.7732 (pttt) REVERT: A 391 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7432 (pm20) REVERT: A 746 GLU cc_start: 0.7306 (mt-10) cc_final: 0.7057 (mt-10) outliers start: 11 outliers final: 5 residues processed: 67 average time/residue: 0.0646 time to fit residues: 5.5870 Evaluate side-chains 67 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 59 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 215 TRP Chi-restraints excluded: chain A residue 219 TYR Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 391 GLU Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 529 ASN Chi-restraints excluded: chain A residue 775 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 19 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 13 optimal weight: 3.9990 chunk 31 optimal weight: 0.4980 chunk 23 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 529 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.149842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.126044 restraints weight = 5118.477| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 1.82 r_work: 0.3322 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4497 Z= 0.139 Angle : 0.562 9.577 6131 Z= 0.286 Chirality : 0.042 0.137 687 Planarity : 0.004 0.030 743 Dihedral : 4.604 51.873 588 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 2.36 % Allowed : 14.59 % Favored : 83.05 % 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: 1.57 (0.36), residues: 541 helix: 1.55 (0.26), residues: 387 sheet: None (None), residues: 0 loop : -0.14 (0.50), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 769 TYR 0.021 0.002 TYR A 219 PHE 0.012 0.001 PHE A 580 TRP 0.011 0.001 TRP A 728 HIS 0.001 0.000 HIS A 601 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.14 ( 4497) covalent geometry : angle 0.56218 / 0.29 ( 6131) hydrogen bonds : bond 0.03911 / 2.62 ( 283) hydrogen bonds : angle 4.41107 / 3.12 ( 828) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 60 time to evaluate : 0.156 Fit side-chains REVERT: A 204 MET cc_start: 0.6787 (OUTLIER) cc_final: 0.6489 (mtt) REVERT: A 215 TRP cc_start: 0.7892 (OUTLIER) cc_final: 0.7301 (t60) REVERT: A 323 LYS cc_start: 0.7973 (mmtm) cc_final: 0.7667 (pttt) REVERT: A 391 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7434 (pm20) REVERT: A 737 MET cc_start: 0.8147 (mmm) cc_final: 0.7469 (tpt) REVERT: A 746 GLU cc_start: 0.7274 (mt-10) cc_final: 0.7010 (mt-10) REVERT: A 771 LYS cc_start: 0.8228 (OUTLIER) cc_final: 0.7685 (pmtt) outliers start: 11 outliers final: 6 residues processed: 68 average time/residue: 0.0521 time to fit residues: 4.8679 Evaluate side-chains 68 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 215 TRP Chi-restraints excluded: chain A residue 219 TYR Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 391 GLU Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 529 ASN Chi-restraints excluded: chain A residue 771 LYS Chi-restraints excluded: chain A residue 775 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 39 optimal weight: 2.9990 chunk 41 optimal weight: 0.4980 chunk 30 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 21 optimal weight: 0.8980 chunk 13 optimal weight: 4.9990 chunk 15 optimal weight: 0.4980 chunk 31 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.147329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.123094 restraints weight = 5170.484| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 1.87 r_work: 0.3315 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4497 Z= 0.137 Angle : 0.561 10.501 6131 Z= 0.285 Chirality : 0.042 0.137 687 Planarity : 0.004 0.031 743 Dihedral : 4.588 51.038 588 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.36 % Allowed : 14.81 % Favored : 82.83 % 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: 1.57 (0.36), residues: 541 helix: 1.54 (0.26), residues: 387 sheet: None (None), residues: 0 loop : -0.14 (0.50), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 769 TYR 0.020 0.002 TYR A 219 PHE 0.010 0.001 PHE A 580 TRP 0.012 0.001 TRP A 728 HIS 0.001 0.000 HIS A 601 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 ( 4497) covalent geometry : angle 0.56141 / 0.28 ( 6131) hydrogen bonds : bond 0.03897 / 2.61 ( 283) hydrogen bonds : angle 4.41812 / 3.12 ( 828) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 time to evaluate : 0.155 Fit side-chains REVERT: A 204 MET cc_start: 0.6857 (OUTLIER) cc_final: 0.6567 (mtt) REVERT: A 215 TRP cc_start: 0.8137 (OUTLIER) cc_final: 0.7578 (t60) REVERT: A 323 LYS cc_start: 0.7995 (mmtm) cc_final: 0.7719 (pttt) REVERT: A 391 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7487 (pm20) REVERT: A 746 GLU cc_start: 0.7351 (mt-10) cc_final: 0.7087 (mt-10) REVERT: A 771 LYS cc_start: 0.8289 (OUTLIER) cc_final: 0.7694 (pmtt) outliers start: 11 outliers final: 6 residues processed: 67 average time/residue: 0.0585 time to fit residues: 5.2991 Evaluate side-chains 67 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 215 TRP Chi-restraints excluded: chain A residue 219 TYR Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 391 GLU Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 771 LYS Chi-restraints excluded: chain A residue 775 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 47 optimal weight: 0.5980 chunk 1 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 39 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 529 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.149318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.126148 restraints weight = 5117.463| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 1.77 r_work: 0.3322 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4497 Z= 0.143 Angle : 0.574 11.120 6131 Z= 0.290 Chirality : 0.042 0.137 687 Planarity : 0.004 0.031 743 Dihedral : 4.590 49.897 588 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.36 % Allowed : 15.02 % Favored : 82.62 % 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: 1.52 (0.36), residues: 541 helix: 1.49 (0.26), residues: 387 sheet: None (None), residues: 0 loop : -0.10 (0.51), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 769 TYR 0.020 0.002 TYR A 219 PHE 0.010 0.001 PHE A 568 TRP 0.014 0.001 TRP A 728 HIS 0.001 0.000 HIS A 738 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.14 ( 4497) covalent geometry : angle 0.57383 / 0.29 ( 6131) hydrogen bonds : bond 0.03954 / 2.65 ( 283) hydrogen bonds : angle 4.41532 / 3.12 ( 828) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 61 time to evaluate : 0.152 Fit side-chains REVERT: A 204 MET cc_start: 0.6841 (OUTLIER) cc_final: 0.6559 (mtt) REVERT: A 215 TRP cc_start: 0.8002 (OUTLIER) cc_final: 0.7350 (t60) REVERT: A 323 LYS cc_start: 0.7994 (mmtm) cc_final: 0.7680 (pttt) REVERT: A 391 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7432 (pm20) REVERT: A 746 GLU cc_start: 0.7265 (mt-10) cc_final: 0.7006 (mt-10) REVERT: A 771 LYS cc_start: 0.8238 (OUTLIER) cc_final: 0.7612 (pmtt) outliers start: 11 outliers final: 7 residues processed: 69 average time/residue: 0.0671 time to fit residues: 6.0222 Evaluate side-chains 72 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 61 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 215 TRP Chi-restraints excluded: chain A residue 219 TYR Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 391 GLU Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 529 ASN Chi-restraints excluded: chain A residue 771 LYS Chi-restraints excluded: chain A residue 775 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 16 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 44 optimal weight: 0.6980 chunk 36 optimal weight: 0.3980 chunk 27 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 chunk 49 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 529 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.151858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.128614 restraints weight = 5174.487| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 1.78 r_work: 0.3333 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4497 Z= 0.132 Angle : 0.577 10.230 6131 Z= 0.290 Chirality : 0.042 0.137 687 Planarity : 0.004 0.031 743 Dihedral : 4.558 49.811 588 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.36 % Allowed : 15.02 % Favored : 82.62 % 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: 1.54 (0.36), residues: 541 helix: 1.49 (0.26), residues: 387 sheet: None (None), residues: 0 loop : -0.05 (0.51), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 769 TYR 0.020 0.001 TYR A 219 PHE 0.010 0.001 PHE A 526 TRP 0.013 0.001 TRP A 728 HIS 0.001 0.000 HIS A 601 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.13 ( 4497) covalent geometry : angle 0.57710 / 0.29 ( 6131) hydrogen bonds : bond 0.03902 / 2.59 ( 283) hydrogen bonds : angle 4.40053 / 3.11 ( 828) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1211.96 seconds wall clock time: 21 minutes 28.94 seconds (1288.94 seconds total)