Starting phenix.real_space_refine on Tue Mar 3 12:44:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9r1h_53509/03_2026/9r1h_53509.cif Found real_map, /net/cci-nas-00/data/ceres_data/9r1h_53509/03_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_53509/03_2026/9r1h_53509.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9r1h_53509/03_2026/9r1h_53509.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9r1h_53509/03_2026/9r1h_53509.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9r1h_53509/03_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-5986/lib/python3.9/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, 9 Unusual residues: {' CL': 1, ' NA': 1} Inner-chain residues flagged as termini: ['pdbres="GLY A 803 "'] Classifications: {'peptide': 1, 'undetermined': 2, 'water': 2} Modifications used: {'COO': 1} Link IDs: {None: 4} 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: 1.03, per 1000 atoms: 0.24 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: 0.27 Conformation dependent library (CDL) restraints added in 201.1 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: 0.15 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: 0.68 Time building geometry restraints manager: 0.38 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 2.470 nonbonded pdb=" O GLY A 206 " pdb="NA NA A 801 " model vdw 2.323 2.470 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 2.470 ... (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: 2.640 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: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 5.620 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 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 covalent geometry : bond 0.00346 ( 4497) covalent geometry : angle 0.73898 ( 6131) hydrogen bonds : bond 0.13474 ( 283) hydrogen bonds : angle 7.10984 ( 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 : 0.161 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: 0.0737 time to fit residues: 6.3311 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 : 0.158 ------------------------------------------------------------------------------- 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... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.151298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.128184 restraints weight = 5130.557| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 1.74 r_work: 0.3356 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3228 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.1268 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 : 0.581 8.400 6131 Z= 0.310 Chirality : 0.043 0.144 687 Planarity : 0.005 0.034 743 Dihedral : 5.587 52.431 594 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Rotamer: Outliers : 2.15 % Allowed : 12.45 % Favored : 85.41 % 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: 0.56 (0.34), residues: 541 helix: 0.87 (0.25), residues: 385 sheet: None (None), residues: 0 loop : -0.71 (0.44), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 766 TYR 0.020 0.002 TYR A 219 PHE 0.011 0.001 PHE A 518 TRP 0.015 0.001 TRP A 713 HIS 0.000 0.000 HIS A 601 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 4497) covalent geometry : angle 0.58130 ( 6131) hydrogen bonds : bond 0.04464 ( 283) hydrogen bonds : angle 4.94268 ( 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 71 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 0.130 Fit side-chains REVERT: A 408 TYR cc_start: 0.7998 (t80) cc_final: 0.7690 (t80) REVERT: A 438 ILE cc_start: 0.7228 (mm) cc_final: 0.7020 (mt) REVERT: A 654 TYR cc_start: 0.8803 (m-80) cc_final: 0.8563 (m-80) REVERT: A 735 ILE cc_start: 0.7391 (mt) cc_final: 0.7129 (mt) outliers start: 10 outliers final: 5 residues processed: 69 average time/residue: 0.0565 time to fit residues: 5.3364 Evaluate side-chains 61 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 56 time to evaluate : 0.145 ------------------------------------------------------------------------------- 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: 5.9990 chunk 52 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 48 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3663 r_free = 0.3663 target = 0.145069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.121417 restraints weight = 5101.530| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 1.82 r_work: 0.3232 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4497 Z= 0.148 Angle : 0.569 8.563 6131 Z= 0.299 Chirality : 0.043 0.145 687 Planarity : 0.005 0.033 743 Dihedral : 5.138 59.125 590 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 3.22 % Allowed : 12.66 % 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: 1.11 (0.36), residues: 541 helix: 1.24 (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 0.003 0.000 ARG A 599 TYR 0.023 0.002 TYR A 219 PHE 0.009 0.001 PHE A 568 TRP 0.012 0.001 TRP A 713 HIS 0.001 0.000 HIS A 765 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 4497) covalent geometry : angle 0.56885 ( 6131) hydrogen bonds : bond 0.04287 ( 283) hydrogen bonds : angle 4.65481 ( 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 77 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 62 time to evaluate : 0.146 Fit side-chains REVERT: A 204 MET cc_start: 0.6748 (OUTLIER) cc_final: 0.6388 (mtt) REVERT: A 391 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7346 (pm20) REVERT: A 408 TYR cc_start: 0.8066 (t80) cc_final: 0.7754 (t80) REVERT: A 735 ILE cc_start: 0.7342 (mt) cc_final: 0.7107 (mt) outliers start: 15 outliers final: 9 residues processed: 73 average time/residue: 0.0584 time to fit residues: 5.6639 Evaluate side-chains 67 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 56 time to evaluate : 0.149 ------------------------------------------------------------------------------- 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 529 ASN Chi-restraints excluded: chain A residue 545 ILE 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 27 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 28 optimal weight: 0.5980 chunk 14 optimal weight: 0.6980 chunk 38 optimal weight: 0.3980 chunk 34 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3644 r_free = 0.3644 target = 0.144699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.120491 restraints weight = 5103.306| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 1.85 r_work: 0.3252 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4497 Z= 0.125 Angle : 0.541 7.706 6131 Z= 0.281 Chirality : 0.042 0.138 687 Planarity : 0.004 0.032 743 Dihedral : 4.979 59.576 590 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 2.36 % Allowed : 13.09 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.36), residues: 541 helix: 1.43 (0.26), residues: 387 sheet: None (None), residues: 0 loop : -0.37 (0.49), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 599 TYR 0.019 0.001 TYR A 219 PHE 0.009 0.001 PHE A 580 TRP 0.012 0.001 TRP A 713 HIS 0.001 0.000 HIS A 601 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 4497) covalent geometry : angle 0.54124 ( 6131) hydrogen bonds : bond 0.03930 ( 283) hydrogen bonds : angle 4.48431 ( 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: 11 poor density : 59 time to evaluate : 0.152 Fit side-chains REVERT: A 204 MET cc_start: 0.6744 (OUTLIER) cc_final: 0.6406 (mtt) REVERT: A 408 TYR cc_start: 0.8073 (t80) cc_final: 0.7798 (t80) REVERT: A 735 ILE cc_start: 0.7370 (mt) cc_final: 0.7131 (mt) REVERT: A 746 GLU cc_start: 0.7153 (mt-10) cc_final: 0.6883 (mt-10) outliers start: 11 outliers final: 8 residues processed: 69 average time/residue: 0.0699 time to fit residues: 6.1708 Evaluate side-chains 66 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.139 ------------------------------------------------------------------------------- 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 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: 2.9990 chunk 7 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 chunk 51 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 529 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.141420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.116323 restraints weight = 5214.310| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 2.00 r_work: 0.3199 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 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 0.030 4497 Z= 0.141 Angle : 0.562 8.520 6131 Z= 0.290 Chirality : 0.043 0.136 687 Planarity : 0.004 0.030 743 Dihedral : 4.962 57.295 590 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 3.00 % Allowed : 13.09 % Favored : 83.91 % 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: 1.37 (0.36), residues: 541 helix: 1.46 (0.26), residues: 387 sheet: None (None), residues: 0 loop : -0.41 (0.48), 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 476 TRP 0.011 0.001 TRP A 713 HIS 0.001 0.000 HIS A 601 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 4497) covalent geometry : angle 0.56187 ( 6131) hydrogen bonds : bond 0.04031 ( 283) hydrogen bonds : angle 4.48334 ( 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 70 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 56 time to evaluate : 0.176 Fit side-chains REVERT: A 215 TRP cc_start: 0.8115 (OUTLIER) cc_final: 0.7590 (t60) REVERT: A 391 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7468 (pm20) REVERT: A 735 ILE cc_start: 0.7732 (mt) cc_final: 0.7477 (mt) outliers start: 14 outliers final: 8 residues processed: 68 average time/residue: 0.0618 time to fit residues: 5.6392 Evaluate side-chains 65 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 55 time to evaluate : 0.155 ------------------------------------------------------------------------------- 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 266 ILE Chi-restraints excluded: chain A residue 303 VAL 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 775 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 2 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 50 optimal weight: 0.0050 chunk 29 optimal weight: 3.9990 chunk 20 optimal weight: 0.4980 chunk 9 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 529 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.150837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.127864 restraints weight = 5148.443| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 1.75 r_work: 0.3278 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4497 Z= 0.130 Angle : 0.548 8.982 6131 Z= 0.282 Chirality : 0.042 0.137 687 Planarity : 0.004 0.030 743 Dihedral : 4.875 55.713 590 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 3.22 % Allowed : 13.73 % 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: 1.43 (0.36), residues: 541 helix: 1.49 (0.26), residues: 387 sheet: None (None), residues: 0 loop : -0.34 (0.49), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 531 TYR 0.020 0.002 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 covalent geometry : bond 0.00312 ( 4497) covalent geometry : angle 0.54824 ( 6131) hydrogen bonds : bond 0.03860 ( 283) hydrogen bonds : angle 4.41141 ( 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 74 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 59 time to evaluate : 0.173 Fit side-chains REVERT: A 204 MET cc_start: 0.6727 (OUTLIER) cc_final: 0.6411 (mtt) REVERT: A 215 TRP cc_start: 0.7889 (OUTLIER) cc_final: 0.7371 (t60) REVERT: A 323 LYS cc_start: 0.8011 (mmtm) cc_final: 0.7694 (pttt) REVERT: A 391 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7425 (pm20) REVERT: A 735 ILE cc_start: 0.7528 (mt) cc_final: 0.7290 (mt) REVERT: A 746 GLU cc_start: 0.7238 (mt-10) cc_final: 0.6991 (mt-10) outliers start: 15 outliers final: 7 residues processed: 71 average time/residue: 0.0622 time to fit residues: 5.8159 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 : 0.162 ------------------------------------------------------------------------------- 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 303 VAL 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 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: 0.9980 chunk 28 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 49 optimal weight: 2.9990 chunk 32 optimal weight: 0.4980 chunk 47 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 50 optimal weight: 0.9980 chunk 42 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 529 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.146542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.122506 restraints weight = 5077.285| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 1.83 r_work: 0.3335 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4497 Z= 0.132 Angle : 0.550 8.906 6131 Z= 0.280 Chirality : 0.042 0.150 687 Planarity : 0.004 0.031 743 Dihedral : 4.818 53.741 590 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 2.58 % Allowed : 15.02 % Favored : 82.40 % 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: 1.51 (0.36), residues: 541 helix: 1.55 (0.26), residues: 387 sheet: None (None), residues: 0 loop : -0.30 (0.49), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 531 TYR 0.020 0.002 TYR A 219 PHE 0.010 0.001 PHE A 580 TRP 0.011 0.001 TRP A 482 HIS 0.001 0.000 HIS A 601 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 4497) covalent geometry : angle 0.55041 ( 6131) hydrogen bonds : bond 0.03837 ( 283) hydrogen bonds : angle 4.38381 ( 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 66 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 54 time to evaluate : 0.158 Fit side-chains REVERT: A 204 MET cc_start: 0.6792 (OUTLIER) cc_final: 0.6465 (mtt) REVERT: A 215 TRP cc_start: 0.8096 (OUTLIER) cc_final: 0.7588 (t60) REVERT: A 323 LYS cc_start: 0.8025 (mmtm) cc_final: 0.7708 (pttt) REVERT: A 391 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7484 (pm20) REVERT: A 735 ILE cc_start: 0.7748 (mt) cc_final: 0.7507 (mt) REVERT: A 746 GLU cc_start: 0.7369 (mt-10) cc_final: 0.7131 (mt-10) REVERT: A 771 LYS cc_start: 0.8289 (OUTLIER) cc_final: 0.7725 (pmtt) outliers start: 12 outliers final: 7 residues processed: 64 average time/residue: 0.0597 time to fit residues: 5.0767 Evaluate side-chains 65 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 54 time to evaluate : 0.143 ------------------------------------------------------------------------------- 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 771 LYS 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: 0.9990 chunk 34 optimal weight: 0.0870 chunk 33 optimal weight: 0.9980 chunk 4 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 13 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 529 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.150819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.127607 restraints weight = 5118.924| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 1.76 r_work: 0.3322 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4497 Z= 0.134 Angle : 0.562 9.765 6131 Z= 0.285 Chirality : 0.042 0.138 687 Planarity : 0.004 0.031 743 Dihedral : 4.809 52.754 590 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.58 % Allowed : 14.81 % 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: 1.55 (0.26), residues: 387 sheet: None (None), residues: 0 loop : -0.23 (0.50), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 766 TYR 0.020 0.002 TYR A 219 PHE 0.009 0.001 PHE A 568 TRP 0.011 0.001 TRP A 482 HIS 0.001 0.000 HIS A 601 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 4497) covalent geometry : angle 0.56178 ( 6131) hydrogen bonds : bond 0.03859 ( 283) hydrogen bonds : angle 4.38746 ( 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 68 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 56 time to evaluate : 0.098 Fit side-chains REVERT: A 204 MET cc_start: 0.6767 (OUTLIER) cc_final: 0.6449 (mtt) REVERT: A 215 TRP cc_start: 0.7925 (OUTLIER) cc_final: 0.7403 (t60) REVERT: A 323 LYS cc_start: 0.8025 (mmtm) cc_final: 0.7673 (pttt) REVERT: A 391 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7453 (pm20) REVERT: A 735 ILE cc_start: 0.7566 (mt) cc_final: 0.7328 (mt) REVERT: A 737 MET cc_start: 0.8122 (mmm) cc_final: 0.7447 (tpt) REVERT: A 746 GLU cc_start: 0.7286 (mt-10) cc_final: 0.7026 (mt-10) outliers start: 12 outliers final: 7 residues processed: 66 average time/residue: 0.0621 time to fit residues: 5.4503 Evaluate side-chains 65 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 55 time to evaluate : 0.147 ------------------------------------------------------------------------------- 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 775 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 39 optimal weight: 0.4980 chunk 41 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 21 optimal weight: 3.9990 chunk 13 optimal weight: 0.2980 chunk 15 optimal weight: 0.5980 chunk 31 optimal weight: 0.0970 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 529 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.153417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.130135 restraints weight = 5109.329| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 1.76 r_work: 0.3307 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4497 Z= 0.113 Angle : 0.541 10.713 6131 Z= 0.272 Chirality : 0.041 0.138 687 Planarity : 0.004 0.031 743 Dihedral : 4.654 51.671 590 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 2.58 % Allowed : 14.59 % 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: 1.73 (0.36), residues: 541 helix: 1.71 (0.26), residues: 383 sheet: None (None), residues: 0 loop : -0.14 (0.50), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 531 TYR 0.016 0.001 TYR A 219 PHE 0.009 0.001 PHE A 476 TRP 0.011 0.001 TRP A 713 HIS 0.001 0.000 HIS A 601 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 4497) covalent geometry : angle 0.54122 ( 6131) hydrogen bonds : bond 0.03539 ( 283) hydrogen bonds : angle 4.27602 ( 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 72 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 0.134 Fit side-chains REVERT: A 204 MET cc_start: 0.6731 (OUTLIER) cc_final: 0.6446 (mtt) REVERT: A 215 TRP cc_start: 0.7834 (OUTLIER) cc_final: 0.7385 (t60) REVERT: A 323 LYS cc_start: 0.8054 (mmtm) cc_final: 0.7712 (pttt) REVERT: A 391 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7403 (pm20) REVERT: A 735 ILE cc_start: 0.7517 (mt) cc_final: 0.7286 (mt) REVERT: A 746 GLU cc_start: 0.7242 (mt-10) cc_final: 0.6980 (mt-10) REVERT: A 771 LYS cc_start: 0.8202 (OUTLIER) cc_final: 0.7659 (pmtt) outliers start: 12 outliers final: 6 residues processed: 70 average time/residue: 0.0666 time to fit residues: 6.0653 Evaluate side-chains 65 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 55 time to evaluate : 0.147 ------------------------------------------------------------------------------- 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 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: 0.6980 chunk 1 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 3 optimal weight: 0.5980 chunk 38 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 39 optimal weight: 0.7980 chunk 41 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 529 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.150811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.127668 restraints weight = 5131.949| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 1.76 r_work: 0.3343 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4497 Z= 0.144 Angle : 0.571 11.246 6131 Z= 0.288 Chirality : 0.042 0.136 687 Planarity : 0.004 0.031 743 Dihedral : 4.787 50.519 590 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.15 % Allowed : 14.81 % 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: 1.59 (0.36), residues: 541 helix: 1.58 (0.26), residues: 385 sheet: None (None), residues: 0 loop : -0.13 (0.51), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 556 TYR 0.020 0.002 TYR A 219 PHE 0.020 0.001 PHE A 580 TRP 0.013 0.001 TRP A 728 HIS 0.001 0.000 HIS A 601 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 4497) covalent geometry : angle 0.57103 ( 6131) hydrogen bonds : bond 0.03889 ( 283) hydrogen bonds : angle 4.37851 ( 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 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 Fit side-chains REVERT: A 204 MET cc_start: 0.6824 (OUTLIER) cc_final: 0.6521 (mtt) REVERT: A 215 TRP cc_start: 0.7851 (OUTLIER) cc_final: 0.7326 (t60) REVERT: A 323 LYS cc_start: 0.7941 (mmtm) cc_final: 0.7662 (pttt) REVERT: A 391 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7386 (pm20) REVERT: A 735 ILE cc_start: 0.7497 (mt) cc_final: 0.7289 (mt) REVERT: A 746 GLU cc_start: 0.7221 (mt-10) cc_final: 0.6964 (mt-10) REVERT: A 771 LYS cc_start: 0.8166 (OUTLIER) cc_final: 0.7584 (pmtt) outliers start: 10 outliers final: 6 residues processed: 64 average time/residue: 0.0538 time to fit residues: 4.7548 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 : 0.146 ------------------------------------------------------------------------------- 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 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: 0.9980 chunk 15 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 44 optimal weight: 0.6980 chunk 36 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 2 optimal weight: 0.5980 chunk 49 optimal weight: 0.5980 chunk 21 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 529 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.146162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.121795 restraints weight = 5195.694| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 1.88 r_work: 0.3275 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4497 Z= 0.129 Angle : 0.556 9.025 6131 Z= 0.282 Chirality : 0.042 0.136 687 Planarity : 0.004 0.031 743 Dihedral : 4.724 49.799 590 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % 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: 1.67 (0.36), residues: 541 helix: 1.62 (0.26), residues: 385 sheet: None (None), residues: 0 loop : -0.06 (0.51), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 556 TYR 0.019 0.001 TYR A 219 PHE 0.009 0.001 PHE A 580 TRP 0.015 0.001 TRP A 728 HIS 0.001 0.000 HIS A 601 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 4497) covalent geometry : angle 0.55616 ( 6131) hydrogen bonds : bond 0.03773 ( 283) hydrogen bonds : angle 4.34605 ( 828) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1233.55 seconds wall clock time: 21 minutes 46.61 seconds (1306.61 seconds total)