Starting phenix.real_space_refine on Wed Mar 4 07:05:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7b5e_12027/03_2026/7b5e_12027.cif Found real_map, /net/cci-nas-00/data/ceres_data/7b5e_12027/03_2026/7b5e_12027.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7b5e_12027/03_2026/7b5e_12027.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7b5e_12027/03_2026/7b5e_12027.map" model { file = "/net/cci-nas-00/data/ceres_data/7b5e_12027/03_2026/7b5e_12027.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7b5e_12027/03_2026/7b5e_12027.cif" } resolution = 4.1 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 4 9.91 5 S 74 5.16 5 C 7678 2.51 5 N 1936 2.21 5 O 2072 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 54 residue(s): 0.01s 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: 11764 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 718, 5880 Classifications: {'peptide': 718} Link IDs: {'PTRANS': 31, 'TRANS': 686} Chain breaks: 4 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: B Time building chain proxies: 4.26, per 1000 atoms: 0.36 Number of scatterers: 11764 At special positions: 0 Unit cell: (122.452, 98.164, 121.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 4 19.99 S 74 16.00 O 2072 8.00 N 1936 7.00 C 7678 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 370 " - pdb=" SG CYS A 395 " distance=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 836 " distance=2.04 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 386 " distance=2.03 Simple disulfide: pdb=" SG CYS A 625 " - pdb=" SG CYS A 630 " distance=2.03 Simple disulfide: pdb=" SG CYS B 370 " - pdb=" SG CYS B 395 " distance=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 836 " distance=2.04 Simple disulfide: pdb=" SG CYS B 382 " - pdb=" SG CYS B 386 " distance=2.03 Simple disulfide: pdb=" SG CYS B 625 " - pdb=" SG CYS B 630 " distance=2.03 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: 0.92 Conformation dependent library (CDL) restraints added in 542.3 milliseconds 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2752 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 6 sheets defined 63.0% alpha, 1.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 166 through 181 Proline residue: A 177 - end of helix Processing helix chain 'A' and resid 204 through 211 removed outlier: 3.664A pdb=" N GLU A 211 " --> pdb=" O PRO A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 257 removed outlier: 3.651A pdb=" N THR A 257 " --> pdb=" O ILE A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 275 Processing helix chain 'A' and resid 296 through 305 Processing helix chain 'A' and resid 307 through 311 Processing helix chain 'A' and resid 316 through 325 Processing helix chain 'A' and resid 325 through 359 removed outlier: 3.752A pdb=" N GLY A 329 " --> pdb=" O GLY A 325 " (cutoff:3.500A) Proline residue: A 344 - end of helix Processing helix chain 'A' and resid 363 through 371 removed outlier: 3.899A pdb=" N MET A 367 " --> pdb=" O ASN A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 393 Processing helix chain 'A' and resid 394 through 403 removed outlier: 3.760A pdb=" N LEU A 403 " --> pdb=" O ARG A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 438 Processing helix chain 'A' and resid 452 through 466 Processing helix chain 'A' and resid 489 through 518 removed outlier: 4.285A pdb=" N ASN A 493 " --> pdb=" O ALA A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 568 Processing helix chain 'A' and resid 572 through 592 Processing helix chain 'A' and resid 593 through 602 Processing helix chain 'A' and resid 630 through 648 removed outlier: 4.194A pdb=" N LEU A 634 " --> pdb=" O CYS A 630 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLN A 646 " --> pdb=" O MET A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 668 Proline residue: A 658 - end of helix Processing helix chain 'A' and resid 685 through 693 removed outlier: 4.320A pdb=" N ASN A 692 " --> pdb=" O GLU A 688 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU A 693 " --> pdb=" O VAL A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 716 Processing helix chain 'A' and resid 722 through 745 removed outlier: 4.211A pdb=" N PHE A 726 " --> pdb=" O LEU A 722 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ARG A 736 " --> pdb=" O ILE A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 782 removed outlier: 4.110A pdb=" N VAL A 772 " --> pdb=" O GLY A 768 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N ILE A 773 " --> pdb=" O LYS A 769 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N PHE A 777 " --> pdb=" O ILE A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 785 through 794 Processing helix chain 'A' and resid 803 through 809 Processing helix chain 'A' and resid 815 through 817 No H-bonds generated for 'chain 'A' and resid 815 through 817' Processing helix chain 'A' and resid 854 through 885 removed outlier: 3.899A pdb=" N TRP A 858 " --> pdb=" O SER A 854 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 908 Processing helix chain 'B' and resid 166 through 181 Proline residue: B 177 - end of helix Processing helix chain 'B' and resid 204 through 211 removed outlier: 3.664A pdb=" N GLU B 211 " --> pdb=" O PRO B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 257 removed outlier: 3.651A pdb=" N THR B 257 " --> pdb=" O ILE B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 275 Processing helix chain 'B' and resid 296 through 305 Processing helix chain 'B' and resid 307 through 311 Processing helix chain 'B' and resid 316 through 325 Processing helix chain 'B' and resid 325 through 359 removed outlier: 3.752A pdb=" N GLY B 329 " --> pdb=" O GLY B 325 " (cutoff:3.500A) Proline residue: B 344 - end of helix Processing helix chain 'B' and resid 363 through 371 removed outlier: 3.899A pdb=" N MET B 367 " --> pdb=" O ASN B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 393 Processing helix chain 'B' and resid 394 through 403 removed outlier: 3.760A pdb=" N LEU B 403 " --> pdb=" O ARG B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 438 Processing helix chain 'B' and resid 452 through 466 Processing helix chain 'B' and resid 489 through 518 removed outlier: 4.285A pdb=" N ASN B 493 " --> pdb=" O ALA B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 568 Processing helix chain 'B' and resid 572 through 592 Processing helix chain 'B' and resid 593 through 602 Processing helix chain 'B' and resid 630 through 648 removed outlier: 4.194A pdb=" N LEU B 634 " --> pdb=" O CYS B 630 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLN B 646 " --> pdb=" O MET B 642 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 668 Proline residue: B 658 - end of helix Processing helix chain 'B' and resid 685 through 693 removed outlier: 4.320A pdb=" N ASN B 692 " --> pdb=" O GLU B 688 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LEU B 693 " --> pdb=" O VAL B 689 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 716 Processing helix chain 'B' and resid 722 through 745 removed outlier: 4.211A pdb=" N PHE B 726 " --> pdb=" O LEU B 722 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ARG B 736 " --> pdb=" O ILE B 732 " (cutoff:3.500A) Processing helix chain 'B' and resid 759 through 782 removed outlier: 4.111A pdb=" N VAL B 772 " --> pdb=" O GLY B 768 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N ILE B 773 " --> pdb=" O LYS B 769 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N PHE B 777 " --> pdb=" O ILE B 773 " (cutoff:3.500A) Processing helix chain 'B' and resid 785 through 794 Processing helix chain 'B' and resid 803 through 809 Processing helix chain 'B' and resid 815 through 817 No H-bonds generated for 'chain 'B' and resid 815 through 817' Processing helix chain 'B' and resid 854 through 885 removed outlier: 3.898A pdb=" N TRP B 858 " --> pdb=" O SER B 854 " (cutoff:3.500A) Processing helix chain 'B' and resid 895 through 908 Processing sheet with id=AA1, first strand: chain 'A' and resid 186 through 188 Processing sheet with id=AA2, first strand: chain 'A' and resid 217 through 218 Processing sheet with id=AA3, first strand: chain 'A' and resid 810 through 813 Processing sheet with id=AA4, first strand: chain 'B' and resid 186 through 188 Processing sheet with id=AA5, first strand: chain 'B' and resid 217 through 218 Processing sheet with id=AA6, first strand: chain 'B' and resid 810 through 813 652 hydrogen bonds defined for protein. 1926 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: 1.46 Time building geometry restraints manager: 1.28 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: 3639 1.34 - 1.46: 2725 1.46 - 1.58: 5572 1.58 - 1.70: 0 1.70 - 1.81: 122 Bond restraints: 12058 Sorted by residual: bond pdb=" C ALA B 723 " pdb=" N PRO B 724 " ideal model delta sigma weight residual 1.335 1.370 -0.036 1.19e-02 7.06e+03 8.91e+00 bond pdb=" C ALA A 723 " pdb=" N PRO A 724 " ideal model delta sigma weight residual 1.335 1.370 -0.035 1.19e-02 7.06e+03 8.82e+00 bond pdb=" C ASP A 203 " pdb=" N PRO A 204 " ideal model delta sigma weight residual 1.337 1.362 -0.025 1.11e-02 8.12e+03 5.27e+00 bond pdb=" C ASP B 203 " pdb=" N PRO B 204 " ideal model delta sigma weight residual 1.337 1.362 -0.025 1.11e-02 8.12e+03 5.08e+00 bond pdb=" C SER A 527 " pdb=" N PRO A 528 " ideal model delta sigma weight residual 1.334 1.375 -0.041 2.34e-02 1.83e+03 3.05e+00 ... (remaining 12053 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.50: 15895 2.50 - 5.00: 365 5.00 - 7.50: 36 7.50 - 9.99: 14 9.99 - 12.49: 2 Bond angle restraints: 16312 Sorted by residual: angle pdb=" N VAL A 181 " pdb=" CA VAL A 181 " pdb=" C VAL A 181 " ideal model delta sigma weight residual 111.91 108.42 3.49 8.90e-01 1.26e+00 1.54e+01 angle pdb=" N VAL B 181 " pdb=" CA VAL B 181 " pdb=" C VAL B 181 " ideal model delta sigma weight residual 111.91 108.42 3.49 8.90e-01 1.26e+00 1.53e+01 angle pdb=" N ASP A 123 " pdb=" CA ASP A 123 " pdb=" C ASP A 123 " ideal model delta sigma weight residual 111.02 115.59 -4.57 1.25e+00 6.40e-01 1.34e+01 angle pdb=" N ASP B 123 " pdb=" CA ASP B 123 " pdb=" C ASP B 123 " ideal model delta sigma weight residual 111.02 115.58 -4.56 1.25e+00 6.40e-01 1.33e+01 angle pdb=" CA LEU A 381 " pdb=" CB LEU A 381 " pdb=" CG LEU A 381 " ideal model delta sigma weight residual 116.30 128.79 -12.49 3.50e+00 8.16e-02 1.27e+01 ... (remaining 16307 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.00: 5973 14.00 - 28.00: 884 28.00 - 42.00: 273 42.00 - 56.01: 64 56.01 - 70.01: 20 Dihedral angle restraints: 7214 sinusoidal: 2962 harmonic: 4252 Sorted by residual: dihedral pdb=" CB CYS B 625 " pdb=" SG CYS B 625 " pdb=" SG CYS B 630 " pdb=" CB CYS B 630 " ideal model delta sinusoidal sigma weight residual -86.00 -151.87 65.87 1 1.00e+01 1.00e-02 5.68e+01 dihedral pdb=" CB CYS A 625 " pdb=" SG CYS A 625 " pdb=" SG CYS A 630 " pdb=" CB CYS A 630 " ideal model delta sinusoidal sigma weight residual -86.00 -151.86 65.86 1 1.00e+01 1.00e-02 5.67e+01 dihedral pdb=" CA THR A 235 " pdb=" C THR A 235 " pdb=" N ASP A 236 " pdb=" CA ASP A 236 " ideal model delta harmonic sigma weight residual 180.00 155.71 24.29 0 5.00e+00 4.00e-02 2.36e+01 ... (remaining 7211 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 1462 0.072 - 0.144: 305 0.144 - 0.216: 19 0.216 - 0.289: 6 0.289 - 0.361: 2 Chirality restraints: 1794 Sorted by residual: chirality pdb=" CB ILE B 786 " pdb=" CA ILE B 786 " pdb=" CG1 ILE B 786 " pdb=" CG2 ILE B 786 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.25e+00 chirality pdb=" CB ILE A 786 " pdb=" CA ILE A 786 " pdb=" CG1 ILE A 786 " pdb=" CG2 ILE A 786 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.24e+00 chirality pdb=" CB VAL A 310 " pdb=" CA VAL A 310 " pdb=" CG1 VAL A 310 " pdb=" CG2 VAL A 310 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.78e+00 ... (remaining 1791 not shown) Planarity restraints: 2044 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A 206 " 0.059 5.00e-02 4.00e+02 8.94e-02 1.28e+01 pdb=" N PRO A 207 " -0.155 5.00e-02 4.00e+02 pdb=" CA PRO A 207 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO A 207 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN B 206 " -0.059 5.00e-02 4.00e+02 8.93e-02 1.28e+01 pdb=" N PRO B 207 " 0.155 5.00e-02 4.00e+02 pdb=" CA PRO B 207 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO B 207 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 406 " -0.047 5.00e-02 4.00e+02 7.07e-02 8.00e+00 pdb=" N PRO A 407 " 0.122 5.00e-02 4.00e+02 pdb=" CA PRO A 407 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 407 " -0.039 5.00e-02 4.00e+02 ... (remaining 2041 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 3347 2.80 - 3.33: 11951 3.33 - 3.85: 19704 3.85 - 4.37: 21530 4.37 - 4.90: 35729 Nonbonded interactions: 92261 Sorted by model distance: nonbonded pdb=" O VAL A 778 " pdb=" OG1 THR A 782 " model vdw 2.275 3.040 nonbonded pdb=" O VAL B 778 " pdb=" OG1 THR B 782 " model vdw 2.275 3.040 nonbonded pdb=" O LYS B 740 " pdb=" OG1 THR B 744 " model vdw 2.278 3.040 nonbonded pdb=" O LYS A 740 " pdb=" OG1 THR A 744 " model vdw 2.279 3.040 nonbonded pdb=" OG SER B 387 " pdb=" O ASP B 825 " model vdw 2.293 3.040 ... (remaining 92256 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.080 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: 0.200 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 12.710 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 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:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 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 : 0.006 0.056 12066 Z= 0.285 Angle : 0.936 12.492 16328 Z= 0.514 Chirality : 0.057 0.361 1794 Planarity : 0.008 0.089 2044 Dihedral : 15.024 70.006 4438 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 0.31 % Allowed : 10.56 % Favored : 89.12 % 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: -3.56 (0.18), residues: 1416 helix: -1.68 (0.15), residues: 834 sheet: None (None), residues: 0 loop : -3.37 (0.21), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 125 TYR 0.022 0.002 TYR A 666 PHE 0.017 0.002 PHE A 585 TRP 0.014 0.002 TRP B 760 HIS 0.010 0.002 HIS B 402 Details of bonding type rmsd covalent geometry : bond 0.00629 (12058) covalent geometry : angle 0.93452 (16312) SS BOND : bond 0.00559 ( 8) SS BOND : angle 1.79796 ( 16) hydrogen bonds : bond 0.09855 ( 652) hydrogen bonds : angle 5.99207 ( 1926) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 181 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 TYR cc_start: 0.8626 (t80) cc_final: 0.8365 (t80) REVERT: A 416 MET cc_start: 0.7452 (tpp) cc_final: 0.7159 (tpp) REVERT: A 424 MET cc_start: 0.8724 (tpp) cc_final: 0.8424 (tpp) REVERT: A 436 TYR cc_start: 0.6872 (t80) cc_final: 0.5979 (t80) REVERT: A 508 VAL cc_start: 0.8668 (t) cc_final: 0.8414 (p) REVERT: A 580 LEU cc_start: 0.8626 (tp) cc_final: 0.8323 (tt) REVERT: B 197 VAL cc_start: 0.9060 (OUTLIER) cc_final: 0.8857 (t) REVERT: B 436 TYR cc_start: 0.6566 (t80) cc_final: 0.6344 (t80) REVERT: B 524 MET cc_start: -0.1256 (ttm) cc_final: -0.2110 (tmm) REVERT: B 760 TRP cc_start: 0.8467 (m100) cc_final: 0.8225 (m-90) outliers start: 4 outliers final: 0 residues processed: 183 average time/residue: 0.1155 time to fit residues: 30.1349 Evaluate side-chains 126 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 125 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.4980 chunk 55 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 215 GLN ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 ASN B 183 HIS ** B 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 692 ASN ** B 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 ASN B 898 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.104752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.087457 restraints weight = 33221.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.089071 restraints weight = 21306.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.089955 restraints weight = 15889.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.090771 restraints weight = 13392.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.090983 restraints weight = 11855.115| |-----------------------------------------------------------------------------| r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12066 Z= 0.128 Angle : 0.634 9.936 16328 Z= 0.329 Chirality : 0.042 0.253 1794 Planarity : 0.006 0.068 2044 Dihedral : 5.179 20.080 1584 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 0.08 % Allowed : 5.40 % Favored : 94.52 % 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: -1.82 (0.20), residues: 1416 helix: -0.11 (0.17), residues: 828 sheet: -3.71 (0.86), residues: 24 loop : -2.80 (0.23), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 683 TYR 0.024 0.001 TYR A 436 PHE 0.012 0.001 PHE A 867 TRP 0.016 0.001 TRP A 760 HIS 0.004 0.001 HIS A 402 Details of bonding type rmsd covalent geometry : bond 0.00264 (12058) covalent geometry : angle 0.63399 (16312) SS BOND : bond 0.00342 ( 8) SS BOND : angle 0.79562 ( 16) hydrogen bonds : bond 0.04365 ( 652) hydrogen bonds : angle 4.74922 ( 1926) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 187 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 416 MET cc_start: 0.7532 (tpp) cc_final: 0.7158 (tpp) REVERT: A 500 MET cc_start: 0.7995 (mtp) cc_final: 0.7298 (mtm) REVERT: A 704 MET cc_start: 0.8259 (mmm) cc_final: 0.8010 (mmt) REVERT: B 704 MET cc_start: 0.8284 (tpp) cc_final: 0.7932 (mmt) REVERT: B 760 TRP cc_start: 0.8347 (m100) cc_final: 0.8032 (m-90) REVERT: B 900 GLU cc_start: 0.8351 (pt0) cc_final: 0.7912 (mm-30) outliers start: 1 outliers final: 0 residues processed: 188 average time/residue: 0.1031 time to fit residues: 28.2919 Evaluate side-chains 121 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 36 optimal weight: 2.9990 chunk 97 optimal weight: 7.9990 chunk 44 optimal weight: 0.7980 chunk 82 optimal weight: 0.9980 chunk 56 optimal weight: 7.9990 chunk 130 optimal weight: 4.9990 chunk 15 optimal weight: 7.9990 chunk 93 optimal weight: 10.0000 chunk 102 optimal weight: 8.9990 chunk 105 optimal weight: 7.9990 chunk 7 optimal weight: 7.9990 overall best weight: 3.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 692 ASN ** A 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 435 ASN ** B 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 896 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.100033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.082746 restraints weight = 34307.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.084164 restraints weight = 22657.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.085089 restraints weight = 17297.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.085585 restraints weight = 14636.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.085786 restraints weight = 13325.914| |-----------------------------------------------------------------------------| r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 12066 Z= 0.223 Angle : 0.708 9.624 16328 Z= 0.370 Chirality : 0.045 0.256 1794 Planarity : 0.006 0.062 2044 Dihedral : 5.234 20.601 1584 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.98 % Favored : 92.02 % Rotamer: Outliers : 0.08 % Allowed : 4.93 % Favored : 94.99 % 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 (0.21), residues: 1416 helix: 0.28 (0.17), residues: 824 sheet: -3.97 (0.83), residues: 24 loop : -2.62 (0.24), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 128 TYR 0.020 0.002 TYR B 436 PHE 0.019 0.002 PHE A 585 TRP 0.018 0.002 TRP A 760 HIS 0.009 0.001 HIS B 402 Details of bonding type rmsd covalent geometry : bond 0.00504 (12058) covalent geometry : angle 0.70697 (16312) SS BOND : bond 0.01057 ( 8) SS BOND : angle 1.16484 ( 16) hydrogen bonds : bond 0.04716 ( 652) hydrogen bonds : angle 4.77648 ( 1926) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 162 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 341 MET cc_start: 0.8200 (tpp) cc_final: 0.7992 (tpp) REVERT: A 500 MET cc_start: 0.8201 (mtp) cc_final: 0.7463 (mtm) REVERT: A 588 LYS cc_start: 0.8245 (tttp) cc_final: 0.8015 (ttpt) REVERT: A 632 MET cc_start: 0.8884 (mmm) cc_final: 0.8644 (tpp) REVERT: B 338 TYR cc_start: 0.8754 (t80) cc_final: 0.8302 (t80) REVERT: B 580 LEU cc_start: 0.8373 (tp) cc_final: 0.8137 (tt) REVERT: B 760 TRP cc_start: 0.8570 (m100) cc_final: 0.8208 (m-90) REVERT: B 900 GLU cc_start: 0.8436 (pt0) cc_final: 0.8105 (mm-30) outliers start: 1 outliers final: 0 residues processed: 163 average time/residue: 0.1064 time to fit residues: 25.4139 Evaluate side-chains 111 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 13 optimal weight: 9.9990 chunk 45 optimal weight: 5.9990 chunk 70 optimal weight: 7.9990 chunk 58 optimal weight: 0.5980 chunk 108 optimal weight: 6.9990 chunk 97 optimal weight: 4.9990 chunk 37 optimal weight: 6.9990 chunk 9 optimal weight: 0.9980 chunk 85 optimal weight: 0.8980 chunk 43 optimal weight: 0.2980 chunk 107 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 230 HIS ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 435 ASN ** A 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 HIS ** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 375 ASN B 435 ASN B 896 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.104068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.087084 restraints weight = 33363.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.088597 restraints weight = 21788.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.089640 restraints weight = 16386.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.090183 restraints weight = 13594.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.090708 restraints weight = 12232.332| |-----------------------------------------------------------------------------| r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12066 Z= 0.125 Angle : 0.622 10.228 16328 Z= 0.318 Chirality : 0.042 0.250 1794 Planarity : 0.005 0.058 2044 Dihedral : 4.840 18.850 1584 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 0.08 % Allowed : 4.38 % Favored : 95.54 % 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: -0.79 (0.21), residues: 1416 helix: 0.72 (0.17), residues: 840 sheet: -3.53 (0.81), residues: 24 loop : -2.41 (0.25), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 125 TYR 0.022 0.001 TYR A 182 PHE 0.020 0.001 PHE B 499 TRP 0.022 0.001 TRP A 760 HIS 0.006 0.001 HIS A 230 Details of bonding type rmsd covalent geometry : bond 0.00263 (12058) covalent geometry : angle 0.62204 (16312) SS BOND : bond 0.00374 ( 8) SS BOND : angle 0.90789 ( 16) hydrogen bonds : bond 0.04201 ( 652) hydrogen bonds : angle 4.50932 ( 1926) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 179 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 391 MET cc_start: 0.7956 (ppp) cc_final: 0.7711 (tmm) REVERT: A 405 ASP cc_start: 0.8345 (t0) cc_final: 0.8085 (t70) REVERT: A 500 MET cc_start: 0.8017 (mtp) cc_final: 0.7790 (mtp) REVERT: A 508 VAL cc_start: 0.8776 (t) cc_final: 0.8529 (p) REVERT: B 391 MET cc_start: 0.7924 (ppp) cc_final: 0.7705 (tmm) REVERT: B 405 ASP cc_start: 0.8645 (t0) cc_final: 0.8308 (t70) REVERT: B 704 MET cc_start: 0.8375 (tpp) cc_final: 0.8138 (mmm) REVERT: B 760 TRP cc_start: 0.8426 (m100) cc_final: 0.8139 (m-90) outliers start: 1 outliers final: 0 residues processed: 180 average time/residue: 0.0912 time to fit residues: 24.3504 Evaluate side-chains 124 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 106 optimal weight: 0.0000 chunk 29 optimal weight: 5.9990 chunk 46 optimal weight: 4.9990 chunk 117 optimal weight: 1.9990 chunk 90 optimal weight: 5.9990 chunk 65 optimal weight: 6.9990 chunk 97 optimal weight: 8.9990 chunk 86 optimal weight: 0.8980 chunk 78 optimal weight: 0.0970 chunk 135 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 overall best weight: 0.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 709 GLN A 730 ASN ** B 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 896 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.105721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.089025 restraints weight = 33177.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.090664 restraints weight = 21301.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.091616 restraints weight = 15794.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.092427 restraints weight = 13160.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.092579 restraints weight = 11568.523| |-----------------------------------------------------------------------------| r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 12066 Z= 0.119 Angle : 0.611 10.054 16328 Z= 0.310 Chirality : 0.042 0.262 1794 Planarity : 0.005 0.056 2044 Dihedral : 4.609 16.612 1584 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.47 (0.22), residues: 1416 helix: 1.03 (0.17), residues: 836 sheet: -3.39 (0.84), residues: 24 loop : -2.35 (0.25), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 219 TYR 0.023 0.001 TYR B 761 PHE 0.021 0.001 PHE A 499 TRP 0.046 0.002 TRP A 760 HIS 0.004 0.001 HIS B 402 Details of bonding type rmsd covalent geometry : bond 0.00247 (12058) covalent geometry : angle 0.61016 (16312) SS BOND : bond 0.00290 ( 8) SS BOND : angle 1.28554 ( 16) hydrogen bonds : bond 0.04036 ( 652) hydrogen bonds : angle 4.40057 ( 1926) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 405 ASP cc_start: 0.8327 (t0) cc_final: 0.8092 (t70) REVERT: A 632 MET cc_start: 0.8754 (mmm) cc_final: 0.8471 (tpt) REVERT: A 660 MET cc_start: 0.5240 (mmt) cc_final: 0.4999 (mmp) REVERT: B 405 ASP cc_start: 0.8502 (t0) cc_final: 0.8194 (t70) REVERT: B 535 ARG cc_start: 0.5514 (mmp-170) cc_final: 0.5221 (mmp-170) REVERT: B 704 MET cc_start: 0.8375 (tpp) cc_final: 0.8100 (mmm) REVERT: B 760 TRP cc_start: 0.8355 (m100) cc_final: 0.8076 (m-90) outliers start: 0 outliers final: 0 residues processed: 200 average time/residue: 0.0969 time to fit residues: 28.8477 Evaluate side-chains 130 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 88 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 64 optimal weight: 9.9990 chunk 100 optimal weight: 8.9990 chunk 119 optimal weight: 10.0000 chunk 110 optimal weight: 0.8980 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 896 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.103781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.087044 restraints weight = 33540.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.088585 restraints weight = 22160.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.089610 restraints weight = 16589.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.090141 restraints weight = 13775.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.090666 restraints weight = 12402.173| |-----------------------------------------------------------------------------| r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.3121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12066 Z= 0.158 Angle : 0.646 10.610 16328 Z= 0.331 Chirality : 0.044 0.268 1794 Planarity : 0.005 0.054 2044 Dihedral : 4.672 17.354 1584 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % 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: -0.46 (0.22), residues: 1416 helix: 1.00 (0.17), residues: 836 sheet: -3.29 (0.86), residues: 24 loop : -2.29 (0.25), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 213 TYR 0.023 0.002 TYR A 182 PHE 0.023 0.001 PHE A 712 TRP 0.016 0.001 TRP B 760 HIS 0.006 0.001 HIS A 402 Details of bonding type rmsd covalent geometry : bond 0.00355 (12058) covalent geometry : angle 0.64493 (16312) SS BOND : bond 0.00403 ( 8) SS BOND : angle 1.10357 ( 16) hydrogen bonds : bond 0.04214 ( 652) hydrogen bonds : angle 4.47944 ( 1926) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 0.457 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 338 TYR cc_start: 0.8458 (t80) cc_final: 0.8093 (t80) REVERT: A 405 ASP cc_start: 0.8320 (t0) cc_final: 0.8115 (t70) REVERT: A 500 MET cc_start: 0.8177 (mtp) cc_final: 0.7520 (mtm) REVERT: B 405 ASP cc_start: 0.8552 (t0) cc_final: 0.8251 (t70) REVERT: B 535 ARG cc_start: 0.5614 (mmp-170) cc_final: 0.5247 (mmm160) REVERT: B 760 TRP cc_start: 0.8470 (m100) cc_final: 0.8147 (m-90) outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.0948 time to fit residues: 24.8778 Evaluate side-chains 124 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 47 optimal weight: 10.0000 chunk 78 optimal weight: 0.0000 chunk 139 optimal weight: 0.9990 chunk 92 optimal weight: 0.5980 chunk 126 optimal weight: 8.9990 chunk 132 optimal weight: 5.9990 chunk 137 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 chunk 111 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 overall best weight: 0.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 730 ASN ** B 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 896 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.106565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.090310 restraints weight = 33071.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.091876 restraints weight = 21480.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.092920 restraints weight = 16073.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.093468 restraints weight = 13310.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.094045 restraints weight = 11939.611| |-----------------------------------------------------------------------------| r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.3425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12066 Z= 0.121 Angle : 0.622 10.084 16328 Z= 0.315 Chirality : 0.042 0.239 1794 Planarity : 0.005 0.053 2044 Dihedral : 4.508 16.935 1584 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.22), residues: 1416 helix: 1.14 (0.18), residues: 832 sheet: -3.16 (0.88), residues: 24 loop : -2.16 (0.25), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 125 TYR 0.022 0.001 TYR A 761 PHE 0.023 0.001 PHE A 499 TRP 0.013 0.001 TRP B 760 HIS 0.005 0.001 HIS A 453 Details of bonding type rmsd covalent geometry : bond 0.00254 (12058) covalent geometry : angle 0.62121 (16312) SS BOND : bond 0.00299 ( 8) SS BOND : angle 0.94979 ( 16) hydrogen bonds : bond 0.04008 ( 652) hydrogen bonds : angle 4.38201 ( 1926) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 0.510 Fit side-chains revert: symmetry clash REVERT: A 500 MET cc_start: 0.8116 (mtp) cc_final: 0.7458 (mtm) REVERT: A 508 VAL cc_start: 0.8771 (t) cc_final: 0.8556 (p) REVERT: A 632 MET cc_start: 0.8662 (mmm) cc_final: 0.8455 (tpt) REVERT: A 660 MET cc_start: 0.5139 (mmp) cc_final: 0.4937 (mmp) REVERT: B 405 ASP cc_start: 0.8313 (t0) cc_final: 0.8063 (t70) REVERT: B 508 VAL cc_start: 0.8741 (t) cc_final: 0.8520 (p) outliers start: 0 outliers final: 0 residues processed: 189 average time/residue: 0.0951 time to fit residues: 26.9626 Evaluate side-chains 128 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 95 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 68 optimal weight: 6.9990 chunk 48 optimal weight: 9.9990 chunk 12 optimal weight: 0.6980 chunk 131 optimal weight: 9.9990 chunk 11 optimal weight: 5.9990 chunk 132 optimal weight: 6.9990 chunk 106 optimal weight: 0.0970 chunk 122 optimal weight: 0.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 896 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.105973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.089322 restraints weight = 33120.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.090847 restraints weight = 22115.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.091755 restraints weight = 16658.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.092545 restraints weight = 13984.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.092873 restraints weight = 12377.308| |-----------------------------------------------------------------------------| r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.3554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12066 Z= 0.129 Angle : 0.635 10.458 16328 Z= 0.321 Chirality : 0.042 0.233 1794 Planarity : 0.005 0.052 2044 Dihedral : 4.528 17.479 1584 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % 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: -0.24 (0.22), residues: 1416 helix: 1.08 (0.17), residues: 850 sheet: -3.05 (0.86), residues: 24 loop : -2.10 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 125 TYR 0.023 0.001 TYR A 182 PHE 0.020 0.001 PHE A 499 TRP 0.019 0.001 TRP B 760 HIS 0.014 0.001 HIS B 230 Details of bonding type rmsd covalent geometry : bond 0.00281 (12058) covalent geometry : angle 0.63471 (16312) SS BOND : bond 0.00302 ( 8) SS BOND : angle 0.89545 ( 16) hydrogen bonds : bond 0.04022 ( 652) hydrogen bonds : angle 4.39388 ( 1926) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 500 MET cc_start: 0.8063 (mtp) cc_final: 0.7370 (mtm) REVERT: A 508 VAL cc_start: 0.8761 (t) cc_final: 0.8532 (p) REVERT: A 606 PHE cc_start: 0.6966 (m-80) cc_final: 0.6273 (t80) REVERT: A 660 MET cc_start: 0.5095 (mmp) cc_final: 0.4879 (mmp) REVERT: B 508 VAL cc_start: 0.8739 (t) cc_final: 0.8484 (p) REVERT: B 535 ARG cc_start: 0.5986 (mmp-170) cc_final: 0.5730 (mmm160) REVERT: B 745 GLU cc_start: 0.7569 (pt0) cc_final: 0.7262 (tt0) REVERT: B 760 TRP cc_start: 0.8374 (m100) cc_final: 0.7557 (m-90) outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 0.0842 time to fit residues: 23.8345 Evaluate side-chains 128 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 46 optimal weight: 4.9990 chunk 42 optimal weight: 5.9990 chunk 132 optimal weight: 0.9990 chunk 126 optimal weight: 6.9990 chunk 139 optimal weight: 0.9990 chunk 23 optimal weight: 9.9990 chunk 86 optimal weight: 0.9980 chunk 7 optimal weight: 7.9990 chunk 77 optimal weight: 0.8980 chunk 59 optimal weight: 0.7980 chunk 29 optimal weight: 8.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.106880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.090661 restraints weight = 32768.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.092096 restraints weight = 21334.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.093153 restraints weight = 16119.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.093773 restraints weight = 13273.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.094292 restraints weight = 11781.067| |-----------------------------------------------------------------------------| r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.3745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12066 Z= 0.123 Angle : 0.626 9.694 16328 Z= 0.316 Chirality : 0.042 0.226 1794 Planarity : 0.004 0.052 2044 Dihedral : 4.434 16.715 1584 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % 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: -0.16 (0.22), residues: 1416 helix: 1.06 (0.17), residues: 862 sheet: -3.07 (0.85), residues: 24 loop : -1.97 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 219 TYR 0.018 0.001 TYR A 761 PHE 0.020 0.001 PHE A 499 TRP 0.018 0.001 TRP B 760 HIS 0.004 0.001 HIS B 402 Details of bonding type rmsd covalent geometry : bond 0.00263 (12058) covalent geometry : angle 0.62570 (16312) SS BOND : bond 0.00329 ( 8) SS BOND : angle 0.74515 ( 16) hydrogen bonds : bond 0.03907 ( 652) hydrogen bonds : angle 4.35013 ( 1926) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 191 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 391 MET cc_start: 0.7930 (ppp) cc_final: 0.7655 (tmm) REVERT: A 500 MET cc_start: 0.8059 (mtp) cc_final: 0.7348 (mtm) REVERT: A 508 VAL cc_start: 0.8599 (t) cc_final: 0.8369 (p) REVERT: A 606 PHE cc_start: 0.6930 (m-80) cc_final: 0.6306 (t80) REVERT: A 660 MET cc_start: 0.5192 (mmp) cc_final: 0.4985 (mmp) REVERT: B 508 VAL cc_start: 0.8718 (t) cc_final: 0.8450 (p) REVERT: B 745 GLU cc_start: 0.7437 (pt0) cc_final: 0.7185 (tt0) REVERT: B 760 TRP cc_start: 0.8284 (m100) cc_final: 0.7538 (m-90) outliers start: 0 outliers final: 0 residues processed: 191 average time/residue: 0.0943 time to fit residues: 27.5184 Evaluate side-chains 137 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 122 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 118 optimal weight: 5.9990 chunk 22 optimal weight: 20.0000 chunk 14 optimal weight: 0.2980 chunk 86 optimal weight: 0.8980 chunk 70 optimal weight: 0.0770 chunk 91 optimal weight: 9.9990 chunk 27 optimal weight: 0.9990 overall best weight: 0.5940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 896 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.107798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.091322 restraints weight = 33259.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.092790 restraints weight = 21812.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.093905 restraints weight = 16634.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.094533 restraints weight = 13741.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.094809 restraints weight = 12231.495| |-----------------------------------------------------------------------------| r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.3936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12066 Z= 0.122 Angle : 0.631 9.785 16328 Z= 0.319 Chirality : 0.042 0.221 1794 Planarity : 0.004 0.052 2044 Dihedral : 4.404 17.420 1584 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % 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: -0.12 (0.22), residues: 1416 helix: 1.11 (0.17), residues: 854 sheet: -2.99 (0.88), residues: 24 loop : -1.96 (0.26), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 219 TYR 0.040 0.001 TYR B 761 PHE 0.019 0.001 PHE A 499 TRP 0.014 0.001 TRP B 760 HIS 0.003 0.001 HIS A 402 Details of bonding type rmsd covalent geometry : bond 0.00255 (12058) covalent geometry : angle 0.62973 (16312) SS BOND : bond 0.00344 ( 8) SS BOND : angle 1.32913 ( 16) hydrogen bonds : bond 0.03863 ( 652) hydrogen bonds : angle 4.34008 ( 1926) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 391 MET cc_start: 0.7920 (ppp) cc_final: 0.7667 (tmm) REVERT: A 500 MET cc_start: 0.8024 (mtp) cc_final: 0.7408 (mtm) REVERT: A 508 VAL cc_start: 0.8577 (t) cc_final: 0.8344 (p) REVERT: A 606 PHE cc_start: 0.6998 (m-80) cc_final: 0.6330 (t80) REVERT: A 660 MET cc_start: 0.5234 (mmp) cc_final: 0.5027 (mmp) REVERT: B 508 VAL cc_start: 0.8664 (t) cc_final: 0.8438 (p) REVERT: B 760 TRP cc_start: 0.8288 (m100) cc_final: 0.7511 (m-90) outliers start: 0 outliers final: 0 residues processed: 189 average time/residue: 0.0851 time to fit residues: 24.5532 Evaluate side-chains 138 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 26 optimal weight: 6.9990 chunk 120 optimal weight: 6.9990 chunk 19 optimal weight: 0.9980 chunk 134 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 102 optimal weight: 0.3980 chunk 105 optimal weight: 20.0000 chunk 23 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 92 optimal weight: 0.6980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 431 GLN ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 896 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.107737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.091221 restraints weight = 32949.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.092587 restraints weight = 21834.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.093670 restraints weight = 16792.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.094292 restraints weight = 13903.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.094801 restraints weight = 12398.901| |-----------------------------------------------------------------------------| r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.3995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12066 Z= 0.124 Angle : 0.626 9.378 16328 Z= 0.318 Chirality : 0.042 0.218 1794 Planarity : 0.004 0.051 2044 Dihedral : 4.365 17.019 1584 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 0.08 % Allowed : 0.08 % Favored : 99.84 % 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: -0.08 (0.22), residues: 1416 helix: 1.11 (0.17), residues: 858 sheet: -2.95 (0.87), residues: 24 loop : -1.89 (0.26), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 219 TYR 0.039 0.001 TYR B 761 PHE 0.019 0.001 PHE A 499 TRP 0.018 0.001 TRP B 760 HIS 0.003 0.001 HIS A 402 Details of bonding type rmsd covalent geometry : bond 0.00268 (12058) covalent geometry : angle 0.62524 (16312) SS BOND : bond 0.00323 ( 8) SS BOND : angle 1.22184 ( 16) hydrogen bonds : bond 0.03822 ( 652) hydrogen bonds : angle 4.32693 ( 1926) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1653.67 seconds wall clock time: 29 minutes 36.88 seconds (1776.88 seconds total)