Starting phenix.real_space_refine on Fri Jul 3 02:51:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7b5e_12027/07_2026/7b5e_12027.cif Found real_map, /net/cci-nas-00/data/ceres_data/7b5e_12027/07_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7b5e_12027/07_2026/7b5e_12027.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7b5e_12027/07_2026/7b5e_12027.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7b5e_12027/07_2026/7b5e_12027.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7b5e_12027/07_2026/7b5e_12027.map" model { file = "/net/cci-nas-00/data/ceres_data/7b5e_12027/07_2026/7b5e_12027.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7b5e_12027/07_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-6108/lib/python3.11/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: 5.22, per 1000 atoms: 0.44 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: 1.07 Conformation dependent library (CDL) restraints added in 530.0 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: 0.23 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: 1.58 Time building geometry restraints manager: 1.38 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: 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: 1.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.140 Find NCS groups from input model: 0.060 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:0.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 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/Z covalent geometry : bond 0.00629 / 0.28 (12058) covalent geometry : angle 0.93452 / 0.51 (16312) SS BOND : bond 0.00559 / 0.31 ( 8) SS BOND : angle 1.79796 / 0.98 ( 16) hydrogen bonds : bond 0.09855 / 6.78 ( 652) hydrogen bonds : angle 5.99207 / 4.05 ( 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 : 0.303 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: 0.6345 (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: 0.0995 time to fit residues: 26.0902 Evaluate side-chains 127 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 126 time to evaluate : 0.462 ------------------------------------------------------------------------------- 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... ** 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 = 43)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.087471 restraints weight = 33221.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.089083 restraints weight = 21278.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.090128 restraints weight = 15865.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.090673 restraints weight = 13176.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.090673 restraints weight = 11894.547| |-----------------------------------------------------------------------------| r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 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/Z covalent geometry : bond 0.00264 / 0.13 (12058) covalent geometry : angle 0.63399 / 0.33 (16312) SS BOND : bond 0.00342 / 0.15 ( 8) SS BOND : angle 0.79562 / 0.44 ( 16) hydrogen bonds : bond 0.04365 / 2.89 ( 652) hydrogen bonds : angle 4.74922 / 3.23 ( 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 : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 416 MET cc_start: 0.7530 (tpp) cc_final: 0.7160 (tpp) REVERT: A 500 MET cc_start: 0.7988 (mtp) cc_final: 0.7288 (mtm) REVERT: A 704 MET cc_start: 0.8254 (mmm) cc_final: 0.8003 (mmt) REVERT: B 704 MET cc_start: 0.8294 (tpp) cc_final: 0.7939 (mmt) REVERT: B 760 TRP cc_start: 0.8350 (m100) cc_final: 0.8036 (m-90) REVERT: B 900 GLU cc_start: 0.8374 (pt0) cc_final: 0.7917 (mm-30) outliers start: 1 outliers final: 0 residues processed: 188 average time/residue: 0.0960 time to fit residues: 26.4753 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 : 0.459 ------------------------------------------------------------------------------- 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: 0.0870 chunk 82 optimal weight: 1.9990 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: 3.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.099991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.082779 restraints weight = 34253.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.084237 restraints weight = 22354.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.085186 restraints weight = 16864.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.085644 restraints weight = 14150.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.086002 restraints weight = 12887.122| |-----------------------------------------------------------------------------| r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 12066 Z= 0.223 Angle : 0.707 9.513 16328 Z= 0.370 Chirality : 0.046 0.249 1794 Planarity : 0.006 0.062 2044 Dihedral : 5.251 20.676 1584 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % 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: -1.39 (0.21), residues: 1416 helix: 0.27 (0.17), residues: 824 sheet: -3.94 (0.84), residues: 24 loop : -2.63 (0.24), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 128 TYR 0.024 0.002 TYR A 436 PHE 0.020 0.002 PHE A 585 TRP 0.018 0.002 TRP A 760 HIS 0.009 0.001 HIS A 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00502 / 0.22 (12058) covalent geometry : angle 0.70675 / 0.37 (16312) SS BOND : bond 0.00382 / 0.19 ( 8) SS BOND : angle 1.21365 / 0.67 ( 16) hydrogen bonds : bond 0.04723 / 3.14 ( 652) hydrogen bonds : angle 4.78654 / 3.25 ( 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 165 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 164 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 500 MET cc_start: 0.8196 (mtp) cc_final: 0.7465 (mtm) REVERT: A 588 LYS cc_start: 0.8237 (tttp) cc_final: 0.8001 (ttpt) REVERT: A 632 MET cc_start: 0.8889 (mmm) cc_final: 0.8656 (tpp) REVERT: B 338 TYR cc_start: 0.8751 (t80) cc_final: 0.8288 (t80) REVERT: B 580 LEU cc_start: 0.8374 (tp) cc_final: 0.8133 (tt) REVERT: B 760 TRP cc_start: 0.8567 (m100) cc_final: 0.8202 (m-90) REVERT: B 900 GLU cc_start: 0.8419 (pt0) cc_final: 0.8093 (mm-30) outliers start: 1 outliers final: 0 residues processed: 165 average time/residue: 0.0971 time to fit residues: 23.6175 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 : 0.349 ------------------------------------------------------------------------------- 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: 4.9990 chunk 70 optimal weight: 5.9990 chunk 58 optimal weight: 0.9990 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: 0.9990 chunk 43 optimal weight: 8.9990 chunk 107 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 435 ASN B 896 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.101884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.084942 restraints weight = 33714.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.086427 restraints weight = 22135.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.087395 restraints weight = 16619.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.087869 restraints weight = 13925.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.088307 restraints weight = 12648.493| |-----------------------------------------------------------------------------| r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12066 Z= 0.160 Angle : 0.647 9.932 16328 Z= 0.334 Chirality : 0.043 0.255 1794 Planarity : 0.005 0.059 2044 Dihedral : 4.998 19.766 1584 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 0.08 % Allowed : 4.85 % Favored : 95.07 % 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: -0.94 (0.21), residues: 1416 helix: 0.58 (0.17), residues: 836 sheet: -3.68 (0.81), residues: 24 loop : -2.42 (0.24), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 621 TYR 0.022 0.002 TYR A 182 PHE 0.018 0.001 PHE B 499 TRP 0.022 0.001 TRP A 760 HIS 0.007 0.001 HIS B 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 (12058) covalent geometry : angle 0.64686 / 0.33 (16312) SS BOND : bond 0.00483 / 0.26 ( 8) SS BOND : angle 0.89516 / 0.51 ( 16) hydrogen bonds : bond 0.04407 / 2.91 ( 652) hydrogen bonds : angle 4.59710 / 3.14 ( 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 169 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 168 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 405 ASP cc_start: 0.8448 (t0) cc_final: 0.8150 (t70) REVERT: A 500 MET cc_start: 0.8122 (mtp) cc_final: 0.7887 (mtp) REVERT: A 508 VAL cc_start: 0.8897 (t) cc_final: 0.8629 (p) REVERT: A 760 TRP cc_start: 0.7802 (m-90) cc_final: 0.7545 (m-90) REVERT: B 230 HIS cc_start: 0.6649 (t70) cc_final: 0.6397 (t70) REVERT: B 405 ASP cc_start: 0.8668 (t0) cc_final: 0.8382 (t70) REVERT: B 704 MET cc_start: 0.8331 (tpp) cc_final: 0.7988 (mmt) REVERT: B 760 TRP cc_start: 0.8615 (m100) cc_final: 0.8170 (m-90) outliers start: 1 outliers final: 0 residues processed: 169 average time/residue: 0.0921 time to fit residues: 23.2794 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: 0.0470 chunk 29 optimal weight: 7.9990 chunk 46 optimal weight: 6.9990 chunk 117 optimal weight: 0.7980 chunk 90 optimal weight: 4.9990 chunk 65 optimal weight: 5.9990 chunk 97 optimal weight: 7.9990 chunk 86 optimal weight: 1.9990 chunk 78 optimal weight: 0.7980 chunk 135 optimal weight: 7.9990 chunk 53 optimal weight: 0.9980 overall best weight: 0.9280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 ** 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 375 ASN B 896 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.105158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.088327 restraints weight = 33326.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.089942 restraints weight = 21556.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.090889 restraints weight = 15983.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.091706 restraints weight = 13321.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.092068 restraints weight = 11734.792| |-----------------------------------------------------------------------------| r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12066 Z= 0.124 Angle : 0.613 10.091 16328 Z= 0.312 Chirality : 0.042 0.269 1794 Planarity : 0.005 0.056 2044 Dihedral : 4.680 17.223 1584 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % 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: -0.51 (0.22), residues: 1416 helix: 0.97 (0.17), residues: 838 sheet: -3.54 (0.82), residues: 24 loop : -2.32 (0.25), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 256 TYR 0.017 0.001 TYR B 436 PHE 0.020 0.001 PHE B 499 TRP 0.015 0.001 TRP B 760 HIS 0.004 0.001 HIS A 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (12058) covalent geometry : angle 0.61192 / 0.31 (16312) SS BOND : bond 0.00268 / 0.12 ( 8) SS BOND : angle 1.31748 / 0.72 ( 16) hydrogen bonds : bond 0.04095 / 2.69 ( 652) hydrogen bonds : angle 4.43155 / 3.03 ( 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 183 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 391 MET cc_start: 0.7916 (ppp) cc_final: 0.7524 (tmm) REVERT: A 405 ASP cc_start: 0.8276 (t0) cc_final: 0.7975 (t70) REVERT: A 436 TYR cc_start: 0.7095 (t80) cc_final: 0.6764 (t80) REVERT: A 500 MET cc_start: 0.7985 (mtp) cc_final: 0.7740 (mtp) REVERT: A 508 VAL cc_start: 0.8808 (t) cc_final: 0.8582 (p) REVERT: B 391 MET cc_start: 0.7774 (ppp) cc_final: 0.7416 (ppp) REVERT: B 405 ASP cc_start: 0.8499 (t0) cc_final: 0.8229 (t70) REVERT: B 535 ARG cc_start: 0.5616 (mmp-170) cc_final: 0.5341 (mmp-170) outliers start: 0 outliers final: 0 residues processed: 183 average time/residue: 0.0988 time to fit residues: 26.9834 Evaluate side-chains 135 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.414 ------------------------------------------------------------------------------- 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: 4.9990 chunk 20 optimal weight: 0.5980 chunk 73 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 126 optimal weight: 0.9980 chunk 77 optimal weight: 5.9990 chunk 14 optimal weight: 0.0270 chunk 64 optimal weight: 7.9990 chunk 100 optimal weight: 6.9990 chunk 119 optimal weight: 9.9990 chunk 110 optimal weight: 6.9990 overall best weight: 1.7242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 A 730 ASN ** B 199 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 = 0.3798 r_free = 0.3798 target = 0.104119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.087266 restraints weight = 33685.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.088783 restraints weight = 21994.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.089683 restraints weight = 16492.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.090441 restraints weight = 13805.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.090662 restraints weight = 12234.190| |-----------------------------------------------------------------------------| r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.3123 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= 0.141 Angle : 0.630 10.837 16328 Z= 0.322 Chirality : 0.043 0.266 1794 Planarity : 0.005 0.055 2044 Dihedral : 4.638 17.109 1584 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.22), residues: 1416 helix: 1.03 (0.17), residues: 838 sheet: -3.35 (0.84), residues: 24 loop : -2.25 (0.25), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 213 TYR 0.024 0.001 TYR A 182 PHE 0.021 0.001 PHE B 499 TRP 0.017 0.001 TRP A 760 HIS 0.005 0.001 HIS A 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (12058) covalent geometry : angle 0.63013 / 0.32 (16312) SS BOND : bond 0.00416 / 0.19 ( 8) SS BOND : angle 0.92576 / 0.52 ( 16) hydrogen bonds : bond 0.04150 / 2.74 ( 652) hydrogen bonds : angle 4.43271 / 3.03 ( 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 179 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 TYR cc_start: 0.8480 (t80) cc_final: 0.8142 (t80) REVERT: A 405 ASP cc_start: 0.8269 (t0) cc_final: 0.8010 (t70) REVERT: A 500 MET cc_start: 0.7967 (mtp) cc_final: 0.7225 (mtm) REVERT: A 508 VAL cc_start: 0.8838 (t) cc_final: 0.8588 (p) REVERT: A 632 MET cc_start: 0.8806 (mmm) cc_final: 0.8409 (tpt) REVERT: A 760 TRP cc_start: 0.7770 (m-90) cc_final: 0.7553 (m-90) REVERT: B 405 ASP cc_start: 0.8523 (t0) cc_final: 0.8163 (t70) REVERT: B 535 ARG cc_start: 0.5605 (mmp-170) cc_final: 0.5251 (mmm160) REVERT: B 760 TRP cc_start: 0.8432 (m100) cc_final: 0.8188 (m-90) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.0981 time to fit residues: 26.2238 Evaluate side-chains 131 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.469 ------------------------------------------------------------------------------- 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: 0.8980 chunk 139 optimal weight: 0.9990 chunk 92 optimal weight: 0.3980 chunk 126 optimal weight: 2.9990 chunk 132 optimal weight: 10.0000 chunk 137 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 111 optimal weight: 4.9990 chunk 12 optimal weight: 6.9990 chunk 127 optimal weight: 0.3980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 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 = 0.3825 r_free = 0.3825 target = 0.105802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.089597 restraints weight = 33073.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.091125 restraints weight = 21364.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.092173 restraints weight = 16015.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.092599 restraints weight = 13266.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.093148 restraints weight = 12054.466| |-----------------------------------------------------------------------------| r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.3377 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 : 0.620 9.999 16328 Z= 0.315 Chirality : 0.042 0.239 1794 Planarity : 0.005 0.054 2044 Dihedral : 4.516 17.310 1584 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % 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: -0.30 (0.22), residues: 1416 helix: 1.10 (0.17), residues: 838 sheet: -3.14 (0.89), residues: 24 loop : -2.18 (0.25), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 125 TYR 0.020 0.001 TYR A 761 PHE 0.023 0.001 PHE A 499 TRP 0.022 0.001 TRP A 760 HIS 0.004 0.001 HIS A 453 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (12058) covalent geometry : angle 0.62013 / 0.31 (16312) SS BOND : bond 0.00300 / 0.14 ( 8) SS BOND : angle 0.69744 / 0.39 ( 16) hydrogen bonds : bond 0.04050 / 2.65 ( 652) hydrogen bonds : angle 4.37078 / 3.00 ( 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 188 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 405 ASP cc_start: 0.8101 (t0) cc_final: 0.7901 (t0) REVERT: A 508 VAL cc_start: 0.8793 (t) cc_final: 0.8552 (p) REVERT: A 606 PHE cc_start: 0.6894 (m-80) cc_final: 0.6226 (t80) REVERT: B 508 VAL cc_start: 0.8795 (t) cc_final: 0.8564 (p) REVERT: B 760 TRP cc_start: 0.8304 (m100) cc_final: 0.7875 (m-90) outliers start: 0 outliers final: 0 residues processed: 188 average time/residue: 0.1017 time to fit residues: 28.2913 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 : 0.501 ------------------------------------------------------------------------------- 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: 5.9990 chunk 17 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 68 optimal weight: 6.9990 chunk 48 optimal weight: 10.0000 chunk 12 optimal weight: 4.9990 chunk 131 optimal weight: 10.0000 chunk 11 optimal weight: 4.9990 chunk 132 optimal weight: 5.9990 chunk 106 optimal weight: 0.8980 chunk 122 optimal weight: 0.8980 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 685 GLN ** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 685 GLN B 709 GLN B 896 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.102491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.085636 restraints weight = 33637.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.086944 restraints weight = 22344.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.087943 restraints weight = 17153.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.088490 restraints weight = 14355.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.088872 restraints weight = 12923.827| |-----------------------------------------------------------------------------| r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.3337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12066 Z= 0.192 Angle : 0.697 10.024 16328 Z= 0.358 Chirality : 0.045 0.240 1794 Planarity : 0.005 0.053 2044 Dihedral : 4.780 19.118 1584 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.22), residues: 1416 helix: 0.93 (0.18), residues: 832 sheet: -3.31 (0.86), residues: 24 loop : -2.27 (0.25), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 128 TYR 0.026 0.002 TYR A 182 PHE 0.026 0.002 PHE B 712 TRP 0.070 0.002 TRP A 760 HIS 0.007 0.001 HIS A 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.19 (12058) covalent geometry : angle 0.69608 / 0.36 (16312) SS BOND : bond 0.00534 / 0.28 ( 8) SS BOND : angle 1.05437 / 0.57 ( 16) hydrogen bonds : bond 0.04474 / 2.95 ( 652) hydrogen bonds : angle 4.54592 / 3.11 ( 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 173 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 405 ASP cc_start: 0.8337 (t0) cc_final: 0.8102 (t0) REVERT: A 424 MET cc_start: 0.8936 (tpp) cc_final: 0.8678 (tpp) REVERT: A 500 MET cc_start: 0.8119 (mtp) cc_final: 0.7310 (mtm) REVERT: B 760 TRP cc_start: 0.8493 (m100) cc_final: 0.8053 (m-90) outliers start: 0 outliers final: 0 residues processed: 173 average time/residue: 0.1026 time to fit residues: 26.5660 Evaluate side-chains 123 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.560 ------------------------------------------------------------------------------- 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: 0.5980 chunk 42 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 126 optimal weight: 7.9990 chunk 139 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 86 optimal weight: 3.9990 chunk 7 optimal weight: 0.0970 chunk 77 optimal weight: 0.8980 chunk 59 optimal weight: 7.9990 chunk 29 optimal weight: 10.0000 overall best weight: 1.0580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 431 GLN ** 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 = 0.3830 r_free = 0.3830 target = 0.106160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.089678 restraints weight = 32937.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.091196 restraints weight = 21901.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.092187 restraints weight = 16525.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 17)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.092711 restraints weight = 13748.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.093213 restraints weight = 12411.655| |-----------------------------------------------------------------------------| r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.3611 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= 0.131 Angle : 0.650 9.892 16328 Z= 0.331 Chirality : 0.043 0.239 1794 Planarity : 0.005 0.053 2044 Dihedral : 4.610 17.488 1584 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % 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: -0.34 (0.22), residues: 1416 helix: 0.96 (0.17), residues: 852 sheet: -3.12 (0.87), residues: 24 loop : -2.08 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 125 TYR 0.039 0.001 TYR A 703 PHE 0.025 0.001 PHE A 499 TRP 0.115 0.002 TRP A 760 HIS 0.005 0.001 HIS A 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (12058) covalent geometry : angle 0.64836 / 0.33 (16312) SS BOND : bond 0.00500 / 0.24 ( 8) SS BOND : angle 1.61192 / 0.85 ( 16) hydrogen bonds : bond 0.04117 / 2.69 ( 652) hydrogen bonds : angle 4.43311 / 3.06 ( 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 181 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 391 MET cc_start: 0.7958 (ppp) cc_final: 0.7687 (tmm) REVERT: A 424 MET cc_start: 0.8895 (tpp) cc_final: 0.8629 (tpp) REVERT: A 432 MET cc_start: 0.7625 (ttm) cc_final: 0.7415 (tmm) REVERT: A 500 MET cc_start: 0.8037 (mtp) cc_final: 0.7214 (mtm) REVERT: A 508 VAL cc_start: 0.8715 (t) cc_final: 0.8473 (p) REVERT: A 606 PHE cc_start: 0.7136 (m-80) cc_final: 0.6315 (t80) REVERT: B 508 VAL cc_start: 0.8791 (t) cc_final: 0.8564 (p) REVERT: B 660 MET cc_start: 0.4911 (mmp) cc_final: 0.4658 (mmp) outliers start: 0 outliers final: 0 residues processed: 181 average time/residue: 0.0956 time to fit residues: 26.0197 Evaluate side-chains 131 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.410 ------------------------------------------------------------------------------- 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: 0.9990 chunk 16 optimal weight: 2.9990 chunk 35 optimal weight: 0.0970 chunk 12 optimal weight: 0.0670 chunk 118 optimal weight: 5.9990 chunk 22 optimal weight: 10.0000 chunk 14 optimal weight: 7.9990 chunk 86 optimal weight: 0.9980 chunk 70 optimal weight: 7.9990 chunk 91 optimal weight: 5.9990 chunk 27 optimal weight: 0.8980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 296 ASN ** 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 = 0.3854 r_free = 0.3854 target = 0.107726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.091314 restraints weight = 32876.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.092881 restraints weight = 21685.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.093975 restraints weight = 16303.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.094516 restraints weight = 13486.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.095122 restraints weight = 12103.578| |-----------------------------------------------------------------------------| r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.3864 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= 0.122 Angle : 0.630 9.874 16328 Z= 0.320 Chirality : 0.042 0.227 1794 Planarity : 0.005 0.054 2044 Dihedral : 4.429 16.425 1584 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % 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: -0.19 (0.22), residues: 1416 helix: 1.05 (0.17), residues: 856 sheet: -3.04 (0.88), residues: 24 loop : -1.98 (0.26), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 125 TYR 0.021 0.001 TYR A 182 PHE 0.021 0.001 PHE A 585 TRP 0.014 0.002 TRP B 760 HIS 0.003 0.001 HIS B 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 (12058) covalent geometry : angle 0.62947 / 0.32 (16312) SS BOND : bond 0.00262 / 0.13 ( 8) SS BOND : angle 1.12634 / 0.60 ( 16) hydrogen bonds : bond 0.03974 / 2.59 ( 652) hydrogen bonds : angle 4.35865 / 3.01 ( 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 188 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 391 MET cc_start: 0.7921 (ppp) cc_final: 0.7645 (tmm) REVERT: A 424 MET cc_start: 0.8852 (tpp) cc_final: 0.8582 (tpp) REVERT: A 500 MET cc_start: 0.7867 (mtp) cc_final: 0.7100 (mtm) REVERT: A 508 VAL cc_start: 0.8713 (t) cc_final: 0.8474 (p) REVERT: A 606 PHE cc_start: 0.7064 (m-80) cc_final: 0.6321 (t80) REVERT: B 508 VAL cc_start: 0.8660 (t) cc_final: 0.8415 (p) REVERT: B 660 MET cc_start: 0.4945 (mmp) cc_final: 0.4659 (mmp) outliers start: 0 outliers final: 0 residues processed: 188 average time/residue: 0.0998 time to fit residues: 28.2854 Evaluate side-chains 143 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 0.466 ------------------------------------------------------------------------------- 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: 7.9990 chunk 120 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 134 optimal weight: 0.0980 chunk 51 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 chunk 105 optimal weight: 0.9990 chunk 23 optimal weight: 8.9990 chunk 17 optimal weight: 0.9990 chunk 31 optimal weight: 0.4980 chunk 92 optimal weight: 8.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 898 HIS ** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.108168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.091769 restraints weight = 33162.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.093435 restraints weight = 21932.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.094345 restraints weight = 16350.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.095102 restraints weight = 13711.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.095314 restraints weight = 12199.165| |-----------------------------------------------------------------------------| r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.4044 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= 0.120 Angle : 0.625 9.651 16328 Z= 0.316 Chirality : 0.042 0.227 1794 Planarity : 0.005 0.053 2044 Dihedral : 4.361 16.605 1584 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % 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: 1.07 (0.17), residues: 858 sheet: -2.96 (0.90), residues: 24 loop : -1.88 (0.27), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 125 TYR 0.016 0.001 TYR A 761 PHE 0.022 0.001 PHE B 585 TRP 0.020 0.002 TRP A 760 HIS 0.003 0.000 HIS B 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 (12058) covalent geometry : angle 0.62429 / 0.32 (16312) SS BOND : bond 0.00272 / 0.13 ( 8) SS BOND : angle 0.94536 / 0.51 ( 16) hydrogen bonds : bond 0.03868 / 2.51 ( 652) hydrogen bonds : angle 4.34575 / 3.00 ( 1926) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1693.59 seconds wall clock time: 30 minutes 13.89 seconds (1813.89 seconds total)