Starting phenix.real_space_refine on Thu Jul 2 08:39:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8emr_28262/07_2026/8emr_28262.cif Found real_map, /net/cci-nas-00/data/ceres_data/8emr_28262/07_2026/8emr_28262.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8emr_28262/07_2026/8emr_28262.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8emr_28262/07_2026/8emr_28262.map" model { file = "/net/cci-nas-00/data/ceres_data/8emr_28262/07_2026/8emr_28262.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8emr_28262/07_2026/8emr_28262.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8emr_28262/07_2026/8emr_28262.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8emr_28262/07_2026/8emr_28262.cif" } resolution = 2.92 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= -0.001 sd= 0.030 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 2 9.91 5 S 35 5.16 5 C 4880 2.51 5 N 1329 2.21 5 O 1439 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 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: 7685 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 859, 6930 Classifications: {'peptide': 859} Modifications used: {'COO': 1} Link IDs: {'PCIS': 4, 'PTRANS': 56, 'TRANS': 798} Chain breaks: 2 Chain: "B" Number of atoms: 703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 703 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 6, 'TRANS': 86} Chain: "D" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "B" 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} Time building chain proxies: 1.35, per 1000 atoms: 0.18 Number of scatterers: 7685 At special positions: 0 Unit cell: (70.2, 87.48, 122.04, 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 2 19.99 S 35 16.00 O 1439 8.00 N 1329 7.00 C 4880 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 41 " - pdb=" SG CYS A 47 " distance=2.03 Simple disulfide: pdb=" SG CYS A 633 " - pdb=" SG CYS A 644 " distance=2.03 Simple disulfide: pdb=" SG CYS B 77 " - pdb=" SG CYS B 99 " distance=2.03 Simple disulfide: pdb=" SG CYS B 100 " - pdb=" SG CYS B 116 " 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 Links applied ALPHA1-3 " BMA D 3 " - " MAN D 4 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " NAG-ASN " NAG D 1 " - " ASN A 97 " Time building additional restraints: 0.42 Conformation dependent library (CDL) restraints added in 361.5 milliseconds 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1758 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 11 sheets defined 22.0% alpha, 24.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 34 through 38 removed outlier: 3.530A pdb=" N ASN A 37 " --> pdb=" O ASP A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 52 Processing helix chain 'A' and resid 371 through 384 Processing helix chain 'A' and resid 390 through 395 Processing helix chain 'A' and resid 405 through 419 removed outlier: 3.873A pdb=" N VAL A 409 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 433 Processing helix chain 'A' and resid 448 through 459 removed outlier: 3.662A pdb=" N LYS A 459 " --> pdb=" O ARG A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 487 removed outlier: 3.900A pdb=" N GLU A 481 " --> pdb=" O TYR A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 524 Processing helix chain 'A' and resid 571 through 573 No H-bonds generated for 'chain 'A' and resid 571 through 573' Processing helix chain 'A' and resid 574 through 590 Processing helix chain 'A' and resid 607 through 611 removed outlier: 3.674A pdb=" N ARG A 610 " --> pdb=" O GLY A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 638 removed outlier: 4.580A pdb=" N ILE A 630 " --> pdb=" O LEU A 626 " (cutoff:3.500A) Proline residue: A 631 - end of helix Processing helix chain 'A' and resid 656 through 668 Processing helix chain 'A' and resid 690 through 707 removed outlier: 3.661A pdb=" N ASP A 695 " --> pdb=" O SER A 691 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ILE A 696 " --> pdb=" O GLN A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 707 through 722 Processing helix chain 'A' and resid 728 through 733 removed outlier: 4.434A pdb=" N GLN A 732 " --> pdb=" O PRO A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 742 removed outlier: 3.804A pdb=" N ASN A 741 " --> pdb=" O THR A 738 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE A 742 " --> pdb=" O THR A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 821 through 826 Processing helix chain 'A' and resid 852 through 857 removed outlier: 3.572A pdb=" N THR A 856 " --> pdb=" O PHE A 852 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 51 Processing helix chain 'B' and resid 90 through 92 No H-bonds generated for 'chain 'B' and resid 90 through 92' Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 69 removed outlier: 10.464A pdb=" N LEU A 64 " --> pdb=" O ILE A 79 " (cutoff:3.500A) removed outlier: 11.898A pdb=" N ILE A 79 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N SER A 66 " --> pdb=" O HIS A 77 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N HIS A 77 " --> pdb=" O SER A 66 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLY A 93 " --> pdb=" O ALA A 126 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 60 through 69 removed outlier: 10.464A pdb=" N LEU A 64 " --> pdb=" O ILE A 79 " (cutoff:3.500A) removed outlier: 11.898A pdb=" N ILE A 79 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N SER A 66 " --> pdb=" O HIS A 77 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N HIS A 77 " --> pdb=" O SER A 66 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N HIS A 255 " --> pdb=" O HIS A 305 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 129 through 133 removed outlier: 3.559A pdb=" N SER A 129 " --> pdb=" O THR A 141 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N GLU A 139 " --> pdb=" O SER A 131 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N ARG A 133 " --> pdb=" O SER A 137 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N SER A 137 " --> pdb=" O ARG A 133 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG A 157 " --> pdb=" O THR A 152 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LEU A 158 " --> pdb=" O SER A 169 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N SER A 169 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N LEU A 160 " --> pdb=" O LEU A 167 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 129 through 133 removed outlier: 3.559A pdb=" N SER A 129 " --> pdb=" O THR A 141 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N GLU A 139 " --> pdb=" O SER A 131 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N ARG A 133 " --> pdb=" O SER A 137 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N SER A 137 " --> pdb=" O ARG A 133 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG A 157 " --> pdb=" O THR A 152 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LEU A 158 " --> pdb=" O SER A 169 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N SER A 169 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N LEU A 160 " --> pdb=" O LEU A 167 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 228 through 229 Processing sheet with id=AA6, first strand: chain 'A' and resid 537 through 540 removed outlier: 7.299A pdb=" N HIS A 397 " --> pdb=" O ALA A 675 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 726 through 727 removed outlier: 3.876A pdb=" N LEU A 752 " --> pdb=" O LEU A 748 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 764 through 769 Processing sheet with id=AA9, first strand: chain 'A' and resid 808 through 812 removed outlier: 6.081A pdb=" N ILE A 828 " --> pdb=" O ILE A 889 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ARG A 891 " --> pdb=" O ILE A 828 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N TRP A 888 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N GLY A 932 " --> pdb=" O TRP A 888 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N GLU A 890 " --> pdb=" O LYS A 930 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 839 through 846 Processing sheet with id=AB2, first strand: chain 'B' and resid 74 through 76 277 hydrogen bonds defined for protein. 732 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: 1.19 Time building geometry restraints manager: 0.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1278 1.32 - 1.44: 2277 1.44 - 1.57: 4299 1.57 - 1.69: 0 1.69 - 1.82: 53 Bond restraints: 7907 Sorted by residual: bond pdb=" CA ARG A 818 " pdb=" C ARG A 818 " ideal model delta sigma weight residual 1.523 1.441 0.082 1.30e-02 5.92e+03 4.02e+01 bond pdb=" C ARG A 817 " pdb=" N ARG A 818 " ideal model delta sigma weight residual 1.335 1.405 -0.070 1.31e-02 5.83e+03 2.83e+01 bond pdb=" CA SER A 819 " pdb=" C SER A 819 " ideal model delta sigma weight residual 1.525 1.459 0.066 1.25e-02 6.40e+03 2.82e+01 bond pdb=" C SER A 819 " pdb=" O SER A 819 " ideal model delta sigma weight residual 1.235 1.191 0.044 1.08e-02 8.57e+03 1.64e+01 bond pdb=" C ARG A 818 " pdb=" O ARG A 818 " ideal model delta sigma weight residual 1.237 1.191 0.045 1.17e-02 7.31e+03 1.51e+01 ... (remaining 7902 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.44: 10423 1.44 - 2.89: 252 2.89 - 4.33: 58 4.33 - 5.78: 29 5.78 - 7.22: 6 Bond angle restraints: 10768 Sorted by residual: angle pdb=" N GLY A 612 " pdb=" CA GLY A 612 " pdb=" C GLY A 612 " ideal model delta sigma weight residual 110.20 115.31 -5.11 1.32e+00 5.74e-01 1.50e+01 angle pdb=" N ARG A 817 " pdb=" CA ARG A 817 " pdb=" C ARG A 817 " ideal model delta sigma weight residual 109.41 103.74 5.67 1.52e+00 4.33e-01 1.39e+01 angle pdb=" C ARG A 817 " pdb=" N ARG A 818 " pdb=" CA ARG A 818 " ideal model delta sigma weight residual 120.28 125.13 -4.85 1.34e+00 5.57e-01 1.31e+01 angle pdb=" C MET A 814 " pdb=" N ARG A 815 " pdb=" CA ARG A 815 " ideal model delta sigma weight residual 123.05 118.19 4.86 1.40e+00 5.10e-01 1.20e+01 angle pdb=" CA ARG A 817 " pdb=" C ARG A 817 " pdb=" N ARG A 818 " ideal model delta sigma weight residual 115.42 121.07 -5.65 1.64e+00 3.72e-01 1.19e+01 ... (remaining 10763 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 4200 17.75 - 35.50: 371 35.50 - 53.25: 54 53.25 - 71.00: 9 71.00 - 88.75: 4 Dihedral angle restraints: 4638 sinusoidal: 1892 harmonic: 2746 Sorted by residual: dihedral pdb=" CB CYS B 100 " pdb=" SG CYS B 100 " pdb=" SG CYS B 116 " pdb=" CB CYS B 116 " ideal model delta sinusoidal sigma weight residual -86.00 -156.29 70.29 1 1.00e+01 1.00e-02 6.36e+01 dihedral pdb=" CB CYS B 77 " pdb=" SG CYS B 77 " pdb=" SG CYS B 99 " pdb=" CB CYS B 99 " ideal model delta sinusoidal sigma weight residual 93.00 60.24 32.76 1 1.00e+01 1.00e-02 1.53e+01 dihedral pdb=" C MET A 814 " pdb=" N MET A 814 " pdb=" CA MET A 814 " pdb=" CB MET A 814 " ideal model delta harmonic sigma weight residual -122.60 -132.11 9.51 0 2.50e+00 1.60e-01 1.45e+01 ... (remaining 4635 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 1066 0.090 - 0.181: 75 0.181 - 0.271: 0 0.271 - 0.362: 1 0.362 - 0.452: 1 Chirality restraints: 1143 Sorted by residual: chirality pdb=" CA MET A 814 " pdb=" N MET A 814 " pdb=" C MET A 814 " pdb=" CB MET A 814 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.11e+00 chirality pdb=" C5 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C6 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" CA TRP A 503 " pdb=" N TRP A 503 " pdb=" C TRP A 503 " pdb=" CB TRP A 503 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.80e-01 ... (remaining 1140 not shown) Planarity restraints: 1413 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 489 " 0.020 2.00e-02 2.50e+03 1.70e-02 5.75e+00 pdb=" CG TYR A 489 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 TYR A 489 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR A 489 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR A 489 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 489 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR A 489 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR A 489 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE B 87 " 0.030 5.00e-02 4.00e+02 4.62e-02 3.41e+00 pdb=" N PRO B 88 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO B 88 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 88 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 306 " 0.027 5.00e-02 4.00e+02 4.11e-02 2.70e+00 pdb=" N PRO A 307 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 307 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 307 " 0.023 5.00e-02 4.00e+02 ... (remaining 1410 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1713 2.79 - 3.32: 6617 3.32 - 3.84: 12673 3.84 - 4.37: 15067 4.37 - 4.90: 26466 Nonbonded interactions: 62536 Sorted by model distance: nonbonded pdb=" OH TYR A 257 " pdb=" O PHE A 740 " model vdw 2.263 3.040 nonbonded pdb=" O ARG B 91 " pdb="CA CA B 601 " model vdw 2.275 2.510 nonbonded pdb=" OD2 ASP A 848 " pdb=" OG1 THR A 851 " model vdw 2.284 3.040 nonbonded pdb=" O VAL B 96 " pdb="CA CA B 601 " model vdw 2.303 2.510 nonbonded pdb=" OD2 ASP B 104 " pdb="CA CA B 601 " model vdw 2.316 2.510 ... (remaining 62531 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: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.210 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: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.840 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 7915 Z= 0.211 Angle : 0.628 7.221 10788 Z= 0.332 Chirality : 0.046 0.452 1143 Planarity : 0.005 0.046 1412 Dihedral : 13.168 88.749 2868 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 0.12 % Allowed : 0.24 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: -0.58 (0.27), residues: 944 helix: 1.26 (0.42), residues: 153 sheet: 0.46 (0.36), residues: 241 loop : -1.32 (0.25), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 817 TYR 0.042 0.001 TYR A 489 PHE 0.014 0.001 PHE A 673 TRP 0.017 0.001 TRP A 503 HIS 0.004 0.001 HIS A 480 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.21 ( 7907) covalent geometry : angle 0.62433 / 0.33 (10768) SS BOND : bond 0.00176 / 0.08 ( 4) SS BOND : angle 0.54094 / 0.31 ( 8) hydrogen bonds : bond 0.16260 / 10.61 ( 253) hydrogen bonds : angle 6.21787 / 4.08 ( 732) link_ALPHA1-3 : bond 0.00509 / 0.27 ( 1) link_ALPHA1-3 : angle 1.62715 / 0.85 ( 3) link_BETA1-4 : bond 0.00959 / 0.50 ( 2) link_BETA1-4 : angle 1.44881 / 0.72 ( 6) link_NAG-ASN : bond 0.00045 / 0.02 ( 1) link_NAG-ASN : angle 3.42205 / 1.87 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 131 time to evaluate : 0.288 Fit side-chains REVERT: A 416 PHE cc_start: 0.7537 (m-80) cc_final: 0.7329 (m-10) REVERT: A 524 MET cc_start: 0.8008 (tpp) cc_final: 0.7781 (tpp) REVERT: A 543 MET cc_start: 0.8380 (mtp) cc_final: 0.8090 (mtp) REVERT: A 699 ASP cc_start: 0.8455 (t0) cc_final: 0.8222 (t0) REVERT: A 882 HIS cc_start: 0.7791 (m-70) cc_final: 0.6588 (p90) REVERT: A 908 LYS cc_start: 0.8374 (mmtm) cc_final: 0.8086 (mmmt) REVERT: A 942 HIS cc_start: 0.6925 (m-70) cc_final: 0.6307 (t-90) REVERT: B 63 ASP cc_start: 0.6869 (p0) cc_final: 0.6656 (p0) outliers start: 1 outliers final: 0 residues processed: 132 average time/residue: 0.4621 time to fit residues: 64.7262 Evaluate side-chains 85 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.2980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 7.9990 chunk 74 optimal weight: 0.4980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 328 ASN A 676 HIS A 741 ASN A 841 GLN A 853 ASN B 76 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.129283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.114367 restraints weight = 12871.222| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 2.19 r_work: 0.3355 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7915 Z= 0.132 Angle : 0.550 6.655 10788 Z= 0.276 Chirality : 0.043 0.146 1143 Planarity : 0.005 0.044 1412 Dihedral : 4.498 45.865 1052 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.53 % Allowed : 9.04 % Favored : 88.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: -0.38 (0.28), residues: 944 helix: 1.85 (0.44), residues: 154 sheet: 0.39 (0.35), residues: 250 loop : -1.25 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 864 TYR 0.011 0.001 TYR A 257 PHE 0.010 0.001 PHE A 101 TRP 0.012 0.001 TRP A 503 HIS 0.005 0.001 HIS A 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.13 ( 7907) covalent geometry : angle 0.54608 / 0.28 (10768) SS BOND : bond 0.00237 / 0.11 ( 4) SS BOND : angle 0.66507 / 0.37 ( 8) hydrogen bonds : bond 0.03805 / 2.51 ( 253) hydrogen bonds : angle 4.92668 / 3.30 ( 732) link_ALPHA1-3 : bond 0.00579 / 0.30 ( 1) link_ALPHA1-3 : angle 1.39276 / 0.76 ( 3) link_BETA1-4 : bond 0.00667 / 0.34 ( 2) link_BETA1-4 : angle 1.49977 / 0.78 ( 6) link_NAG-ASN : bond 0.00302 / 0.16 ( 1) link_NAG-ASN : angle 3.11625 / 1.63 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 83 time to evaluate : 0.225 Fit side-chains REVERT: A 107 GLU cc_start: 0.8261 (mm-30) cc_final: 0.7868 (mp0) REVERT: A 416 PHE cc_start: 0.7553 (m-80) cc_final: 0.7305 (m-10) REVERT: A 489 TYR cc_start: 0.7779 (OUTLIER) cc_final: 0.6566 (m-80) REVERT: A 561 GLN cc_start: 0.7923 (OUTLIER) cc_final: 0.7602 (pm20) REVERT: A 699 ASP cc_start: 0.8497 (t0) cc_final: 0.8265 (t0) REVERT: A 908 LYS cc_start: 0.8419 (mmtm) cc_final: 0.8144 (mmmt) REVERT: A 942 HIS cc_start: 0.7439 (m-70) cc_final: 0.6482 (t-90) outliers start: 21 outliers final: 6 residues processed: 97 average time/residue: 0.4342 time to fit residues: 44.7964 Evaluate side-chains 82 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 561 GLN Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain A residue 918 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 87 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 15 optimal weight: 0.0370 chunk 54 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 67 optimal weight: 0.0070 chunk 2 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 42 optimal weight: 0.0670 overall best weight: 0.3614 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 676 HIS A 741 ASN A 855 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.130168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.115546 restraints weight = 12718.014| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 2.14 r_work: 0.3373 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3271 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.1563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 7915 Z= 0.093 Angle : 0.503 6.503 10788 Z= 0.249 Chirality : 0.042 0.152 1143 Planarity : 0.004 0.039 1412 Dihedral : 4.291 42.118 1052 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.77 % Allowed : 10.12 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: -0.23 (0.28), residues: 944 helix: 2.14 (0.45), residues: 154 sheet: 0.44 (0.35), residues: 250 loop : -1.18 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 588 TYR 0.010 0.001 TYR A 257 PHE 0.011 0.001 PHE A 101 TRP 0.012 0.001 TRP A 503 HIS 0.002 0.001 HIS A 572 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.09 ( 7907) covalent geometry : angle 0.49919 / 0.25 (10768) SS BOND : bond 0.00182 / 0.09 ( 4) SS BOND : angle 0.50460 / 0.28 ( 8) hydrogen bonds : bond 0.03147 / 2.09 ( 253) hydrogen bonds : angle 4.59901 / 3.09 ( 732) link_ALPHA1-3 : bond 0.00665 / 0.35 ( 1) link_ALPHA1-3 : angle 1.53066 / 0.82 ( 3) link_BETA1-4 : bond 0.00659 / 0.33 ( 2) link_BETA1-4 : angle 1.44766 / 0.76 ( 6) link_NAG-ASN : bond 0.00298 / 0.16 ( 1) link_NAG-ASN : angle 2.76958 / 1.44 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 86 time to evaluate : 0.204 Fit side-chains REVERT: A 107 GLU cc_start: 0.8283 (mm-30) cc_final: 0.7889 (mt-10) REVERT: A 416 PHE cc_start: 0.7553 (m-80) cc_final: 0.7326 (m-10) REVERT: A 489 TYR cc_start: 0.7800 (OUTLIER) cc_final: 0.6797 (m-80) REVERT: A 561 GLN cc_start: 0.7985 (OUTLIER) cc_final: 0.7618 (pm20) REVERT: A 699 ASP cc_start: 0.8442 (t0) cc_final: 0.8212 (t0) REVERT: A 908 LYS cc_start: 0.8392 (mmtm) cc_final: 0.8149 (mmmt) REVERT: A 942 HIS cc_start: 0.7381 (m-70) cc_final: 0.6483 (t-90) REVERT: B 56 CYS cc_start: 0.8235 (t) cc_final: 0.7898 (t) outliers start: 23 outliers final: 5 residues processed: 99 average time/residue: 0.5058 time to fit residues: 53.4482 Evaluate side-chains 84 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 77 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 561 GLN Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain A residue 918 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 93 optimal weight: 0.0010 chunk 57 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 12 optimal weight: 0.0980 chunk 42 optimal weight: 9.9990 chunk 21 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 chunk 70 optimal weight: 0.6980 overall best weight: 0.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 676 HIS A 741 ASN A 855 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.128914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.114175 restraints weight = 12911.496| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 2.16 r_work: 0.3354 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3252 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 7915 Z= 0.103 Angle : 0.507 6.471 10788 Z= 0.250 Chirality : 0.042 0.150 1143 Planarity : 0.004 0.041 1412 Dihedral : 4.267 39.735 1052 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.29 % Allowed : 10.96 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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 (0.28), residues: 944 helix: 2.18 (0.45), residues: 154 sheet: 0.50 (0.35), residues: 247 loop : -1.17 (0.26), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 588 TYR 0.009 0.001 TYR A 257 PHE 0.011 0.001 PHE A 101 TRP 0.012 0.001 TRP A 503 HIS 0.003 0.001 HIS A 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.10 ( 7907) covalent geometry : angle 0.50333 / 0.25 (10768) SS BOND : bond 0.00200 / 0.10 ( 4) SS BOND : angle 0.55046 / 0.30 ( 8) hydrogen bonds : bond 0.03087 / 2.05 ( 253) hydrogen bonds : angle 4.48514 / 3.01 ( 732) link_ALPHA1-3 : bond 0.00674 / 0.35 ( 1) link_ALPHA1-3 : angle 1.47213 / 0.78 ( 3) link_BETA1-4 : bond 0.00629 / 0.32 ( 2) link_BETA1-4 : angle 1.42660 / 0.75 ( 6) link_NAG-ASN : bond 0.00178 / 0.09 ( 1) link_NAG-ASN : angle 2.77272 / 1.45 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 85 time to evaluate : 0.288 Fit side-chains REVERT: A 107 GLU cc_start: 0.8277 (mm-30) cc_final: 0.7890 (mt-10) REVERT: A 416 PHE cc_start: 0.7611 (m-80) cc_final: 0.7401 (m-10) REVERT: A 489 TYR cc_start: 0.7815 (OUTLIER) cc_final: 0.6781 (m-80) REVERT: A 561 GLN cc_start: 0.8008 (OUTLIER) cc_final: 0.7634 (pm20) REVERT: A 699 ASP cc_start: 0.8453 (t0) cc_final: 0.8226 (t0) REVERT: A 908 LYS cc_start: 0.8351 (mmtm) cc_final: 0.8133 (mmmt) REVERT: B 54 ASP cc_start: 0.7877 (m-30) cc_final: 0.7503 (m-30) REVERT: B 56 CYS cc_start: 0.8101 (t) cc_final: 0.7735 (t) outliers start: 19 outliers final: 7 residues processed: 97 average time/residue: 0.5014 time to fit residues: 51.9280 Evaluate side-chains 88 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 79 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 561 GLN Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 857 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 81 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 91 optimal weight: 0.8980 chunk 38 optimal weight: 0.0050 chunk 14 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 11 optimal weight: 0.1980 chunk 78 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 2 optimal weight: 0.0970 overall best weight: 0.3592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 676 HIS A 741 ASN A 855 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.129537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.114763 restraints weight = 12807.118| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 2.14 r_work: 0.3362 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 7915 Z= 0.088 Angle : 0.489 6.405 10788 Z= 0.241 Chirality : 0.042 0.152 1143 Planarity : 0.004 0.040 1412 Dihedral : 4.154 36.919 1052 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 2.41 % Allowed : 11.33 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: -0.15 (0.28), residues: 944 helix: 2.24 (0.45), residues: 154 sheet: 0.56 (0.35), residues: 240 loop : -1.15 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 588 TYR 0.008 0.001 TYR A 257 PHE 0.011 0.001 PHE A 101 TRP 0.012 0.001 TRP A 503 HIS 0.003 0.001 HIS A 572 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.09 ( 7907) covalent geometry : angle 0.48527 / 0.24 (10768) SS BOND : bond 0.00200 / 0.10 ( 4) SS BOND : angle 0.53488 / 0.29 ( 8) hydrogen bonds : bond 0.02870 / 1.91 ( 253) hydrogen bonds : angle 4.35337 / 2.93 ( 732) link_ALPHA1-3 : bond 0.00736 / 0.39 ( 1) link_ALPHA1-3 : angle 1.51789 / 0.80 ( 3) link_BETA1-4 : bond 0.00552 / 0.28 ( 2) link_BETA1-4 : angle 1.35896 / 0.71 ( 6) link_NAG-ASN : bond 0.00199 / 0.10 ( 1) link_NAG-ASN : angle 2.62336 / 1.38 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 85 time to evaluate : 0.311 Fit side-chains REVERT: A 107 GLU cc_start: 0.8320 (mm-30) cc_final: 0.7967 (mt-10) REVERT: A 489 TYR cc_start: 0.7792 (OUTLIER) cc_final: 0.6886 (m-80) REVERT: A 561 GLN cc_start: 0.7971 (OUTLIER) cc_final: 0.7631 (pm20) REVERT: A 699 ASP cc_start: 0.8441 (t0) cc_final: 0.8216 (t0) REVERT: A 908 LYS cc_start: 0.8334 (mmtm) cc_final: 0.8129 (mmmt) REVERT: A 942 HIS cc_start: 0.7453 (m90) cc_final: 0.6485 (t-90) REVERT: B 54 ASP cc_start: 0.8021 (m-30) cc_final: 0.7692 (m-30) REVERT: B 56 CYS cc_start: 0.8082 (t) cc_final: 0.7820 (t) outliers start: 20 outliers final: 6 residues processed: 97 average time/residue: 0.5181 time to fit residues: 53.5718 Evaluate side-chains 90 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 82 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 561 GLN Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain A residue 715 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 82 optimal weight: 0.0000 chunk 11 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 67 optimal weight: 0.0020 chunk 83 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 34 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 676 HIS A 741 ASN A 855 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.128789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.114066 restraints weight = 12850.043| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.16 r_work: 0.3353 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 7915 Z= 0.102 Angle : 0.509 7.579 10788 Z= 0.249 Chirality : 0.042 0.149 1143 Planarity : 0.004 0.039 1412 Dihedral : 4.182 35.991 1052 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 2.05 % Allowed : 12.65 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: -0.14 (0.28), residues: 944 helix: 2.24 (0.45), residues: 154 sheet: 0.49 (0.35), residues: 245 loop : -1.10 (0.26), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 588 TYR 0.008 0.001 TYR A 498 PHE 0.011 0.001 PHE A 101 TRP 0.012 0.001 TRP A 503 HIS 0.003 0.001 HIS A 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.10 ( 7907) covalent geometry : angle 0.50540 / 0.25 (10768) SS BOND : bond 0.00225 / 0.11 ( 4) SS BOND : angle 0.55219 / 0.30 ( 8) hydrogen bonds : bond 0.02972 / 1.98 ( 253) hydrogen bonds : angle 4.34211 / 2.92 ( 732) link_ALPHA1-3 : bond 0.00693 / 0.36 ( 1) link_ALPHA1-3 : angle 1.47683 / 0.78 ( 3) link_BETA1-4 : bond 0.00593 / 0.30 ( 2) link_BETA1-4 : angle 1.36682 / 0.71 ( 6) link_NAG-ASN : bond 0.00170 / 0.09 ( 1) link_NAG-ASN : angle 2.68143 / 1.41 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 87 time to evaluate : 0.299 Fit side-chains REVERT: A 107 GLU cc_start: 0.8319 (mm-30) cc_final: 0.7966 (mt-10) REVERT: A 228 GLU cc_start: 0.6949 (mp0) cc_final: 0.6577 (mp0) REVERT: A 377 ARG cc_start: 0.8971 (OUTLIER) cc_final: 0.7689 (mpp80) REVERT: A 489 TYR cc_start: 0.7830 (OUTLIER) cc_final: 0.7049 (m-80) REVERT: A 561 GLN cc_start: 0.8002 (OUTLIER) cc_final: 0.7632 (pm20) REVERT: A 699 ASP cc_start: 0.8493 (t0) cc_final: 0.8270 (t0) REVERT: B 54 ASP cc_start: 0.8057 (OUTLIER) cc_final: 0.7745 (m-30) REVERT: B 56 CYS cc_start: 0.8146 (t) cc_final: 0.7918 (t) outliers start: 17 outliers final: 7 residues processed: 98 average time/residue: 0.4958 time to fit residues: 51.8007 Evaluate side-chains 93 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 82 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 377 ARG Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 561 GLN Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 918 GLN Chi-restraints excluded: chain B residue 54 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 25 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 32 optimal weight: 0.1980 chunk 26 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 40 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 676 HIS A 678 HIS A 741 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.126396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.111768 restraints weight = 12935.686| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 2.12 r_work: 0.3314 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7915 Z= 0.142 Angle : 0.547 6.688 10788 Z= 0.270 Chirality : 0.044 0.153 1143 Planarity : 0.004 0.040 1412 Dihedral : 4.455 38.894 1052 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 2.77 % Allowed : 12.41 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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 (0.28), residues: 944 helix: 2.13 (0.44), residues: 154 sheet: 0.32 (0.34), residues: 245 loop : -1.15 (0.26), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 478 TYR 0.009 0.001 TYR A 509 PHE 0.012 0.001 PHE B 48 TRP 0.012 0.001 TRP A 503 HIS 0.004 0.001 HIS A 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.14 ( 7907) covalent geometry : angle 0.54353 / 0.27 (10768) SS BOND : bond 0.00253 / 0.12 ( 4) SS BOND : angle 0.60818 / 0.33 ( 8) hydrogen bonds : bond 0.03397 / 2.24 ( 253) hydrogen bonds : angle 4.47466 / 3.03 ( 732) link_ALPHA1-3 : bond 0.00689 / 0.36 ( 1) link_ALPHA1-3 : angle 1.43117 / 0.75 ( 3) link_BETA1-4 : bond 0.00673 / 0.34 ( 2) link_BETA1-4 : angle 1.46938 / 0.77 ( 6) link_NAG-ASN : bond 0.00116 / 0.06 ( 1) link_NAG-ASN : angle 2.95794 / 1.57 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 86 time to evaluate : 0.280 Fit side-chains REVERT: A 107 GLU cc_start: 0.8337 (mm-30) cc_final: 0.7931 (mt-10) REVERT: A 228 GLU cc_start: 0.6952 (mp0) cc_final: 0.6677 (mp0) REVERT: A 377 ARG cc_start: 0.8965 (OUTLIER) cc_final: 0.7673 (mpp80) REVERT: A 478 ARG cc_start: 0.5596 (OUTLIER) cc_final: 0.5359 (ttp80) REVERT: A 561 GLN cc_start: 0.8149 (OUTLIER) cc_final: 0.7769 (pm20) REVERT: A 699 ASP cc_start: 0.8490 (t0) cc_final: 0.8246 (t0) REVERT: B 54 ASP cc_start: 0.8074 (OUTLIER) cc_final: 0.7769 (m-30) REVERT: B 56 CYS cc_start: 0.7983 (t) cc_final: 0.7719 (t) outliers start: 23 outliers final: 9 residues processed: 101 average time/residue: 0.4844 time to fit residues: 52.2347 Evaluate side-chains 93 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 80 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 377 ARG Chi-restraints excluded: chain A residue 478 ARG Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 561 GLN Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 918 GLN Chi-restraints excluded: chain B residue 54 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 7 optimal weight: 0.6980 chunk 59 optimal weight: 10.0000 chunk 55 optimal weight: 0.0070 chunk 1 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 68 optimal weight: 0.0570 chunk 56 optimal weight: 4.9990 chunk 36 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 676 HIS A 678 HIS A 692 GLN A 741 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.128046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.113392 restraints weight = 12817.863| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 2.12 r_work: 0.3338 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 7915 Z= 0.099 Angle : 0.519 6.665 10788 Z= 0.255 Chirality : 0.042 0.152 1143 Planarity : 0.004 0.040 1412 Dihedral : 4.322 36.898 1052 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 1.81 % Allowed : 13.73 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: -0.18 (0.28), residues: 944 helix: 2.18 (0.44), residues: 155 sheet: 0.47 (0.35), residues: 239 loop : -1.12 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 309 TYR 0.009 0.001 TYR A 705 PHE 0.011 0.001 PHE A 101 TRP 0.011 0.001 TRP A 503 HIS 0.005 0.001 HIS A 678 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.10 ( 7907) covalent geometry : angle 0.51592 / 0.25 (10768) SS BOND : bond 0.00224 / 0.11 ( 4) SS BOND : angle 0.53963 / 0.30 ( 8) hydrogen bonds : bond 0.02982 / 1.98 ( 253) hydrogen bonds : angle 4.33486 / 2.92 ( 732) link_ALPHA1-3 : bond 0.00688 / 0.36 ( 1) link_ALPHA1-3 : angle 1.48650 / 0.78 ( 3) link_BETA1-4 : bond 0.00584 / 0.30 ( 2) link_BETA1-4 : angle 1.38961 / 0.72 ( 6) link_NAG-ASN : bond 0.00147 / 0.08 ( 1) link_NAG-ASN : angle 2.72887 / 1.44 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 84 time to evaluate : 0.287 Fit side-chains REVERT: A 107 GLU cc_start: 0.8324 (mm-30) cc_final: 0.7937 (mt-10) REVERT: A 228 GLU cc_start: 0.6833 (mp0) cc_final: 0.6566 (mp0) REVERT: A 561 GLN cc_start: 0.7947 (OUTLIER) cc_final: 0.7573 (pm20) REVERT: A 699 ASP cc_start: 0.8479 (t0) cc_final: 0.8248 (t0) REVERT: B 54 ASP cc_start: 0.8057 (OUTLIER) cc_final: 0.7765 (m-30) outliers start: 15 outliers final: 6 residues processed: 94 average time/residue: 0.4673 time to fit residues: 47.0664 Evaluate side-chains 91 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 83 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 561 GLN Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain B residue 54 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 69 optimal weight: 0.9980 chunk 20 optimal weight: 0.0470 chunk 27 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 59 optimal weight: 10.0000 chunk 83 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 overall best weight: 0.7880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 676 HIS A 678 HIS A 692 GLN A 741 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.127721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.112647 restraints weight = 12870.079| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.35 r_work: 0.3317 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7915 Z= 0.130 Angle : 0.545 7.041 10788 Z= 0.269 Chirality : 0.043 0.155 1143 Planarity : 0.004 0.039 1412 Dihedral : 4.456 38.042 1052 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 1.69 % Allowed : 14.22 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: -0.26 (0.28), residues: 944 helix: 2.06 (0.44), residues: 155 sheet: 0.33 (0.35), residues: 244 loop : -1.12 (0.26), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 478 TYR 0.013 0.001 TYR A 705 PHE 0.012 0.001 PHE B 48 TRP 0.011 0.001 TRP A 503 HIS 0.005 0.001 HIS A 678 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 ( 7907) covalent geometry : angle 0.54175 / 0.27 (10768) SS BOND : bond 0.00260 / 0.12 ( 4) SS BOND : angle 0.60508 / 0.33 ( 8) hydrogen bonds : bond 0.03286 / 2.17 ( 253) hydrogen bonds : angle 4.41332 / 2.99 ( 732) link_ALPHA1-3 : bond 0.00634 / 0.33 ( 1) link_ALPHA1-3 : angle 1.43899 / 0.75 ( 3) link_BETA1-4 : bond 0.00591 / 0.30 ( 2) link_BETA1-4 : angle 1.43457 / 0.75 ( 6) link_NAG-ASN : bond 0.00138 / 0.07 ( 1) link_NAG-ASN : angle 2.86994 / 1.52 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 84 time to evaluate : 0.231 Fit side-chains REVERT: A 72 ASP cc_start: 0.7626 (p0) cc_final: 0.7409 (p0) REVERT: A 107 GLU cc_start: 0.8372 (mm-30) cc_final: 0.7993 (mt-10) REVERT: A 228 GLU cc_start: 0.7050 (mp0) cc_final: 0.6773 (mp0) REVERT: A 377 ARG cc_start: 0.9076 (OUTLIER) cc_final: 0.7879 (mpp80) REVERT: A 561 GLN cc_start: 0.8184 (OUTLIER) cc_final: 0.7886 (pm20) REVERT: A 699 ASP cc_start: 0.8547 (t0) cc_final: 0.8313 (t0) REVERT: A 918 GLN cc_start: 0.8494 (OUTLIER) cc_final: 0.8155 (mp10) REVERT: B 54 ASP cc_start: 0.8143 (m-30) cc_final: 0.7845 (m-30) outliers start: 14 outliers final: 8 residues processed: 91 average time/residue: 0.5000 time to fit residues: 48.2785 Evaluate side-chains 93 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 82 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 377 ARG Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 561 GLN Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain A residue 918 GLN Chi-restraints excluded: chain B residue 67 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 52 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 72 optimal weight: 0.2980 chunk 45 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 31 optimal weight: 6.9990 chunk 13 optimal weight: 3.9990 chunk 92 optimal weight: 5.9990 chunk 11 optimal weight: 0.2980 chunk 77 optimal weight: 0.7980 chunk 28 optimal weight: 0.0020 overall best weight: 0.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 676 HIS A 678 HIS A 692 GLN A 741 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.127932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.113002 restraints weight = 12825.544| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 2.28 r_work: 0.3339 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 7915 Z= 0.100 Angle : 0.524 7.414 10788 Z= 0.257 Chirality : 0.042 0.152 1143 Planarity : 0.004 0.039 1412 Dihedral : 4.301 35.656 1052 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 1.57 % Allowed : 14.34 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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 (0.28), residues: 944 helix: 2.12 (0.44), residues: 155 sheet: 0.49 (0.35), residues: 239 loop : -1.09 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 445 TYR 0.006 0.001 TYR A 498 PHE 0.012 0.001 PHE A 101 TRP 0.010 0.001 TRP A 503 HIS 0.006 0.001 HIS A 678 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.10 ( 7907) covalent geometry : angle 0.52028 / 0.26 (10768) SS BOND : bond 0.00218 / 0.10 ( 4) SS BOND : angle 0.53525 / 0.30 ( 8) hydrogen bonds : bond 0.02951 / 1.95 ( 253) hydrogen bonds : angle 4.29526 / 2.90 ( 732) link_ALPHA1-3 : bond 0.00679 / 0.36 ( 1) link_ALPHA1-3 : angle 1.50275 / 0.79 ( 3) link_BETA1-4 : bond 0.00672 / 0.34 ( 2) link_BETA1-4 : angle 1.39429 / 0.72 ( 6) link_NAG-ASN : bond 0.00124 / 0.07 ( 1) link_NAG-ASN : angle 2.67018 / 1.41 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 81 time to evaluate : 0.262 Fit side-chains REVERT: A 72 ASP cc_start: 0.7589 (p0) cc_final: 0.7389 (p0) REVERT: A 107 GLU cc_start: 0.8306 (mm-30) cc_final: 0.7930 (mt-10) REVERT: A 228 GLU cc_start: 0.6958 (mp0) cc_final: 0.6668 (mp0) REVERT: A 377 ARG cc_start: 0.9003 (OUTLIER) cc_final: 0.7708 (mpp80) REVERT: A 478 ARG cc_start: 0.5675 (OUTLIER) cc_final: 0.5318 (ttp80) REVERT: A 561 GLN cc_start: 0.8036 (OUTLIER) cc_final: 0.7806 (pm20) REVERT: A 699 ASP cc_start: 0.8482 (t0) cc_final: 0.8250 (t0) REVERT: A 721 GLU cc_start: 0.8734 (mm-30) cc_final: 0.8076 (mt-10) REVERT: B 54 ASP cc_start: 0.8037 (m-30) cc_final: 0.7768 (m-30) outliers start: 13 outliers final: 7 residues processed: 89 average time/residue: 0.4698 time to fit residues: 44.4532 Evaluate side-chains 91 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 81 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 377 ARG Chi-restraints excluded: chain A residue 478 ARG Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 561 GLN Chi-restraints excluded: chain A residue 624 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 0 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 chunk 79 optimal weight: 0.0000 chunk 54 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 83 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 8 optimal weight: 0.2980 chunk 28 optimal weight: 0.0010 chunk 18 optimal weight: 0.8980 overall best weight: 0.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 676 HIS A 678 HIS A 692 GLN A 741 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.128528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.113624 restraints weight = 12892.981| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 2.28 r_work: 0.3354 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 7915 Z= 0.095 Angle : 0.517 7.429 10788 Z= 0.252 Chirality : 0.042 0.154 1143 Planarity : 0.004 0.039 1412 Dihedral : 4.189 33.052 1052 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 1.45 % Allowed : 14.70 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: -0.10 (0.28), residues: 944 helix: 2.05 (0.44), residues: 157 sheet: 0.48 (0.35), residues: 242 loop : -1.00 (0.27), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 445 TYR 0.007 0.001 TYR A 257 PHE 0.012 0.001 PHE A 101 TRP 0.009 0.001 TRP A 503 HIS 0.005 0.001 HIS A 678 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.09 ( 7907) covalent geometry : angle 0.51382 / 0.25 (10768) SS BOND : bond 0.00204 / 0.10 ( 4) SS BOND : angle 0.54852 / 0.30 ( 8) hydrogen bonds : bond 0.02895 / 1.92 ( 253) hydrogen bonds : angle 4.22655 / 2.85 ( 732) link_ALPHA1-3 : bond 0.00626 / 0.33 ( 1) link_ALPHA1-3 : angle 1.51103 / 0.79 ( 3) link_BETA1-4 : bond 0.00552 / 0.28 ( 2) link_BETA1-4 : angle 1.34904 / 0.70 ( 6) link_NAG-ASN : bond 0.00156 / 0.08 ( 1) link_NAG-ASN : angle 2.59128 / 1.37 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2306.55 seconds wall clock time: 40 minutes 6.28 seconds (2406.28 seconds total)