Starting phenix.real_space_refine on Thu Feb 5 05:44:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9oga_70459/02_2026/9oga_70459_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9oga_70459/02_2026/9oga_70459.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9oga_70459/02_2026/9oga_70459.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9oga_70459/02_2026/9oga_70459.map" model { file = "/net/cci-nas-00/data/ceres_data/9oga_70459/02_2026/9oga_70459_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9oga_70459/02_2026/9oga_70459_trim.cif" } resolution = 3.37 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= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians S 51 5.16 5 C 4766 2.51 5 N 1239 2.21 5 O 1359 1.98 5 F 6 1.80 5 H 7424 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14845 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 14814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 912, 14814 Classifications: {'peptide': 912} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 35, 'TRANS': 876} Chain breaks: 4 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'V6A': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.45, per 1000 atoms: 0.17 Number of scatterers: 14845 At special positions: 0 Unit cell: (70.21, 109.858, 111.51, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 51 16.00 F 6 9.00 O 1359 8.00 N 1239 7.00 C 4766 6.00 H 7424 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.31 Conformation dependent library (CDL) restraints added in 429.0 milliseconds 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1764 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 1 sheets defined 86.6% alpha, 0.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 127 through 140 Processing helix chain 'A' and resid 141 through 146 Processing helix chain 'A' and resid 150 through 157 Processing helix chain 'A' and resid 163 through 178 removed outlier: 4.125A pdb=" N GLU A 176 " --> pdb=" O LYS A 172 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLU A 177 " --> pdb=" O LEU A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 200 No H-bonds generated for 'chain 'A' and resid 198 through 200' Processing helix chain 'A' and resid 201 through 216 removed outlier: 4.046A pdb=" N ILE A 205 " --> pdb=" O GLU A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 233 Processing helix chain 'A' and resid 237 through 242 removed outlier: 3.679A pdb=" N ILE A 241 " --> pdb=" O PRO A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 254 Processing helix chain 'A' and resid 257 through 274 removed outlier: 4.678A pdb=" N ASN A 262 " --> pdb=" O PRO A 258 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N VAL A 263 " --> pdb=" O MET A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 298 removed outlier: 3.730A pdb=" N GLN A 296 " --> pdb=" O MET A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 311 Processing helix chain 'A' and resid 312 through 339 removed outlier: 6.418A pdb=" N GLN A 335 " --> pdb=" O LYS A 331 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N LEU A 336 " --> pdb=" O GLU A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 359 removed outlier: 3.540A pdb=" N GLU A 359 " --> pdb=" O LEU A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 384 removed outlier: 3.614A pdb=" N SER A 384 " --> pdb=" O LEU A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 423 Proline residue: A 411 - end of helix removed outlier: 4.415A pdb=" N PHE A 414 " --> pdb=" O LEU A 410 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N LYS A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 468 removed outlier: 3.524A pdb=" N ILE A 451 " --> pdb=" O ASP A 447 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN A 452 " --> pdb=" O THR A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 486 Processing helix chain 'A' and resid 490 through 504 Processing helix chain 'A' and resid 509 through 531 removed outlier: 3.523A pdb=" N THR A 519 " --> pdb=" O ARG A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 551 Processing helix chain 'A' and resid 551 through 556 Processing helix chain 'A' and resid 558 through 574 removed outlier: 3.546A pdb=" N HIS A 574 " --> pdb=" O PHE A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 595 removed outlier: 3.872A pdb=" N LYS A 594 " --> pdb=" O LYS A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 601 removed outlier: 3.873A pdb=" N PHE A 599 " --> pdb=" O CYS A 595 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL A 600 " --> pdb=" O ARG A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 616 removed outlier: 3.750A pdb=" N GLU A 613 " --> pdb=" O PRO A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 622 Processing helix chain 'A' and resid 626 through 643 removed outlier: 3.635A pdb=" N ALA A 643 " --> pdb=" O TYR A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 658 removed outlier: 4.121A pdb=" N HIS A 652 " --> pdb=" O THR A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 658 through 675 Processing helix chain 'A' and resid 676 through 680 Processing helix chain 'A' and resid 681 through 703 Processing helix chain 'A' and resid 706 through 736 removed outlier: 3.815A pdb=" N ARG A 712 " --> pdb=" O ILE A 708 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE A 713 " --> pdb=" O GLN A 709 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N LEU A 715 " --> pdb=" O GLY A 711 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N ASP A 716 " --> pdb=" O ARG A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 741 Processing helix chain 'A' and resid 742 through 766 removed outlier: 3.541A pdb=" N ARG A 765 " --> pdb=" O GLY A 761 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 776 Processing helix chain 'A' and resid 776 through 791 removed outlier: 4.748A pdb=" N ILE A 786 " --> pdb=" O ASP A 782 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N ASP A 787 " --> pdb=" O ALA A 783 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 796 Processing helix chain 'A' and resid 797 through 812 removed outlier: 4.280A pdb=" N LEU A 801 " --> pdb=" O GLU A 797 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 817 removed outlier: 3.531A pdb=" N THR A 816 " --> pdb=" O GLY A 813 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N ALA A 817 " --> pdb=" O HIS A 814 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 813 through 817' Processing helix chain 'A' and resid 818 through 826 Processing helix chain 'A' and resid 826 through 837 removed outlier: 3.607A pdb=" N ASN A 832 " --> pdb=" O GLU A 828 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N MET A 833 " --> pdb=" O CYS A 829 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N LYS A 836 " --> pdb=" O ASN A 832 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N ASP A 837 " --> pdb=" O MET A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 841 through 859 Processing helix chain 'A' and resid 860 through 866 removed outlier: 4.022A pdb=" N LEU A 864 " --> pdb=" O PHE A 860 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 883 removed outlier: 3.755A pdb=" N LEU A 873 " --> pdb=" O THR A 869 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 905 Processing helix chain 'A' and resid 907 through 933 removed outlier: 6.111A pdb=" N CYS A 920 " --> pdb=" O GLN A 916 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N ASP A 921 " --> pdb=" O THR A 917 " (cutoff:3.500A) Processing helix chain 'A' and resid 935 through 937 No H-bonds generated for 'chain 'A' and resid 935 through 937' Processing helix chain 'A' and resid 938 through 955 Processing helix chain 'A' and resid 969 through 986 Processing helix chain 'A' and resid 990 through 1004 Processing helix chain 'A' and resid 1007 through 1027 Processing helix chain 'A' and resid 1031 through 1033 No H-bonds generated for 'chain 'A' and resid 1031 through 1033' Processing helix chain 'A' and resid 1034 through 1055 removed outlier: 3.539A pdb=" N SER A1055 " --> pdb=" O LYS A1051 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 432 through 435 removed outlier: 3.826A pdb=" N GLU A 439 " --> pdb=" O ASN A 435 " (cutoff:3.500A) 540 hydrogen bonds defined for protein. 1587 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: 3.58 Time building geometry restraints manager: 1.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 7408 1.03 - 1.23: 17 1.23 - 1.42: 3119 1.42 - 1.62: 4370 1.62 - 1.81: 85 Bond restraints: 14999 Sorted by residual: bond pdb=" C13 V6A A1101 " pdb=" N04 V6A A1101 " ideal model delta sigma weight residual 1.356 1.452 -0.096 2.00e-02 2.50e+03 2.30e+01 bond pdb=" C14 V6A A1101 " pdb=" N05 V6A A1101 " ideal model delta sigma weight residual 1.372 1.454 -0.082 2.00e-02 2.50e+03 1.69e+01 bond pdb=" C05 V6A A1101 " pdb=" C09 V6A A1101 " ideal model delta sigma weight residual 1.462 1.520 -0.058 2.00e-02 2.50e+03 8.41e+00 bond pdb=" N04 V6A A1101 " pdb=" N05 V6A A1101 " ideal model delta sigma weight residual 1.360 1.407 -0.047 2.00e-02 2.50e+03 5.42e+00 bond pdb=" C13 V6A A1101 " pdb=" O01 V6A A1101 " ideal model delta sigma weight residual 1.217 1.185 0.032 2.00e-02 2.50e+03 2.57e+00 ... (remaining 14994 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.50: 26512 1.50 - 3.01: 573 3.01 - 4.51: 57 4.51 - 6.02: 18 6.02 - 7.52: 2 Bond angle restraints: 27162 Sorted by residual: angle pdb=" N GLU A 976 " pdb=" CA GLU A 976 " pdb=" CB GLU A 976 " ideal model delta sigma weight residual 110.28 115.61 -5.33 1.55e+00 4.16e-01 1.18e+01 angle pdb=" C GLN A 975 " pdb=" N GLU A 976 " pdb=" CA GLU A 976 " ideal model delta sigma weight residual 120.31 115.76 4.55 1.52e+00 4.33e-01 8.97e+00 angle pdb=" CB MET A 508 " pdb=" CG MET A 508 " pdb=" SD MET A 508 " ideal model delta sigma weight residual 112.70 105.18 7.52 3.00e+00 1.11e-01 6.28e+00 angle pdb=" CA GLU A 976 " pdb=" CB GLU A 976 " pdb=" CG GLU A 976 " ideal model delta sigma weight residual 114.10 118.79 -4.69 2.00e+00 2.50e-01 5.50e+00 angle pdb=" CB MET A 348 " pdb=" CG MET A 348 " pdb=" SD MET A 348 " ideal model delta sigma weight residual 112.70 119.11 -6.41 3.00e+00 1.11e-01 4.57e+00 ... (remaining 27157 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.33: 6431 17.33 - 34.65: 449 34.65 - 51.98: 102 51.98 - 69.30: 29 69.30 - 86.63: 19 Dihedral angle restraints: 7030 sinusoidal: 3845 harmonic: 3185 Sorted by residual: dihedral pdb=" CD ARG A 474 " pdb=" NE ARG A 474 " pdb=" CZ ARG A 474 " pdb=" NH1 ARG A 474 " ideal model delta sinusoidal sigma weight residual 0.00 74.86 -74.86 1 1.00e+01 1.00e-02 7.09e+01 dihedral pdb=" CD ARG A 340 " pdb=" NE ARG A 340 " pdb=" CZ ARG A 340 " pdb=" NH1 ARG A 340 " ideal model delta sinusoidal sigma weight residual 0.00 36.18 -36.18 1 1.00e+01 1.00e-02 1.85e+01 dihedral pdb=" CA ASP A 837 " pdb=" C ASP A 837 " pdb=" N PHE A 838 " pdb=" CA PHE A 838 " ideal model delta harmonic sigma weight residual -180.00 -161.07 -18.93 0 5.00e+00 4.00e-02 1.43e+01 ... (remaining 7027 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 729 0.027 - 0.054: 280 0.054 - 0.081: 108 0.081 - 0.108: 41 0.108 - 0.135: 14 Chirality restraints: 1172 Sorted by residual: chirality pdb=" CA VAL A 257 " pdb=" N VAL A 257 " pdb=" C VAL A 257 " pdb=" CB VAL A 257 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.58e-01 chirality pdb=" CA ILE A 236 " pdb=" N ILE A 236 " pdb=" C ILE A 236 " pdb=" CB ILE A 236 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.37e-01 chirality pdb=" CA ILE A 205 " pdb=" N ILE A 205 " pdb=" C ILE A 205 " pdb=" CB ILE A 205 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.32e-01 ... (remaining 1169 not shown) Planarity restraints: 2181 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 474 " -0.927 9.50e-02 1.11e+02 3.10e-01 1.12e+02 pdb=" NE ARG A 474 " 0.068 2.00e-02 2.50e+03 pdb=" CZ ARG A 474 " -0.041 2.00e-02 2.50e+03 pdb=" NH1 ARG A 474 " 0.021 2.00e-02 2.50e+03 pdb=" NH2 ARG A 474 " 0.007 2.00e-02 2.50e+03 pdb="HH11 ARG A 474 " 0.000 2.00e-02 2.50e+03 pdb="HH12 ARG A 474 " -0.008 2.00e-02 2.50e+03 pdb="HH21 ARG A 474 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG A 474 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 340 " -0.513 9.50e-02 1.11e+02 1.72e-01 3.91e+01 pdb=" NE ARG A 340 " 0.041 2.00e-02 2.50e+03 pdb=" CZ ARG A 340 " -0.039 2.00e-02 2.50e+03 pdb=" NH1 ARG A 340 " 0.026 2.00e-02 2.50e+03 pdb=" NH2 ARG A 340 " 0.004 2.00e-02 2.50e+03 pdb="HH11 ARG A 340 " 0.001 2.00e-02 2.50e+03 pdb="HH12 ARG A 340 " -0.007 2.00e-02 2.50e+03 pdb="HH21 ARG A 340 " 0.000 2.00e-02 2.50e+03 pdb="HH22 ARG A 340 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 261 " 0.019 2.00e-02 2.50e+03 3.70e-02 1.37e+01 pdb=" C ARG A 261 " -0.064 2.00e-02 2.50e+03 pdb=" O ARG A 261 " 0.024 2.00e-02 2.50e+03 pdb=" N ASN A 262 " 0.022 2.00e-02 2.50e+03 ... (remaining 2178 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.16: 543 2.16 - 2.77: 30002 2.77 - 3.38: 44007 3.38 - 3.99: 53647 3.99 - 4.60: 85787 Nonbonded interactions: 213986 Sorted by model distance: nonbonded pdb=" O LYS A 245 " pdb=" HG1 THR A 249 " model vdw 1.556 2.450 nonbonded pdb=" O MET A 354 " pdb=" HG SER A 358 " model vdw 1.572 2.450 nonbonded pdb=" OE1 GLU A 635 " pdb="HH21 ARG A 697 " model vdw 1.573 2.450 nonbonded pdb="HH21 ARG A 442 " pdb=" OD2 ASP A 582 " model vdw 1.594 2.450 nonbonded pdb="HH11 ARG A 749 " pdb=" OE2 GLU A 797 " model vdw 1.599 2.450 ... (remaining 213981 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 1.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.080 Extract box with map and model: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.800 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 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 : 0.004 0.096 7576 Z= 0.210 Angle : 0.608 7.519 10265 Z= 0.335 Chirality : 0.037 0.135 1172 Planarity : 0.015 0.409 1309 Dihedral : 14.130 86.626 2827 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.77 % Favored : 98.12 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.85 (0.28), residues: 902 helix: 1.57 (0.20), residues: 677 sheet: None (None), residues: 0 loop : 0.37 (0.44), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.055 0.003 ARG A 474 TYR 0.013 0.001 TYR A 372 PHE 0.016 0.002 PHE A 882 TRP 0.016 0.002 TRP A 489 HIS 0.006 0.001 HIS A 884 Details of bonding type rmsd covalent geometry : bond 0.00416 ( 7575) covalent geometry : angle 0.60819 (10265) hydrogen bonds : bond 0.11724 ( 540) hydrogen bonds : angle 6.27680 ( 1587) Misc. bond : bond 0.00016 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 MET cc_start: 0.9443 (mmp) cc_final: 0.9236 (mmm) REVERT: A 371 GLU cc_start: 0.8636 (tm-30) cc_final: 0.8318 (tm-30) REVERT: A 799 GLU cc_start: 0.8793 (mm-30) cc_final: 0.7969 (mm-30) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.1601 time to fit residues: 17.9813 Evaluate side-chains 64 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 333 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.078735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.061408 restraints weight = 66568.759| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 3.55 r_work: 0.2976 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.0843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 7576 Z= 0.169 Angle : 0.547 6.977 10265 Z= 0.297 Chirality : 0.036 0.131 1172 Planarity : 0.005 0.103 1309 Dihedral : 7.393 87.292 982 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.00 % Favored : 97.89 % Rotamer: Outliers : 0.12 % Allowed : 3.37 % Favored : 96.51 % 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: 2.15 (0.28), residues: 902 helix: 1.84 (0.19), residues: 687 sheet: -2.54 (1.14), residues: 10 loop : 0.35 (0.47), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 474 TYR 0.013 0.001 TYR A 372 PHE 0.023 0.002 PHE A 882 TRP 0.010 0.001 TRP A 762 HIS 0.004 0.001 HIS A 577 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 7575) covalent geometry : angle 0.54708 (10265) hydrogen bonds : bond 0.04796 ( 540) hydrogen bonds : angle 4.99143 ( 1587) Misc. bond : bond 0.00165 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 67 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 MET cc_start: 0.8803 (mmp) cc_final: 0.8373 (tmm) REVERT: A 371 GLU cc_start: 0.9130 (tm-30) cc_final: 0.8729 (tm-30) REVERT: A 799 GLU cc_start: 0.9078 (mm-30) cc_final: 0.8320 (mm-30) outliers start: 1 outliers final: 1 residues processed: 68 average time/residue: 0.1748 time to fit residues: 16.5403 Evaluate side-chains 63 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 62 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 589 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 25 optimal weight: 0.7980 chunk 32 optimal weight: 4.9990 chunk 90 optimal weight: 0.0770 chunk 39 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 19 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 overall best weight: 0.8940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 543 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.078684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.060696 restraints weight = 67093.108| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 3.71 r_work: 0.2996 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.1108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7576 Z= 0.125 Angle : 0.489 5.496 10265 Z= 0.262 Chirality : 0.035 0.131 1172 Planarity : 0.004 0.036 1309 Dihedral : 7.121 89.517 982 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.66 % Favored : 98.23 % Rotamer: Outliers : 0.24 % Allowed : 3.73 % Favored : 96.03 % 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: 2.60 (0.28), residues: 902 helix: 2.19 (0.19), residues: 689 sheet: -2.61 (1.23), residues: 10 loop : 0.43 (0.47), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 697 TYR 0.011 0.001 TYR A 372 PHE 0.021 0.001 PHE A 882 TRP 0.011 0.001 TRP A 762 HIS 0.003 0.001 HIS A 577 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 7575) covalent geometry : angle 0.48937 (10265) hydrogen bonds : bond 0.04303 ( 540) hydrogen bonds : angle 4.64384 ( 1587) Misc. bond : bond 0.00078 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 67 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 371 GLU cc_start: 0.9100 (tm-30) cc_final: 0.8757 (tm-30) REVERT: A 799 GLU cc_start: 0.9101 (mm-30) cc_final: 0.8321 (mm-30) outliers start: 2 outliers final: 0 residues processed: 69 average time/residue: 0.1407 time to fit residues: 14.5582 Evaluate side-chains 63 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 29 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 87 optimal weight: 5.9990 chunk 64 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 23 optimal weight: 0.3980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.078088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.060698 restraints weight = 66161.318| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 3.63 r_work: 0.2996 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.1309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7576 Z= 0.126 Angle : 0.482 5.248 10265 Z= 0.257 Chirality : 0.034 0.133 1172 Planarity : 0.003 0.036 1309 Dihedral : 6.985 88.291 982 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.77 % Favored : 98.12 % Rotamer: Outliers : 0.12 % Allowed : 4.45 % Favored : 95.43 % 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: 2.85 (0.28), residues: 902 helix: 2.38 (0.19), residues: 689 sheet: -2.74 (1.30), residues: 10 loop : 0.47 (0.48), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 697 TYR 0.010 0.001 TYR A 372 PHE 0.020 0.001 PHE A 882 TRP 0.010 0.001 TRP A 762 HIS 0.003 0.001 HIS A 577 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 7575) covalent geometry : angle 0.48182 (10265) hydrogen bonds : bond 0.04009 ( 540) hydrogen bonds : angle 4.50438 ( 1587) Misc. bond : bond 0.00096 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 70 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 TYR cc_start: 0.8783 (m-80) cc_final: 0.8559 (m-80) REVERT: A 292 MET cc_start: 0.9019 (tmm) cc_final: 0.8790 (tmm) REVERT: A 371 GLU cc_start: 0.9108 (tm-30) cc_final: 0.8756 (tm-30) REVERT: A 459 GLU cc_start: 0.8877 (mt-10) cc_final: 0.8511 (tt0) REVERT: A 799 GLU cc_start: 0.9120 (mm-30) cc_final: 0.8384 (mm-30) REVERT: A 921 ASP cc_start: 0.8869 (m-30) cc_final: 0.8504 (t0) outliers start: 1 outliers final: 0 residues processed: 70 average time/residue: 0.1228 time to fit residues: 13.5868 Evaluate side-chains 63 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 4 optimal weight: 10.0000 chunk 25 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 70 optimal weight: 0.0070 chunk 68 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 71 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 77 optimal weight: 5.9990 chunk 58 optimal weight: 4.9990 overall best weight: 1.3002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.078152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.060158 restraints weight = 67203.604| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 3.76 r_work: 0.2980 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7576 Z= 0.143 Angle : 0.483 5.379 10265 Z= 0.258 Chirality : 0.035 0.132 1172 Planarity : 0.003 0.038 1309 Dihedral : 6.854 86.207 982 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.00 % Favored : 97.89 % Rotamer: Outliers : 0.12 % Allowed : 4.81 % 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: 3.03 (0.28), residues: 902 helix: 2.51 (0.19), residues: 690 sheet: None (None), residues: 0 loop : 0.34 (0.46), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 697 TYR 0.009 0.001 TYR A 372 PHE 0.019 0.001 PHE A 882 TRP 0.010 0.001 TRP A 762 HIS 0.003 0.001 HIS A 333 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 7575) covalent geometry : angle 0.48297 (10265) hydrogen bonds : bond 0.03894 ( 540) hydrogen bonds : angle 4.44344 ( 1587) Misc. bond : bond 0.00114 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 65 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 MET cc_start: 0.9444 (mmp) cc_final: 0.9211 (mmm) REVERT: A 292 MET cc_start: 0.9037 (tmm) cc_final: 0.8788 (tmm) REVERT: A 371 GLU cc_start: 0.9125 (tm-30) cc_final: 0.8809 (tm-30) REVERT: A 459 GLU cc_start: 0.8894 (mt-10) cc_final: 0.8584 (tt0) REVERT: A 921 ASP cc_start: 0.8868 (m-30) cc_final: 0.8497 (t0) outliers start: 1 outliers final: 1 residues processed: 65 average time/residue: 0.1346 time to fit residues: 13.2755 Evaluate side-chains 62 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 61 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1046 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 7 optimal weight: 6.9990 chunk 40 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 9 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 951 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.077160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.059646 restraints weight = 67243.325| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 3.62 r_work: 0.2939 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7576 Z= 0.206 Angle : 0.518 5.632 10265 Z= 0.280 Chirality : 0.036 0.135 1172 Planarity : 0.004 0.042 1309 Dihedral : 6.821 84.137 982 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.44 % Favored : 97.45 % Rotamer: Outliers : 0.48 % Allowed : 4.57 % Favored : 94.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.00 (0.28), residues: 902 helix: 2.52 (0.19), residues: 690 sheet: None (None), residues: 0 loop : 0.19 (0.46), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1043 TYR 0.010 0.001 TYR A 657 PHE 0.018 0.001 PHE A 882 TRP 0.010 0.001 TRP A 762 HIS 0.005 0.001 HIS A 333 Details of bonding type rmsd covalent geometry : bond 0.00441 ( 7575) covalent geometry : angle 0.51752 (10265) hydrogen bonds : bond 0.03973 ( 540) hydrogen bonds : angle 4.53048 ( 1587) Misc. bond : bond 0.00171 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 62 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 MET cc_start: 0.9450 (mmp) cc_final: 0.9211 (mmm) REVERT: A 292 MET cc_start: 0.9041 (tmm) cc_final: 0.8791 (tmm) REVERT: A 371 GLU cc_start: 0.9104 (tm-30) cc_final: 0.8740 (tm-30) REVERT: A 459 GLU cc_start: 0.8920 (mt-10) cc_final: 0.8606 (tt0) REVERT: A 921 ASP cc_start: 0.8883 (m-30) cc_final: 0.8509 (t0) outliers start: 4 outliers final: 2 residues processed: 64 average time/residue: 0.1134 time to fit residues: 11.4634 Evaluate side-chains 62 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 60 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 1046 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 17 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 4 optimal weight: 10.0000 chunk 68 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 543 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.077480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.059375 restraints weight = 66380.470| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 3.72 r_work: 0.2948 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7576 Z= 0.146 Angle : 0.494 6.121 10265 Z= 0.262 Chirality : 0.035 0.132 1172 Planarity : 0.003 0.039 1309 Dihedral : 6.709 83.029 982 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.88 % Favored : 98.00 % Rotamer: Outliers : 0.24 % Allowed : 5.17 % Favored : 94.58 % 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: 3.14 (0.28), residues: 902 helix: 2.62 (0.19), residues: 690 sheet: None (None), residues: 0 loop : 0.23 (0.46), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1043 TYR 0.009 0.001 TYR A 372 PHE 0.017 0.001 PHE A 882 TRP 0.011 0.001 TRP A 762 HIS 0.003 0.001 HIS A 375 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 7575) covalent geometry : angle 0.49369 (10265) hydrogen bonds : bond 0.03868 ( 540) hydrogen bonds : angle 4.40113 ( 1587) Misc. bond : bond 0.00115 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 63 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 MET cc_start: 0.9438 (mmp) cc_final: 0.9219 (mmm) REVERT: A 292 MET cc_start: 0.9049 (tmm) cc_final: 0.8798 (tmm) REVERT: A 371 GLU cc_start: 0.9111 (tm-30) cc_final: 0.8739 (tm-30) REVERT: A 459 GLU cc_start: 0.8907 (mt-10) cc_final: 0.8615 (tt0) REVERT: A 921 ASP cc_start: 0.8870 (m-30) cc_final: 0.8509 (t0) outliers start: 2 outliers final: 2 residues processed: 63 average time/residue: 0.1518 time to fit residues: 14.0960 Evaluate side-chains 63 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 61 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 1046 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 16 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 53 optimal weight: 0.5980 chunk 62 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 73 optimal weight: 0.5980 chunk 0 optimal weight: 8.9990 chunk 83 optimal weight: 0.8980 chunk 61 optimal weight: 0.5980 chunk 78 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 543 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.078270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.060289 restraints weight = 66814.744| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 3.68 r_work: 0.2970 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7576 Z= 0.122 Angle : 0.486 6.998 10265 Z= 0.256 Chirality : 0.034 0.134 1172 Planarity : 0.003 0.038 1309 Dihedral : 6.583 82.277 982 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.00 % Favored : 97.89 % Rotamer: Outliers : 0.36 % Allowed : 5.29 % Favored : 94.34 % 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: 3.23 (0.29), residues: 902 helix: 2.72 (0.19), residues: 688 sheet: -2.67 (1.46), residues: 10 loop : 0.34 (0.48), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 887 TYR 0.008 0.001 TYR A 372 PHE 0.016 0.001 PHE A 882 TRP 0.011 0.001 TRP A 762 HIS 0.003 0.001 HIS A 375 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 7575) covalent geometry : angle 0.48606 (10265) hydrogen bonds : bond 0.03729 ( 540) hydrogen bonds : angle 4.29134 ( 1587) Misc. bond : bond 0.00082 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 65 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 MET cc_start: 0.9419 (mmp) cc_final: 0.9203 (mmm) REVERT: A 292 MET cc_start: 0.9032 (tmm) cc_final: 0.8791 (tmm) REVERT: A 371 GLU cc_start: 0.9111 (tm-30) cc_final: 0.8719 (tm-30) REVERT: A 459 GLU cc_start: 0.8844 (mt-10) cc_final: 0.8563 (tt0) REVERT: A 921 ASP cc_start: 0.8831 (m-30) cc_final: 0.8488 (t0) outliers start: 3 outliers final: 2 residues processed: 66 average time/residue: 0.1494 time to fit residues: 14.4430 Evaluate side-chains 65 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 63 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 1046 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 60 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 64 optimal weight: 0.3980 chunk 37 optimal weight: 7.9990 chunk 57 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.077481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.059439 restraints weight = 67571.249| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 3.73 r_work: 0.2945 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7576 Z= 0.169 Angle : 0.508 8.959 10265 Z= 0.270 Chirality : 0.035 0.184 1172 Planarity : 0.004 0.039 1309 Dihedral : 6.548 82.192 982 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.36 % Allowed : 5.29 % Favored : 94.34 % 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: 3.24 (0.28), residues: 902 helix: 2.71 (0.19), residues: 688 sheet: None (None), residues: 0 loop : 0.26 (0.47), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 887 TYR 0.009 0.001 TYR A 657 PHE 0.016 0.001 PHE A 882 TRP 0.010 0.001 TRP A 762 HIS 0.003 0.001 HIS A 333 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 7575) covalent geometry : angle 0.50753 (10265) hydrogen bonds : bond 0.03762 ( 540) hydrogen bonds : angle 4.35544 ( 1587) Misc. bond : bond 0.00136 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 64 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 MET cc_start: 0.9428 (mmp) cc_final: 0.9227 (mmm) REVERT: A 292 MET cc_start: 0.9037 (tmm) cc_final: 0.8796 (tmm) REVERT: A 371 GLU cc_start: 0.9128 (tm-30) cc_final: 0.8759 (tm-30) REVERT: A 459 GLU cc_start: 0.8918 (mt-10) cc_final: 0.8623 (tt0) REVERT: A 921 ASP cc_start: 0.8842 (m-30) cc_final: 0.8493 (t0) outliers start: 3 outliers final: 2 residues processed: 65 average time/residue: 0.1594 time to fit residues: 15.2117 Evaluate side-chains 64 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 62 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 1046 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 10 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.077960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.060436 restraints weight = 66954.343| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 3.62 r_work: 0.2974 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7576 Z= 0.128 Angle : 0.500 10.135 10265 Z= 0.261 Chirality : 0.035 0.184 1172 Planarity : 0.003 0.038 1309 Dihedral : 6.454 81.622 982 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.24 % Allowed : 5.66 % Favored : 94.10 % 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: 3.25 (0.29), residues: 902 helix: 2.75 (0.19), residues: 688 sheet: -2.70 (1.46), residues: 10 loop : 0.32 (0.48), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 887 TYR 0.016 0.001 TYR A 381 PHE 0.015 0.001 PHE A 882 TRP 0.012 0.001 TRP A 762 HIS 0.003 0.001 HIS A 375 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 7575) covalent geometry : angle 0.50042 (10265) hydrogen bonds : bond 0.03684 ( 540) hydrogen bonds : angle 4.26459 ( 1587) Misc. bond : bond 0.00093 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 64 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 MET cc_start: 0.9032 (tmm) cc_final: 0.8803 (tmm) REVERT: A 371 GLU cc_start: 0.9113 (tm-30) cc_final: 0.8742 (tm-30) REVERT: A 459 GLU cc_start: 0.8853 (mt-10) cc_final: 0.8564 (tt0) REVERT: A 508 MET cc_start: 0.8866 (mmm) cc_final: 0.8553 (mmm) REVERT: A 921 ASP cc_start: 0.8820 (m-30) cc_final: 0.8490 (t0) outliers start: 2 outliers final: 2 residues processed: 64 average time/residue: 0.1587 time to fit residues: 15.0860 Evaluate side-chains 65 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 63 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 1046 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 70 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.076967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.059472 restraints weight = 67312.795| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 3.58 r_work: 0.2950 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7576 Z= 0.196 Angle : 0.530 9.630 10265 Z= 0.283 Chirality : 0.036 0.180 1172 Planarity : 0.004 0.039 1309 Dihedral : 6.444 81.834 982 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.36 % Allowed : 5.90 % Favored : 93.74 % 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: 3.14 (0.28), residues: 902 helix: 2.67 (0.19), residues: 689 sheet: None (None), residues: 0 loop : 0.08 (0.46), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 887 TYR 0.010 0.001 TYR A 657 PHE 0.015 0.001 PHE A 329 TRP 0.010 0.001 TRP A 762 HIS 0.004 0.001 HIS A 333 Details of bonding type rmsd covalent geometry : bond 0.00420 ( 7575) covalent geometry : angle 0.52967 (10265) hydrogen bonds : bond 0.03801 ( 540) hydrogen bonds : angle 4.38720 ( 1587) Misc. bond : bond 0.00159 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2712.67 seconds wall clock time: 46 minutes 52.73 seconds (2812.73 seconds total)