Starting phenix.real_space_refine on Wed Feb 4 01:54:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qii_53188/02_2026/9qii_53188_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qii_53188/02_2026/9qii_53188.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9qii_53188/02_2026/9qii_53188.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qii_53188/02_2026/9qii_53188.map" model { file = "/net/cci-nas-00/data/ceres_data/9qii_53188/02_2026/9qii_53188_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qii_53188/02_2026/9qii_53188_neut.cif" } resolution = 3.99 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= 0.026 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 P 9 5.49 5 S 37 5.16 5 C 5139 2.51 5 N 1348 2.21 5 O 1544 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 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: 8077 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 8010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1011, 8010 Classifications: {'peptide': 1011} Link IDs: {'CIS': 1, 'PCIS': 4, 'PTRANS': 50, 'TRANS': 955} Chain: "B" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'ATP': 1, 'IHP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.88, per 1000 atoms: 0.23 Number of scatterers: 8077 At special positions: 0 Unit cell: (79.2, 100.65, 119.625, 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) S 37 16.00 P 9 15.00 O 1544 8.00 N 1348 7.00 C 5139 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.57 Conformation dependent library (CDL) restraints added in 246.4 milliseconds 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1922 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 8 sheets defined 48.6% alpha, 11.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'B' and resid 40 through 45 Processing helix chain 'B' and resid 45 through 52 removed outlier: 3.889A pdb=" N TYR B 49 " --> pdb=" O SER B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 60 removed outlier: 3.920A pdb=" N LYS B 58 " --> pdb=" O THR B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 84 Processing helix chain 'B' and resid 98 through 103 Processing helix chain 'B' and resid 108 through 114 removed outlier: 3.645A pdb=" N VAL B 112 " --> pdb=" O SER B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 130 removed outlier: 3.643A pdb=" N VAL B 122 " --> pdb=" O ARG B 118 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LYS B 124 " --> pdb=" O GLU B 120 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N HIS B 125 " --> pdb=" O ALA B 121 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU B 128 " --> pdb=" O LYS B 124 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LEU B 129 " --> pdb=" O HIS B 125 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ASN B 130 " --> pdb=" O ILE B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 154 removed outlier: 3.930A pdb=" N LYS B 153 " --> pdb=" O PHE B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 177 Processing helix chain 'B' and resid 301 through 308 removed outlier: 3.746A pdb=" N LYS B 307 " --> pdb=" O GLU B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 340 Processing helix chain 'B' and resid 347 through 365 removed outlier: 3.790A pdb=" N GLU B 363 " --> pdb=" O THR B 359 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR B 364 " --> pdb=" O SER B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 382 Processing helix chain 'B' and resid 387 through 408 Processing helix chain 'B' and resid 421 through 427 removed outlier: 3.923A pdb=" N VAL B 425 " --> pdb=" O ALA B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 437 removed outlier: 4.101A pdb=" N PHE B 436 " --> pdb=" O GLU B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 451 Processing helix chain 'B' and resid 451 through 460 Processing helix chain 'B' and resid 469 through 483 Processing helix chain 'B' and resid 503 through 508 Processing helix chain 'B' and resid 513 through 517 Processing helix chain 'B' and resid 520 through 533 Processing helix chain 'B' and resid 546 through 552 removed outlier: 4.046A pdb=" N THR B 551 " --> pdb=" O THR B 548 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 561 Processing helix chain 'B' and resid 570 through 585 removed outlier: 3.716A pdb=" N ARG B 574 " --> pdb=" O ASN B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 623 through 630 Processing helix chain 'B' and resid 633 through 650 removed outlier: 3.558A pdb=" N THR B 637 " --> pdb=" O ALA B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 663 Processing helix chain 'B' and resid 665 through 675 Processing helix chain 'B' and resid 681 through 691 Processing helix chain 'B' and resid 695 through 712 Processing helix chain 'B' and resid 712 through 722 Processing helix chain 'B' and resid 751 through 769 Processing helix chain 'B' and resid 779 through 789 removed outlier: 4.320A pdb=" N GLU B 789 " --> pdb=" O ASN B 785 " (cutoff:3.500A) Processing helix chain 'B' and resid 817 through 834 Processing helix chain 'B' and resid 839 through 843 Processing helix chain 'B' and resid 857 through 873 Processing helix chain 'B' and resid 879 through 889 Processing helix chain 'B' and resid 894 through 914 Processing helix chain 'B' and resid 967 through 980 Processing helix chain 'B' and resid 1001 through 1007 removed outlier: 3.563A pdb=" N LEU B1005 " --> pdb=" O ALA B1002 " (cutoff:3.500A) Processing helix chain 'B' and resid 1008 through 1013 Processing sheet with id=AA1, first strand: chain 'B' and resid 134 through 136 removed outlier: 6.419A pdb=" N VAL B 88 " --> pdb=" O THR B 136 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N VAL B 64 " --> pdb=" O THR B 89 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N HIS B 91 " --> pdb=" O VAL B 64 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N LEU B 66 " --> pdb=" O HIS B 91 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N CYS B 156 " --> pdb=" O HIS B 63 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N VAL B 157 " --> pdb=" O ILE B 184 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N ALA B 186 " --> pdb=" O VAL B 157 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N LEU B 159 " --> pdb=" O ALA B 186 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N VAL B 188 " --> pdb=" O LEU B 159 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU B 419 " --> pdb=" O SER B 193 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 203 through 205 Processing sheet with id=AA3, first strand: chain 'B' and resid 260 through 262 removed outlier: 4.222A pdb=" N PHE B 244 " --> pdb=" O VAL B 291 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ILE B 250 " --> pdb=" O GLY B 285 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N GLY B 285 " --> pdb=" O ILE B 250 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N GLY B 286 " --> pdb=" O ILE B 218 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N SER B 272 " --> pdb=" O VAL B 265 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N VAL B 265 " --> pdb=" O SER B 272 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 538 through 541 removed outlier: 6.218A pdb=" N ILE B 493 " --> pdb=" O ASP B 539 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N HIS B 541 " --> pdb=" O ILE B 493 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL B 495 " --> pdb=" O HIS B 541 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N ILE B 463 " --> pdb=" O THR B 494 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N THR B 496 " --> pdb=" O ILE B 463 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N LEU B 465 " --> pdb=" O THR B 496 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE B 565 " --> pdb=" O PHE B 464 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ILE B 564 " --> pdb=" O LEU B 589 " (cutoff:3.500A) removed outlier: 8.571A pdb=" N SER B 591 " --> pdb=" O ILE B 564 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N THR B 566 " --> pdb=" O SER B 591 " (cutoff:3.500A) removed outlier: 9.089A pdb=" N THR B 593 " --> pdb=" O THR B 566 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N CYS B 924 " --> pdb=" O THR B 600 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL B 602 " --> pdb=" O LYS B 922 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N LYS B 922 " --> pdb=" O VAL B 602 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 944 through 947 removed outlier: 6.548A pdb=" N ILE B 950 " --> pdb=" O ILE B 946 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 958 through 961 removed outlier: 6.679A pdb=" N TRP B 958 " --> pdb=" O ARG B1044 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N TYR B1046 " --> pdb=" O TRP B 958 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N VAL B 960 " --> pdb=" O TYR B1046 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 986 through 988 removed outlier: 5.883A pdb=" N VAL B 986 " --> pdb=" O LEU B 993 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 1027 through 1028 376 hydrogen bonds defined for protein. 1035 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: 1.37 Time building geometry restraints manager: 0.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2611 1.34 - 1.46: 1809 1.46 - 1.58: 3780 1.58 - 1.70: 9 1.70 - 1.82: 53 Bond restraints: 8262 Sorted by residual: bond pdb=" C ILE B 981 " pdb=" N GLU B 982 " ideal model delta sigma weight residual 1.331 1.303 0.028 2.07e-02 2.33e+03 1.86e+00 bond pdb=" CB ASN B 234 " pdb=" CG ASN B 234 " ideal model delta sigma weight residual 1.516 1.545 -0.029 2.50e-02 1.60e+03 1.38e+00 bond pdb=" CA PRO B1041 " pdb=" C PRO B1041 " ideal model delta sigma weight residual 1.517 1.509 0.008 6.70e-03 2.23e+04 1.38e+00 bond pdb=" CB TRP B 416 " pdb=" CG TRP B 416 " ideal model delta sigma weight residual 1.498 1.462 0.036 3.10e-02 1.04e+03 1.34e+00 bond pdb=" C SER B 874 " pdb=" N ILE B 875 " ideal model delta sigma weight residual 1.332 1.313 0.019 1.73e-02 3.34e+03 1.20e+00 ... (remaining 8257 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.32: 11038 2.32 - 4.64: 160 4.64 - 6.95: 14 6.95 - 9.27: 6 9.27 - 11.59: 4 Bond angle restraints: 11222 Sorted by residual: angle pdb=" CA LEU B 585 " pdb=" CB LEU B 585 " pdb=" CG LEU B 585 " ideal model delta sigma weight residual 116.30 127.89 -11.59 3.50e+00 8.16e-02 1.10e+01 angle pdb=" CA LEU B 828 " pdb=" CB LEU B 828 " pdb=" CG LEU B 828 " ideal model delta sigma weight residual 116.30 127.19 -10.89 3.50e+00 8.16e-02 9.69e+00 angle pdb=" N PHE B 479 " pdb=" CA PHE B 479 " pdb=" CB PHE B 479 " ideal model delta sigma weight residual 110.12 114.68 -4.56 1.47e+00 4.63e-01 9.64e+00 angle pdb=" CA LEU B 689 " pdb=" CB LEU B 689 " pdb=" CG LEU B 689 " ideal model delta sigma weight residual 116.30 126.62 -10.32 3.50e+00 8.16e-02 8.69e+00 angle pdb=" CA MET B 844 " pdb=" CB MET B 844 " pdb=" CG MET B 844 " ideal model delta sigma weight residual 114.10 119.72 -5.62 2.00e+00 2.50e-01 7.91e+00 ... (remaining 11217 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.41: 4540 17.41 - 34.82: 399 34.82 - 52.23: 75 52.23 - 69.64: 19 69.64 - 87.05: 11 Dihedral angle restraints: 5044 sinusoidal: 2087 harmonic: 2957 Sorted by residual: dihedral pdb=" CA MET B 59 " pdb=" C MET B 59 " pdb=" N ALA B 60 " pdb=" CA ALA B 60 " ideal model delta harmonic sigma weight residual 180.00 160.90 19.10 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA GLU B 280 " pdb=" C GLU B 280 " pdb=" N PRO B 281 " pdb=" CA PRO B 281 " ideal model delta harmonic sigma weight residual 180.00 161.58 18.42 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CA PHE B 244 " pdb=" C PHE B 244 " pdb=" N LEU B 245 " pdb=" CA LEU B 245 " ideal model delta harmonic sigma weight residual -180.00 -162.49 -17.51 0 5.00e+00 4.00e-02 1.23e+01 ... (remaining 5041 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 843 0.034 - 0.068: 287 0.068 - 0.102: 107 0.102 - 0.135: 30 0.135 - 0.169: 1 Chirality restraints: 1268 Sorted by residual: chirality pdb=" CA ASN B 234 " pdb=" N ASN B 234 " pdb=" C ASN B 234 " pdb=" CB ASN B 234 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.17e-01 chirality pdb=" CA VAL B 814 " pdb=" N VAL B 814 " pdb=" C VAL B 814 " pdb=" CB VAL B 814 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.05e-01 chirality pdb=" CA ILE B 622 " pdb=" N ILE B 622 " pdb=" C ILE B 622 " pdb=" CB ILE B 622 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.86e-01 ... (remaining 1265 not shown) Planarity restraints: 1430 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET B 998 " -0.009 2.00e-02 2.50e+03 1.79e-02 3.20e+00 pdb=" C MET B 998 " 0.031 2.00e-02 2.50e+03 pdb=" O MET B 998 " -0.011 2.00e-02 2.50e+03 pdb=" N PRO B 999 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B1045 " 0.012 2.00e-02 2.50e+03 1.14e-02 2.62e+00 pdb=" CG TYR B1045 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 TYR B1045 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR B1045 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR B1045 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR B1045 " 0.011 2.00e-02 2.50e+03 pdb=" CZ TYR B1045 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR B1045 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 280 " -0.007 2.00e-02 2.50e+03 1.35e-02 1.82e+00 pdb=" C GLU B 280 " 0.023 2.00e-02 2.50e+03 pdb=" O GLU B 280 " -0.009 2.00e-02 2.50e+03 pdb=" N PRO B 281 " -0.008 2.00e-02 2.50e+03 ... (remaining 1427 not shown) Histogram of nonbonded interaction distances: 2.56 - 3.03: 5502 3.03 - 3.50: 9520 3.50 - 3.97: 13687 3.97 - 4.43: 16809 4.43 - 4.90: 24021 Nonbonded interactions: 69539 Sorted by model distance: nonbonded pdb=" N ASP B 781 " pdb=" OD1 ASP B 781 " model vdw 2.564 3.120 nonbonded pdb=" O GLU B 233 " pdb=" OD1 ASN B 234 " model vdw 2.576 3.040 nonbonded pdb=" N ASP B 965 " pdb=" OD1 ASP B 965 " model vdw 2.581 3.120 nonbonded pdb=" O LYS B 687 " pdb=" OG SER B 690 " model vdw 2.590 3.040 nonbonded pdb=" O2' ATP B1102 " pdb=" O3' ATP B1102 " model vdw 2.596 2.432 ... (remaining 69534 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.550 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:0.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8831 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 : 0.005 0.036 8262 Z= 0.253 Angle : 0.702 11.588 11222 Z= 0.360 Chirality : 0.041 0.169 1268 Planarity : 0.004 0.033 1430 Dihedral : 14.293 87.051 3122 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.78 % Allowed : 11.42 % Favored : 87.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.10 % 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: 0.98 (0.28), residues: 1009 helix: 1.51 (0.25), residues: 433 sheet: -0.52 (0.49), residues: 127 loop : 0.29 (0.33), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 691 TYR 0.027 0.002 TYR B1045 PHE 0.022 0.002 PHE B 966 TRP 0.011 0.002 TRP B 660 HIS 0.005 0.001 HIS B 855 Details of bonding type rmsd covalent geometry : bond 0.00498 ( 8262) covalent geometry : angle 0.70205 (11222) hydrogen bonds : bond 0.13671 ( 376) hydrogen bonds : angle 7.25461 ( 1035) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 33 time to evaluate : 0.205 Fit side-chains REVERT: B 253 MET cc_start: 0.6024 (mpp) cc_final: 0.4890 (mpp) REVERT: B 474 GLU cc_start: 0.9762 (mm-30) cc_final: 0.9148 (mt-10) REVERT: B 475 MET cc_start: 0.9673 (mmm) cc_final: 0.9358 (mmm) REVERT: B 620 GLU cc_start: 0.9469 (mm-30) cc_final: 0.9104 (tm-30) REVERT: B 909 MET cc_start: 0.9743 (tmm) cc_final: 0.9437 (tmm) outliers start: 7 outliers final: 6 residues processed: 39 average time/residue: 0.0644 time to fit residues: 4.0853 Evaluate side-chains 39 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 33 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 247 PHE Chi-restraints excluded: chain B residue 682 CYS Chi-restraints excluded: chain B residue 720 HIS Chi-restraints excluded: chain B residue 826 PHE Chi-restraints excluded: chain B residue 891 ILE Chi-restraints excluded: chain B residue 1001 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 10.0000 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.043665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.038230 restraints weight = 90526.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.039185 restraints weight = 44108.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.039771 restraints weight = 25722.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.040229 restraints weight = 17588.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.040665 restraints weight = 12207.437| |-----------------------------------------------------------------------------| r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.0679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8262 Z= 0.136 Angle : 0.548 10.604 11222 Z= 0.278 Chirality : 0.040 0.169 1268 Planarity : 0.004 0.033 1430 Dihedral : 6.958 80.139 1158 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.23 % Allowed : 11.53 % Favored : 87.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.28), residues: 1009 helix: 1.72 (0.25), residues: 444 sheet: -0.40 (0.46), residues: 134 loop : 0.19 (0.34), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 48 TYR 0.013 0.001 TYR B1045 PHE 0.013 0.001 PHE B 656 TRP 0.009 0.001 TRP B 696 HIS 0.003 0.001 HIS B 377 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 8262) covalent geometry : angle 0.54842 (11222) hydrogen bonds : bond 0.03518 ( 376) hydrogen bonds : angle 5.58282 ( 1035) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 36 time to evaluate : 0.327 Fit side-chains revert: symmetry clash REVERT: B 253 MET cc_start: 0.5729 (mpp) cc_final: 0.5360 (mpp) REVERT: B 365 LEU cc_start: 0.9390 (OUTLIER) cc_final: 0.8986 (mm) REVERT: B 474 GLU cc_start: 0.9742 (mm-30) cc_final: 0.9013 (mt-10) REVERT: B 475 MET cc_start: 0.9668 (mmm) cc_final: 0.9372 (mmm) REVERT: B 620 GLU cc_start: 0.9171 (mm-30) cc_final: 0.8960 (tm-30) REVERT: B 909 MET cc_start: 0.9753 (tmm) cc_final: 0.9454 (tmm) outliers start: 11 outliers final: 6 residues processed: 45 average time/residue: 0.0772 time to fit residues: 5.3663 Evaluate side-chains 39 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 32 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 435 GLU Chi-restraints excluded: chain B residue 682 CYS Chi-restraints excluded: chain B residue 720 HIS Chi-restraints excluded: chain B residue 826 PHE Chi-restraints excluded: chain B residue 1001 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 4 optimal weight: 0.9980 chunk 9 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 89 optimal weight: 6.9990 chunk 100 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 70 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 41 optimal weight: 6.9990 chunk 64 optimal weight: 8.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.028062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2531 r_free = 0.2531 target = 0.021993 restraints weight = 83452.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2561 r_free = 0.2561 target = 0.022698 restraints weight = 56540.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2585 r_free = 0.2585 target = 0.023230 restraints weight = 42451.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2603 r_free = 0.2603 target = 0.023633 restraints weight = 33950.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2615 r_free = 0.2615 target = 0.023910 restraints weight = 28432.004| |-----------------------------------------------------------------------------| r_work (final): 0.2608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.0927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8262 Z= 0.144 Angle : 0.539 8.894 11222 Z= 0.274 Chirality : 0.039 0.167 1268 Planarity : 0.004 0.033 1430 Dihedral : 6.822 80.536 1154 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.68 % Allowed : 10.97 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.10 % 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: 1.26 (0.28), residues: 1009 helix: 1.89 (0.25), residues: 439 sheet: -0.48 (0.47), residues: 129 loop : 0.30 (0.34), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 880 TYR 0.013 0.001 TYR B1045 PHE 0.013 0.001 PHE B 656 TRP 0.008 0.001 TRP B 696 HIS 0.003 0.001 HIS B 377 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 8262) covalent geometry : angle 0.53892 (11222) hydrogen bonds : bond 0.03172 ( 376) hydrogen bonds : angle 5.26556 ( 1035) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 34 time to evaluate : 0.335 Fit side-chains revert: symmetry clash REVERT: B 253 MET cc_start: 0.6264 (mpp) cc_final: 0.5974 (mpp) REVERT: B 365 LEU cc_start: 0.9421 (OUTLIER) cc_final: 0.9082 (mm) REVERT: B 423 ASP cc_start: 0.9322 (OUTLIER) cc_final: 0.8501 (t0) REVERT: B 474 GLU cc_start: 0.9758 (mm-30) cc_final: 0.9520 (mm-30) REVERT: B 475 MET cc_start: 0.9647 (mmm) cc_final: 0.9342 (mmm) REVERT: B 620 GLU cc_start: 0.9403 (mm-30) cc_final: 0.9097 (tm-30) REVERT: B 909 MET cc_start: 0.9775 (tmm) cc_final: 0.9447 (tmm) outliers start: 15 outliers final: 7 residues processed: 48 average time/residue: 0.0565 time to fit residues: 4.4997 Evaluate side-chains 42 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 33 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 435 GLU Chi-restraints excluded: chain B residue 682 CYS Chi-restraints excluded: chain B residue 720 HIS Chi-restraints excluded: chain B residue 826 PHE Chi-restraints excluded: chain B residue 891 ILE Chi-restraints excluded: chain B residue 1001 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 21 optimal weight: 0.0870 chunk 81 optimal weight: 0.8980 chunk 65 optimal weight: 5.9990 chunk 27 optimal weight: 6.9990 chunk 41 optimal weight: 5.9990 chunk 39 optimal weight: 0.0000 chunk 4 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 95 optimal weight: 0.0060 chunk 85 optimal weight: 4.9990 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.045886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.040364 restraints weight = 87943.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.041316 restraints weight = 42222.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.041915 restraints weight = 24142.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.042397 restraints weight = 16487.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.042835 restraints weight = 11598.145| |-----------------------------------------------------------------------------| r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.1384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8262 Z= 0.090 Angle : 0.524 11.228 11222 Z= 0.256 Chirality : 0.040 0.170 1268 Planarity : 0.003 0.034 1430 Dihedral : 6.510 79.919 1154 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.67 % Allowed : 12.21 % Favored : 87.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.10 % 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: 1.33 (0.28), residues: 1009 helix: 2.00 (0.25), residues: 439 sheet: -0.36 (0.45), residues: 134 loop : 0.24 (0.34), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 48 TYR 0.010 0.001 TYR B1045 PHE 0.013 0.001 PHE B 656 TRP 0.007 0.001 TRP B 696 HIS 0.003 0.000 HIS B 636 Details of bonding type rmsd covalent geometry : bond 0.00189 ( 8262) covalent geometry : angle 0.52444 (11222) hydrogen bonds : bond 0.02796 ( 376) hydrogen bonds : angle 4.94195 ( 1035) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 36 time to evaluate : 0.360 Fit side-chains REVERT: B 365 LEU cc_start: 0.9387 (OUTLIER) cc_final: 0.9089 (mm) REVERT: B 474 GLU cc_start: 0.9745 (mm-30) cc_final: 0.9495 (mm-30) REVERT: B 475 MET cc_start: 0.9669 (mmm) cc_final: 0.9435 (mmm) REVERT: B 620 GLU cc_start: 0.9270 (mm-30) cc_final: 0.9037 (tm-30) REVERT: B 909 MET cc_start: 0.9829 (tmm) cc_final: 0.9532 (tmm) outliers start: 6 outliers final: 4 residues processed: 41 average time/residue: 0.0804 time to fit residues: 5.0459 Evaluate side-chains 37 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 32 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 720 HIS Chi-restraints excluded: chain B residue 785 ASN Chi-restraints excluded: chain B residue 826 PHE Chi-restraints excluded: chain B residue 936 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 70 optimal weight: 10.0000 chunk 35 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 40 optimal weight: 8.9990 chunk 2 optimal weight: 4.9990 chunk 41 optimal weight: 6.9990 chunk 53 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 100 optimal weight: 10.0000 chunk 7 optimal weight: 4.9990 chunk 28 optimal weight: 8.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.043110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.037654 restraints weight = 91900.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.038601 restraints weight = 45035.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.039196 restraints weight = 26159.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.039698 restraints weight = 17903.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.039859 restraints weight = 12278.488| |-----------------------------------------------------------------------------| r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.1221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8262 Z= 0.168 Angle : 0.547 9.038 11222 Z= 0.277 Chirality : 0.039 0.166 1268 Planarity : 0.004 0.034 1430 Dihedral : 6.516 80.226 1151 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.12 % Allowed : 12.43 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.10 % 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: 1.45 (0.29), residues: 1009 helix: 2.04 (0.25), residues: 440 sheet: -0.13 (0.45), residues: 132 loop : 0.31 (0.34), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 691 TYR 0.011 0.001 TYR B 994 PHE 0.045 0.002 PHE B 479 TRP 0.008 0.001 TRP B 696 HIS 0.003 0.001 HIS B 377 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 8262) covalent geometry : angle 0.54732 (11222) hydrogen bonds : bond 0.02943 ( 376) hydrogen bonds : angle 4.98572 ( 1035) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 33 time to evaluate : 0.323 Fit side-chains revert: symmetry clash REVERT: B 365 LEU cc_start: 0.9381 (OUTLIER) cc_final: 0.9049 (mm) REVERT: B 474 GLU cc_start: 0.9742 (mm-30) cc_final: 0.9424 (mm-30) REVERT: B 475 MET cc_start: 0.9656 (mmm) cc_final: 0.9408 (mmm) REVERT: B 620 GLU cc_start: 0.9240 (mm-30) cc_final: 0.9039 (tm-30) REVERT: B 909 MET cc_start: 0.9764 (tmm) cc_final: 0.9448 (tmm) outliers start: 10 outliers final: 7 residues processed: 42 average time/residue: 0.0651 time to fit residues: 4.5552 Evaluate side-chains 41 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 33 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 435 GLU Chi-restraints excluded: chain B residue 682 CYS Chi-restraints excluded: chain B residue 720 HIS Chi-restraints excluded: chain B residue 785 ASN Chi-restraints excluded: chain B residue 826 PHE Chi-restraints excluded: chain B residue 936 THR Chi-restraints excluded: chain B residue 944 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 27 optimal weight: 3.9990 chunk 33 optimal weight: 10.0000 chunk 99 optimal weight: 7.9990 chunk 95 optimal weight: 0.1980 chunk 89 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 70 optimal weight: 8.9990 chunk 16 optimal weight: 7.9990 chunk 88 optimal weight: 1.9990 chunk 2 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 overall best weight: 1.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 561 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.043802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.038367 restraints weight = 89695.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.039308 restraints weight = 43757.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.039864 restraints weight = 25275.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.040455 restraints weight = 17539.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.040815 restraints weight = 11620.797| |-----------------------------------------------------------------------------| r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.1363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8262 Z= 0.123 Angle : 0.527 10.938 11222 Z= 0.262 Chirality : 0.039 0.167 1268 Planarity : 0.003 0.036 1430 Dihedral : 6.443 79.804 1151 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.23 % Allowed : 12.21 % Favored : 86.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.10 % 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: 1.49 (0.29), residues: 1009 helix: 2.06 (0.25), residues: 441 sheet: -0.06 (0.46), residues: 132 loop : 0.32 (0.34), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 809 TYR 0.008 0.001 TYR B 979 PHE 0.014 0.001 PHE B 656 TRP 0.008 0.001 TRP B 696 HIS 0.003 0.001 HIS B 377 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 8262) covalent geometry : angle 0.52737 (11222) hydrogen bonds : bond 0.02781 ( 376) hydrogen bonds : angle 4.90767 ( 1035) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 32 time to evaluate : 0.291 Fit side-chains revert: symmetry clash REVERT: B 253 MET cc_start: 0.5856 (mpp) cc_final: 0.4796 (tpp) REVERT: B 365 LEU cc_start: 0.9376 (OUTLIER) cc_final: 0.9103 (mm) REVERT: B 474 GLU cc_start: 0.9744 (mm-30) cc_final: 0.9418 (mm-30) REVERT: B 475 MET cc_start: 0.9654 (mmm) cc_final: 0.9420 (mmm) REVERT: B 909 MET cc_start: 0.9776 (tmm) cc_final: 0.9462 (tmm) outliers start: 11 outliers final: 8 residues processed: 42 average time/residue: 0.0590 time to fit residues: 4.2464 Evaluate side-chains 40 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 31 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 435 GLU Chi-restraints excluded: chain B residue 682 CYS Chi-restraints excluded: chain B residue 720 HIS Chi-restraints excluded: chain B residue 785 ASN Chi-restraints excluded: chain B residue 826 PHE Chi-restraints excluded: chain B residue 891 ILE Chi-restraints excluded: chain B residue 936 THR Chi-restraints excluded: chain B residue 944 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 28 optimal weight: 7.9990 chunk 80 optimal weight: 6.9990 chunk 16 optimal weight: 8.9990 chunk 48 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 chunk 50 optimal weight: 7.9990 chunk 65 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 4 optimal weight: 7.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.028275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.2538 r_free = 0.2538 target = 0.022167 restraints weight = 82853.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2568 r_free = 0.2568 target = 0.022846 restraints weight = 56635.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2590 r_free = 0.2590 target = 0.023360 restraints weight = 42958.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2608 r_free = 0.2608 target = 0.023761 restraints weight = 34654.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 16)----------------| | r_work = 0.2618 r_free = 0.2618 target = 0.023999 restraints weight = 29196.436| |-----------------------------------------------------------------------------| r_work (final): 0.2611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.1466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8262 Z= 0.140 Angle : 0.545 10.802 11222 Z= 0.272 Chirality : 0.039 0.166 1268 Planarity : 0.003 0.035 1430 Dihedral : 6.458 79.595 1151 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.68 % Allowed : 12.32 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.29), residues: 1009 helix: 2.02 (0.25), residues: 441 sheet: 0.00 (0.48), residues: 125 loop : 0.38 (0.34), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 809 TYR 0.012 0.001 TYR B 769 PHE 0.039 0.001 PHE B 479 TRP 0.008 0.001 TRP B 696 HIS 0.003 0.001 HIS B 377 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 8262) covalent geometry : angle 0.54520 (11222) hydrogen bonds : bond 0.02811 ( 376) hydrogen bonds : angle 4.90811 ( 1035) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 32 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 253 MET cc_start: 0.6209 (mpp) cc_final: 0.5173 (tpp) REVERT: B 365 LEU cc_start: 0.9413 (OUTLIER) cc_final: 0.9138 (mm) REVERT: B 474 GLU cc_start: 0.9745 (mm-30) cc_final: 0.9148 (mt-10) REVERT: B 475 MET cc_start: 0.9664 (mmm) cc_final: 0.8995 (mmm) REVERT: B 909 MET cc_start: 0.9766 (tmm) cc_final: 0.9433 (tmm) outliers start: 15 outliers final: 10 residues processed: 45 average time/residue: 0.0644 time to fit residues: 4.7327 Evaluate side-chains 43 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 32 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 LYS Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 435 GLU Chi-restraints excluded: chain B residue 682 CYS Chi-restraints excluded: chain B residue 720 HIS Chi-restraints excluded: chain B residue 785 ASN Chi-restraints excluded: chain B residue 826 PHE Chi-restraints excluded: chain B residue 936 THR Chi-restraints excluded: chain B residue 944 THR Chi-restraints excluded: chain B residue 998 MET Chi-restraints excluded: chain B residue 1001 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 70 optimal weight: 0.8980 chunk 10 optimal weight: 9.9990 chunk 95 optimal weight: 8.9990 chunk 21 optimal weight: 9.9990 chunk 25 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 90 optimal weight: 0.9990 chunk 75 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.028726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2552 r_free = 0.2552 target = 0.022550 restraints weight = 82047.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2580 r_free = 0.2580 target = 0.023243 restraints weight = 56161.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2605 r_free = 0.2605 target = 0.023779 restraints weight = 42550.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2623 r_free = 0.2623 target = 0.024188 restraints weight = 34305.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.2633 r_free = 0.2633 target = 0.024445 restraints weight = 28828.399| |-----------------------------------------------------------------------------| r_work (final): 0.2626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8262 Z= 0.107 Angle : 0.548 14.254 11222 Z= 0.264 Chirality : 0.039 0.167 1268 Planarity : 0.003 0.036 1430 Dihedral : 6.340 79.036 1151 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.12 % Allowed : 12.99 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.10 % 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: 1.57 (0.29), residues: 1009 helix: 2.08 (0.25), residues: 442 sheet: 0.03 (0.48), residues: 125 loop : 0.40 (0.34), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 586 TYR 0.009 0.001 TYR B 769 PHE 0.015 0.001 PHE B 656 TRP 0.007 0.001 TRP B 696 HIS 0.003 0.001 HIS B 636 Details of bonding type rmsd covalent geometry : bond 0.00228 ( 8262) covalent geometry : angle 0.54769 (11222) hydrogen bonds : bond 0.02655 ( 376) hydrogen bonds : angle 4.81215 ( 1035) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 32 time to evaluate : 0.342 Fit side-chains revert: symmetry clash REVERT: B 365 LEU cc_start: 0.9406 (OUTLIER) cc_final: 0.8890 (mt) REVERT: B 474 GLU cc_start: 0.9742 (mm-30) cc_final: 0.9141 (mt-10) REVERT: B 475 MET cc_start: 0.9667 (mmm) cc_final: 0.8972 (mmm) REVERT: B 909 MET cc_start: 0.9760 (tmm) cc_final: 0.9428 (tmm) REVERT: B 1009 MET cc_start: 0.9337 (mpp) cc_final: 0.9083 (pmm) outliers start: 10 outliers final: 6 residues processed: 40 average time/residue: 0.0669 time to fit residues: 4.5129 Evaluate side-chains 38 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 31 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 435 GLU Chi-restraints excluded: chain B residue 682 CYS Chi-restraints excluded: chain B residue 720 HIS Chi-restraints excluded: chain B residue 785 ASN Chi-restraints excluded: chain B residue 826 PHE Chi-restraints excluded: chain B residue 998 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 44 optimal weight: 6.9990 chunk 8 optimal weight: 6.9990 chunk 31 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 5 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 chunk 23 optimal weight: 8.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 94 optimal weight: 8.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.028060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2522 r_free = 0.2522 target = 0.021976 restraints weight = 84852.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2553 r_free = 0.2553 target = 0.022696 restraints weight = 57579.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2576 r_free = 0.2576 target = 0.023220 restraints weight = 43207.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2593 r_free = 0.2593 target = 0.023622 restraints weight = 34610.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2608 r_free = 0.2608 target = 0.023940 restraints weight = 28967.571| |-----------------------------------------------------------------------------| r_work (final): 0.2599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8262 Z= 0.159 Angle : 0.574 12.451 11222 Z= 0.282 Chirality : 0.040 0.166 1268 Planarity : 0.004 0.045 1430 Dihedral : 6.445 79.443 1151 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.34 % Allowed : 12.65 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.10 % 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: 1.63 (0.28), residues: 1009 helix: 2.12 (0.25), residues: 434 sheet: 0.26 (0.51), residues: 101 loop : 0.39 (0.33), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 947 TYR 0.011 0.001 TYR B 769 PHE 0.038 0.002 PHE B 479 TRP 0.007 0.001 TRP B 696 HIS 0.003 0.001 HIS B 377 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 8262) covalent geometry : angle 0.57392 (11222) hydrogen bonds : bond 0.02803 ( 376) hydrogen bonds : angle 4.87268 ( 1035) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 32 time to evaluate : 0.336 Fit side-chains revert: symmetry clash REVERT: B 365 LEU cc_start: 0.9418 (OUTLIER) cc_final: 0.8895 (mt) REVERT: B 423 ASP cc_start: 0.9295 (OUTLIER) cc_final: 0.8521 (t0) REVERT: B 474 GLU cc_start: 0.9748 (mm-30) cc_final: 0.9169 (mt-10) REVERT: B 475 MET cc_start: 0.9677 (mmm) cc_final: 0.9004 (mmm) REVERT: B 909 MET cc_start: 0.9768 (tmm) cc_final: 0.9440 (tmm) REVERT: B 1009 MET cc_start: 0.9373 (mpp) cc_final: 0.9143 (pmm) outliers start: 12 outliers final: 10 residues processed: 41 average time/residue: 0.0627 time to fit residues: 4.2747 Evaluate side-chains 44 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 32 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 253 MET Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 435 GLU Chi-restraints excluded: chain B residue 637 THR Chi-restraints excluded: chain B residue 682 CYS Chi-restraints excluded: chain B residue 720 HIS Chi-restraints excluded: chain B residue 785 ASN Chi-restraints excluded: chain B residue 826 PHE Chi-restraints excluded: chain B residue 936 THR Chi-restraints excluded: chain B residue 998 MET Chi-restraints excluded: chain B residue 1001 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 14 optimal weight: 0.0770 chunk 70 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 76 optimal weight: 6.9990 chunk 4 optimal weight: 1.9990 chunk 87 optimal weight: 9.9990 chunk 42 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 overall best weight: 0.9942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.028978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2554 r_free = 0.2554 target = 0.022711 restraints weight = 81255.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2583 r_free = 0.2583 target = 0.023445 restraints weight = 55191.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2607 r_free = 0.2607 target = 0.023999 restraints weight = 41445.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2624 r_free = 0.2624 target = 0.024395 restraints weight = 33337.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2636 r_free = 0.2636 target = 0.024690 restraints weight = 27929.158| |-----------------------------------------------------------------------------| r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8262 Z= 0.097 Angle : 0.555 12.386 11222 Z= 0.266 Chirality : 0.040 0.167 1268 Planarity : 0.003 0.048 1430 Dihedral : 6.239 78.389 1151 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.01 % Allowed : 13.21 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.10 % 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: 1.64 (0.29), residues: 1009 helix: 2.12 (0.26), residues: 442 sheet: 0.36 (0.48), residues: 116 loop : 0.33 (0.33), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 947 TYR 0.009 0.001 TYR B 769 PHE 0.016 0.001 PHE B 656 TRP 0.007 0.001 TRP B 696 HIS 0.003 0.001 HIS B 377 Details of bonding type rmsd covalent geometry : bond 0.00209 ( 8262) covalent geometry : angle 0.55522 (11222) hydrogen bonds : bond 0.02574 ( 376) hydrogen bonds : angle 4.72448 ( 1035) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 32 time to evaluate : 0.332 Fit side-chains REVERT: B 365 LEU cc_start: 0.9425 (OUTLIER) cc_final: 0.8942 (mt) REVERT: B 474 GLU cc_start: 0.9742 (mm-30) cc_final: 0.9134 (mt-10) REVERT: B 475 MET cc_start: 0.9667 (mmm) cc_final: 0.8981 (mmm) REVERT: B 909 MET cc_start: 0.9778 (tmm) cc_final: 0.9446 (tmm) REVERT: B 1009 MET cc_start: 0.9319 (mpp) cc_final: 0.9118 (pmm) outliers start: 9 outliers final: 6 residues processed: 39 average time/residue: 0.0661 time to fit residues: 4.3153 Evaluate side-chains 38 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 31 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 637 THR Chi-restraints excluded: chain B residue 682 CYS Chi-restraints excluded: chain B residue 720 HIS Chi-restraints excluded: chain B residue 826 PHE Chi-restraints excluded: chain B residue 936 THR Chi-restraints excluded: chain B residue 998 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 46 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 18 optimal weight: 7.9990 chunk 25 optimal weight: 7.9990 chunk 12 optimal weight: 0.0470 chunk 85 optimal weight: 4.9990 chunk 27 optimal weight: 8.9990 chunk 87 optimal weight: 0.9980 chunk 58 optimal weight: 7.9990 overall best weight: 1.4082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.028770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2548 r_free = 0.2548 target = 0.022569 restraints weight = 82187.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2576 r_free = 0.2576 target = 0.023266 restraints weight = 56199.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2601 r_free = 0.2601 target = 0.023827 restraints weight = 42464.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2617 r_free = 0.2617 target = 0.024215 restraints weight = 34218.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2630 r_free = 0.2630 target = 0.024507 restraints weight = 28748.647| |-----------------------------------------------------------------------------| r_work (final): 0.2622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8262 Z= 0.108 Angle : 0.555 11.856 11222 Z= 0.268 Chirality : 0.039 0.167 1268 Planarity : 0.003 0.047 1430 Dihedral : 6.235 78.589 1151 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.01 % Allowed : 13.33 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.10 % 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: 1.64 (0.29), residues: 1009 helix: 2.13 (0.26), residues: 442 sheet: 0.24 (0.49), residues: 106 loop : 0.35 (0.33), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 947 TYR 0.009 0.001 TYR B 769 PHE 0.037 0.001 PHE B 479 TRP 0.006 0.001 TRP B 696 HIS 0.002 0.001 HIS B 377 Details of bonding type rmsd covalent geometry : bond 0.00231 ( 8262) covalent geometry : angle 0.55534 (11222) hydrogen bonds : bond 0.02579 ( 376) hydrogen bonds : angle 4.75484 ( 1035) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1148.37 seconds wall clock time: 20 minutes 52.22 seconds (1252.22 seconds total)