Starting phenix.real_space_refine on Sat Jul 4 04:41:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9y7h_72655/07_2026/9y7h_72655_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9y7h_72655/07_2026/9y7h_72655.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9y7h_72655/07_2026/9y7h_72655_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9y7h_72655/07_2026/9y7h_72655_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9y7h_72655/07_2026/9y7h_72655.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9y7h_72655/07_2026/9y7h_72655.map" } resolution = 4.4 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= 0.018 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 Ca 1 9.91 5 S 51 5.16 5 C 5625 2.51 5 N 1545 2.21 5 O 1691 1.98 5 H 8789 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17702 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 11888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 741, 11888 Classifications: {'peptide': 741} Link IDs: {'PTRANS': 46, 'TRANS': 694} Chain breaks: 3 Chain: "B" Number of atoms: 4990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 4990 Classifications: {'peptide': 332} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 326} Chain: "G" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 807 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 4, 'TRANS': 47} Chain: "A" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'ME7': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Time building chain proxies: 2.72, per 1000 atoms: 0.15 Number of scatterers: 17702 At special positions: 0 Unit cell: (86.24, 105.105, 121.275, 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) Ca 1 19.99 S 51 16.00 O 1691 8.00 N 1545 7.00 C 5625 6.00 H 8789 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=0, symmetry=0 Time building additional restraints: 1.68 Conformation dependent library (CDL) restraints added in 614.6 milliseconds 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2122 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 14 sheets defined 29.1% alpha, 14.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 19 through 25 Processing helix chain 'A' and resid 83 through 90 Processing helix chain 'A' and resid 99 through 101 No H-bonds generated for 'chain 'A' and resid 99 through 101' Processing helix chain 'A' and resid 127 through 140 Processing helix chain 'A' and resid 141 through 146 removed outlier: 3.549A pdb=" N GLN A 145 " --> pdb=" O ASN A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 163 removed outlier: 3.665A pdb=" N PHE A 152 " --> pdb=" O SER A 148 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLN A 163 " --> pdb=" O LYS A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 179 Processing helix chain 'A' and resid 182 through 194 Processing helix chain 'A' and resid 204 through 208 removed outlier: 3.502A pdb=" N GLU A 207 " --> pdb=" O ARG A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 219 Processing helix chain 'A' and resid 223 through 234 Processing helix chain 'A' and resid 243 through 253 Processing helix chain 'A' and resid 268 through 279 Processing helix chain 'A' and resid 292 through 302 removed outlier: 4.284A pdb=" N GLY A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 314 removed outlier: 4.024A pdb=" N LEU A 313 " --> pdb=" O PRO A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 355 removed outlier: 3.747A pdb=" N ARG A 351 " --> pdb=" O VAL A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 397 removed outlier: 4.457A pdb=" N ALA A 397 " --> pdb=" O LEU A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 400 No H-bonds generated for 'chain 'A' and resid 398 through 400' Processing helix chain 'A' and resid 418 through 432 Processing helix chain 'A' and resid 433 through 437 removed outlier: 3.671A pdb=" N ALA A 436 " --> pdb=" O PHE A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 460 removed outlier: 3.817A pdb=" N MET A 460 " --> pdb=" O GLN A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 582 removed outlier: 3.777A pdb=" N SER A 582 " --> pdb=" O THR A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 592 Processing helix chain 'A' and resid 604 through 612 Processing helix chain 'A' and resid 621 through 632 removed outlier: 3.503A pdb=" N LYS A 631 " --> pdb=" O GLU A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 641 Processing helix chain 'A' and resid 661 through 667 removed outlier: 3.612A pdb=" N ASN A 666 " --> pdb=" O GLN A 662 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N VAL A 667 " --> pdb=" O LEU A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 691 removed outlier: 4.253A pdb=" N VAL A 689 " --> pdb=" O LEU A 685 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE A 690 " --> pdb=" O ASN A 686 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLU A 691 " --> pdb=" O ALA A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 707 removed outlier: 3.595A pdb=" N ARG A 706 " --> pdb=" O PRO A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 869 through 878 Processing helix chain 'B' and resid 9 through 26 Processing helix chain 'B' and resid 29 through 37 removed outlier: 3.686A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE B 37 " --> pdb=" O ILE B 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 11 through 24 Processing helix chain 'G' and resid 29 through 46 removed outlier: 3.511A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 29 removed outlier: 3.559A pdb=" N VAL A 106 " --> pdb=" O LEU A 118 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 44 through 45 Processing sheet with id=AA3, first strand: chain 'A' and resid 170 through 171 Processing sheet with id=AA4, first strand: chain 'A' and resid 241 through 242 Processing sheet with id=AA5, first strand: chain 'A' and resid 365 through 366 removed outlier: 3.507A pdb=" N VAL A 387 " --> pdb=" O ILE A 377 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 783 through 786 removed outlier: 4.859A pdb=" N LYS A 785 " --> pdb=" O ASN A 726 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ASN A 726 " --> pdb=" O LYS A 785 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ILE A 733 " --> pdb=" O LEU A 839 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N LEU A 839 " --> pdb=" O ILE A 733 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N GLY A 735 " --> pdb=" O ALA A 837 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ALA A 837 " --> pdb=" O GLY A 735 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 745 through 750 removed outlier: 3.639A pdb=" N ILE A 796 " --> pdb=" O ARG A 809 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY A 807 " --> pdb=" O ALA A 798 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N GLU A 800 " --> pdb=" O PHE A 805 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N PHE A 805 " --> pdb=" O GLU A 800 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 61 through 63 removed outlier: 3.652A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE B 80 " --> pdb=" O SER B 72 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 123 through 124 Processing sheet with id=AB1, first strand: chain 'B' and resid 146 through 153 removed outlier: 6.579A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.689A pdb=" N SER B 191 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL B 200 " --> pdb=" O SER B 191 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.592A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N CYS B 250 " --> pdb=" O TYR B 264 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.725A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 315 through 320 268 hydrogen bonds defined for protein. 756 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: 3.36 Time building geometry restraints manager: 2.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 8773 1.03 - 1.23: 20 1.23 - 1.42: 3776 1.42 - 1.62: 5230 1.62 - 1.81: 82 Bond restraints: 17881 Sorted by residual: bond pdb=" N ARG B 8 " pdb=" H1 ARG B 8 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.49e+01 bond pdb=" C ILE A 170 " pdb=" O ILE A 170 " ideal model delta sigma weight residual 1.240 1.231 0.009 1.26e-02 6.30e+03 5.01e-01 bond pdb=" N CYS B 121 " pdb=" CA CYS B 121 " ideal model delta sigma weight residual 1.457 1.466 -0.009 1.29e-02 6.01e+03 4.77e-01 bond pdb=" CB GLN A 670 " pdb=" CG GLN A 670 " ideal model delta sigma weight residual 1.520 1.500 0.020 3.00e-02 1.11e+03 4.42e-01 bond pdb=" CB ASN A 658 " pdb=" CG ASN A 658 " ideal model delta sigma weight residual 1.516 1.500 0.016 2.50e-02 1.60e+03 4.20e-01 ... (remaining 17876 not shown) Histogram of bond angle deviations from ideal: 0.00 - 11.20: 32261 11.20 - 22.41: 1 22.41 - 33.61: 5 33.61 - 44.82: 0 44.82 - 56.02: 2 Bond angle restraints: 32269 Sorted by residual: angle pdb=" C CYS B 114 " pdb=" N GLY B 115 " pdb=" H GLY B 115 " ideal model delta sigma weight residual 124.93 68.91 56.02 3.00e+00 1.11e-01 3.49e+02 angle pdb=" CA GLY B 115 " pdb=" N GLY B 115 " pdb=" H GLY B 115 " ideal model delta sigma weight residual 114.63 58.85 55.78 3.00e+00 1.11e-01 3.46e+02 angle pdb="HG21 THR A 115 " pdb=" CG2 THR A 115 " pdb="HG22 THR A 115 " ideal model delta sigma weight residual 109.00 79.22 29.78 3.00e+00 1.11e-01 9.85e+01 angle pdb="HG22 THR A 115 " pdb=" CG2 THR A 115 " pdb="HG23 THR A 115 " ideal model delta sigma weight residual 109.00 79.37 29.63 3.00e+00 1.11e-01 9.76e+01 angle pdb=" CB THR A 115 " pdb=" CG2 THR A 115 " pdb="HG21 THR A 115 " ideal model delta sigma weight residual 110.00 81.51 28.49 3.00e+00 1.11e-01 9.02e+01 ... (remaining 32264 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.06: 8155 27.06 - 54.11: 242 54.11 - 81.17: 24 81.17 - 108.23: 2 108.23 - 135.29: 1 Dihedral angle restraints: 8424 sinusoidal: 4626 harmonic: 3798 Sorted by residual: dihedral pdb=" NAO ME7 A 901 " pdb=" CAI ME7 A 901 " pdb=" CAJ ME7 A 901 " pdb=" NAP ME7 A 901 " ideal model delta sinusoidal sigma weight residual -179.98 -44.69 -135.29 1 3.00e+01 1.11e-03 1.82e+01 dihedral pdb=" CA PHE A 412 " pdb=" C PHE A 412 " pdb=" N GLU A 413 " pdb=" CA GLU A 413 " ideal model delta harmonic sigma weight residual 180.00 159.73 20.27 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" CA ASN A 675 " pdb=" C ASN A 675 " pdb=" N PHE A 676 " pdb=" CA PHE A 676 " ideal model delta harmonic sigma weight residual 180.00 160.36 19.64 0 5.00e+00 4.00e-02 1.54e+01 ... (remaining 8421 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 875 0.030 - 0.060: 348 0.060 - 0.090: 66 0.090 - 0.120: 68 0.120 - 0.150: 11 Chirality restraints: 1368 Sorted by residual: chirality pdb=" CA ILE A 796 " pdb=" N ILE A 796 " pdb=" C ILE A 796 " pdb=" CB ILE A 796 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.62e-01 chirality pdb=" CA ILE B 273 " pdb=" N ILE B 273 " pdb=" C ILE B 273 " pdb=" CB ILE B 273 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.09e-01 chirality pdb=" CA VAL B 296 " pdb=" N VAL B 296 " pdb=" C VAL B 296 " pdb=" CB VAL B 296 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.04e-01 ... (remaining 1365 not shown) Planarity restraints: 2657 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 280 " -0.028 5.00e-02 4.00e+02 4.18e-02 2.79e+00 pdb=" N PRO A 281 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 281 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 281 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 811 " -0.021 5.00e-02 4.00e+02 3.10e-02 1.54e+00 pdb=" N PRO A 812 " 0.054 5.00e-02 4.00e+02 pdb=" CA PRO A 812 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 812 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 783 " 0.019 5.00e-02 4.00e+02 2.83e-02 1.28e+00 pdb=" N PRO A 784 " -0.049 5.00e-02 4.00e+02 pdb=" CA PRO A 784 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 784 " 0.016 5.00e-02 4.00e+02 ... (remaining 2654 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.18: 710 2.18 - 2.78: 36149 2.78 - 3.39: 48074 3.39 - 3.99: 60766 3.99 - 4.60: 94483 Nonbonded interactions: 240182 Sorted by model distance: nonbonded pdb=" H GLY B 115 " pdb=" HA2 GLY B 115 " model vdw 1.571 1.816 nonbonded pdb=" O CYS B 114 " pdb=" H GLY B 115 " model vdw 1.706 1.960 nonbonded pdb=" H ASN A 595 " pdb="HD22 ASN A 595 " model vdw 1.756 2.100 nonbonded pdb=" H ASN A 165 " pdb=" H ARG A 169 " model vdw 1.758 2.100 nonbonded pdb=" HE2 HIS A 332 " pdb="CA CA A 902 " model vdw 1.793 2.780 ... (remaining 240177 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.050 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: 0.110 Extract box with map and model: 0.230 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 15.850 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 9092 Z= 0.122 Angle : 0.474 7.319 12308 Z= 0.254 Chirality : 0.039 0.150 1368 Planarity : 0.004 0.042 1600 Dihedral : 11.309 135.286 3406 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.92 % Favored : 92.90 % Rotamer: Outliers : 1.64 % Allowed : 7.68 % Favored : 90.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.49 (0.26), residues: 1113 helix: 0.82 (0.33), residues: 270 sheet: -1.48 (0.36), residues: 227 loop : -1.65 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 44 TYR 0.011 0.001 TYR A 157 PHE 0.008 0.001 PHE A 28 TRP 0.005 0.001 TRP B 82 HIS 0.002 0.001 HIS G 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 ( 9092) covalent geometry : angle 0.47426 / 0.25 (12308) hydrogen bonds : bond 0.17962 / 11.58 ( 268) hydrogen bonds : angle 6.37973 / 4.35 ( 756) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 151 time to evaluate : 0.486 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: 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: symmetry clash REVERT: A 138 LEU cc_start: 0.9298 (mt) cc_final: 0.9076 (mm) REVERT: A 140 MET cc_start: 0.9241 (mmt) cc_final: 0.8946 (mmm) REVERT: A 170 ILE cc_start: 0.9469 (mt) cc_final: 0.9263 (tt) REVERT: A 416 VAL cc_start: 0.8911 (t) cc_final: 0.8709 (t) REVERT: A 425 MET cc_start: 0.9141 (tmm) cc_final: 0.8798 (tmm) REVERT: A 626 MET cc_start: 0.9111 (ttp) cc_final: 0.8666 (tpp) REVERT: A 741 ARG cc_start: 0.8404 (mtp180) cc_final: 0.8133 (mtp180) REVERT: B 145 TYR cc_start: 0.7956 (p90) cc_final: 0.7325 (p90) outliers start: 16 outliers final: 11 residues processed: 164 average time/residue: 0.2690 time to fit residues: 57.5425 Evaluate side-chains 105 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 7.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.1980 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 0.7980 chunk 106 optimal weight: 5.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 595 ASN A 666 ASN A 675 ASN ** A 821 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.111446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.081106 restraints weight = 55037.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.081759 restraints weight = 38382.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.083896 restraints weight = 27506.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.083859 restraints weight = 20723.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.084754 restraints weight = 20594.139| |-----------------------------------------------------------------------------| r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9092 Z= 0.175 Angle : 0.558 7.383 12308 Z= 0.301 Chirality : 0.040 0.155 1368 Planarity : 0.005 0.102 1600 Dihedral : 5.775 134.627 1229 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.16 % Favored : 90.66 % Rotamer: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % 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: -1.73 (0.25), residues: 1113 helix: 0.35 (0.30), residues: 283 sheet: -1.46 (0.36), residues: 227 loop : -1.79 (0.25), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 197 TYR 0.011 0.001 TYR A 157 PHE 0.029 0.002 PHE A 296 TRP 0.006 0.001 TRP A 131 HIS 0.012 0.001 HIS A 821 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.18 ( 9092) covalent geometry : angle 0.55765 / 0.30 (12308) hydrogen bonds : bond 0.04928 / 3.13 ( 268) hydrogen bonds : angle 5.66770 / 3.93 ( 756) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.496 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: 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 121 MET cc_start: 0.8639 (tpt) cc_final: 0.8353 (tpp) REVERT: A 140 MET cc_start: 0.9198 (mmt) cc_final: 0.8948 (mmm) REVERT: A 241 LEU cc_start: 0.8778 (mp) cc_final: 0.8237 (tp) REVERT: A 398 GLU cc_start: 0.8409 (tm-30) cc_final: 0.7994 (tm-30) REVERT: A 416 VAL cc_start: 0.8985 (t) cc_final: 0.8724 (t) REVERT: A 626 MET cc_start: 0.9223 (ttp) cc_final: 0.8641 (tpp) REVERT: A 741 ARG cc_start: 0.8328 (mtp180) cc_final: 0.8108 (mtp180) REVERT: B 78 LYS cc_start: 0.8819 (tptm) cc_final: 0.8548 (mmmt) REVERT: B 145 TYR cc_start: 0.7912 (p90) cc_final: 0.7229 (p90) REVERT: G 21 MET cc_start: 0.9022 (mmt) cc_final: 0.8781 (mmm) outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.2459 time to fit residues: 44.4241 Evaluate side-chains 99 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 70 optimal weight: 1.9990 chunk 97 optimal weight: 6.9990 chunk 12 optimal weight: 0.8980 chunk 96 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 84 optimal weight: 8.9990 chunk 46 optimal weight: 4.9990 chunk 36 optimal weight: 0.0040 chunk 1 optimal weight: 0.5980 chunk 95 optimal weight: 4.9990 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 163 GLN ** A 821 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.111952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.080468 restraints weight = 55326.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.079775 restraints weight = 45545.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.081711 restraints weight = 32678.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.083075 restraints weight = 23706.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.083112 restraints weight = 20923.109| |-----------------------------------------------------------------------------| r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9092 Z= 0.119 Angle : 0.510 7.385 12308 Z= 0.271 Chirality : 0.039 0.150 1368 Planarity : 0.004 0.041 1600 Dihedral : 5.666 134.120 1229 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.64 % Favored : 92.18 % Rotamer: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % 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: -1.53 (0.26), residues: 1113 helix: 0.49 (0.31), residues: 284 sheet: -1.41 (0.36), residues: 231 loop : -1.61 (0.26), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 197 TYR 0.010 0.001 TYR A 157 PHE 0.018 0.001 PHE A 296 TRP 0.005 0.001 TRP B 211 HIS 0.004 0.001 HIS A 821 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 ( 9092) covalent geometry : angle 0.50994 / 0.27 (12308) hydrogen bonds : bond 0.03966 / 2.52 ( 268) hydrogen bonds : angle 5.29333 / 3.68 ( 756) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.513 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 MET cc_start: 0.8615 (tpt) cc_final: 0.8409 (tpp) REVERT: A 140 MET cc_start: 0.9255 (mmt) cc_final: 0.8927 (mmm) REVERT: A 241 LEU cc_start: 0.8659 (mp) cc_final: 0.8345 (tp) REVERT: A 398 GLU cc_start: 0.8461 (tm-30) cc_final: 0.8001 (tm-30) REVERT: A 416 VAL cc_start: 0.9010 (t) cc_final: 0.8767 (t) REVERT: A 590 MET cc_start: 0.9007 (mmm) cc_final: 0.8657 (mmm) REVERT: A 626 MET cc_start: 0.9176 (ttp) cc_final: 0.8597 (tpp) REVERT: A 741 ARG cc_start: 0.8345 (mtp180) cc_final: 0.8098 (mtp180) REVERT: B 78 LYS cc_start: 0.8776 (tptm) cc_final: 0.8505 (mmmt) REVERT: B 217 MET cc_start: 0.7209 (mmp) cc_final: 0.6907 (mmm) outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.2498 time to fit residues: 40.3093 Evaluate side-chains 98 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 25 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 86 optimal weight: 8.9990 chunk 66 optimal weight: 0.5980 chunk 65 optimal weight: 0.7980 chunk 42 optimal weight: 0.0070 chunk 52 optimal weight: 1.9990 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.112817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.081819 restraints weight = 55541.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.080393 restraints weight = 48141.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.081972 restraints weight = 35855.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.083129 restraints weight = 28071.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.083171 restraints weight = 24651.990| |-----------------------------------------------------------------------------| r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9092 Z= 0.111 Angle : 0.498 7.419 12308 Z= 0.265 Chirality : 0.039 0.149 1368 Planarity : 0.004 0.063 1600 Dihedral : 5.591 133.833 1229 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.91 % Favored : 91.91 % Rotamer: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % 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: -1.45 (0.26), residues: 1113 helix: 0.59 (0.31), residues: 283 sheet: -1.34 (0.36), residues: 228 loop : -1.59 (0.26), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 44 TYR 0.008 0.001 TYR A 157 PHE 0.017 0.001 PHE A 636 TRP 0.004 0.001 TRP A 54 HIS 0.003 0.001 HIS A 808 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 ( 9092) covalent geometry : angle 0.49826 / 0.26 (12308) hydrogen bonds : bond 0.03487 / 2.21 ( 268) hydrogen bonds : angle 5.13408 / 3.59 ( 756) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.488 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: 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 140 MET cc_start: 0.9234 (mmt) cc_final: 0.8869 (mmm) REVERT: A 241 LEU cc_start: 0.8630 (mp) cc_final: 0.8334 (tp) REVERT: A 398 GLU cc_start: 0.8457 (tm-30) cc_final: 0.8009 (tm-30) REVERT: A 416 VAL cc_start: 0.9027 (t) cc_final: 0.8799 (t) REVERT: A 626 MET cc_start: 0.9126 (ttp) cc_final: 0.8560 (tpp) REVERT: A 741 ARG cc_start: 0.8272 (mtp180) cc_final: 0.8009 (mtp180) REVERT: B 188 MET cc_start: 0.7569 (mpp) cc_final: 0.7362 (mpp) outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 0.2449 time to fit residues: 40.8153 Evaluate side-chains 97 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 96 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 69 optimal weight: 0.3980 chunk 13 optimal weight: 0.9990 chunk 56 optimal weight: 0.0570 chunk 72 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 103 optimal weight: 8.9990 chunk 35 optimal weight: 0.1980 chunk 64 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 595 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.112839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.081410 restraints weight = 54962.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.082583 restraints weight = 36820.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.084146 restraints weight = 26568.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.085294 restraints weight = 19013.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.085377 restraints weight = 16818.950| |-----------------------------------------------------------------------------| r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9092 Z= 0.099 Angle : 0.495 7.427 12308 Z= 0.261 Chirality : 0.039 0.149 1368 Planarity : 0.004 0.037 1600 Dihedral : 5.549 133.231 1229 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.92 % Favored : 92.90 % Rotamer: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.39 (0.26), residues: 1113 helix: 0.69 (0.31), residues: 291 sheet: -1.35 (0.36), residues: 224 loop : -1.58 (0.26), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 197 TYR 0.011 0.001 TYR A 406 PHE 0.026 0.001 PHE A 704 TRP 0.003 0.001 TRP A 54 HIS 0.003 0.001 HIS A 808 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.10 ( 9092) covalent geometry : angle 0.49469 / 0.26 (12308) hydrogen bonds : bond 0.03255 / 2.09 ( 268) hydrogen bonds : angle 4.95407 / 3.48 ( 756) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.498 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: 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 140 MET cc_start: 0.9242 (mmt) cc_final: 0.8836 (mmm) REVERT: A 241 LEU cc_start: 0.8540 (mp) cc_final: 0.8180 (tp) REVERT: A 416 VAL cc_start: 0.9038 (t) cc_final: 0.8808 (t) REVERT: A 626 MET cc_start: 0.9147 (ttp) cc_final: 0.8538 (tpp) REVERT: A 691 GLU cc_start: 0.8526 (pp20) cc_final: 0.8206 (pp20) REVERT: A 741 ARG cc_start: 0.8232 (mtp180) cc_final: 0.7983 (mtp180) REVERT: B 188 MET cc_start: 0.7655 (mpp) cc_final: 0.7422 (mpp) REVERT: B 190 LEU cc_start: 0.9159 (tp) cc_final: 0.8942 (tt) outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 0.2134 time to fit residues: 35.9215 Evaluate side-chains 99 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 66 optimal weight: 0.0870 chunk 96 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 44 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 overall best weight: 0.7558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 595 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.112659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.081378 restraints weight = 54958.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.081921 restraints weight = 41079.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.083394 restraints weight = 31307.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.084249 restraints weight = 21907.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.084339 restraints weight = 19852.451| |-----------------------------------------------------------------------------| r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9092 Z= 0.115 Angle : 0.486 7.457 12308 Z= 0.258 Chirality : 0.039 0.147 1368 Planarity : 0.004 0.040 1600 Dihedral : 5.495 132.696 1229 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.73 % Favored : 92.09 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % 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: -1.36 (0.26), residues: 1113 helix: 0.76 (0.32), residues: 286 sheet: -1.36 (0.36), residues: 225 loop : -1.57 (0.26), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 707 TYR 0.010 0.001 TYR A 406 PHE 0.015 0.001 PHE A 636 TRP 0.003 0.001 TRP A 776 HIS 0.005 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 ( 9092) covalent geometry : angle 0.48553 / 0.26 (12308) hydrogen bonds : bond 0.03209 / 2.06 ( 268) hydrogen bonds : angle 4.96167 / 3.53 ( 756) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.383 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: 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 140 MET cc_start: 0.9256 (mmt) cc_final: 0.8803 (mmm) REVERT: A 241 LEU cc_start: 0.8575 (mp) cc_final: 0.8220 (tp) REVERT: A 398 GLU cc_start: 0.8066 (tt0) cc_final: 0.7692 (tm-30) REVERT: A 416 VAL cc_start: 0.9068 (t) cc_final: 0.8864 (t) REVERT: A 626 MET cc_start: 0.9106 (ttp) cc_final: 0.8516 (tpp) REVERT: A 691 GLU cc_start: 0.8538 (pp20) cc_final: 0.8199 (pp20) REVERT: A 741 ARG cc_start: 0.8283 (mtp180) cc_final: 0.8025 (mtp180) REVERT: B 188 MET cc_start: 0.7578 (mpp) cc_final: 0.7344 (mpp) REVERT: B 190 LEU cc_start: 0.9249 (tp) cc_final: 0.9007 (tt) REVERT: B 270 ILE cc_start: 0.9022 (mp) cc_final: 0.8779 (pt) outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.2116 time to fit residues: 36.3474 Evaluate side-chains 100 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 26 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 77 optimal weight: 20.0000 chunk 73 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 101 optimal weight: 0.9980 chunk 111 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 677 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.109331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.078163 restraints weight = 55798.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.078571 restraints weight = 42033.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.080707 restraints weight = 30615.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.080633 restraints weight = 21764.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.080923 restraints weight = 21253.755| |-----------------------------------------------------------------------------| r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 9092 Z= 0.245 Angle : 0.566 7.423 12308 Z= 0.304 Chirality : 0.041 0.140 1368 Planarity : 0.004 0.040 1600 Dihedral : 5.733 132.262 1229 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.15 % Favored : 89.67 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % 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: -1.83 (0.25), residues: 1113 helix: 0.26 (0.30), residues: 290 sheet: -1.52 (0.35), residues: 230 loop : -1.86 (0.25), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 150 TYR 0.017 0.002 TYR A 157 PHE 0.026 0.002 PHE A 296 TRP 0.006 0.001 TRP A 131 HIS 0.008 0.002 HIS A 332 Details of bonding type rmsd/Z covalent geometry : bond 0.00551 / 0.25 ( 9092) covalent geometry : angle 0.56648 / 0.30 (12308) hydrogen bonds : bond 0.03997 / 2.62 ( 268) hydrogen bonds : angle 5.38220 / 3.83 ( 756) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.505 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: 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 140 MET cc_start: 0.9228 (mmt) cc_final: 0.8948 (mmm) REVERT: A 241 LEU cc_start: 0.8576 (mp) cc_final: 0.8167 (tp) REVERT: A 416 VAL cc_start: 0.9080 (t) cc_final: 0.8871 (t) REVERT: B 188 MET cc_start: 0.7656 (mpp) cc_final: 0.7441 (mpp) outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.2368 time to fit residues: 38.3797 Evaluate side-chains 93 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 96 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 chunk 56 optimal weight: 0.6980 chunk 85 optimal weight: 7.9990 chunk 83 optimal weight: 7.9990 chunk 101 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 76 optimal weight: 8.9990 chunk 19 optimal weight: 0.7980 chunk 69 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.110908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.080222 restraints weight = 55324.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.078797 restraints weight = 48657.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.080253 restraints weight = 38957.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.081313 restraints weight = 29563.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.081580 restraints weight = 24620.902| |-----------------------------------------------------------------------------| r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9092 Z= 0.143 Angle : 0.522 7.388 12308 Z= 0.277 Chirality : 0.040 0.148 1368 Planarity : 0.004 0.039 1600 Dihedral : 5.690 132.372 1229 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.36 % Favored : 91.46 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % 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: -1.71 (0.25), residues: 1113 helix: 0.34 (0.30), residues: 297 sheet: -1.45 (0.35), residues: 229 loop : -1.81 (0.25), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 707 TYR 0.012 0.001 TYR A 157 PHE 0.054 0.002 PHE A 676 TRP 0.005 0.001 TRP A 54 HIS 0.006 0.001 HIS A 332 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 ( 9092) covalent geometry : angle 0.52214 / 0.28 (12308) hydrogen bonds : bond 0.03438 / 2.24 ( 268) hydrogen bonds : angle 5.16165 / 3.66 ( 756) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.513 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: 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: symmetry clash REVERT: A 140 MET cc_start: 0.9199 (mmt) cc_final: 0.8910 (mmm) REVERT: A 416 VAL cc_start: 0.9076 (t) cc_final: 0.8842 (t) REVERT: A 626 MET cc_start: 0.8875 (ttp) cc_final: 0.8476 (tpp) REVERT: B 145 TYR cc_start: 0.7775 (p90) cc_final: 0.7076 (p90) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.2133 time to fit residues: 34.7767 Evaluate side-chains 94 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 98 optimal weight: 8.9990 chunk 100 optimal weight: 0.9990 chunk 96 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.110258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.078634 restraints weight = 55428.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.078239 restraints weight = 45495.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.080318 restraints weight = 32384.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.081054 restraints weight = 23957.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.081443 restraints weight = 21835.643| |-----------------------------------------------------------------------------| r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 9092 Z= 0.178 Angle : 0.539 7.405 12308 Z= 0.287 Chirality : 0.040 0.164 1368 Planarity : 0.004 0.040 1600 Dihedral : 5.671 132.400 1229 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.61 % Favored : 90.21 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % 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: -1.74 (0.25), residues: 1113 helix: 0.33 (0.30), residues: 290 sheet: -1.44 (0.35), residues: 228 loop : -1.82 (0.25), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 874 TYR 0.013 0.001 TYR A 157 PHE 0.048 0.002 PHE A 676 TRP 0.006 0.001 TRP A 131 HIS 0.009 0.002 HIS A 821 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.18 ( 9092) covalent geometry : angle 0.53935 / 0.29 (12308) hydrogen bonds : bond 0.03594 / 2.33 ( 268) hydrogen bonds : angle 5.22808 / 3.73 ( 756) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.503 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: 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 140 MET cc_start: 0.9204 (mmt) cc_final: 0.8913 (mmm) REVERT: A 416 VAL cc_start: 0.9063 (t) cc_final: 0.8840 (t) REVERT: A 626 MET cc_start: 0.8902 (ttp) cc_final: 0.8415 (tpp) REVERT: B 145 TYR cc_start: 0.7828 (p90) cc_final: 0.7129 (p90) REVERT: B 188 MET cc_start: 0.7586 (mpp) cc_final: 0.7374 (mpp) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.2227 time to fit residues: 35.9463 Evaluate side-chains 94 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 33 optimal weight: 1.9990 chunk 80 optimal weight: 7.9990 chunk 95 optimal weight: 5.9990 chunk 92 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 50 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 105 optimal weight: 6.9990 chunk 100 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.110242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.078833 restraints weight = 55245.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.078170 restraints weight = 45363.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.080244 restraints weight = 33051.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.081018 restraints weight = 24829.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.081472 restraints weight = 22150.247| |-----------------------------------------------------------------------------| r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9092 Z= 0.151 Angle : 0.524 7.400 12308 Z= 0.277 Chirality : 0.040 0.153 1368 Planarity : 0.004 0.039 1600 Dihedral : 5.643 132.118 1229 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.54 % Favored : 91.28 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -1.70 (0.25), residues: 1113 helix: 0.35 (0.30), residues: 299 sheet: -1.39 (0.35), residues: 228 loop : -1.83 (0.25), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 707 TYR 0.012 0.001 TYR A 157 PHE 0.020 0.001 PHE A 296 TRP 0.006 0.001 TRP A 131 HIS 0.006 0.001 HIS A 821 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 ( 9092) covalent geometry : angle 0.52410 / 0.28 (12308) hydrogen bonds : bond 0.03434 / 2.22 ( 268) hydrogen bonds : angle 5.16751 / 3.69 ( 756) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.490 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: 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 140 MET cc_start: 0.9209 (mmt) cc_final: 0.8910 (mmm) REVERT: A 416 VAL cc_start: 0.9061 (t) cc_final: 0.8833 (t) REVERT: A 626 MET cc_start: 0.8891 (ttp) cc_final: 0.8426 (tpp) REVERT: B 188 MET cc_start: 0.7511 (mpp) cc_final: 0.7301 (mpp) REVERT: B 289 TYR cc_start: 0.9091 (m-10) cc_final: 0.8808 (m-10) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.1997 time to fit residues: 32.6971 Evaluate side-chains 94 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 37 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 99 optimal weight: 6.9990 chunk 95 optimal weight: 1.9990 chunk 106 optimal weight: 8.9990 chunk 9 optimal weight: 0.5980 chunk 4 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.110058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.078889 restraints weight = 55952.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.079393 restraints weight = 41905.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.081062 restraints weight = 30252.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.081944 restraints weight = 21523.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.081835 restraints weight = 19588.011| |-----------------------------------------------------------------------------| r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.3017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9092 Z= 0.174 Angle : 0.541 8.468 12308 Z= 0.285 Chirality : 0.040 0.153 1368 Planarity : 0.004 0.040 1600 Dihedral : 5.682 132.187 1229 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.79 % Favored : 90.03 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % 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: -1.78 (0.25), residues: 1113 helix: 0.29 (0.30), residues: 299 sheet: -1.43 (0.35), residues: 228 loop : -1.89 (0.25), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 707 TYR 0.012 0.001 TYR A 157 PHE 0.032 0.002 PHE A 676 TRP 0.008 0.001 TRP A 131 HIS 0.008 0.001 HIS A 821 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.17 ( 9092) covalent geometry : angle 0.54119 / 0.29 (12308) hydrogen bonds : bond 0.03514 / 2.29 ( 268) hydrogen bonds : angle 5.21775 / 3.72 ( 756) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2678.96 seconds wall clock time: 46 minutes 36.68 seconds (2796.68 seconds total)