Starting phenix.real_space_refine on Thu Mar 5 02:26:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9y7h_72655/03_2026/9y7h_72655_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9y7h_72655/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9y7h_72655/03_2026/9y7h_72655.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9y7h_72655/03_2026/9y7h_72655.map" model { file = "/net/cci-nas-00/data/ceres_data/9y7h_72655/03_2026/9y7h_72655_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9y7h_72655/03_2026/9y7h_72655_trim.cif" } 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-5986/lib/python3.9/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, 17 Unusual residues: {' CA': 1, 'ME7': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.17, per 1000 atoms: 0.18 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: 1.58 Conformation dependent library (CDL) restraints added in 487.3 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: 0.57 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: 4.00 Time building geometry restraints manager: 2.17 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 2.040 ... (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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.030 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: 0.070 Extract box with map and model: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.360 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 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 covalent geometry : bond 0.00275 ( 9092) covalent geometry : angle 0.47426 (12308) hydrogen bonds : bond 0.17962 ( 268) hydrogen bonds : angle 6.37973 ( 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 : 0.427 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: 0.3050 time to fit residues: 63.9315 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 : 0.476 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 340 GLN 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.111734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.081063 restraints weight = 55320.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.081838 restraints weight = 39864.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.083702 restraints weight = 30790.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.084109 restraints weight = 20646.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.084355 restraints weight = 20102.543| |-----------------------------------------------------------------------------| r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9092 Z= 0.175 Angle : 0.559 7.378 12308 Z= 0.302 Chirality : 0.040 0.153 1368 Planarity : 0.005 0.103 1600 Dihedral : 5.773 134.644 1229 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 9.35 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: -1.74 (0.25), residues: 1113 helix: 0.34 (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 0.027 0.002 PHE A 296 TRP 0.006 0.001 TRP A 131 HIS 0.008 0.001 HIS A 821 Details of bonding type rmsd covalent geometry : bond 0.00398 ( 9092) covalent geometry : angle 0.55913 (12308) hydrogen bonds : bond 0.04961 ( 268) hydrogen bonds : angle 5.67843 ( 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 132 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 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: A 121 MET cc_start: 0.8616 (tpt) cc_final: 0.8331 (tpp) REVERT: A 140 MET cc_start: 0.9197 (mmt) cc_final: 0.8940 (mmm) REVERT: A 241 LEU cc_start: 0.8801 (mp) cc_final: 0.8257 (tp) REVERT: A 398 GLU cc_start: 0.8414 (tm-30) cc_final: 0.7995 (tm-30) REVERT: A 416 VAL cc_start: 0.8990 (t) cc_final: 0.8739 (t) REVERT: A 626 MET cc_start: 0.9201 (ttp) cc_final: 0.8619 (tpp) REVERT: A 741 ARG cc_start: 0.8316 (mtp180) cc_final: 0.8073 (mtp180) REVERT: B 145 TYR cc_start: 0.7923 (p90) cc_final: 0.7221 (p90) REVERT: G 20 LYS cc_start: 0.9193 (ttpp) cc_final: 0.8835 (ttpp) REVERT: G 21 MET cc_start: 0.9077 (mmt) cc_final: 0.8631 (mmm) outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.2539 time to fit residues: 44.3024 Evaluate side-chains 96 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.463 ------------------------------------------------------------------------------- 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: 0.9980 chunk 96 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 84 optimal weight: 8.9990 chunk 46 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 95 optimal weight: 5.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3499 r_free = 0.3499 target = 0.111260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.080420 restraints weight = 55876.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.080983 restraints weight = 44738.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.082639 restraints weight = 32096.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.083347 restraints weight = 22413.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.083504 restraints weight = 20869.544| |-----------------------------------------------------------------------------| r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9092 Z= 0.161 Angle : 0.529 7.361 12308 Z= 0.283 Chirality : 0.040 0.159 1368 Planarity : 0.004 0.040 1600 Dihedral : 5.754 134.097 1229 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.54 % Favored : 91.28 % Rotamer: Outliers : 0.10 % Allowed : 0.92 % 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: -1.74 (0.25), residues: 1113 helix: 0.27 (0.30), residues: 289 sheet: -1.50 (0.35), residues: 234 loop : -1.75 (0.25), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 197 TYR 0.012 0.001 TYR A 157 PHE 0.022 0.001 PHE A 296 TRP 0.005 0.001 TRP B 211 HIS 0.006 0.001 HIS A 821 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 9092) covalent geometry : angle 0.52923 (12308) hydrogen bonds : bond 0.04225 ( 268) hydrogen bonds : angle 5.43630 ( 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 121 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 120 time to evaluate : 0.493 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: 0.8604 (tpt) cc_final: 0.8403 (tpp) REVERT: A 140 MET cc_start: 0.9205 (mmt) cc_final: 0.8964 (mmm) REVERT: A 398 GLU cc_start: 0.8555 (tm-30) cc_final: 0.8039 (tm-30) REVERT: A 416 VAL cc_start: 0.8997 (t) cc_final: 0.8747 (t) REVERT: A 590 MET cc_start: 0.8995 (mmm) cc_final: 0.8746 (mmm) REVERT: A 626 MET cc_start: 0.9190 (ttp) cc_final: 0.8610 (tpp) REVERT: A 741 ARG cc_start: 0.8321 (mtp180) cc_final: 0.8095 (mtp180) REVERT: B 217 MET cc_start: 0.6997 (mmp) cc_final: 0.6779 (mmm) outliers start: 1 outliers final: 0 residues processed: 121 average time/residue: 0.2528 time to fit residues: 40.8602 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 : 0.474 ------------------------------------------------------------------------------- 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: 0.4980 chunk 36 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 chunk 42 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.111228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.079429 restraints weight = 55304.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.079150 restraints weight = 39701.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.081028 restraints weight = 28610.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.082465 restraints weight = 20918.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.082655 restraints weight = 17995.967| |-----------------------------------------------------------------------------| r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9092 Z= 0.127 Angle : 0.509 7.385 12308 Z= 0.270 Chirality : 0.039 0.149 1368 Planarity : 0.004 0.047 1600 Dihedral : 5.686 134.045 1229 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.36 % Favored : 91.46 % Rotamer: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % 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: -1.61 (0.25), residues: 1113 helix: 0.47 (0.31), residues: 284 sheet: -1.43 (0.36), residues: 227 loop : -1.70 (0.25), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 197 TYR 0.010 0.001 TYR A 157 PHE 0.017 0.001 PHE A 296 TRP 0.005 0.001 TRP A 54 HIS 0.004 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 9092) covalent geometry : angle 0.50905 (12308) hydrogen bonds : bond 0.03714 ( 268) hydrogen bonds : angle 5.20960 ( 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 121 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.438 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: A 140 MET cc_start: 0.9190 (mmt) cc_final: 0.8901 (mmm) REVERT: A 241 LEU cc_start: 0.8590 (mp) cc_final: 0.8317 (tp) REVERT: A 319 MET cc_start: 0.8534 (mtm) cc_final: 0.8220 (mtm) REVERT: A 398 GLU cc_start: 0.8549 (tm-30) cc_final: 0.8050 (tm-30) REVERT: A 416 VAL cc_start: 0.8990 (t) cc_final: 0.8770 (t) REVERT: A 626 MET cc_start: 0.9178 (ttp) cc_final: 0.8402 (tpp) REVERT: A 691 GLU cc_start: 0.8489 (pp20) cc_final: 0.8281 (tm-30) REVERT: A 741 ARG cc_start: 0.8236 (mtp180) cc_final: 0.7987 (mtp180) REVERT: B 188 MET cc_start: 0.7599 (mpp) cc_final: 0.7354 (mpp) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.2451 time to fit residues: 39.8717 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 : 0.490 ------------------------------------------------------------------------------- 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: 5.9990 chunk 23 optimal weight: 2.9990 chunk 69 optimal weight: 0.4980 chunk 13 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 72 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 chunk 103 optimal weight: 2.9990 chunk 35 optimal weight: 0.5980 chunk 64 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.112320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.080995 restraints weight = 54881.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.081154 restraints weight = 41949.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.083224 restraints weight = 30187.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.083448 restraints weight = 21614.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.083636 restraints weight = 20909.800| |-----------------------------------------------------------------------------| r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9092 Z= 0.118 Angle : 0.501 7.388 12308 Z= 0.267 Chirality : 0.039 0.148 1368 Planarity : 0.004 0.039 1600 Dihedral : 5.647 133.628 1229 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.00 % Favored : 91.82 % 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: -1.56 (0.26), residues: 1113 helix: 0.56 (0.31), residues: 284 sheet: -1.42 (0.36), residues: 226 loop : -1.68 (0.25), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 197 TYR 0.012 0.001 TYR A 406 PHE 0.016 0.001 PHE A 296 TRP 0.004 0.001 TRP A 54 HIS 0.003 0.001 HIS A 808 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 9092) covalent geometry : angle 0.50085 (12308) hydrogen bonds : bond 0.03474 ( 268) hydrogen bonds : angle 5.10239 ( 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 : 0.472 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: A 140 MET cc_start: 0.9250 (mmt) cc_final: 0.8892 (mmm) REVERT: A 241 LEU cc_start: 0.8573 (mp) cc_final: 0.8254 (tp) REVERT: A 416 VAL cc_start: 0.9024 (t) cc_final: 0.8781 (t) REVERT: A 626 MET cc_start: 0.9105 (ttp) cc_final: 0.8384 (tpp) REVERT: A 691 GLU cc_start: 0.8468 (pp20) cc_final: 0.8251 (tm-30) REVERT: A 741 ARG cc_start: 0.8285 (mtp180) cc_final: 0.8013 (mtp180) REVERT: B 188 MET cc_start: 0.7646 (mpp) cc_final: 0.7429 (mpp) outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 0.2463 time to fit residues: 41.0200 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 : 0.460 ------------------------------------------------------------------------------- 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: 0.6980 chunk 96 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 43 optimal weight: 0.0170 chunk 44 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.112462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.080819 restraints weight = 54954.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.079996 restraints weight = 46203.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.081999 restraints weight = 33201.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.084070 restraints weight = 24254.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.083953 restraints weight = 20565.486| |-----------------------------------------------------------------------------| r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 9092 Z= 0.103 Angle : 0.487 7.420 12308 Z= 0.258 Chirality : 0.039 0.149 1368 Planarity : 0.004 0.040 1600 Dihedral : 5.568 134.262 1229 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.73 % Favored : 92.09 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % 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: -1.42 (0.26), residues: 1113 helix: 0.69 (0.31), residues: 291 sheet: -1.37 (0.36), residues: 226 loop : -1.62 (0.26), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 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 54 HIS 0.003 0.001 HIS A 808 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 9092) covalent geometry : angle 0.48711 (12308) hydrogen bonds : bond 0.03253 ( 268) hydrogen bonds : angle 4.94585 ( 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 123 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.407 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: A 140 MET cc_start: 0.9245 (mmt) cc_final: 0.8837 (mmm) REVERT: A 398 GLU cc_start: 0.8057 (tt0) cc_final: 0.7658 (tm-30) REVERT: A 416 VAL cc_start: 0.9040 (t) cc_final: 0.8813 (t) REVERT: A 626 MET cc_start: 0.9103 (ttp) cc_final: 0.8358 (tpp) REVERT: A 691 GLU cc_start: 0.8569 (pp20) cc_final: 0.8184 (pp20) REVERT: A 741 ARG cc_start: 0.8260 (mtp180) cc_final: 0.8007 (mtp180) REVERT: B 188 MET cc_start: 0.7510 (mpp) cc_final: 0.7292 (mpp) REVERT: G 21 MET cc_start: 0.9095 (mmm) cc_final: 0.8849 (mmm) outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.2262 time to fit residues: 38.0492 Evaluate side-chains 101 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.454 ------------------------------------------------------------------------------- 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: 5.9990 chunk 51 optimal weight: 1.9990 chunk 77 optimal weight: 8.9990 chunk 73 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 101 optimal weight: 5.9990 chunk 111 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 677 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.108997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.077814 restraints weight = 55520.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.078283 restraints weight = 41012.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.079843 restraints weight = 30563.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.080854 restraints weight = 21976.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.080941 restraints weight = 19504.830| |-----------------------------------------------------------------------------| r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 9092 Z= 0.247 Angle : 0.575 7.433 12308 Z= 0.309 Chirality : 0.041 0.141 1368 Planarity : 0.004 0.038 1600 Dihedral : 5.792 132.716 1229 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.33 % Favored : 89.49 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % 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: -1.94 (0.25), residues: 1113 helix: 0.16 (0.30), residues: 290 sheet: -1.54 (0.35), residues: 231 loop : -1.96 (0.25), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 874 TYR 0.017 0.002 TYR B 289 PHE 0.027 0.002 PHE A 296 TRP 0.006 0.001 TRP A 131 HIS 0.006 0.001 HIS A 821 Details of bonding type rmsd covalent geometry : bond 0.00557 ( 9092) covalent geometry : angle 0.57508 (12308) hydrogen bonds : bond 0.04121 ( 268) hydrogen bonds : angle 5.42096 ( 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 115 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.487 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: 0.9248 (mmt) cc_final: 0.9004 (mmm) REVERT: A 241 LEU cc_start: 0.8548 (mp) cc_final: 0.8156 (tp) REVERT: A 416 VAL cc_start: 0.9060 (t) cc_final: 0.8858 (t) REVERT: B 145 TYR cc_start: 0.7729 (p90) cc_final: 0.7002 (p90) outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.2378 time to fit residues: 36.9731 Evaluate side-chains 91 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.439 ------------------------------------------------------------------------------- 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: 0.8980 chunk 74 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 85 optimal weight: 5.9990 chunk 83 optimal weight: 4.9990 chunk 101 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 76 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.110742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.079237 restraints weight = 55207.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.078480 restraints weight = 46182.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.080849 restraints weight = 34445.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.081564 restraints weight = 24942.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.082034 restraints weight = 23079.342| |-----------------------------------------------------------------------------| r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9092 Z= 0.146 Angle : 0.524 7.406 12308 Z= 0.279 Chirality : 0.040 0.160 1368 Planarity : 0.004 0.040 1600 Dihedral : 5.726 132.490 1229 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.91 % Favored : 91.91 % Rotamer: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % 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: 0.32 (0.30), residues: 296 sheet: -1.40 (0.35), residues: 229 loop : -1.84 (0.25), residues: 588 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 0.051 0.002 PHE A 676 TRP 0.005 0.001 TRP A 131 HIS 0.006 0.001 HIS A 332 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 9092) covalent geometry : angle 0.52416 (12308) hydrogen bonds : bond 0.03448 ( 268) hydrogen bonds : angle 5.15990 ( 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 : 0.484 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: A 59 MET cc_start: 0.7647 (tmm) cc_final: 0.7388 (tmm) REVERT: A 140 MET cc_start: 0.9186 (mmt) cc_final: 0.8889 (mmm) REVERT: A 416 VAL cc_start: 0.9043 (t) cc_final: 0.8815 (t) REVERT: A 626 MET cc_start: 0.8907 (ttp) cc_final: 0.8463 (tpp) REVERT: B 145 TYR cc_start: 0.7824 (p90) cc_final: 0.7099 (p90) REVERT: B 188 MET cc_start: 0.7640 (mpp) cc_final: 0.7425 (mpp) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.2201 time to fit residues: 35.3066 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 : 0.483 ------------------------------------------------------------------------------- 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: 5.9990 chunk 100 optimal weight: 0.9980 chunk 96 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 101 optimal weight: 4.9990 chunk 42 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.110530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.079783 restraints weight = 55335.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.080350 restraints weight = 42780.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.082331 restraints weight = 31849.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.082403 restraints weight = 22552.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.082689 restraints weight = 21355.724| |-----------------------------------------------------------------------------| r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 9092 Z= 0.157 Angle : 0.520 7.416 12308 Z= 0.277 Chirality : 0.040 0.146 1368 Planarity : 0.004 0.040 1600 Dihedral : 5.658 132.414 1229 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.72 % Favored : 91.11 % 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: -1.76 (0.25), residues: 1113 helix: 0.28 (0.30), residues: 299 sheet: -1.44 (0.35), residues: 231 loop : -1.85 (0.25), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 707 TYR 0.014 0.001 TYR B 289 PHE 0.052 0.002 PHE A 676 TRP 0.005 0.001 TRP A 131 HIS 0.009 0.001 HIS A 821 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 9092) covalent geometry : angle 0.52020 (12308) hydrogen bonds : bond 0.03524 ( 268) hydrogen bonds : angle 5.18010 ( 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 115 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.480 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 59 MET cc_start: 0.7646 (tmm) cc_final: 0.7426 (tmm) REVERT: A 140 MET cc_start: 0.9200 (mmt) cc_final: 0.8910 (mmm) REVERT: A 197 PHE cc_start: 0.8368 (p90) cc_final: 0.8150 (p90) REVERT: A 416 VAL cc_start: 0.9049 (t) cc_final: 0.8825 (t) REVERT: A 626 MET cc_start: 0.8896 (ttp) cc_final: 0.8465 (tpp) REVERT: B 59 TYR cc_start: 0.8108 (m-80) cc_final: 0.7775 (m-10) REVERT: B 145 TYR cc_start: 0.7766 (p90) cc_final: 0.7132 (p90) REVERT: B 188 MET cc_start: 0.7754 (mpp) cc_final: 0.7528 (mpp) outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.2221 time to fit residues: 35.1669 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 : 0.406 ------------------------------------------------------------------------------- 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: 0.9990 chunk 80 optimal weight: 8.9990 chunk 95 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 105 optimal weight: 0.6980 chunk 100 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.110775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.079583 restraints weight = 54828.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.080175 restraints weight = 39274.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.082318 restraints weight = 27952.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.082325 restraints weight = 20647.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.082606 restraints weight = 19689.505| |-----------------------------------------------------------------------------| r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.2972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 9092 Z= 0.127 Angle : 0.511 7.434 12308 Z= 0.270 Chirality : 0.040 0.148 1368 Planarity : 0.004 0.039 1600 Dihedral : 5.615 132.083 1229 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.45 % Favored : 91.37 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % 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: -1.67 (0.25), residues: 1113 helix: 0.39 (0.30), residues: 299 sheet: -1.38 (0.36), residues: 228 loop : -1.82 (0.25), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 707 TYR 0.013 0.001 TYR A 406 PHE 0.018 0.001 PHE A 296 TRP 0.005 0.001 TRP A 356 HIS 0.005 0.001 HIS A 821 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 9092) covalent geometry : angle 0.51103 (12308) hydrogen bonds : bond 0.03337 ( 268) hydrogen bonds : angle 5.10323 ( 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 117 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.476 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: 0.9181 (mmt) cc_final: 0.8888 (mmm) REVERT: A 178 MET cc_start: 0.8887 (ttp) cc_final: 0.8524 (ttm) REVERT: A 416 VAL cc_start: 0.9061 (t) cc_final: 0.8829 (t) REVERT: A 626 MET cc_start: 0.8874 (ttp) cc_final: 0.8447 (tpp) REVERT: B 59 TYR cc_start: 0.8104 (m-80) cc_final: 0.7750 (m-10) REVERT: B 145 TYR cc_start: 0.7817 (p90) cc_final: 0.7128 (p90) REVERT: B 188 MET cc_start: 0.7632 (mpp) cc_final: 0.7399 (mpp) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.2252 time to fit residues: 36.2799 Evaluate side-chains 96 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.511 ------------------------------------------------------------------------------- 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: 3.9990 chunk 95 optimal weight: 0.3980 chunk 106 optimal weight: 6.9990 chunk 9 optimal weight: 0.4980 chunk 4 optimal weight: 0.5980 chunk 93 optimal weight: 4.9990 chunk 71 optimal weight: 0.1980 chunk 0 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.111745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.080113 restraints weight = 55066.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.079261 restraints weight = 45520.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.081323 restraints weight = 33177.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.082270 restraints weight = 24968.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.082776 restraints weight = 22307.548| |-----------------------------------------------------------------------------| r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.3061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 9092 Z= 0.099 Angle : 0.494 7.431 12308 Z= 0.262 Chirality : 0.039 0.149 1368 Planarity : 0.003 0.041 1600 Dihedral : 5.523 131.422 1229 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.64 % Favored : 92.18 % 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: -1.50 (0.26), residues: 1113 helix: 0.65 (0.31), residues: 293 sheet: -1.38 (0.34), residues: 242 loop : -1.71 (0.26), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 707 TYR 0.009 0.001 TYR A 157 PHE 0.013 0.001 PHE A 296 TRP 0.006 0.001 TRP B 339 HIS 0.004 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00232 ( 9092) covalent geometry : angle 0.49437 (12308) hydrogen bonds : bond 0.03054 ( 268) hydrogen bonds : angle 4.95028 ( 756) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2680.54 seconds wall clock time: 46 minutes 46.21 seconds (2806.21 seconds total)