Starting phenix.real_space_refine on Tue Mar 3 16:11:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6s5t_10100/03_2026/6s5t_10100.cif Found real_map, /net/cci-nas-00/data/ceres_data/6s5t_10100/03_2026/6s5t_10100.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6s5t_10100/03_2026/6s5t_10100.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6s5t_10100/03_2026/6s5t_10100.map" model { file = "/net/cci-nas-00/data/ceres_data/6s5t_10100/03_2026/6s5t_10100.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6s5t_10100/03_2026/6s5t_10100.cif" } resolution = 4.15 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= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 22 5.16 5 C 4429 2.51 5 N 1186 2.21 5 O 1318 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 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: 6958 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 752, 5977 Classifications: {'peptide': 752} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 43} Link IDs: {'PTRANS': 31, 'TRANS': 720} Unresolved non-hydrogen bonds: 160 Unresolved non-hydrogen angles: 193 Unresolved non-hydrogen dihedrals: 129 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 3, 'ASP:plan': 8, 'GLN:plan1': 4, 'GLU:plan': 10, 'ASN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 104 Chain: "B" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 950 Classifications: {'peptide': 144} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 2, 'TRANS': 141} Unresolved non-hydrogen bonds: 193 Unresolved non-hydrogen angles: 243 Unresolved non-hydrogen dihedrals: 153 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 13, 'GLN:plan1': 2, 'ASP:plan': 10, 'ASN:plan1': 4, 'ARG:plan': 4, 'PHE:plan': 2, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 148 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.60, per 1000 atoms: 0.23 Number of scatterers: 6958 At special positions: 0 Unit cell: (101.76, 106.56, 86.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 22 16.00 P 3 15.00 O 1318 8.00 N 1186 7.00 C 4429 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.65 Conformation dependent library (CDL) restraints added in 278.0 milliseconds 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1704 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 8 sheets defined 58.9% alpha, 8.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 135 through 158 Processing helix chain 'A' and resid 164 through 182 removed outlier: 3.586A pdb=" N ILE A 168 " --> pdb=" O PRO A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 206 Proline residue: A 197 - end of helix removed outlier: 3.794A pdb=" N SER A 204 " --> pdb=" O THR A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 220 removed outlier: 3.802A pdb=" N GLU A 218 " --> pdb=" O ASN A 214 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LYS A 219 " --> pdb=" O GLU A 215 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER A 220 " --> pdb=" O LEU A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 235 removed outlier: 3.724A pdb=" N SER A 235 " --> pdb=" O ARG A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 246 Processing helix chain 'A' and resid 251 through 261 removed outlier: 3.566A pdb=" N LYS A 260 " --> pdb=" O ALA A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 269 removed outlier: 3.556A pdb=" N LEU A 268 " --> pdb=" O SER A 265 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE A 269 " --> pdb=" O VAL A 266 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 265 through 269' Processing helix chain 'A' and resid 270 through 281 Processing helix chain 'A' and resid 303 through 311 Processing helix chain 'A' and resid 342 through 344 No H-bonds generated for 'chain 'A' and resid 342 through 344' Processing helix chain 'A' and resid 374 through 391 removed outlier: 4.324A pdb=" N LEU A 378 " --> pdb=" O PRO A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 396 removed outlier: 3.826A pdb=" N LEU A 395 " --> pdb=" O HIS A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 419 Processing helix chain 'A' and resid 420 through 422 No H-bonds generated for 'chain 'A' and resid 420 through 422' Processing helix chain 'A' and resid 424 through 432 removed outlier: 3.677A pdb=" N ILE A 432 " --> pdb=" O PHE A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 450 Processing helix chain 'A' and resid 459 through 481 removed outlier: 3.555A pdb=" N LEU A 463 " --> pdb=" O ASP A 459 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU A 480 " --> pdb=" O VAL A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 530 Processing helix chain 'A' and resid 550 through 553 Processing helix chain 'A' and resid 556 through 563 removed outlier: 3.532A pdb=" N PHE A 563 " --> pdb=" O THR A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 568 removed outlier: 3.913A pdb=" N LEU A 567 " --> pdb=" O PHE A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 576 removed outlier: 3.690A pdb=" N PHE A 576 " --> pdb=" O PRO A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 592 removed outlier: 3.644A pdb=" N ARG A 592 " --> pdb=" O GLY A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 623 removed outlier: 3.918A pdb=" N TYR A 597 " --> pdb=" O LEU A 593 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR A 602 " --> pdb=" O LEU A 598 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE A 603 " --> pdb=" O TYR A 599 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU A 608 " --> pdb=" O ALA A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 654 removed outlier: 3.645A pdb=" N GLU A 637 " --> pdb=" O ALA A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 657 through 667 removed outlier: 3.551A pdb=" N THR A 663 " --> pdb=" O SER A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 682 Processing helix chain 'A' and resid 685 through 689 Processing helix chain 'A' and resid 690 through 702 Processing helix chain 'A' and resid 738 through 774 removed outlier: 3.660A pdb=" N GLU A 742 " --> pdb=" O LEU A 738 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU A 751 " --> pdb=" O ALA A 747 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU A 758 " --> pdb=" O GLY A 754 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE A 763 " --> pdb=" O ASP A 759 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS A 764 " --> pdb=" O LYS A 760 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS A 771 " --> pdb=" O GLU A 767 " (cutoff:3.500A) Processing helix chain 'A' and resid 780 through 793 removed outlier: 3.656A pdb=" N ASP A 793 " --> pdb=" O ALA A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 800 through 817 Processing helix chain 'A' and resid 826 through 846 removed outlier: 3.632A pdb=" N ARG A 846 " --> pdb=" O GLN A 842 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 20 Processing helix chain 'B' and resid 32 through 40 removed outlier: 3.793A pdb=" N VAL B 36 " --> pdb=" O GLU B 32 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG B 38 " --> pdb=" O GLY B 34 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER B 39 " --> pdb=" O THR B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 57 Processing helix chain 'B' and resid 65 through 77 Processing helix chain 'B' and resid 82 through 92 Processing helix chain 'B' and resid 102 through 113 removed outlier: 3.502A pdb=" N LEU B 106 " --> pdb=" O SER B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 128 Processing helix chain 'B' and resid 139 through 146 Processing sheet with id=AA1, first strand: chain 'A' and resid 105 through 109 Processing sheet with id=AA2, first strand: chain 'A' and resid 121 through 124 removed outlier: 3.923A pdb=" N SER A 585 " --> pdb=" O LYS A 132 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 291 through 294 Processing sheet with id=AA4, first strand: chain 'A' and resid 346 through 350 removed outlier: 7.022A pdb=" N LEU A 346 " --> pdb=" O SER A 357 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N SER A 357 " --> pdb=" O LEU A 346 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ARG A 348 " --> pdb=" O LEU A 355 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N VAL A 442 " --> pdb=" O LEU A 405 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 346 through 350 removed outlier: 7.022A pdb=" N LEU A 346 " --> pdb=" O SER A 357 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N SER A 357 " --> pdb=" O LEU A 346 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ARG A 348 " --> pdb=" O LEU A 355 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 482 through 483 Processing sheet with id=AA7, first strand: chain 'B' and resid 28 through 29 Processing sheet with id=AA8, first strand: chain 'B' and resid 100 through 101 381 hydrogen bonds defined for protein. 1080 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.05 Time building geometry restraints manager: 0.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2242 1.34 - 1.46: 1722 1.46 - 1.58: 3098 1.58 - 1.70: 5 1.70 - 1.82: 41 Bond restraints: 7108 Sorted by residual: bond pdb=" N3B ANP A 901 " pdb=" PG ANP A 901 " ideal model delta sigma weight residual 1.795 1.641 0.154 2.00e-02 2.50e+03 5.96e+01 bond pdb=" O3A ANP A 901 " pdb=" PB ANP A 901 " ideal model delta sigma weight residual 1.700 1.604 0.096 2.00e-02 2.50e+03 2.31e+01 bond pdb=" O5' ANP A 901 " pdb=" PA ANP A 901 " ideal model delta sigma weight residual 1.655 1.602 0.053 2.00e-02 2.50e+03 7.06e+00 bond pdb=" C TYR A 222 " pdb=" N PRO A 223 " ideal model delta sigma weight residual 1.334 1.355 -0.021 8.40e-03 1.42e+04 6.44e+00 bond pdb=" C LEU A 117 " pdb=" N PRO A 118 " ideal model delta sigma weight residual 1.329 1.357 -0.028 1.18e-02 7.18e+03 5.65e+00 ... (remaining 7103 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.14: 8400 2.14 - 4.28: 1144 4.28 - 6.42: 91 6.42 - 8.56: 10 8.56 - 10.70: 1 Bond angle restraints: 9646 Sorted by residual: angle pdb=" CA PHE A 269 " pdb=" CB PHE A 269 " pdb=" CG PHE A 269 " ideal model delta sigma weight residual 113.80 118.84 -5.04 1.00e+00 1.00e+00 2.54e+01 angle pdb=" C THR A 654 " pdb=" CA THR A 654 " pdb=" CB THR A 654 " ideal model delta sigma weight residual 109.02 116.89 -7.87 1.68e+00 3.54e-01 2.19e+01 angle pdb=" CA ASP A 542 " pdb=" CB ASP A 542 " pdb=" CG ASP A 542 " ideal model delta sigma weight residual 112.60 117.26 -4.66 1.00e+00 1.00e+00 2.17e+01 angle pdb=" C THR A 451 " pdb=" CA THR A 451 " pdb=" CB THR A 451 " ideal model delta sigma weight residual 110.19 116.95 -6.76 1.62e+00 3.81e-01 1.74e+01 angle pdb=" C ASP A 542 " pdb=" CA ASP A 542 " pdb=" CB ASP A 542 " ideal model delta sigma weight residual 110.42 118.64 -8.22 1.99e+00 2.53e-01 1.71e+01 ... (remaining 9641 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.54: 4124 35.54 - 71.08: 154 71.08 - 106.63: 5 106.63 - 142.17: 0 142.17 - 177.71: 1 Dihedral angle restraints: 4284 sinusoidal: 1649 harmonic: 2635 Sorted by residual: dihedral pdb=" O1B ANP A 901 " pdb=" N3B ANP A 901 " pdb=" PB ANP A 901 " pdb=" PG ANP A 901 " ideal model delta sinusoidal sigma weight residual 35.15 -142.56 177.71 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" CA TYR A 222 " pdb=" C TYR A 222 " pdb=" N PRO A 223 " pdb=" CA PRO A 223 " ideal model delta harmonic sigma weight residual -180.00 -157.03 -22.97 0 5.00e+00 4.00e-02 2.11e+01 dihedral pdb=" C THR A 654 " pdb=" N THR A 654 " pdb=" CA THR A 654 " pdb=" CB THR A 654 " ideal model delta harmonic sigma weight residual -122.00 -133.28 11.28 0 2.50e+00 1.60e-01 2.03e+01 ... (remaining 4281 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 681 0.081 - 0.162: 307 0.162 - 0.242: 90 0.242 - 0.323: 11 0.323 - 0.404: 2 Chirality restraints: 1091 Sorted by residual: chirality pdb=" CA ASN A 271 " pdb=" N ASN A 271 " pdb=" C ASN A 271 " pdb=" CB ASN A 271 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.08e+00 chirality pdb=" CA THR A 654 " pdb=" N THR A 654 " pdb=" C THR A 654 " pdb=" CB THR A 654 " both_signs ideal model delta sigma weight residual False 2.53 2.15 0.37 2.00e-01 2.50e+01 3.50e+00 chirality pdb=" CA ASP A 542 " pdb=" N ASP A 542 " pdb=" C ASP A 542 " pdb=" CB ASP A 542 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.31 2.00e-01 2.50e+01 2.33e+00 ... (remaining 1088 not shown) Planarity restraints: 1236 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 606 " -0.013 2.00e-02 2.50e+03 7.66e-03 1.17e+00 pdb=" CG TYR A 606 " 0.015 2.00e-02 2.50e+03 pdb=" CD1 TYR A 606 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR A 606 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR A 606 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR A 606 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR A 606 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 606 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 393 " 0.068 9.50e-02 1.11e+02 3.13e-02 1.07e+00 pdb=" NE ARG A 393 " -0.000 2.00e-02 2.50e+03 pdb=" CZ ARG A 393 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG A 393 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 393 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 242 " 0.005 2.00e-02 2.50e+03 1.02e-02 1.04e+00 pdb=" C ILE A 242 " -0.018 2.00e-02 2.50e+03 pdb=" O ILE A 242 " 0.007 2.00e-02 2.50e+03 pdb=" N HIS A 243 " 0.006 2.00e-02 2.50e+03 ... (remaining 1233 not shown) Histogram of nonbonded interaction distances: 2.45 - 2.94: 2628 2.94 - 3.43: 6963 3.43 - 3.92: 11094 3.92 - 4.41: 12009 4.41 - 4.90: 19812 Nonbonded interactions: 52506 Sorted by model distance: nonbonded pdb=" O GLN A 350 " pdb=" OG1 THR A 353 " model vdw 2.450 3.040 nonbonded pdb=" ND2 ASN A 470 " pdb=" O ARG A 536 " model vdw 2.525 3.120 nonbonded pdb=" NE2 GLN A 842 " pdb=" O GLU B 115 " model vdw 2.525 3.120 nonbonded pdb=" O TRP A 845 " pdb=" N GLU A 847 " model vdw 2.525 3.120 nonbonded pdb=" O GLU A 294 " pdb=" OG SER A 297 " model vdw 2.526 3.040 ... (remaining 52501 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: 0.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 7.850 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 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 : 0.007 0.154 7108 Z= 0.451 Angle : 1.477 10.703 9646 Z= 0.994 Chirality : 0.094 0.404 1091 Planarity : 0.003 0.031 1236 Dihedral : 17.703 177.709 2580 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.56 % Allowed : 7.06 % Favored : 92.38 % Rotamer: Outliers : 3.93 % Allowed : 13.90 % Favored : 82.16 % Cbeta Deviations : 0.35 % 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: -4.05 (0.22), residues: 892 helix: -2.73 (0.17), residues: 498 sheet: -0.64 (0.92), residues: 32 loop : -2.63 (0.26), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 393 TYR 0.015 0.003 TYR A 606 PHE 0.017 0.002 PHE A 269 TRP 0.005 0.002 TRP A 845 HIS 0.006 0.001 HIS A 800 Details of bonding type rmsd covalent geometry : bond 0.00695 ( 7108) covalent geometry : angle 1.47682 ( 9646) hydrogen bonds : bond 0.27093 ( 368) hydrogen bonds : angle 8.97721 ( 1080) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 175 time to evaluate : 0.270 Fit side-chains REVERT: A 117 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8358 (mp) REVERT: A 218 GLU cc_start: 0.9049 (mm-30) cc_final: 0.8752 (tp30) REVERT: A 239 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8247 (mp) REVERT: A 245 TYR cc_start: 0.8840 (m-80) cc_final: 0.8598 (m-10) REVERT: A 282 TYR cc_start: 0.9150 (m-80) cc_final: 0.8788 (m-10) REVERT: A 339 TYR cc_start: 0.7710 (t80) cc_final: 0.7469 (t80) REVERT: A 345 ARG cc_start: 0.8060 (mtt180) cc_final: 0.7682 (mtp85) REVERT: A 381 GLU cc_start: 0.8667 (tp30) cc_final: 0.8349 (tp30) REVERT: A 461 GLU cc_start: 0.8142 (tt0) cc_final: 0.7531 (tm-30) REVERT: A 480 GLU cc_start: 0.8583 (tp30) cc_final: 0.8093 (tm-30) REVERT: A 490 ILE cc_start: 0.8975 (OUTLIER) cc_final: 0.8698 (pt) REVERT: A 640 ASN cc_start: 0.8543 (OUTLIER) cc_final: 0.8217 (t0) REVERT: A 682 MET cc_start: 0.9016 (mtt) cc_final: 0.8714 (mtm) REVERT: A 732 TYR cc_start: 0.8997 (t80) cc_final: 0.8729 (t80) REVERT: A 735 GLU cc_start: 0.9302 (pm20) cc_final: 0.8929 (pm20) REVERT: A 771 LYS cc_start: 0.8429 (mttt) cc_final: 0.8006 (mtpp) REVERT: A 817 TYR cc_start: 0.8676 (m-80) cc_final: 0.8471 (m-10) REVERT: A 834 ARG cc_start: 0.8956 (mtp180) cc_final: 0.8746 (ttp-170) REVERT: B 22 LYS cc_start: 0.8635 (mttt) cc_final: 0.7919 (mtmt) REVERT: B 32 GLU cc_start: 0.8675 (pp20) cc_final: 0.7897 (mp0) REVERT: B 68 GLU cc_start: 0.8208 (tm-30) cc_final: 0.7938 (tm-30) REVERT: B 115 GLU cc_start: 0.5243 (mt-10) cc_final: 0.4820 (mt-10) outliers start: 28 outliers final: 8 residues processed: 196 average time/residue: 0.0830 time to fit residues: 21.6652 Evaluate side-chains 140 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 128 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 9.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 6.9990 chunk 74 optimal weight: 6.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 GLN A 189 ASN A 214 ASN ** A 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 308 ASN A 517 GLN A 534 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.150705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.115740 restraints weight = 10151.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.117293 restraints weight = 8202.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.117824 restraints weight = 7144.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.119164 restraints weight = 6666.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.119395 restraints weight = 6220.407| |-----------------------------------------------------------------------------| r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7108 Z= 0.126 Angle : 0.572 6.344 9646 Z= 0.301 Chirality : 0.039 0.146 1091 Planarity : 0.004 0.047 1236 Dihedral : 9.174 178.107 1001 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.14 % Allowed : 1.54 % Favored : 98.31 % 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: -1.41 (0.26), residues: 892 helix: -0.36 (0.22), residues: 497 sheet: -0.41 (0.91), residues: 33 loop : -1.71 (0.29), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 849 TYR 0.015 0.001 TYR A 147 PHE 0.019 0.002 PHE A 475 TRP 0.007 0.001 TRP A 845 HIS 0.002 0.001 HIS A 171 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 7108) covalent geometry : angle 0.57237 ( 9646) hydrogen bonds : bond 0.04813 ( 368) hydrogen bonds : angle 4.46883 ( 1080) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 175 time to evaluate : 0.266 Fit side-chains REVERT: A 114 ASP cc_start: 0.7606 (t0) cc_final: 0.7084 (t0) REVERT: A 218 GLU cc_start: 0.8412 (mm-30) cc_final: 0.8212 (tp30) REVERT: A 308 ASN cc_start: 0.8863 (OUTLIER) cc_final: 0.8514 (m-40) REVERT: A 317 GLU cc_start: 0.8184 (tp30) cc_final: 0.7836 (tm-30) REVERT: A 414 GLU cc_start: 0.8680 (mp0) cc_final: 0.8420 (mp0) REVERT: A 480 GLU cc_start: 0.8449 (tp30) cc_final: 0.7811 (tm-30) REVERT: A 642 MET cc_start: 0.8827 (tpp) cc_final: 0.8589 (tpp) REVERT: A 650 ILE cc_start: 0.9027 (mm) cc_final: 0.8633 (tt) REVERT: A 771 LYS cc_start: 0.8710 (mttt) cc_final: 0.8172 (mtpt) REVERT: B 22 LYS cc_start: 0.8562 (mttt) cc_final: 0.7821 (mtmt) REVERT: B 25 ASP cc_start: 0.8193 (p0) cc_final: 0.7961 (p0) REVERT: B 32 GLU cc_start: 0.8152 (pp20) cc_final: 0.7929 (mp0) REVERT: B 37 MET cc_start: 0.8827 (mmm) cc_final: 0.8593 (mmm) outliers start: 1 outliers final: 0 residues processed: 176 average time/residue: 0.0890 time to fit residues: 20.6700 Evaluate side-chains 122 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 121 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 30 optimal weight: 9.9990 chunk 2 optimal weight: 9.9990 chunk 7 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 29 optimal weight: 9.9990 chunk 41 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 83 optimal weight: 9.9990 chunk 11 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 HIS A 234 HIS ** A 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 800 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.146439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.112798 restraints weight = 10274.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.112367 restraints weight = 10931.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.113869 restraints weight = 10336.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.113657 restraints weight = 8220.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.113786 restraints weight = 7579.932| |-----------------------------------------------------------------------------| r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 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 0.033 7108 Z= 0.158 Angle : 0.556 7.114 9646 Z= 0.290 Chirality : 0.041 0.144 1091 Planarity : 0.004 0.048 1236 Dihedral : 8.802 177.082 1001 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 0.14 % Allowed : 2.53 % Favored : 97.33 % 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: -0.56 (0.27), residues: 892 helix: 0.47 (0.23), residues: 499 sheet: -0.38 (0.89), residues: 33 loop : -1.55 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 849 TYR 0.017 0.002 TYR A 274 PHE 0.015 0.002 PHE A 261 TRP 0.004 0.001 TRP A 845 HIS 0.003 0.001 HIS A 208 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 7108) covalent geometry : angle 0.55647 ( 9646) hydrogen bonds : bond 0.04708 ( 368) hydrogen bonds : angle 4.23979 ( 1080) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 153 time to evaluate : 0.315 Fit side-chains revert: symmetry clash REVERT: A 114 ASP cc_start: 0.7661 (t0) cc_final: 0.7320 (t0) REVERT: A 172 TYR cc_start: 0.9147 (t80) cc_final: 0.8945 (t80) REVERT: A 218 GLU cc_start: 0.8367 (mm-30) cc_final: 0.8143 (tp30) REVERT: A 534 ASN cc_start: 0.8304 (t0) cc_final: 0.8094 (t0) REVERT: A 650 ILE cc_start: 0.9025 (mm) cc_final: 0.8665 (tt) REVERT: A 771 LYS cc_start: 0.8707 (mttt) cc_final: 0.8359 (mtpt) REVERT: A 825 TYR cc_start: 0.8752 (m-80) cc_final: 0.8303 (m-10) REVERT: B 22 LYS cc_start: 0.8575 (mttt) cc_final: 0.7963 (mtmt) REVERT: B 25 ASP cc_start: 0.8259 (p0) cc_final: 0.8026 (p0) outliers start: 1 outliers final: 0 residues processed: 154 average time/residue: 0.0692 time to fit residues: 14.8658 Evaluate side-chains 120 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 77 optimal weight: 10.0000 chunk 24 optimal weight: 0.0050 chunk 8 optimal weight: 1.9990 chunk 26 optimal weight: 8.9990 chunk 33 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 69 optimal weight: 0.0010 chunk 0 optimal weight: 10.0000 chunk 12 optimal weight: 5.9990 chunk 61 optimal weight: 9.9990 chunk 55 optimal weight: 0.7980 overall best weight: 0.7602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 HIS ** A 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 HIS A 308 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.152538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.120577 restraints weight = 10291.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.119672 restraints weight = 10173.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.120911 restraints weight = 10029.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.121094 restraints weight = 8194.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.121385 restraints weight = 7358.063| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.3465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7108 Z= 0.104 Angle : 0.516 7.559 9646 Z= 0.264 Chirality : 0.038 0.140 1091 Planarity : 0.004 0.052 1236 Dihedral : 8.314 174.740 1001 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % 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: -0.07 (0.28), residues: 892 helix: 0.89 (0.24), residues: 501 sheet: -0.24 (0.87), residues: 33 loop : -1.37 (0.31), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 394 TYR 0.014 0.001 TYR A 147 PHE 0.015 0.001 PHE A 475 TRP 0.005 0.001 TRP A 635 HIS 0.002 0.000 HIS A 302 Details of bonding type rmsd covalent geometry : bond 0.00226 ( 7108) covalent geometry : angle 0.51608 ( 9646) hydrogen bonds : bond 0.03636 ( 368) hydrogen bonds : angle 3.85512 ( 1080) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 0.252 Fit side-chains revert: symmetry clash REVERT: A 114 ASP cc_start: 0.7451 (t0) cc_final: 0.7112 (t0) REVERT: A 245 TYR cc_start: 0.8279 (m-80) cc_final: 0.7563 (m-10) REVERT: A 422 SER cc_start: 0.8404 (t) cc_final: 0.8144 (p) REVERT: A 480 GLU cc_start: 0.8358 (tp30) cc_final: 0.7781 (tm-30) REVERT: A 534 ASN cc_start: 0.8462 (t0) cc_final: 0.8097 (t0) REVERT: A 682 MET cc_start: 0.7717 (mtm) cc_final: 0.7459 (ttm) REVERT: A 771 LYS cc_start: 0.8736 (mttt) cc_final: 0.8349 (mtpt) REVERT: B 22 LYS cc_start: 0.8540 (mttt) cc_final: 0.8332 (mtpp) outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 0.0726 time to fit residues: 16.3405 Evaluate side-chains 122 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 24 optimal weight: 20.0000 chunk 61 optimal weight: 9.9990 chunk 48 optimal weight: 9.9990 chunk 6 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 8 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 chunk 4 optimal weight: 0.9990 chunk 23 optimal weight: 5.9990 chunk 58 optimal weight: 0.7980 chunk 70 optimal weight: 6.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 HIS ** A 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 299 ASN B 108 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.149418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.118200 restraints weight = 10426.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.116948 restraints weight = 11686.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.117935 restraints weight = 10542.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.118035 restraints weight = 8955.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.118336 restraints weight = 8093.483| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.3565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7108 Z= 0.150 Angle : 0.553 8.094 9646 Z= 0.282 Chirality : 0.041 0.140 1091 Planarity : 0.004 0.050 1236 Dihedral : 8.492 175.153 1001 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % 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: -0.02 (0.28), residues: 892 helix: 0.93 (0.23), residues: 501 sheet: -0.09 (0.88), residues: 33 loop : -1.35 (0.31), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 394 TYR 0.019 0.001 TYR A 274 PHE 0.028 0.002 PHE A 261 TRP 0.006 0.001 TRP A 845 HIS 0.003 0.001 HIS A 651 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 7108) covalent geometry : angle 0.55287 ( 9646) hydrogen bonds : bond 0.04225 ( 368) hydrogen bonds : angle 4.02848 ( 1080) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 0.277 Fit side-chains revert: symmetry clash REVERT: A 245 TYR cc_start: 0.8436 (m-80) cc_final: 0.7496 (m-10) REVERT: A 422 SER cc_start: 0.8345 (t) cc_final: 0.8121 (p) REVERT: A 480 GLU cc_start: 0.8476 (tp30) cc_final: 0.7797 (tm-30) REVERT: A 534 ASN cc_start: 0.8530 (t0) cc_final: 0.8064 (t0) REVERT: A 682 MET cc_start: 0.7965 (mtm) cc_final: 0.7668 (ttm) REVERT: A 771 LYS cc_start: 0.8855 (mttt) cc_final: 0.8405 (mtpt) REVERT: A 825 TYR cc_start: 0.8628 (m-10) cc_final: 0.8326 (m-10) outliers start: 0 outliers final: 0 residues processed: 153 average time/residue: 0.0717 time to fit residues: 15.0373 Evaluate side-chains 119 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 50 optimal weight: 0.7980 chunk 43 optimal weight: 7.9990 chunk 58 optimal weight: 0.0370 chunk 67 optimal weight: 10.0000 chunk 21 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 10 optimal weight: 0.2980 chunk 46 optimal weight: 0.7980 chunk 19 optimal weight: 0.3980 chunk 82 optimal weight: 6.9990 chunk 88 optimal weight: 50.0000 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 ASN A 308 ASN A 765 GLN A 790 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.157210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.123630 restraints weight = 10160.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.124926 restraints weight = 8138.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.126499 restraints weight = 7085.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.127091 restraints weight = 6404.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.127091 restraints weight = 6031.783| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.4075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 7108 Z= 0.101 Angle : 0.508 6.859 9646 Z= 0.259 Chirality : 0.038 0.138 1091 Planarity : 0.004 0.053 1236 Dihedral : 8.104 173.306 1001 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.14 % Allowed : 1.54 % Favored : 98.31 % 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: 0.19 (0.28), residues: 892 helix: 1.01 (0.23), residues: 502 sheet: 0.37 (0.92), residues: 33 loop : -1.15 (0.32), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 338 TYR 0.017 0.001 TYR A 147 PHE 0.015 0.001 PHE A 475 TRP 0.005 0.001 TRP A 635 HIS 0.002 0.000 HIS B 108 Details of bonding type rmsd covalent geometry : bond 0.00217 ( 7108) covalent geometry : angle 0.50845 ( 9646) hydrogen bonds : bond 0.03300 ( 368) hydrogen bonds : angle 3.76813 ( 1080) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 159 time to evaluate : 0.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 THR cc_start: 0.8759 (m) cc_final: 0.8546 (p) REVERT: A 245 TYR cc_start: 0.8222 (m-80) cc_final: 0.7507 (m-10) REVERT: A 253 ASN cc_start: 0.8001 (OUTLIER) cc_final: 0.7550 (m-40) REVERT: A 317 GLU cc_start: 0.7903 (tp30) cc_final: 0.7505 (tm-30) REVERT: A 384 MET cc_start: 0.8555 (tpp) cc_final: 0.8192 (tmm) REVERT: A 388 LEU cc_start: 0.9117 (tp) cc_final: 0.8842 (tp) REVERT: A 422 SER cc_start: 0.8289 (t) cc_final: 0.7740 (p) REVERT: A 480 GLU cc_start: 0.8252 (tp30) cc_final: 0.7868 (tm-30) REVERT: A 534 ASN cc_start: 0.8572 (t0) cc_final: 0.8256 (t0) REVERT: A 590 LYS cc_start: 0.9053 (mttt) cc_final: 0.8636 (mttt) REVERT: A 607 LEU cc_start: 0.8083 (mt) cc_final: 0.7836 (mp) REVERT: A 682 MET cc_start: 0.7608 (mtm) cc_final: 0.7362 (ttm) REVERT: A 771 LYS cc_start: 0.8673 (mttt) cc_final: 0.8302 (mtpt) REVERT: B 25 ASP cc_start: 0.8095 (p0) cc_final: 0.7839 (p0) outliers start: 1 outliers final: 0 residues processed: 160 average time/residue: 0.0777 time to fit residues: 17.0521 Evaluate side-chains 137 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 136 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 29 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 59 optimal weight: 9.9990 chunk 30 optimal weight: 0.9990 chunk 49 optimal weight: 4.9990 chunk 67 optimal weight: 7.9990 chunk 82 optimal weight: 20.0000 chunk 87 optimal weight: 9.9990 chunk 43 optimal weight: 0.7980 chunk 4 optimal weight: 6.9990 chunk 57 optimal weight: 8.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.160792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.130207 restraints weight = 10178.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.130036 restraints weight = 9647.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.130991 restraints weight = 8750.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.131085 restraints weight = 7793.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.131249 restraints weight = 6992.143| |-----------------------------------------------------------------------------| r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.4023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7108 Z= 0.133 Angle : 0.537 8.504 9646 Z= 0.271 Chirality : 0.040 0.141 1091 Planarity : 0.004 0.051 1236 Dihedral : 8.274 174.429 1001 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % 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: 0.28 (0.28), residues: 892 helix: 1.07 (0.23), residues: 502 sheet: 0.44 (0.91), residues: 33 loop : -1.11 (0.32), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 262 TYR 0.019 0.001 TYR A 147 PHE 0.025 0.001 PHE A 675 TRP 0.004 0.001 TRP A 845 HIS 0.004 0.001 HIS A 302 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 7108) covalent geometry : angle 0.53723 ( 9646) hydrogen bonds : bond 0.03833 ( 368) hydrogen bonds : angle 3.84619 ( 1080) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 0.237 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 172 TYR cc_start: 0.9121 (t80) cc_final: 0.8915 (t80) REVERT: A 245 TYR cc_start: 0.8341 (m-80) cc_final: 0.7175 (m-10) REVERT: A 384 MET cc_start: 0.8585 (tpp) cc_final: 0.8249 (tmm) REVERT: A 422 SER cc_start: 0.8298 (t) cc_final: 0.7803 (p) REVERT: A 480 GLU cc_start: 0.8397 (tp30) cc_final: 0.7751 (tm-30) REVERT: A 534 ASN cc_start: 0.8636 (t0) cc_final: 0.8100 (t0) REVERT: A 682 MET cc_start: 0.7859 (mtm) cc_final: 0.7590 (ttm) REVERT: A 771 LYS cc_start: 0.8746 (mttt) cc_final: 0.8288 (mtpt) REVERT: B 25 ASP cc_start: 0.8156 (p0) cc_final: 0.7772 (p0) REVERT: B 68 GLU cc_start: 0.7199 (tm-30) cc_final: 0.6673 (tm-30) outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 0.0714 time to fit residues: 14.4809 Evaluate side-chains 128 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 84 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 55 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 26 optimal weight: 20.0000 chunk 82 optimal weight: 6.9990 chunk 87 optimal weight: 40.0000 chunk 49 optimal weight: 4.9990 chunk 64 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 HIS A 214 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.150516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.119996 restraints weight = 10378.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.118580 restraints weight = 10985.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.119688 restraints weight = 10230.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.119788 restraints weight = 8882.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.120052 restraints weight = 7790.234| |-----------------------------------------------------------------------------| r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.4020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7108 Z= 0.154 Angle : 0.591 8.006 9646 Z= 0.297 Chirality : 0.041 0.148 1091 Planarity : 0.004 0.049 1236 Dihedral : 8.420 174.348 1001 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % 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: 0.24 (0.28), residues: 892 helix: 1.06 (0.23), residues: 501 sheet: 0.38 (0.90), residues: 33 loop : -1.14 (0.32), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 262 TYR 0.018 0.001 TYR A 274 PHE 0.015 0.001 PHE A 785 TRP 0.007 0.001 TRP A 845 HIS 0.002 0.001 HIS A 243 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 7108) covalent geometry : angle 0.59146 ( 9646) hydrogen bonds : bond 0.04176 ( 368) hydrogen bonds : angle 3.97440 ( 1080) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.252 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 172 TYR cc_start: 0.9151 (t80) cc_final: 0.8936 (t80) REVERT: A 245 TYR cc_start: 0.8283 (m-80) cc_final: 0.7614 (m-10) REVERT: A 422 SER cc_start: 0.8316 (t) cc_final: 0.7864 (p) REVERT: A 534 ASN cc_start: 0.8703 (t0) cc_final: 0.8166 (t0) REVERT: A 682 MET cc_start: 0.7874 (mtm) cc_final: 0.7610 (ttm) REVERT: A 771 LYS cc_start: 0.8793 (mttt) cc_final: 0.8300 (mtpt) REVERT: A 842 GLN cc_start: 0.8605 (tt0) cc_final: 0.8230 (mm-40) REVERT: B 68 GLU cc_start: 0.7211 (tm-30) cc_final: 0.6624 (tm-30) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.0752 time to fit residues: 14.6297 Evaluate side-chains 120 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 88 optimal weight: 7.9990 chunk 22 optimal weight: 8.9990 chunk 87 optimal weight: 9.9990 chunk 51 optimal weight: 5.9990 chunk 63 optimal weight: 7.9990 chunk 69 optimal weight: 8.9990 chunk 17 optimal weight: 0.7980 chunk 60 optimal weight: 0.6980 chunk 18 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 86 optimal weight: 5.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 HIS A 214 ASN A 299 ASN A 308 ASN A 790 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.150673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.115309 restraints weight = 10304.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.116408 restraints weight = 8403.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.117818 restraints weight = 7444.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.118408 restraints weight = 6796.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.118408 restraints weight = 6421.487| |-----------------------------------------------------------------------------| r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.4001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 7108 Z= 0.178 Angle : 0.604 7.730 9646 Z= 0.308 Chirality : 0.042 0.156 1091 Planarity : 0.004 0.049 1236 Dihedral : 8.594 174.223 1001 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 0.14 % Allowed : 0.56 % Favored : 99.30 % 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: 0.21 (0.29), residues: 892 helix: 1.02 (0.24), residues: 499 sheet: 0.32 (0.92), residues: 33 loop : -1.11 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 262 TYR 0.025 0.002 TYR A 147 PHE 0.019 0.002 PHE A 785 TRP 0.018 0.002 TRP A 845 HIS 0.002 0.001 HIS A 171 Details of bonding type rmsd covalent geometry : bond 0.00415 ( 7108) covalent geometry : angle 0.60400 ( 9646) hydrogen bonds : bond 0.04515 ( 368) hydrogen bonds : angle 4.16938 ( 1080) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 140 time to evaluate : 0.263 Fit side-chains REVERT: A 172 TYR cc_start: 0.9165 (t80) cc_final: 0.8939 (t80) REVERT: A 245 TYR cc_start: 0.8298 (m-80) cc_final: 0.7687 (m-10) REVERT: A 422 SER cc_start: 0.8374 (t) cc_final: 0.7841 (p) REVERT: A 534 ASN cc_start: 0.8601 (t0) cc_final: 0.8127 (t0) REVERT: A 682 MET cc_start: 0.7935 (mtm) cc_final: 0.7673 (ttm) REVERT: A 771 LYS cc_start: 0.8854 (mttt) cc_final: 0.8321 (mtpt) outliers start: 1 outliers final: 0 residues processed: 141 average time/residue: 0.0722 time to fit residues: 14.1935 Evaluate side-chains 114 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 75 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 82 optimal weight: 9.9990 chunk 58 optimal weight: 3.9990 chunk 88 optimal weight: 40.0000 chunk 62 optimal weight: 0.5980 chunk 13 optimal weight: 6.9990 chunk 28 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 chunk 67 optimal weight: 3.9990 chunk 80 optimal weight: 20.0000 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 HIS A 517 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.145711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.111538 restraints weight = 10470.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.110426 restraints weight = 12306.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.112396 restraints weight = 11034.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.112336 restraints weight = 8136.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.112384 restraints weight = 8282.382| |-----------------------------------------------------------------------------| r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.3948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 7108 Z= 0.213 Angle : 0.670 9.555 9646 Z= 0.340 Chirality : 0.044 0.161 1091 Planarity : 0.004 0.049 1236 Dihedral : 8.830 174.184 1001 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.28), residues: 892 helix: 0.82 (0.24), residues: 499 sheet: 0.13 (0.93), residues: 33 loop : -1.22 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 262 TYR 0.024 0.002 TYR A 147 PHE 0.025 0.002 PHE A 785 TRP 0.020 0.002 TRP A 845 HIS 0.003 0.001 HIS A 171 Details of bonding type rmsd covalent geometry : bond 0.00498 ( 7108) covalent geometry : angle 0.67042 ( 9646) hydrogen bonds : bond 0.04971 ( 368) hydrogen bonds : angle 4.40906 ( 1080) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.227 Fit side-chains REVERT: A 194 LEU cc_start: 0.9005 (mm) cc_final: 0.8752 (mm) REVERT: A 245 TYR cc_start: 0.8288 (m-80) cc_final: 0.7215 (m-10) REVERT: A 422 SER cc_start: 0.8373 (t) cc_final: 0.7803 (p) REVERT: A 534 ASN cc_start: 0.8567 (t0) cc_final: 0.8150 (t0) REVERT: A 682 MET cc_start: 0.7988 (mtm) cc_final: 0.7725 (ttm) REVERT: A 771 LYS cc_start: 0.8929 (mttt) cc_final: 0.8354 (mtpt) outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.0749 time to fit residues: 14.2112 Evaluate side-chains 118 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 18 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 59 optimal weight: 10.0000 chunk 37 optimal weight: 0.7980 chunk 50 optimal weight: 0.6980 chunk 51 optimal weight: 0.8980 chunk 12 optimal weight: 0.0050 chunk 45 optimal weight: 0.2980 chunk 53 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 overall best weight: 0.5394 ------------------------------------------------------------------------------- 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 = 0.3680 r_free = 0.3680 target = 0.154176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.121974 restraints weight = 10217.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.120465 restraints weight = 10735.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.121676 restraints weight = 9604.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.122203 restraints weight = 8157.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.122446 restraints weight = 7663.004| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.4426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 7108 Z= 0.109 Angle : 0.571 8.786 9646 Z= 0.286 Chirality : 0.040 0.147 1091 Planarity : 0.004 0.052 1236 Dihedral : 8.083 171.451 1001 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.29), residues: 892 helix: 1.10 (0.24), residues: 499 sheet: 0.39 (0.92), residues: 33 loop : -1.04 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 262 TYR 0.022 0.001 TYR A 147 PHE 0.022 0.001 PHE A 785 TRP 0.022 0.001 TRP A 845 HIS 0.002 0.000 HIS A 113 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 7108) covalent geometry : angle 0.57130 ( 9646) hydrogen bonds : bond 0.03578 ( 368) hydrogen bonds : angle 3.91025 ( 1080) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1094.71 seconds wall clock time: 19 minutes 43.45 seconds (1183.45 seconds total)