Starting phenix.real_space_refine on Fri Sep 11 02:39:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6s5t_10100/09_2026/6s5t_10100.cif Found real_map, /net/cci-nas-00/data/ceres_data/6s5t_10100/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/6s5t_10100/09_2026/6s5t_10100.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6s5t_10100/09_2026/6s5t_10100.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6s5t_10100/09_2026/6s5t_10100.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6s5t_10100/09_2026/6s5t_10100.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6s5t_10100/09_2026/6s5t_10100.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6s5t_10100/09_2026/6s5t_10100.map" } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/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: 1.74, per 1000 atoms: 0.25 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: 0.58 Conformation dependent library (CDL) restraints added in 449.3 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: 0.18 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: 1.07 Time building geometry restraints manager: 0.77 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: 4108 35.54 - 71.08: 143 71.08 - 106.63: 4 106.63 - 142.17: 0 142.17 - 177.71: 1 Dihedral angle restraints: 4256 sinusoidal: 1621 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 4253 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: 0.360 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: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 8.250 Find NCS groups from input model: 0.030 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 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 : 17.310 177.709 2552 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/Z covalent geometry : bond 0.00695 / 0.45 ( 7108) covalent geometry : angle 1.47682 / 0.99 ( 9646) hydrogen bonds : bond 0.27093 / 18.63 ( 368) hydrogen bonds : angle 8.97721 / 6.34 ( 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 : 0.261 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: 0.0773 time to fit residues: 20.2637 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 : 0.243 ------------------------------------------------------------------------------- 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... 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 = 0.150761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.115412 restraints weight = 10157.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.116926 restraints weight = 8085.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.118312 restraints weight = 6996.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.118805 restraints weight = 6364.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.119263 restraints weight = 6042.549| |-----------------------------------------------------------------------------| r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7108 Z= 0.127 Angle : 0.574 6.300 9646 Z= 0.302 Chirality : 0.039 0.147 1091 Planarity : 0.004 0.047 1236 Dihedral : 7.963 178.531 973 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.14 % Allowed : 1.40 % Favored : 98.46 % 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: 892 helix: -0.38 (0.22), residues: 497 sheet: -0.42 (0.91), residues: 33 loop : -1.71 (0.29), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 849 TYR 0.015 0.001 TYR A 147 PHE 0.019 0.002 PHE A 475 TRP 0.005 0.001 TRP A 845 HIS 0.003 0.001 HIS A 302 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.13 ( 7108) covalent geometry : angle 0.57371 / 0.30 ( 9646) hydrogen bonds : bond 0.04859 / 3.23 ( 368) hydrogen bonds : angle 4.46805 / 3.18 ( 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 : 0.165 Fit side-chains REVERT: A 114 ASP cc_start: 0.7631 (t0) cc_final: 0.7121 (t0) REVERT: A 218 GLU cc_start: 0.8431 (mm-30) cc_final: 0.8229 (tp30) REVERT: A 308 ASN cc_start: 0.8861 (OUTLIER) cc_final: 0.8503 (m-40) REVERT: A 317 GLU cc_start: 0.8090 (tp30) cc_final: 0.7831 (tm-30) REVERT: A 414 GLU cc_start: 0.8702 (mp0) cc_final: 0.8436 (mp0) REVERT: A 480 GLU cc_start: 0.8462 (tp30) cc_final: 0.7819 (tm-30) REVERT: A 642 MET cc_start: 0.8811 (tpp) cc_final: 0.8560 (tpp) REVERT: A 650 ILE cc_start: 0.9027 (mm) cc_final: 0.8632 (tt) REVERT: A 682 MET cc_start: 0.8293 (mtt) cc_final: 0.8079 (mtm) REVERT: A 771 LYS cc_start: 0.8728 (mttt) cc_final: 0.8191 (mtpt) REVERT: B 22 LYS cc_start: 0.8564 (mttt) cc_final: 0.7823 (mtmt) REVERT: B 25 ASP cc_start: 0.8187 (p0) cc_final: 0.7950 (p0) REVERT: B 32 GLU cc_start: 0.8152 (pp20) cc_final: 0.7930 (mp0) REVERT: B 37 MET cc_start: 0.8844 (mmm) cc_final: 0.8603 (mmm) outliers start: 1 outliers final: 0 residues processed: 176 average time/residue: 0.0736 time to fit residues: 17.0743 Evaluate side-chains 124 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 123 time to evaluate : 0.220 ------------------------------------------------------------------------------- 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: 1.9990 chunk 4 optimal weight: 5.9990 chunk 29 optimal weight: 0.0870 chunk 41 optimal weight: 0.9980 chunk 14 optimal weight: 7.9990 chunk 80 optimal weight: 0.9990 chunk 83 optimal weight: 20.0000 chunk 11 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 overall best weight: 0.7762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 208 HIS ** A 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.152581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.120756 restraints weight = 10082.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.120053 restraints weight = 9905.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.121477 restraints weight = 9476.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.121538 restraints weight = 7781.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.121659 restraints weight = 7337.788| |-----------------------------------------------------------------------------| r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 7108 Z= 0.104 Angle : 0.495 6.114 9646 Z= 0.258 Chirality : 0.038 0.134 1091 Planarity : 0.004 0.050 1236 Dihedral : 7.593 177.611 973 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.14 % Allowed : 2.11 % Favored : 97.75 % 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: -0.54 (0.27), residues: 892 helix: 0.46 (0.23), residues: 508 sheet: -0.44 (0.84), residues: 33 loop : -1.52 (0.30), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 849 TYR 0.016 0.001 TYR A 147 PHE 0.016 0.001 PHE A 475 TRP 0.005 0.001 TRP A 635 HIS 0.004 0.001 HIS A 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.10 ( 7108) covalent geometry : angle 0.49510 / 0.26 ( 9646) hydrogen bonds : bond 0.03889 / 2.59 ( 368) hydrogen bonds : angle 3.99422 / 2.83 ( 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 163 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 162 time to evaluate : 0.207 Fit side-chains revert: symmetry clash REVERT: A 114 ASP cc_start: 0.7650 (t0) cc_final: 0.7444 (t0) REVERT: A 245 TYR cc_start: 0.8373 (m-80) cc_final: 0.7681 (m-10) REVERT: A 480 GLU cc_start: 0.8411 (tp30) cc_final: 0.7823 (tm-30) REVERT: A 534 ASN cc_start: 0.8250 (t0) cc_final: 0.8031 (t0) REVERT: A 650 ILE cc_start: 0.8879 (mm) cc_final: 0.8669 (tt) REVERT: A 771 LYS cc_start: 0.8561 (mttt) cc_final: 0.8264 (mtpt) REVERT: B 22 LYS cc_start: 0.8558 (mttt) cc_final: 0.7846 (mtmt) outliers start: 1 outliers final: 0 residues processed: 162 average time/residue: 0.0737 time to fit residues: 16.5581 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 : 0.325 ------------------------------------------------------------------------------- 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: 20.0000 chunk 8 optimal weight: 3.9990 chunk 26 optimal weight: 8.9990 chunk 33 optimal weight: 7.9990 chunk 16 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 12 optimal weight: 1.9990 chunk 61 optimal weight: 8.9990 chunk 55 optimal weight: 7.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 208 HIS A 234 HIS ** A 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 HIS A 308 ASN A 398 HIS A 800 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.142826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.109091 restraints weight = 10564.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.107775 restraints weight = 10568.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.109182 restraints weight = 10711.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.109198 restraints weight = 8321.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.109304 restraints weight = 8214.814| |-----------------------------------------------------------------------------| r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.3138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 7108 Z= 0.244 Angle : 0.676 9.386 9646 Z= 0.347 Chirality : 0.044 0.145 1091 Planarity : 0.005 0.048 1236 Dihedral : 7.908 177.196 973 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % 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: -0.48 (0.27), residues: 892 helix: 0.57 (0.23), residues: 505 sheet: -0.40 (0.90), residues: 31 loop : -1.59 (0.30), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 232 TYR 0.024 0.002 TYR A 274 PHE 0.020 0.002 PHE A 292 TRP 0.010 0.002 TRP A 845 HIS 0.005 0.001 HIS A 651 Details of bonding type rmsd/Z covalent geometry : bond 0.00568 / 0.24 ( 7108) covalent geometry : angle 0.67644 / 0.35 ( 9646) hydrogen bonds : bond 0.05370 / 3.56 ( 368) hydrogen bonds : angle 4.53379 / 3.21 ( 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 148 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 0.276 Fit side-chains revert: symmetry clash REVERT: A 245 TYR cc_start: 0.8435 (m-80) cc_final: 0.7557 (m-10) REVERT: A 461 GLU cc_start: 0.7785 (tt0) cc_final: 0.7431 (tm-30) REVERT: A 534 ASN cc_start: 0.8437 (t0) cc_final: 0.8077 (t0) REVERT: A 650 ILE cc_start: 0.9103 (mm) cc_final: 0.8755 (tt) REVERT: A 771 LYS cc_start: 0.8893 (mttt) cc_final: 0.8483 (mtpt) REVERT: A 825 TYR cc_start: 0.8769 (m-10) cc_final: 0.8458 (m-10) outliers start: 0 outliers final: 0 residues processed: 148 average time/residue: 0.0751 time to fit residues: 15.5706 Evaluate side-chains 115 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.256 ------------------------------------------------------------------------------- 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: 0.9980 chunk 61 optimal weight: 4.9990 chunk 48 optimal weight: 8.9990 chunk 6 optimal weight: 10.0000 chunk 3 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 23 optimal weight: 10.0000 chunk 58 optimal weight: 0.0970 chunk 70 optimal weight: 0.9980 overall best weight: 1.0180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 253 ASN A 299 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.150869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.117563 restraints weight = 10307.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.116935 restraints weight = 11059.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.118832 restraints weight = 9988.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.118828 restraints weight = 7492.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.118952 restraints weight = 7159.029| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.3600 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= 0.110 Angle : 0.530 7.737 9646 Z= 0.269 Chirality : 0.039 0.136 1091 Planarity : 0.004 0.053 1236 Dihedral : 7.404 170.466 973 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % 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: -0.03 (0.28), residues: 892 helix: 0.94 (0.24), residues: 498 sheet: -0.36 (0.85), residues: 33 loop : -1.34 (0.31), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 262 TYR 0.008 0.001 TYR A 274 PHE 0.014 0.001 PHE A 475 TRP 0.004 0.001 TRP A 635 HIS 0.004 0.001 HIS A 302 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 ( 7108) covalent geometry : angle 0.52953 / 0.27 ( 9646) hydrogen bonds : bond 0.03845 / 2.54 ( 368) hydrogen bonds : angle 3.93084 / 2.79 ( 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 161 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 160 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 245 TYR cc_start: 0.8256 (m-80) cc_final: 0.7520 (m-10) REVERT: A 253 ASN cc_start: 0.8096 (OUTLIER) cc_final: 0.7667 (m-40) REVERT: A 422 SER cc_start: 0.8272 (t) cc_final: 0.8068 (p) REVERT: A 534 ASN cc_start: 0.8525 (t0) cc_final: 0.8202 (t0) REVERT: A 549 ILE cc_start: 0.8395 (tp) cc_final: 0.8107 (tt) REVERT: A 682 MET cc_start: 0.7746 (mtm) cc_final: 0.7389 (ttm) REVERT: A 696 MET cc_start: 0.8106 (mmp) cc_final: 0.7410 (mtm) REVERT: A 771 LYS cc_start: 0.8808 (mttt) cc_final: 0.8419 (mtpt) REVERT: B 25 ASP cc_start: 0.8213 (p0) cc_final: 0.7920 (p0) outliers start: 1 outliers final: 0 residues processed: 161 average time/residue: 0.0687 time to fit residues: 15.8239 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 : 0.249 ------------------------------------------------------------------------------- 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: 1.9990 chunk 43 optimal weight: 0.5980 chunk 58 optimal weight: 6.9990 chunk 67 optimal weight: 10.0000 chunk 21 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 10 optimal weight: 8.9990 chunk 46 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 82 optimal weight: 9.9990 chunk 88 optimal weight: 50.0000 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 208 HIS A 350 GLN B 108 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.151730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.118902 restraints weight = 10394.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.117743 restraints weight = 10008.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.118815 restraints weight = 8804.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.119129 restraints weight = 7932.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.119393 restraints weight = 6963.632| |-----------------------------------------------------------------------------| r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.3790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7108 Z= 0.121 Angle : 0.522 8.794 9646 Z= 0.267 Chirality : 0.039 0.134 1091 Planarity : 0.004 0.053 1236 Dihedral : 7.288 168.537 973 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % 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: 0.09 (0.28), residues: 892 helix: 0.95 (0.24), residues: 500 sheet: 0.06 (0.93), residues: 31 loop : -1.19 (0.32), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 262 TYR 0.020 0.001 TYR A 147 PHE 0.011 0.001 PHE A 475 TRP 0.004 0.001 TRP A 845 HIS 0.002 0.001 HIS A 243 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 ( 7108) covalent geometry : angle 0.52182 / 0.27 ( 9646) hydrogen bonds : bond 0.03881 / 2.57 ( 368) hydrogen bonds : angle 3.89598 / 2.76 ( 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 148 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 0.264 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 172 TYR cc_start: 0.9135 (t80) cc_final: 0.8913 (t80) REVERT: A 245 TYR cc_start: 0.8326 (m-80) cc_final: 0.7364 (m-10) REVERT: A 422 SER cc_start: 0.8241 (t) cc_final: 0.7799 (p) REVERT: A 534 ASN cc_start: 0.8560 (t0) cc_final: 0.8057 (t0) REVERT: A 549 ILE cc_start: 0.8455 (tp) cc_final: 0.8189 (tt) REVERT: A 650 ILE cc_start: 0.8904 (mm) cc_final: 0.8702 (tt) REVERT: A 682 MET cc_start: 0.7764 (mtm) cc_final: 0.7372 (ttm) REVERT: A 771 LYS cc_start: 0.8783 (mttt) cc_final: 0.8351 (mtpt) REVERT: B 25 ASP cc_start: 0.8183 (p0) cc_final: 0.7805 (p0) outliers start: 0 outliers final: 0 residues processed: 148 average time/residue: 0.0754 time to fit residues: 15.6387 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 : 0.247 ------------------------------------------------------------------------------- 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: 7.9990 chunk 10 optimal weight: 8.9990 chunk 59 optimal weight: 9.9990 chunk 30 optimal weight: 6.9990 chunk 49 optimal weight: 7.9990 chunk 67 optimal weight: 5.9990 chunk 82 optimal weight: 6.9990 chunk 87 optimal weight: 40.0000 chunk 43 optimal weight: 0.2980 chunk 4 optimal weight: 6.9990 chunk 57 optimal weight: 5.9990 overall best weight: 5.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 208 HIS A 299 ASN A 308 ASN A 674 HIS A 765 GLN A 790 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.147429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.111339 restraints weight = 11300.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.109587 restraints weight = 14410.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.110907 restraints weight = 13475.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.111071 restraints weight = 10643.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.111373 restraints weight = 9970.748| |-----------------------------------------------------------------------------| r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.3604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.043 7108 Z= 0.312 Angle : 0.755 11.343 9646 Z= 0.385 Chirality : 0.047 0.169 1091 Planarity : 0.005 0.063 1236 Dihedral : 7.861 167.475 973 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % 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: -0.37 (0.28), residues: 892 helix: 0.59 (0.23), residues: 499 sheet: -0.13 (0.98), residues: 31 loop : -1.41 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 232 TYR 0.027 0.003 TYR A 147 PHE 0.038 0.002 PHE A 675 TRP 0.007 0.002 TRP A 277 HIS 0.005 0.001 HIS A 651 Details of bonding type rmsd/Z covalent geometry : bond 0.00728 / 0.31 ( 7108) covalent geometry : angle 0.75496 / 0.39 ( 9646) hydrogen bonds : bond 0.05684 / 3.77 ( 368) hydrogen bonds : angle 4.72789 / 3.34 ( 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 144 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 0.267 Fit side-chains REVERT: A 114 ASP cc_start: 0.7652 (t0) cc_final: 0.7413 (t0) REVERT: A 172 TYR cc_start: 0.9227 (t80) cc_final: 0.9017 (t80) REVERT: A 245 TYR cc_start: 0.8520 (m-80) cc_final: 0.7592 (m-10) REVERT: A 339 TYR cc_start: 0.7167 (t80) cc_final: 0.6855 (t80) REVERT: A 461 GLU cc_start: 0.7824 (tt0) cc_final: 0.7116 (mp0) REVERT: A 534 ASN cc_start: 0.8529 (t0) cc_final: 0.8188 (t0) REVERT: A 682 MET cc_start: 0.8098 (mtm) cc_final: 0.7828 (ttm) REVERT: A 771 LYS cc_start: 0.8991 (mttt) cc_final: 0.8465 (mtpt) outliers start: 0 outliers final: 0 residues processed: 144 average time/residue: 0.0765 time to fit residues: 15.3979 Evaluate side-chains 111 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.275 ------------------------------------------------------------------------------- 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: 9.9990 chunk 51 optimal weight: 0.7980 chunk 28 optimal weight: 6.9990 chunk 55 optimal weight: 0.9990 chunk 1 optimal weight: 5.9990 chunk 26 optimal weight: 9.9990 chunk 82 optimal weight: 9.9990 chunk 87 optimal weight: 9.9990 chunk 49 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 214 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.151585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.119581 restraints weight = 10427.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.118248 restraints weight = 11401.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.119585 restraints weight = 10427.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.120087 restraints weight = 8159.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.120248 restraints weight = 7208.114| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.4029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7108 Z= 0.122 Angle : 0.571 10.258 9646 Z= 0.288 Chirality : 0.040 0.160 1091 Planarity : 0.004 0.053 1236 Dihedral : 7.320 164.351 973 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % 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: -0.12 (0.28), residues: 892 helix: 0.76 (0.23), residues: 499 sheet: -0.19 (0.92), residues: 33 loop : -1.22 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 262 TYR 0.030 0.001 TYR A 147 PHE 0.012 0.001 PHE A 174 TRP 0.010 0.001 TRP A 845 HIS 0.004 0.001 HIS A 302 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 ( 7108) covalent geometry : angle 0.57119 / 0.29 ( 9646) hydrogen bonds : bond 0.04036 / 2.65 ( 368) hydrogen bonds : angle 4.05803 / 2.90 ( 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 153 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 0.246 Fit side-chains revert: symmetry clash REVERT: A 245 TYR cc_start: 0.8394 (m-80) cc_final: 0.7359 (m-10) REVERT: A 534 ASN cc_start: 0.8593 (t0) cc_final: 0.8133 (t0) REVERT: A 650 ILE cc_start: 0.8963 (mm) cc_final: 0.8645 (tt) REVERT: A 682 MET cc_start: 0.7879 (mtm) cc_final: 0.7505 (ttm) REVERT: A 771 LYS cc_start: 0.8870 (mttt) cc_final: 0.8395 (mtpt) REVERT: B 25 ASP cc_start: 0.8258 (p0) cc_final: 0.7872 (p0) outliers start: 0 outliers final: 0 residues processed: 153 average time/residue: 0.0769 time to fit residues: 16.5175 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 : 0.246 ------------------------------------------------------------------------------- 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: 50.0000 chunk 22 optimal weight: 10.0000 chunk 87 optimal weight: 5.9990 chunk 51 optimal weight: 6.9990 chunk 63 optimal weight: 0.0770 chunk 69 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 86 optimal weight: 10.0000 overall best weight: 1.7744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 208 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.149909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.116441 restraints weight = 10389.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.115486 restraints weight = 11341.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.117046 restraints weight = 10538.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.117836 restraints weight = 7822.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.117876 restraints weight = 7163.554| |-----------------------------------------------------------------------------| r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.4046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7108 Z= 0.141 Angle : 0.585 11.103 9646 Z= 0.291 Chirality : 0.041 0.161 1091 Planarity : 0.004 0.051 1236 Dihedral : 7.255 163.861 973 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % 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: 0.06 (0.28), residues: 892 helix: 0.87 (0.23), residues: 501 sheet: -0.06 (0.94), residues: 33 loop : -1.10 (0.33), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 262 TYR 0.031 0.002 TYR A 147 PHE 0.020 0.002 PHE A 675 TRP 0.011 0.001 TRP A 845 HIS 0.002 0.000 HIS A 324 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 ( 7108) covalent geometry : angle 0.58548 / 0.29 ( 9646) hydrogen bonds : bond 0.04181 / 2.74 ( 368) hydrogen bonds : angle 4.01636 / 2.86 ( 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 147 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 0.284 Fit side-chains revert: symmetry clash REVERT: A 245 TYR cc_start: 0.8264 (m-80) cc_final: 0.7637 (m-10) REVERT: A 534 ASN cc_start: 0.8567 (t0) cc_final: 0.8163 (t0) REVERT: A 682 MET cc_start: 0.7871 (mtm) cc_final: 0.7515 (ttm) REVERT: A 771 LYS cc_start: 0.8830 (mttt) cc_final: 0.8342 (mtpt) REVERT: B 25 ASP cc_start: 0.8223 (p0) cc_final: 0.7790 (p0) outliers start: 0 outliers final: 0 residues processed: 147 average time/residue: 0.0748 time to fit residues: 15.3634 Evaluate side-chains 121 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.280 ------------------------------------------------------------------------------- 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: 4.9990 chunk 5 optimal weight: 0.5980 chunk 82 optimal weight: 7.9990 chunk 58 optimal weight: 7.9990 chunk 88 optimal weight: 50.0000 chunk 62 optimal weight: 4.9990 chunk 13 optimal weight: 0.1980 chunk 28 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 67 optimal weight: 7.9990 chunk 80 optimal weight: 8.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 208 HIS A 790 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.157525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.128434 restraints weight = 10145.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.126778 restraints weight = 9711.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.127875 restraints weight = 9477.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.128058 restraints weight = 8143.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.128166 restraints weight = 7422.622| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.4138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7108 Z= 0.160 Angle : 0.621 10.756 9646 Z= 0.312 Chirality : 0.042 0.167 1091 Planarity : 0.004 0.051 1236 Dihedral : 7.265 162.406 973 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 0.14 % Allowed : 0.14 % Favored : 99.72 % 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: 0.10 (0.28), residues: 892 helix: 0.88 (0.23), residues: 500 sheet: -0.06 (0.96), residues: 33 loop : -1.04 (0.33), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 262 TYR 0.026 0.002 TYR A 147 PHE 0.032 0.002 PHE A 261 TRP 0.018 0.002 TRP A 845 HIS 0.002 0.001 HIS A 171 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 ( 7108) covalent geometry : angle 0.62071 / 0.31 ( 9646) hydrogen bonds : bond 0.04359 / 2.85 ( 368) hydrogen bonds : angle 4.10313 / 2.93 ( 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 144 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 143 time to evaluate : 0.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 TYR cc_start: 0.9190 (t80) cc_final: 0.8969 (t80) REVERT: A 245 TYR cc_start: 0.8278 (m-80) cc_final: 0.7368 (m-10) REVERT: A 534 ASN cc_start: 0.8582 (t0) cc_final: 0.8128 (t0) REVERT: A 682 MET cc_start: 0.7898 (mtm) cc_final: 0.7595 (ttm) REVERT: A 771 LYS cc_start: 0.8838 (mttt) cc_final: 0.8334 (mtpt) REVERT: B 25 ASP cc_start: 0.8223 (p0) cc_final: 0.7804 (p0) outliers start: 1 outliers final: 0 residues processed: 144 average time/residue: 0.0759 time to fit residues: 15.2908 Evaluate side-chains 126 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.261 ------------------------------------------------------------------------------- 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: 4.9990 chunk 24 optimal weight: 9.9990 chunk 59 optimal weight: 8.9990 chunk 37 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 12 optimal weight: 0.0770 chunk 45 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 overall best weight: 1.1944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 208 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.156568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.125752 restraints weight = 10224.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.124783 restraints weight = 9980.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.126098 restraints weight = 9283.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.126258 restraints weight = 7152.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.126434 restraints weight = 6413.124| |-----------------------------------------------------------------------------| r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.4340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7108 Z= 0.123 Angle : 0.582 7.923 9646 Z= 0.291 Chirality : 0.040 0.152 1091 Planarity : 0.004 0.052 1236 Dihedral : 7.073 160.795 973 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % 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: 0.22 (0.29), residues: 892 helix: 0.97 (0.23), residues: 500 sheet: 0.01 (0.95), residues: 33 loop : -0.97 (0.34), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 668 TYR 0.016 0.001 TYR A 810 PHE 0.022 0.002 PHE A 261 TRP 0.021 0.001 TRP A 845 HIS 0.003 0.000 HIS A 302 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 ( 7108) covalent geometry : angle 0.58186 / 0.29 ( 9646) hydrogen bonds : bond 0.03919 / 2.56 ( 368) hydrogen bonds : angle 3.93858 / 2.82 ( 1080) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1126.60 seconds wall clock time: 20 minutes 17.40 seconds (1217.40 seconds total)