Starting phenix.real_space_refine on Wed Mar 12 00:35:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6s5t_10100/03_2025/6s5t_10100.cif Found real_map, /net/cci-nas-00/data/ceres_data/6s5t_10100/03_2025/6s5t_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_2025/6s5t_10100.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6s5t_10100/03_2025/6s5t_10100.map" model { file = "/net/cci-nas-00/data/ceres_data/6s5t_10100/03_2025/6s5t_10100.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6s5t_10100/03_2025/6s5t_10100.cif" } resolution = 4.15 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: {'GLN:plan1': 4, 'ASN:plan1': 1, 'ASP:plan': 8, 'PHE:plan': 1, 'GLU:plan': 10, 'ARG:plan': 3} 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: {'GLN:plan1': 2, 'TYR:plan': 2, 'ASN:plan1': 4, 'ASP:plan': 10, 'PHE:plan': 2, 'GLU:plan': 13, 'ARG:plan': 4} 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: 4.55, per 1000 atoms: 0.65 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: 1.78 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.80 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: 2.09 Time building geometry restraints manager: 2.06 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: 0.200 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: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 20.120 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.770 ------------------------------------------------------------------------------- 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= 0.449 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.005 0.002 TRP A 845 HIS 0.006 0.001 HIS A 800 PHE 0.017 0.002 PHE A 269 TYR 0.015 0.003 TYR A 606 ARG 0.012 0.001 ARG A 393 *********************** 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 : 0.763 Fit side-chains REVERT: A 117 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8357 (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: 0.8249 (mp) REVERT: A 245 TYR cc_start: 0.8840 (m-80) cc_final: 0.8597 (m-10) REVERT: A 282 TYR cc_start: 0.9150 (m-80) cc_final: 0.8789 (m-10) REVERT: A 339 TYR cc_start: 0.7710 (t80) cc_final: 0.7463 (t80) REVERT: A 345 ARG cc_start: 0.8060 (mtt180) cc_final: 0.7677 (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: 0.7532 (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: 0.8715 (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: 0.8928 (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: 0.8747 (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: 0.8209 (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: 0.1954 time to fit residues: 50.3607 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 : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 75 optimal weight: 5.9990 chunk 67 optimal weight: 9.9990 chunk 37 optimal weight: 3.9990 chunk 23 optimal weight: 9.9990 chunk 45 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 69 optimal weight: 5.9990 chunk 26 optimal weight: 10.0000 chunk 42 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 80 optimal weight: 3.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- 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 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 308 ASN A 517 GLN A 800 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.144547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.113575 restraints weight = 10356.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.112399 restraints weight = 11762.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.113276 restraints weight = 10943.144| |-----------------------------------------------------------------------------| r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 7108 Z= 0.310 Angle : 0.654 6.471 9646 Z= 0.345 Chirality : 0.042 0.144 1091 Planarity : 0.005 0.046 1236 Dihedral : 9.483 178.018 1001 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.26), residues: 892 helix: -0.49 (0.22), residues: 497 sheet: -0.29 (0.84), residues: 38 loop : -1.91 (0.29), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 845 HIS 0.003 0.001 HIS A 171 PHE 0.017 0.002 PHE A 292 TYR 0.018 0.002 TYR A 274 ARG 0.006 0.001 ARG A 394 *********************** 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 162 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 161 time to evaluate : 0.842 Fit side-chains revert: symmetry clash REVERT: A 114 ASP cc_start: 0.7630 (t0) cc_final: 0.7125 (t0) REVERT: A 218 GLU cc_start: 0.8320 (mm-30) cc_final: 0.7941 (tp30) REVERT: A 245 TYR cc_start: 0.8215 (m-80) cc_final: 0.7985 (m-10) REVERT: A 308 ASN cc_start: 0.8923 (OUTLIER) cc_final: 0.8665 (m-40) REVERT: A 642 MET cc_start: 0.8934 (tpp) cc_final: 0.8658 (tpp) REVERT: A 735 GLU cc_start: 0.8897 (pm20) cc_final: 0.8690 (pm20) REVERT: A 771 LYS cc_start: 0.8809 (mttt) cc_final: 0.8333 (mtpt) REVERT: B 22 LYS cc_start: 0.8567 (mttt) cc_final: 0.7879 (mtmt) REVERT: B 25 ASP cc_start: 0.8527 (p0) cc_final: 0.8183 (p0) REVERT: B 32 GLU cc_start: 0.8269 (pp20) cc_final: 0.7980 (mp0) REVERT: B 73 MET cc_start: 0.8905 (tpp) cc_final: 0.8658 (tpp) outliers start: 1 outliers final: 0 residues processed: 162 average time/residue: 0.2098 time to fit residues: 44.6457 Evaluate side-chains 113 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 112 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 68 optimal weight: 1.9990 chunk 48 optimal weight: 10.0000 chunk 21 optimal weight: 0.4980 chunk 77 optimal weight: 4.9990 chunk 54 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 78 optimal weight: 5.9990 chunk 60 optimal weight: 0.5980 chunk 88 optimal weight: 50.0000 chunk 59 optimal weight: 3.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 HIS ** A 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 472 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.148883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.117676 restraints weight = 10261.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.116977 restraints weight = 10589.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.118177 restraints weight = 10358.441| |-----------------------------------------------------------------------------| r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7108 Z= 0.173 Angle : 0.530 6.225 9646 Z= 0.274 Chirality : 0.039 0.142 1091 Planarity : 0.004 0.050 1236 Dihedral : 8.682 175.447 1001 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 0.14 % Allowed : 1.83 % Favored : 98.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.27), residues: 892 helix: 0.42 (0.23), residues: 498 sheet: -0.67 (0.84), residues: 33 loop : -1.56 (0.30), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 635 HIS 0.002 0.001 HIS A 472 PHE 0.017 0.002 PHE A 475 TYR 0.016 0.001 TYR A 147 ARG 0.008 0.000 ARG A 394 *********************** 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 : 0.798 Fit side-chains revert: symmetry clash REVERT: A 114 ASP cc_start: 0.7625 (t0) cc_final: 0.7295 (t0) REVERT: A 147 TYR cc_start: 0.8646 (t80) cc_final: 0.8444 (t80) REVERT: A 771 LYS cc_start: 0.8790 (mttt) cc_final: 0.8312 (mtpt) REVERT: A 825 TYR cc_start: 0.8724 (m-80) cc_final: 0.8240 (m-10) REVERT: B 22 LYS cc_start: 0.8544 (mttt) cc_final: 0.7888 (mtmt) REVERT: B 25 ASP cc_start: 0.8160 (p0) cc_final: 0.7900 (p0) outliers start: 1 outliers final: 0 residues processed: 163 average time/residue: 0.1762 time to fit residues: 39.1973 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 : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 23 optimal weight: 20.0000 chunk 84 optimal weight: 10.0000 chunk 36 optimal weight: 0.9980 chunk 15 optimal weight: 0.0040 chunk 24 optimal weight: 20.0000 chunk 73 optimal weight: 10.0000 chunk 22 optimal weight: 6.9990 chunk 85 optimal weight: 20.0000 chunk 52 optimal weight: 10.0000 chunk 63 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 overall best weight: 2.7998 ------------------------------------------------------------------------------- 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 308 ASN ** A 534 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 = 0.3778 r_free = 0.3778 target = 0.161934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.126824 restraints weight = 10807.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.124970 restraints weight = 8623.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.126834 restraints weight = 7797.159| |-----------------------------------------------------------------------------| r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.3203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7108 Z= 0.279 Angle : 0.587 8.101 9646 Z= 0.306 Chirality : 0.042 0.140 1091 Planarity : 0.004 0.051 1236 Dihedral : 8.797 175.330 1001 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 0.14 % Allowed : 3.09 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.28), residues: 892 helix: 0.70 (0.24), residues: 497 sheet: -0.56 (0.85), residues: 33 loop : -1.56 (0.30), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 845 HIS 0.003 0.001 HIS A 800 PHE 0.016 0.002 PHE A 292 TYR 0.020 0.002 TYR A 274 ARG 0.004 0.000 ARG A 394 *********************** 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 149 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 148 time to evaluate : 0.820 Fit side-chains REVERT: A 114 ASP cc_start: 0.7668 (t0) cc_final: 0.7256 (t0) REVERT: A 650 ILE cc_start: 0.9025 (mm) cc_final: 0.8707 (tt) REVERT: A 682 MET cc_start: 0.7980 (mtm) cc_final: 0.7738 (ttm) REVERT: A 771 LYS cc_start: 0.8830 (mttt) cc_final: 0.8340 (mtpt) REVERT: A 825 TYR cc_start: 0.8970 (m-80) cc_final: 0.8607 (m-10) REVERT: B 25 ASP cc_start: 0.8275 (p0) cc_final: 0.8072 (p0) outliers start: 1 outliers final: 0 residues processed: 149 average time/residue: 0.1799 time to fit residues: 36.3231 Evaluate side-chains 113 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 38 optimal weight: 0.7980 chunk 13 optimal weight: 9.9990 chunk 1 optimal weight: 3.9990 chunk 48 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 4 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 88 optimal weight: 50.0000 chunk 41 optimal weight: 0.8980 chunk 14 optimal weight: 4.9990 chunk 53 optimal weight: 0.6980 overall best weight: 1.8784 ------------------------------------------------------------------------------- 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 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.161997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.126279 restraints weight = 10752.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.124863 restraints weight = 10638.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.126272 restraints weight = 9713.234| |-----------------------------------------------------------------------------| r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.3469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7108 Z= 0.204 Angle : 0.529 7.610 9646 Z= 0.274 Chirality : 0.040 0.134 1091 Planarity : 0.004 0.053 1236 Dihedral : 8.540 173.608 1001 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.00 % Allowed : 2.25 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.28), residues: 892 helix: 0.80 (0.24), residues: 505 sheet: -0.37 (0.86), residues: 33 loop : -1.43 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 845 HIS 0.003 0.001 HIS A 280 PHE 0.013 0.001 PHE A 261 TYR 0.020 0.001 TYR A 147 ARG 0.003 0.000 ARG A 262 *********************** 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 157 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 0.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 GLU cc_start: 0.8630 (tt0) cc_final: 0.8185 (tt0) REVERT: A 245 TYR cc_start: 0.8502 (m-80) cc_final: 0.7010 (m-10) REVERT: A 339 TYR cc_start: 0.7093 (t80) cc_final: 0.6852 (t80) REVERT: A 422 SER cc_start: 0.8337 (t) cc_final: 0.8030 (p) REVERT: A 549 ILE cc_start: 0.8447 (tp) cc_final: 0.8055 (tt) REVERT: A 771 LYS cc_start: 0.8836 (mttt) cc_final: 0.8440 (mtpt) REVERT: A 825 TYR cc_start: 0.8783 (m-80) cc_final: 0.8561 (m-10) REVERT: B 52 MET cc_start: 0.7759 (mmm) cc_final: 0.7379 (mmm) REVERT: B 110 MET cc_start: 0.7920 (mmm) cc_final: 0.7676 (mmm) outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 0.1733 time to fit residues: 37.3655 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 : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 88 optimal weight: 50.0000 chunk 38 optimal weight: 5.9990 chunk 79 optimal weight: 6.9990 chunk 62 optimal weight: 0.9980 chunk 47 optimal weight: 9.9990 chunk 66 optimal weight: 5.9990 chunk 72 optimal weight: 10.0000 chunk 80 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 19 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- 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 350 GLN ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 674 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.149045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.112191 restraints weight = 11223.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.109740 restraints weight = 13680.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.111283 restraints weight = 12631.253| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.3485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 7108 Z= 0.338 Angle : 0.647 9.791 9646 Z= 0.331 Chirality : 0.044 0.158 1091 Planarity : 0.004 0.051 1236 Dihedral : 8.948 173.794 1001 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.28), residues: 892 helix: 0.78 (0.24), residues: 498 sheet: -0.19 (0.92), residues: 31 loop : -1.48 (0.31), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 845 HIS 0.003 0.001 HIS A 302 PHE 0.019 0.002 PHE A 292 TYR 0.022 0.002 TYR A 274 ARG 0.003 0.000 ARG A 394 *********************** 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 142 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 0.738 Fit side-chains revert: symmetry clash REVERT: A 422 SER cc_start: 0.8355 (t) cc_final: 0.7876 (p) REVERT: A 682 MET cc_start: 0.8085 (mtm) cc_final: 0.7725 (ttm) REVERT: A 771 LYS cc_start: 0.8948 (mttt) cc_final: 0.8440 (mtpt) REVERT: A 825 TYR cc_start: 0.8834 (m-80) cc_final: 0.8575 (m-10) REVERT: B 52 MET cc_start: 0.7922 (mmm) cc_final: 0.7645 (mmm) REVERT: B 110 MET cc_start: 0.7890 (mmm) cc_final: 0.7459 (mmt) outliers start: 0 outliers final: 0 residues processed: 142 average time/residue: 0.1899 time to fit residues: 36.4040 Evaluate side-chains 112 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 84 optimal weight: 9.9990 chunk 38 optimal weight: 3.9990 chunk 52 optimal weight: 10.0000 chunk 63 optimal weight: 9.9990 chunk 87 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 69 optimal weight: 5.9990 chunk 88 optimal weight: 50.0000 chunk 3 optimal weight: 5.9990 chunk 55 optimal weight: 0.9990 chunk 59 optimal weight: 10.0000 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 517 GLN ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.151802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.114945 restraints weight = 10814.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.113503 restraints weight = 12849.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.115015 restraints weight = 11143.785| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.3674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7108 Z= 0.259 Angle : 0.591 9.977 9646 Z= 0.302 Chirality : 0.042 0.164 1091 Planarity : 0.004 0.051 1236 Dihedral : 8.678 172.236 1001 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 0.00 % Allowed : 1.69 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.29), residues: 892 helix: 0.88 (0.24), residues: 500 sheet: -0.25 (0.90), residues: 33 loop : -1.37 (0.32), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 845 HIS 0.002 0.001 HIS A 171 PHE 0.012 0.002 PHE A 518 TYR 0.020 0.002 TYR A 147 ARG 0.006 0.000 ARG A 843 *********************** 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 149 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 1.023 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 422 SER cc_start: 0.8324 (t) cc_final: 0.8009 (p) REVERT: A 682 MET cc_start: 0.8018 (mtm) cc_final: 0.7651 (ttm) REVERT: A 771 LYS cc_start: 0.8923 (mttt) cc_final: 0.8451 (mtpt) REVERT: B 25 ASP cc_start: 0.8278 (p0) cc_final: 0.7693 (p0) REVERT: B 110 MET cc_start: 0.7865 (mmm) cc_final: 0.7313 (mpp) outliers start: 0 outliers final: 0 residues processed: 149 average time/residue: 0.1743 time to fit residues: 35.8784 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 : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 2 optimal weight: 0.4980 chunk 4 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 53 optimal weight: 0.9990 chunk 71 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.156451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.119120 restraints weight = 11221.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.118227 restraints weight = 11272.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.120225 restraints weight = 10260.934| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.3995 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= 0.171 Angle : 0.562 9.509 9646 Z= 0.283 Chirality : 0.040 0.140 1091 Planarity : 0.004 0.052 1236 Dihedral : 8.237 171.145 1001 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.14 % Allowed : 0.70 % Favored : 99.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.29), residues: 892 helix: 0.97 (0.24), residues: 500 sheet: -0.21 (0.86), residues: 33 loop : -1.22 (0.33), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 526 HIS 0.003 0.000 HIS A 302 PHE 0.029 0.002 PHE A 675 TYR 0.015 0.001 TYR A 147 ARG 0.004 0.000 ARG A 843 *********************** 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 156 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 155 time to evaluate : 0.815 Fit side-chains revert: symmetry clash REVERT: A 221 GLU cc_start: 0.8618 (mm-30) cc_final: 0.8347 (mm-30) REVERT: A 244 GLU cc_start: 0.8521 (tt0) cc_final: 0.8200 (tt0) REVERT: A 245 TYR cc_start: 0.8478 (m-80) cc_final: 0.6973 (m-10) REVERT: A 253 ASN cc_start: 0.8153 (OUTLIER) cc_final: 0.7704 (m-40) REVERT: A 422 SER cc_start: 0.8347 (t) cc_final: 0.7822 (p) REVERT: A 590 LYS cc_start: 0.9015 (mttt) cc_final: 0.8668 (mttt) REVERT: A 682 MET cc_start: 0.7732 (mtm) cc_final: 0.7447 (ttm) REVERT: A 696 MET cc_start: 0.8001 (mmp) cc_final: 0.7324 (mtm) REVERT: A 771 LYS cc_start: 0.8855 (mttt) cc_final: 0.8376 (mtpt) REVERT: A 843 ARG cc_start: 0.8374 (tpp80) cc_final: 0.7522 (mtt-85) REVERT: B 25 ASP cc_start: 0.8132 (p0) cc_final: 0.7668 (p0) REVERT: B 68 GLU cc_start: 0.7139 (tm-30) cc_final: 0.6927 (tm-30) outliers start: 1 outliers final: 0 residues processed: 156 average time/residue: 0.1730 time to fit residues: 36.8949 Evaluate side-chains 126 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 125 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 64 optimal weight: 3.9990 chunk 44 optimal weight: 8.9990 chunk 86 optimal weight: 9.9990 chunk 22 optimal weight: 8.9990 chunk 87 optimal weight: 4.9990 chunk 48 optimal weight: 9.9990 chunk 56 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 chunk 4 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 HIS ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.153760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.115028 restraints weight = 11018.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.116044 restraints weight = 10682.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.117664 restraints weight = 9103.564| |-----------------------------------------------------------------------------| r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.3973 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= 0.237 Angle : 0.583 10.741 9646 Z= 0.296 Chirality : 0.041 0.149 1091 Planarity : 0.004 0.051 1236 Dihedral : 8.387 172.080 1001 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.29), residues: 892 helix: 1.00 (0.24), residues: 501 sheet: -0.16 (0.87), residues: 33 loop : -1.25 (0.33), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 845 HIS 0.001 0.000 HIS A 171 PHE 0.012 0.002 PHE A 292 TYR 0.023 0.002 TYR A 147 ARG 0.004 0.000 ARG A 262 *********************** 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 148 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 0.765 Fit side-chains revert: symmetry clash REVERT: A 221 GLU cc_start: 0.8607 (mm-30) cc_final: 0.8397 (mm-30) REVERT: A 238 MET cc_start: 0.8362 (ttm) cc_final: 0.8142 (ttm) REVERT: A 422 SER cc_start: 0.8274 (t) cc_final: 0.7759 (p) REVERT: A 682 MET cc_start: 0.7911 (mtm) cc_final: 0.7596 (ttm) REVERT: A 771 LYS cc_start: 0.8878 (mttt) cc_final: 0.8383 (mtpt) REVERT: A 825 TYR cc_start: 0.8520 (m-10) cc_final: 0.8250 (m-10) REVERT: B 25 ASP cc_start: 0.8214 (p0) cc_final: 0.7663 (p0) REVERT: B 68 GLU cc_start: 0.7502 (tm-30) cc_final: 0.6864 (tm-30) REVERT: B 110 MET cc_start: 0.7923 (mmm) cc_final: 0.7685 (mmm) outliers start: 0 outliers final: 0 residues processed: 148 average time/residue: 0.1688 time to fit residues: 34.1601 Evaluate side-chains 125 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 4 optimal weight: 0.9990 chunk 82 optimal weight: 9.9990 chunk 17 optimal weight: 0.9990 chunk 47 optimal weight: 9.9990 chunk 3 optimal weight: 7.9990 chunk 40 optimal weight: 5.9990 chunk 25 optimal weight: 9.9990 chunk 77 optimal weight: 9.9990 chunk 53 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 chunk 61 optimal weight: 10.0000 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 HIS ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.158007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.120259 restraints weight = 10997.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.120127 restraints weight = 10430.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.122364 restraints weight = 9084.655| |-----------------------------------------------------------------------------| r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.4044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7108 Z= 0.236 Angle : 0.605 11.216 9646 Z= 0.306 Chirality : 0.042 0.152 1091 Planarity : 0.004 0.051 1236 Dihedral : 8.370 171.920 1001 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.29), residues: 892 helix: 1.05 (0.24), residues: 500 sheet: -0.29 (0.86), residues: 33 loop : -1.24 (0.33), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 635 HIS 0.003 0.001 HIS A 171 PHE 0.013 0.002 PHE A 174 TYR 0.015 0.001 TYR A 274 ARG 0.005 0.000 ARG A 262 ********************** 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 141 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 218 GLU cc_start: 0.8414 (tp30) cc_final: 0.8192 (tp30) REVERT: A 221 GLU cc_start: 0.8612 (mm-30) cc_final: 0.8391 (mm-30) REVERT: A 245 TYR cc_start: 0.8602 (m-80) cc_final: 0.7486 (m-10) REVERT: A 422 SER cc_start: 0.8224 (t) cc_final: 0.7698 (p) REVERT: A 682 MET cc_start: 0.7843 (mtm) cc_final: 0.7628 (ttm) REVERT: A 696 MET cc_start: 0.7953 (mmp) cc_final: 0.7284 (mtm) REVERT: A 771 LYS cc_start: 0.8906 (mttt) cc_final: 0.8403 (mtpt) REVERT: A 825 TYR cc_start: 0.8554 (m-10) cc_final: 0.8285 (m-10) REVERT: A 843 ARG cc_start: 0.8500 (mmt90) cc_final: 0.7559 (mmm-85) REVERT: B 25 ASP cc_start: 0.8110 (p0) cc_final: 0.7558 (p0) REVERT: B 68 GLU cc_start: 0.7279 (tm-30) cc_final: 0.6791 (tm-30) REVERT: B 110 MET cc_start: 0.7954 (mmm) cc_final: 0.7708 (mmm) outliers start: 0 outliers final: 0 residues processed: 141 average time/residue: 0.1727 time to fit residues: 33.1366 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 : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 64 optimal weight: 2.9990 chunk 82 optimal weight: 6.9990 chunk 34 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 75 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 59 optimal weight: 10.0000 chunk 76 optimal weight: 0.1980 chunk 29 optimal weight: 4.9990 chunk 39 optimal weight: 10.0000 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 HIS ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.153946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.119099 restraints weight = 11077.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.116368 restraints weight = 12400.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.117782 restraints weight = 13483.322| |-----------------------------------------------------------------------------| r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.4048 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= 0.237 Angle : 0.589 11.719 9646 Z= 0.298 Chirality : 0.041 0.155 1091 Planarity : 0.004 0.051 1236 Dihedral : 8.373 171.532 1001 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.29), residues: 892 helix: 1.13 (0.24), residues: 495 sheet: -0.34 (0.88), residues: 33 loop : -1.19 (0.33), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 526 HIS 0.004 0.001 HIS A 280 PHE 0.031 0.002 PHE A 675 TYR 0.024 0.002 TYR A 147 ARG 0.003 0.000 ARG A 262 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2036.11 seconds wall clock time: 36 minutes 19.79 seconds (2179.79 seconds total)