Starting phenix.real_space_refine on Tue Mar 11 15:55:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ca0_45378/03_2025/9ca0_45378_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ca0_45378/03_2025/9ca0_45378.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ca0_45378/03_2025/9ca0_45378.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ca0_45378/03_2025/9ca0_45378.map" model { file = "/net/cci-nas-00/data/ceres_data/9ca0_45378/03_2025/9ca0_45378_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ca0_45378/03_2025/9ca0_45378_neut.cif" } resolution = 3.48 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= 0.001 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Mn 1 7.51 5 P 10 5.49 5 S 39 5.16 5 C 3928 2.51 5 N 1081 2.21 5 O 1206 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 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: 6265 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4845 Classifications: {'peptide': 612} Link IDs: {'PTRANS': 30, 'TRANS': 581} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'PTR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 1219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1219 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 153} Chain: "D" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 143 Classifications: {'DNA': 7} Link IDs: {'rna3p': 6} Chain: "E" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 57 Classifications: {'DNA': 3} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.32, per 1000 atoms: 0.85 Number of scatterers: 6265 At special positions: 0 Unit cell: (73.87, 86.32, 135.29, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Mn 1 24.99 S 39 16.00 P 10 15.00 O 1206 8.00 N 1081 7.00 C 3928 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.92 Conformation dependent library (CDL) restraints added in 962.2 milliseconds 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1442 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 6 sheets defined 41.1% alpha, 15.0% beta 0 base pairs and 4 stacking pairs defined. Time for finding SS restraints: 1.66 Creating SS restraints... Processing helix chain 'A' and resid 10 through 23 Processing helix chain 'A' and resid 68 through 72 Processing helix chain 'A' and resid 77 through 82 removed outlier: 3.741A pdb=" N PHE A 82 " --> pdb=" O ALA A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 96 Processing helix chain 'A' and resid 97 through 105 Processing helix chain 'A' and resid 122 through 134 Processing helix chain 'A' and resid 156 through 166 Processing helix chain 'A' and resid 171 through 190 removed outlier: 3.904A pdb=" N SER A 177 " --> pdb=" O ASN A 173 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL A 178 " --> pdb=" O GLU A 174 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N ALA A 180 " --> pdb=" O LEU A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 200 removed outlier: 4.034A pdb=" N PHE A 195 " --> pdb=" O ALA A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 234 removed outlier: 3.603A pdb=" N PHE A 224 " --> pdb=" O PRO A 220 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N CYS A 225 " --> pdb=" O THR A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 276 Processing helix chain 'A' and resid 302 through 313 Processing helix chain 'A' and resid 317 through 332 Processing helix chain 'A' and resid 349 through 355 Processing helix chain 'A' and resid 363 through 371 Processing helix chain 'A' and resid 404 through 421 removed outlier: 3.725A pdb=" N LEU A 408 " --> pdb=" O ASP A 404 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE A 417 " --> pdb=" O THR A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 455 Processing helix chain 'A' and resid 496 through 507 Processing helix chain 'A' and resid 513 through 524 Processing helix chain 'A' and resid 538 through 552 Processing helix chain 'A' and resid 553 through 556 removed outlier: 3.618A pdb=" N VAL A 556 " --> pdb=" O ALA A 553 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 553 through 556' Processing helix chain 'A' and resid 559 through 573 removed outlier: 3.862A pdb=" N LEU A 570 " --> pdb=" O LYS A 566 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ILE A 571 " --> pdb=" O GLN A 567 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA A 572 " --> pdb=" O LEU A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 598 removed outlier: 3.782A pdb=" N VAL A 581 " --> pdb=" O ASP A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 611 removed outlier: 4.277A pdb=" N LEU A 606 " --> pdb=" O GLY A 602 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N VAL A 609 " --> pdb=" O GLU A 605 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER A 610 " --> pdb=" O LEU A 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 13 Processing helix chain 'B' and resid 17 through 25 Processing helix chain 'B' and resid 32 through 43 Processing helix chain 'B' and resid 44 through 48 removed outlier: 3.656A pdb=" N THR B 47 " --> pdb=" O ASP B 44 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 5.464A pdb=" N SER A 37 " --> pdb=" O SER A 56 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N SER A 56 " --> pdb=" O SER A 37 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N VAL A 4 " --> pdb=" O LYS A 53 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N THR A 55 " --> pdb=" O VAL A 4 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N MET A 6 " --> pdb=" O THR A 55 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N THR A 3 " --> pdb=" O TYR A 111 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N VAL A 113 " --> pdb=" O THR A 3 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N LEU A 5 " --> pdb=" O VAL A 113 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N TRP A 115 " --> pdb=" O LEU A 5 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL A 7 " --> pdb=" O TRP A 115 " (cutoff:3.500A) removed outlier: 8.564A pdb=" N PHE A 148 " --> pdb=" O ASP A 110 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ILE A 112 " --> pdb=" O PHE A 148 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 62 through 66 Processing sheet with id=AA3, first strand: chain 'A' and resid 254 through 256 removed outlier: 6.357A pdb=" N VAL A 242 " --> pdb=" O MET A 483 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N MET A 483 " --> pdb=" O VAL A 242 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N GLN A 244 " --> pdb=" O VAL A 481 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N VAL A 481 " --> pdb=" O GLN A 244 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N LYS A 246 " --> pdb=" O GLY A 479 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 258 through 259 removed outlier: 6.973A pdb=" N LYS A 425 " --> pdb=" O LEU A 448 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER A 432 " --> pdb=" O ALA A 287 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA A 287 " --> pdb=" O SER A 432 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ARG A 434 " --> pdb=" O VAL A 285 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N VAL A 285 " --> pdb=" O ARG A 434 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 494 through 495 removed outlier: 3.941A pdb=" N LEU A 494 " --> pdb=" O LEU A 535 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 64 through 65 removed outlier: 4.350A pdb=" N ASP B 134 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N THR B 107 " --> pdb=" O LEU B 140 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N LEU B 142 " --> pdb=" O THR B 107 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N VAL B 109 " --> pdb=" O LEU B 142 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N LEU B 95 " --> pdb=" O GLU B 110 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ARG B 96 " --> pdb=" O ILE B 76 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ILE B 76 " --> pdb=" O ARG B 96 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N GLN B 98 " --> pdb=" O GLN B 74 " (cutoff:3.500A) 250 hydrogen bonds defined for protein. 702 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 4 stacking parallelities Total time for adding SS restraints: 1.88 Time building geometry restraints manager: 2.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1933 1.33 - 1.45: 886 1.45 - 1.57: 3513 1.57 - 1.69: 18 1.69 - 1.81: 61 Bond restraints: 6411 Sorted by residual: bond pdb=" OH PTR A 336 " pdb=" P PTR A 336 " ideal model delta sigma weight residual 1.769 1.606 0.163 2.00e-02 2.50e+03 6.61e+01 bond pdb=" C SER A 335 " pdb=" N PTR A 336 " ideal model delta sigma weight residual 1.329 1.429 -0.100 1.40e-02 5.10e+03 5.15e+01 bond pdb=" O1P PTR A 336 " pdb=" P PTR A 336 " ideal model delta sigma weight residual 1.522 1.476 0.046 2.00e-02 2.50e+03 5.22e+00 bond pdb=" CZ PTR A 336 " pdb=" OH PTR A 336 " ideal model delta sigma weight residual 1.339 1.300 0.039 2.00e-02 2.50e+03 3.74e+00 bond pdb=" C ASP A 386 " pdb=" N HIS A 387 " ideal model delta sigma weight residual 1.331 1.307 0.024 1.48e-02 4.57e+03 2.66e+00 ... (remaining 6406 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 8581 1.96 - 3.92: 111 3.92 - 5.89: 15 5.89 - 7.85: 5 7.85 - 9.81: 3 Bond angle restraints: 8715 Sorted by residual: angle pdb=" CA SER A 335 " pdb=" C SER A 335 " pdb=" N PTR A 336 " ideal model delta sigma weight residual 116.20 106.58 9.62 2.00e+00 2.50e-01 2.31e+01 angle pdb=" OH PTR A 336 " pdb=" P PTR A 336 " pdb=" O2P PTR A 336 " ideal model delta sigma weight residual 99.92 109.73 -9.81 3.00e+00 1.11e-01 1.07e+01 angle pdb=" N GLN B 11 " pdb=" CA GLN B 11 " pdb=" CB GLN B 11 " ideal model delta sigma weight residual 110.41 115.56 -5.15 1.68e+00 3.54e-01 9.39e+00 angle pdb=" C SER B 10 " pdb=" N GLN B 11 " pdb=" CA GLN B 11 " ideal model delta sigma weight residual 121.58 115.81 5.77 1.95e+00 2.63e-01 8.75e+00 angle pdb=" CA LEU B 41 " pdb=" CB LEU B 41 " pdb=" CG LEU B 41 " ideal model delta sigma weight residual 116.30 124.78 -8.48 3.50e+00 8.16e-02 5.87e+00 ... (remaining 8710 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.76: 3403 16.76 - 33.52: 356 33.52 - 50.28: 90 50.28 - 67.04: 25 67.04 - 83.80: 4 Dihedral angle restraints: 3878 sinusoidal: 1644 harmonic: 2234 Sorted by residual: dihedral pdb=" CA SER A 335 " pdb=" C SER A 335 " pdb=" N PTR A 336 " pdb=" CA PTR A 336 " ideal model delta harmonic sigma weight residual -180.00 -140.35 -39.65 0 5.00e+00 4.00e-02 6.29e+01 dihedral pdb=" CA LEU A 176 " pdb=" C LEU A 176 " pdb=" N SER A 177 " pdb=" CA SER A 177 " ideal model delta harmonic sigma weight residual 180.00 161.65 18.35 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA TYR A 240 " pdb=" C TYR A 240 " pdb=" N TRP A 241 " pdb=" CA TRP A 241 " ideal model delta harmonic sigma weight residual 180.00 162.37 17.63 0 5.00e+00 4.00e-02 1.24e+01 ... (remaining 3875 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 640 0.032 - 0.065: 246 0.065 - 0.097: 53 0.097 - 0.129: 35 0.129 - 0.161: 3 Chirality restraints: 977 Sorted by residual: chirality pdb=" CA PTR A 336 " pdb=" N PTR A 336 " pdb=" C PTR A 336 " pdb=" CB PTR A 336 " both_signs ideal model delta sigma weight residual False 2.35 2.51 -0.16 2.00e-01 2.50e+01 6.52e-01 chirality pdb=" CA ILE B 135 " pdb=" N ILE B 135 " pdb=" C ILE B 135 " pdb=" CB ILE B 135 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.11e-01 chirality pdb=" CG LEU B 71 " pdb=" CB LEU B 71 " pdb=" CD1 LEU B 71 " pdb=" CD2 LEU B 71 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 4.63e-01 ... (remaining 974 not shown) Planarity restraints: 1092 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 335 " 0.053 2.00e-02 2.50e+03 1.11e-01 1.23e+02 pdb=" C SER A 335 " -0.191 2.00e-02 2.50e+03 pdb=" O SER A 335 " 0.079 2.00e-02 2.50e+03 pdb=" N PTR A 336 " 0.059 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 137 " 0.010 2.00e-02 2.50e+03 2.03e-02 4.13e+00 pdb=" C ASN B 137 " -0.035 2.00e-02 2.50e+03 pdb=" O ASN B 137 " 0.013 2.00e-02 2.50e+03 pdb=" N GLY B 138 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG A 377 " -0.027 5.00e-02 4.00e+02 4.08e-02 2.67e+00 pdb=" N PRO A 378 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 378 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 378 " -0.023 5.00e-02 4.00e+02 ... (remaining 1089 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 90 2.66 - 3.22: 5685 3.22 - 3.78: 9085 3.78 - 4.34: 12231 4.34 - 4.90: 20360 Nonbonded interactions: 47451 Sorted by model distance: nonbonded pdb=" OD2 ASP A 119 " pdb="MN MN A 701 " model vdw 2.104 2.320 nonbonded pdb=" OE1 GLN A 196 " pdb=" OH TYR A 548 " model vdw 2.278 3.040 nonbonded pdb=" OE1 GLU A 326 " pdb=" NH2 ARG A 338 " model vdw 2.283 3.120 nonbonded pdb=" O CYS A 217 " pdb=" OG1 THR A 221 " model vdw 2.320 3.040 nonbonded pdb=" OE2 GLU A 496 " pdb=" NH2 ARG A 533 " model vdw 2.323 3.120 ... (remaining 47446 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 individual isotropic 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: 0.010 Normalize map: mean=0, sd=1: 1.790 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: 0.290 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 21.040 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 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 : 0.004 0.163 6411 Z= 0.247 Angle : 0.579 9.812 8715 Z= 0.290 Chirality : 0.040 0.161 977 Planarity : 0.005 0.111 1092 Dihedral : 14.952 83.802 2436 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 0.15 % Allowed : 0.15 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -0.73 (0.29), residues: 766 helix: 0.34 (0.30), residues: 290 sheet: 0.05 (0.49), residues: 123 loop : -1.36 (0.30), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 241 HIS 0.003 0.001 HIS A 60 PHE 0.012 0.001 PHE A 265 TYR 0.010 0.001 TYR A 411 ARG 0.008 0.000 ARG A 524 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 189 time to evaluate : 0.663 Fit side-chains REVERT: A 30 LYS cc_start: 0.8183 (mppt) cc_final: 0.7976 (mppt) REVERT: A 51 ARG cc_start: 0.7325 (ttp-170) cc_final: 0.7054 (ttp80) REVERT: A 56 SER cc_start: 0.7983 (p) cc_final: 0.7750 (p) REVERT: A 77 ASP cc_start: 0.7639 (p0) cc_final: 0.7369 (p0) REVERT: A 105 GLU cc_start: 0.7127 (mm-30) cc_final: 0.6913 (mm-30) REVERT: A 171 ASP cc_start: 0.6878 (m-30) cc_final: 0.6661 (m-30) REVERT: A 214 PHE cc_start: 0.8572 (t80) cc_final: 0.8338 (t80) REVERT: A 240 TYR cc_start: 0.6946 (m-10) cc_final: 0.6689 (m-10) REVERT: A 349 ASP cc_start: 0.7299 (t0) cc_final: 0.6878 (t0) REVERT: A 393 MET cc_start: 0.7731 (mmm) cc_final: 0.7315 (mmm) REVERT: A 482 LYS cc_start: 0.7496 (ptmt) cc_final: 0.7195 (ptmt) REVERT: A 483 MET cc_start: 0.7357 (mpp) cc_final: 0.6627 (mpp) outliers start: 1 outliers final: 1 residues processed: 190 average time/residue: 0.2274 time to fit residues: 55.2880 Evaluate side-chains 179 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 178 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 65 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 19 optimal weight: 0.4980 chunk 39 optimal weight: 0.8980 chunk 31 optimal weight: 0.2980 chunk 60 optimal weight: 0.9980 chunk 23 optimal weight: 0.4980 chunk 36 optimal weight: 0.6980 chunk 44 optimal weight: 0.6980 chunk 69 optimal weight: 2.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN A 323 GLN ** A 387 HIS ** 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 = 0.3445 r_free = 0.3445 target = 0.112533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.100379 restraints weight = 10057.196| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 2.15 r_work: 0.3139 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.1160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 6411 Z= 0.249 Angle : 0.543 7.449 8715 Z= 0.285 Chirality : 0.041 0.183 977 Planarity : 0.004 0.030 1092 Dihedral : 11.409 59.197 954 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 0.90 % Allowed : 11.39 % Favored : 87.71 % 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: -0.58 (0.30), residues: 766 helix: 0.64 (0.30), residues: 301 sheet: -0.22 (0.48), residues: 131 loop : -1.39 (0.31), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 458 HIS 0.005 0.001 HIS A 387 PHE 0.015 0.002 PHE A 66 TYR 0.013 0.002 TYR A 411 ARG 0.006 0.000 ARG A 524 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 183 time to evaluate : 0.666 Fit side-chains revert: symmetry clash REVERT: A 30 LYS cc_start: 0.8534 (mppt) cc_final: 0.8279 (mppt) REVERT: A 51 ARG cc_start: 0.8095 (ttp-170) cc_final: 0.7892 (ttp80) REVERT: A 171 ASP cc_start: 0.7465 (m-30) cc_final: 0.7242 (m-30) REVERT: A 240 TYR cc_start: 0.7782 (m-10) cc_final: 0.7530 (m-10) REVERT: A 272 MET cc_start: 0.7462 (tmm) cc_final: 0.7211 (tmm) REVERT: A 285 VAL cc_start: 0.8917 (t) cc_final: 0.8570 (p) REVERT: A 349 ASP cc_start: 0.7775 (t0) cc_final: 0.7345 (t0) REVERT: A 393 MET cc_start: 0.8286 (mmm) cc_final: 0.7903 (mtt) REVERT: A 482 LYS cc_start: 0.7918 (ptmt) cc_final: 0.7572 (ptmt) REVERT: A 483 MET cc_start: 0.7957 (mpp) cc_final: 0.7410 (mpp) REVERT: A 551 ILE cc_start: 0.8521 (mm) cc_final: 0.8291 (mm) REVERT: A 552 ASP cc_start: 0.8034 (t0) cc_final: 0.7776 (t0) REVERT: A 597 VAL cc_start: 0.8879 (p) cc_final: 0.8652 (p) REVERT: B 22 GLU cc_start: 0.8054 (mp0) cc_final: 0.7236 (mp0) outliers start: 6 outliers final: 2 residues processed: 185 average time/residue: 0.2185 time to fit residues: 51.3393 Evaluate side-chains 174 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 172 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 598 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 35 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 40 optimal weight: 0.7980 chunk 58 optimal weight: 0.4980 chunk 63 optimal weight: 3.9990 chunk 37 optimal weight: 0.2980 chunk 47 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 323 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.111701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.099403 restraints weight = 10012.007| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 2.15 r_work: 0.3122 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6411 Z= 0.283 Angle : 0.529 7.272 8715 Z= 0.276 Chirality : 0.041 0.138 977 Planarity : 0.004 0.033 1092 Dihedral : 11.212 62.569 950 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.85 % Allowed : 13.94 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.52 (0.30), residues: 766 helix: 0.71 (0.30), residues: 301 sheet: -0.14 (0.47), residues: 136 loop : -1.41 (0.31), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 458 HIS 0.004 0.001 HIS A 320 PHE 0.017 0.002 PHE A 66 TYR 0.015 0.002 TYR A 578 ARG 0.006 0.000 ARG A 524 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 178 time to evaluate : 0.679 Fit side-chains revert: symmetry clash REVERT: A 7 VAL cc_start: 0.8573 (OUTLIER) cc_final: 0.8289 (m) REVERT: A 30 LYS cc_start: 0.8550 (mppt) cc_final: 0.8314 (mppt) REVERT: A 171 ASP cc_start: 0.7487 (m-30) cc_final: 0.7262 (m-30) REVERT: A 240 TYR cc_start: 0.7840 (m-10) cc_final: 0.7521 (m-10) REVERT: A 258 ASP cc_start: 0.7687 (OUTLIER) cc_final: 0.7310 (m-30) REVERT: A 285 VAL cc_start: 0.8905 (t) cc_final: 0.8566 (p) REVERT: A 349 ASP cc_start: 0.7780 (t0) cc_final: 0.7343 (t0) REVERT: A 393 MET cc_start: 0.8291 (mmm) cc_final: 0.7929 (mtt) REVERT: A 482 LYS cc_start: 0.7906 (ptmt) cc_final: 0.7516 (ptmt) REVERT: A 483 MET cc_start: 0.7950 (mpp) cc_final: 0.7428 (mpp) REVERT: A 552 ASP cc_start: 0.8042 (t0) cc_final: 0.7813 (t0) REVERT: A 597 VAL cc_start: 0.8865 (p) cc_final: 0.8628 (p) REVERT: B 120 ASN cc_start: 0.8030 (p0) cc_final: 0.7769 (p0) REVERT: B 136 LYS cc_start: 0.7955 (mmmt) cc_final: 0.7700 (mmmt) outliers start: 19 outliers final: 9 residues processed: 183 average time/residue: 0.2159 time to fit residues: 50.4765 Evaluate side-chains 182 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 171 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 598 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 26 optimal weight: 0.9990 chunk 63 optimal weight: 0.0970 chunk 75 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 74 optimal weight: 0.7980 chunk 43 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 54 optimal weight: 0.6980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 323 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.111209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.098761 restraints weight = 10202.248| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 2.17 r_work: 0.3109 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6411 Z= 0.286 Angle : 0.523 7.455 8715 Z= 0.274 Chirality : 0.041 0.137 977 Planarity : 0.004 0.035 1092 Dihedral : 10.882 61.709 950 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.15 % Allowed : 16.19 % Favored : 80.66 % 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: -0.51 (0.30), residues: 766 helix: 0.73 (0.30), residues: 303 sheet: -0.16 (0.46), residues: 136 loop : -1.41 (0.32), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 458 HIS 0.004 0.001 HIS A 320 PHE 0.017 0.002 PHE A 66 TYR 0.016 0.002 TYR A 578 ARG 0.007 0.000 ARG A 524 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 182 time to evaluate : 0.685 Fit side-chains revert: symmetry clash REVERT: A 30 LYS cc_start: 0.8599 (mppt) cc_final: 0.8387 (mppt) REVERT: A 134 LEU cc_start: 0.8147 (mt) cc_final: 0.7889 (mt) REVERT: A 171 ASP cc_start: 0.7491 (m-30) cc_final: 0.7275 (m-30) REVERT: A 240 TYR cc_start: 0.7914 (m-10) cc_final: 0.7533 (m-10) REVERT: A 258 ASP cc_start: 0.7739 (OUTLIER) cc_final: 0.7346 (m-30) REVERT: A 272 MET cc_start: 0.7483 (tmm) cc_final: 0.7208 (tmm) REVERT: A 349 ASP cc_start: 0.7788 (t0) cc_final: 0.7373 (t0) REVERT: A 393 MET cc_start: 0.8275 (mmm) cc_final: 0.7911 (mtt) REVERT: A 482 LYS cc_start: 0.7924 (ptmt) cc_final: 0.7532 (ptmt) REVERT: A 483 MET cc_start: 0.7920 (mpp) cc_final: 0.7416 (mpp) REVERT: A 498 GLU cc_start: 0.7990 (tt0) cc_final: 0.7753 (mt-10) REVERT: A 552 ASP cc_start: 0.8075 (t0) cc_final: 0.7830 (t0) REVERT: A 597 VAL cc_start: 0.8872 (p) cc_final: 0.8633 (p) REVERT: B 22 GLU cc_start: 0.8149 (mm-30) cc_final: 0.7408 (mp0) REVERT: B 120 ASN cc_start: 0.8048 (p0) cc_final: 0.7792 (p0) REVERT: B 136 LYS cc_start: 0.7900 (mmmt) cc_final: 0.7604 (mmmt) outliers start: 21 outliers final: 12 residues processed: 189 average time/residue: 0.2170 time to fit residues: 52.5454 Evaluate side-chains 189 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 176 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 387 HIS Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 598 ASP Chi-restraints excluded: chain B residue 145 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 1 optimal weight: 1.9990 chunk 69 optimal weight: 0.0270 chunk 38 optimal weight: 0.0470 chunk 52 optimal weight: 0.2980 chunk 41 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 chunk 29 optimal weight: 0.9990 chunk 55 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 overall best weight: 0.3336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 323 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.112669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.100322 restraints weight = 10091.058| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 2.17 r_work: 0.3137 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6411 Z= 0.183 Angle : 0.499 8.316 8715 Z= 0.257 Chirality : 0.040 0.152 977 Planarity : 0.004 0.030 1092 Dihedral : 10.674 62.355 950 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.15 % Allowed : 17.54 % Favored : 79.31 % 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: -0.43 (0.30), residues: 766 helix: 0.80 (0.30), residues: 304 sheet: -0.26 (0.48), residues: 126 loop : -1.28 (0.32), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 458 HIS 0.002 0.000 HIS A 320 PHE 0.013 0.001 PHE A 66 TYR 0.012 0.001 TYR A 411 ARG 0.007 0.000 ARG A 524 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 178 time to evaluate : 0.668 Fit side-chains revert: symmetry clash REVERT: A 7 VAL cc_start: 0.8550 (OUTLIER) cc_final: 0.8310 (m) REVERT: A 30 LYS cc_start: 0.8579 (mppt) cc_final: 0.8362 (mppt) REVERT: A 171 ASP cc_start: 0.7475 (m-30) cc_final: 0.7226 (m-30) REVERT: A 240 TYR cc_start: 0.7708 (m-10) cc_final: 0.7450 (m-10) REVERT: A 258 ASP cc_start: 0.7668 (OUTLIER) cc_final: 0.7303 (m-30) REVERT: A 272 MET cc_start: 0.7438 (tmm) cc_final: 0.7162 (tmm) REVERT: A 349 ASP cc_start: 0.7767 (t0) cc_final: 0.7357 (t0) REVERT: A 393 MET cc_start: 0.8272 (mmm) cc_final: 0.7885 (mtt) REVERT: A 482 LYS cc_start: 0.7931 (ptmt) cc_final: 0.7552 (ptmt) REVERT: A 483 MET cc_start: 0.7903 (mpp) cc_final: 0.7410 (mpp) REVERT: A 498 GLU cc_start: 0.7921 (tt0) cc_final: 0.7714 (mt-10) REVERT: A 504 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.7658 (tm-30) REVERT: A 523 GLN cc_start: 0.8430 (tt0) cc_final: 0.8228 (tt0) REVERT: A 552 ASP cc_start: 0.8064 (t0) cc_final: 0.7833 (t0) REVERT: A 597 VAL cc_start: 0.8858 (p) cc_final: 0.8618 (p) REVERT: B 22 GLU cc_start: 0.8203 (mm-30) cc_final: 0.7545 (mp0) REVERT: B 120 ASN cc_start: 0.8034 (p0) cc_final: 0.7770 (p0) outliers start: 21 outliers final: 11 residues processed: 183 average time/residue: 0.2098 time to fit residues: 49.1803 Evaluate side-chains 191 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 177 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 387 HIS Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 504 GLU Chi-restraints excluded: chain B residue 145 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 11 optimal weight: 0.3980 chunk 75 optimal weight: 0.4980 chunk 69 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 54 optimal weight: 0.1980 chunk 47 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 59 optimal weight: 0.3980 chunk 12 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 323 GLN A 520 ASN B 137 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.112423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.100089 restraints weight = 10062.581| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.16 r_work: 0.3132 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6411 Z= 0.219 Angle : 0.514 8.553 8715 Z= 0.261 Chirality : 0.041 0.253 977 Planarity : 0.004 0.041 1092 Dihedral : 10.619 61.705 950 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 3.75 % Allowed : 16.79 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.42 (0.30), residues: 766 helix: 0.79 (0.30), residues: 305 sheet: -0.27 (0.47), residues: 130 loop : -1.27 (0.32), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 458 HIS 0.003 0.001 HIS A 320 PHE 0.015 0.001 PHE A 66 TYR 0.012 0.001 TYR A 578 ARG 0.010 0.000 ARG A 524 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 175 time to evaluate : 0.697 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 VAL cc_start: 0.8551 (OUTLIER) cc_final: 0.8314 (m) REVERT: A 30 LYS cc_start: 0.8570 (mppt) cc_final: 0.8346 (mppt) REVERT: A 171 ASP cc_start: 0.7490 (m-30) cc_final: 0.7240 (m-30) REVERT: A 240 TYR cc_start: 0.7744 (m-10) cc_final: 0.7468 (m-10) REVERT: A 258 ASP cc_start: 0.7684 (OUTLIER) cc_final: 0.7317 (m-30) REVERT: A 349 ASP cc_start: 0.7769 (t0) cc_final: 0.7366 (t0) REVERT: A 393 MET cc_start: 0.8262 (mmm) cc_final: 0.7865 (mtt) REVERT: A 482 LYS cc_start: 0.7890 (ptmt) cc_final: 0.7502 (ptmt) REVERT: A 483 MET cc_start: 0.7917 (mpp) cc_final: 0.7409 (mpp) REVERT: A 498 GLU cc_start: 0.7933 (tt0) cc_final: 0.7689 (mt-10) REVERT: A 503 MET cc_start: 0.8410 (mtt) cc_final: 0.8185 (mtp) REVERT: A 552 ASP cc_start: 0.8096 (t0) cc_final: 0.7866 (t0) REVERT: A 597 VAL cc_start: 0.8861 (OUTLIER) cc_final: 0.8622 (p) REVERT: B 22 GLU cc_start: 0.8215 (mm-30) cc_final: 0.7566 (mp0) REVERT: B 120 ASN cc_start: 0.8019 (p0) cc_final: 0.7752 (p0) outliers start: 25 outliers final: 16 residues processed: 183 average time/residue: 0.2178 time to fit residues: 50.7114 Evaluate side-chains 190 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 171 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 60 HIS Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 387 HIS Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 158 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 26 optimal weight: 0.6980 chunk 2 optimal weight: 0.6980 chunk 50 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 3 optimal weight: 0.0770 chunk 21 optimal weight: 0.0030 chunk 20 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 chunk 58 optimal weight: 0.5980 chunk 63 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 overall best weight: 0.4148 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 323 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.112586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.100333 restraints weight = 10075.071| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 2.15 r_work: 0.3135 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6411 Z= 0.209 Angle : 0.518 8.147 8715 Z= 0.263 Chirality : 0.040 0.164 977 Planarity : 0.004 0.041 1092 Dihedral : 10.596 61.882 950 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 3.45 % Allowed : 18.59 % Favored : 77.96 % 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: -0.45 (0.30), residues: 766 helix: 0.82 (0.30), residues: 305 sheet: -0.33 (0.47), residues: 130 loop : -1.31 (0.32), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 458 HIS 0.003 0.001 HIS A 343 PHE 0.015 0.001 PHE A 66 TYR 0.012 0.001 TYR A 578 ARG 0.009 0.000 ARG A 524 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 171 time to evaluate : 0.747 Fit side-chains revert: symmetry clash REVERT: A 30 LYS cc_start: 0.8567 (mppt) cc_final: 0.8346 (mppt) REVERT: A 171 ASP cc_start: 0.7486 (m-30) cc_final: 0.7233 (m-30) REVERT: A 240 TYR cc_start: 0.7707 (m-10) cc_final: 0.7433 (m-10) REVERT: A 258 ASP cc_start: 0.7696 (OUTLIER) cc_final: 0.7331 (m-30) REVERT: A 272 MET cc_start: 0.7410 (tmm) cc_final: 0.7153 (tmm) REVERT: A 349 ASP cc_start: 0.7779 (t0) cc_final: 0.7370 (t0) REVERT: A 393 MET cc_start: 0.8288 (mmm) cc_final: 0.7899 (mtt) REVERT: A 482 LYS cc_start: 0.7876 (ptmt) cc_final: 0.7495 (ptmt) REVERT: A 483 MET cc_start: 0.7919 (mpp) cc_final: 0.7411 (mpp) REVERT: A 498 GLU cc_start: 0.7892 (tt0) cc_final: 0.7658 (mt-10) REVERT: A 552 ASP cc_start: 0.8091 (t0) cc_final: 0.7845 (t0) REVERT: A 597 VAL cc_start: 0.8844 (OUTLIER) cc_final: 0.8605 (p) REVERT: B 120 ASN cc_start: 0.8018 (p0) cc_final: 0.7759 (p0) outliers start: 23 outliers final: 15 residues processed: 179 average time/residue: 0.2298 time to fit residues: 52.8652 Evaluate side-chains 187 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 170 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 60 HIS Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 158 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 31 optimal weight: 0.9980 chunk 21 optimal weight: 0.0030 chunk 62 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 51 optimal weight: 0.4980 chunk 25 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 64 optimal weight: 0.0470 chunk 38 optimal weight: 0.7980 chunk 67 optimal weight: 0.5980 chunk 32 optimal weight: 0.4980 overall best weight: 0.3288 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 323 GLN A 343 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.113234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.100841 restraints weight = 10023.678| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 2.17 r_work: 0.3145 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6411 Z= 0.180 Angle : 0.517 11.413 8715 Z= 0.259 Chirality : 0.041 0.312 977 Planarity : 0.004 0.028 1092 Dihedral : 10.546 62.214 950 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.15 % Allowed : 19.64 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.48 (0.30), residues: 766 helix: 0.73 (0.30), residues: 305 sheet: -0.30 (0.48), residues: 126 loop : -1.29 (0.32), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 458 HIS 0.002 0.001 HIS A 60 PHE 0.011 0.001 PHE A 66 TYR 0.011 0.001 TYR A 411 ARG 0.004 0.000 ARG A 107 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 169 time to evaluate : 0.656 Fit side-chains revert: symmetry clash REVERT: A 30 LYS cc_start: 0.8517 (mppt) cc_final: 0.8296 (mppt) REVERT: A 52 PHE cc_start: 0.8184 (m-80) cc_final: 0.7817 (t80) REVERT: A 100 LYS cc_start: 0.8020 (OUTLIER) cc_final: 0.7747 (ptpt) REVERT: A 171 ASP cc_start: 0.7438 (m-30) cc_final: 0.7180 (m-30) REVERT: A 240 TYR cc_start: 0.7639 (m-10) cc_final: 0.7397 (m-10) REVERT: A 258 ASP cc_start: 0.7725 (OUTLIER) cc_final: 0.7376 (m-30) REVERT: A 272 MET cc_start: 0.7400 (tmm) cc_final: 0.7150 (tmm) REVERT: A 349 ASP cc_start: 0.7782 (t0) cc_final: 0.7378 (t0) REVERT: A 393 MET cc_start: 0.8302 (mmm) cc_final: 0.7907 (mtt) REVERT: A 482 LYS cc_start: 0.7894 (ptmt) cc_final: 0.7517 (ptmt) REVERT: A 483 MET cc_start: 0.7962 (mpp) cc_final: 0.7460 (mpp) REVERT: A 498 GLU cc_start: 0.7904 (tt0) cc_final: 0.7704 (mt-10) REVERT: A 552 ASP cc_start: 0.8038 (t0) cc_final: 0.7802 (t0) REVERT: A 597 VAL cc_start: 0.8844 (OUTLIER) cc_final: 0.8627 (p) REVERT: B 22 GLU cc_start: 0.8125 (mm-30) cc_final: 0.7385 (mp0) REVERT: B 120 ASN cc_start: 0.7981 (p0) cc_final: 0.7716 (p0) outliers start: 21 outliers final: 14 residues processed: 176 average time/residue: 0.2121 time to fit residues: 47.2982 Evaluate side-chains 184 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 167 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 60 HIS Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 100 LYS Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 597 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 54 optimal weight: 0.8980 chunk 20 optimal weight: 0.0040 chunk 5 optimal weight: 0.3980 chunk 33 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 72 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 75 optimal weight: 0.2980 chunk 34 optimal weight: 0.4980 chunk 50 optimal weight: 0.0010 chunk 32 optimal weight: 0.5980 overall best weight: 0.2398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 323 GLN B 137 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.113673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.100312 restraints weight = 10058.589| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.34 r_work: 0.3132 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6411 Z= 0.156 Angle : 0.503 9.849 8715 Z= 0.252 Chirality : 0.040 0.284 977 Planarity : 0.004 0.029 1092 Dihedral : 10.481 62.810 950 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 3.45 % Allowed : 19.94 % Favored : 76.61 % 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: -0.42 (0.30), residues: 766 helix: 0.78 (0.30), residues: 304 sheet: -0.36 (0.47), residues: 125 loop : -1.21 (0.32), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 458 HIS 0.002 0.000 HIS A 320 PHE 0.011 0.001 PHE A 66 TYR 0.011 0.001 TYR A 411 ARG 0.005 0.000 ARG A 524 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 174 time to evaluate : 0.807 Fit side-chains revert: symmetry clash REVERT: A 30 LYS cc_start: 0.8539 (mppt) cc_final: 0.8305 (mppt) REVERT: A 52 PHE cc_start: 0.8151 (m-80) cc_final: 0.7704 (t80) REVERT: A 98 MET cc_start: 0.7939 (mmm) cc_final: 0.7669 (mmm) REVERT: A 171 ASP cc_start: 0.7374 (m-30) cc_final: 0.7129 (m-30) REVERT: A 240 TYR cc_start: 0.7555 (m-10) cc_final: 0.7300 (m-10) REVERT: A 272 MET cc_start: 0.7424 (tmm) cc_final: 0.7192 (tmm) REVERT: A 349 ASP cc_start: 0.7834 (t0) cc_final: 0.7431 (t0) REVERT: A 482 LYS cc_start: 0.7959 (ptmt) cc_final: 0.7535 (ptmt) REVERT: A 483 MET cc_start: 0.7975 (mpp) cc_final: 0.7494 (mpp) REVERT: A 498 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7555 (mt-10) REVERT: A 552 ASP cc_start: 0.8118 (t0) cc_final: 0.7839 (t0) REVERT: A 597 VAL cc_start: 0.8822 (OUTLIER) cc_final: 0.8609 (p) REVERT: B 22 GLU cc_start: 0.8160 (mm-30) cc_final: 0.7421 (mp0) REVERT: B 120 ASN cc_start: 0.8084 (p0) cc_final: 0.7832 (p0) outliers start: 23 outliers final: 16 residues processed: 182 average time/residue: 0.2241 time to fit residues: 51.5890 Evaluate side-chains 189 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 171 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 60 HIS Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 498 GLU Chi-restraints excluded: chain A residue 504 GLU Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 158 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 31 optimal weight: 0.9980 chunk 21 optimal weight: 0.4980 chunk 17 optimal weight: 0.9990 chunk 61 optimal weight: 6.9990 chunk 9 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 70 optimal weight: 0.3980 chunk 44 optimal weight: 0.6980 chunk 20 optimal weight: 0.0170 chunk 60 optimal weight: 0.9990 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 323 GLN B 137 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.112361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.098978 restraints weight = 10182.664| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 2.34 r_work: 0.3099 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6411 Z= 0.232 Angle : 0.531 9.679 8715 Z= 0.267 Chirality : 0.042 0.276 977 Planarity : 0.004 0.029 1092 Dihedral : 10.545 63.961 950 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.55 % Allowed : 20.99 % Favored : 76.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.45 (0.30), residues: 766 helix: 0.75 (0.30), residues: 305 sheet: -0.36 (0.46), residues: 129 loop : -1.24 (0.33), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 458 HIS 0.003 0.001 HIS A 320 PHE 0.017 0.002 PHE A 66 TYR 0.013 0.001 TYR A 578 ARG 0.005 0.000 ARG A 524 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 175 time to evaluate : 0.713 Fit side-chains revert: symmetry clash REVERT: A 30 LYS cc_start: 0.8536 (mppt) cc_final: 0.8311 (mppt) REVERT: A 52 PHE cc_start: 0.8189 (m-80) cc_final: 0.7783 (t80) REVERT: A 98 MET cc_start: 0.7909 (mmm) cc_final: 0.7627 (mmm) REVERT: A 171 ASP cc_start: 0.7456 (m-30) cc_final: 0.7211 (m-30) REVERT: A 240 TYR cc_start: 0.7754 (m-10) cc_final: 0.7426 (m-10) REVERT: A 349 ASP cc_start: 0.7838 (t0) cc_final: 0.7407 (t0) REVERT: A 370 LEU cc_start: 0.8758 (tp) cc_final: 0.8332 (tt) REVERT: A 482 LYS cc_start: 0.7987 (ptmt) cc_final: 0.7555 (ptmt) REVERT: A 483 MET cc_start: 0.8006 (mpp) cc_final: 0.7540 (mpp) REVERT: A 498 GLU cc_start: 0.7838 (tt0) cc_final: 0.7579 (mt-10) REVERT: A 552 ASP cc_start: 0.8208 (t0) cc_final: 0.7907 (t0) REVERT: A 597 VAL cc_start: 0.8824 (p) cc_final: 0.8616 (p) REVERT: B 22 GLU cc_start: 0.8194 (mm-30) cc_final: 0.7469 (mp0) REVERT: B 120 ASN cc_start: 0.8039 (p0) cc_final: 0.7776 (p0) outliers start: 17 outliers final: 15 residues processed: 181 average time/residue: 0.2184 time to fit residues: 50.4800 Evaluate side-chains 190 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 175 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 60 HIS Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 158 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 76 optimal weight: 0.0570 chunk 21 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 26 optimal weight: 0.0980 chunk 64 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 13 optimal weight: 0.2980 chunk 1 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 63 optimal weight: 0.7980 overall best weight: 0.3898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 323 GLN B 137 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.112747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.099283 restraints weight = 10111.177| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 2.34 r_work: 0.3106 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6411 Z= 0.200 Angle : 0.524 9.385 8715 Z= 0.263 Chirality : 0.041 0.268 977 Planarity : 0.004 0.027 1092 Dihedral : 10.524 64.630 950 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 3.00 % Allowed : 20.54 % Favored : 76.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.45 (0.30), residues: 766 helix: 0.80 (0.30), residues: 303 sheet: -0.42 (0.47), residues: 126 loop : -1.22 (0.32), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 458 HIS 0.003 0.001 HIS A 320 PHE 0.014 0.001 PHE A 66 TYR 0.011 0.001 TYR A 578 ARG 0.005 0.000 ARG A 524 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3732.46 seconds wall clock time: 64 minutes 35.28 seconds (3875.28 seconds total)