Starting phenix.real_space_refine on Tue Jan 14 08:29:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ca0_45378/01_2025/9ca0_45378_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ca0_45378/01_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_45378/01_2025/9ca0_45378.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ca0_45378/01_2025/9ca0_45378.map" model { file = "/net/cci-nas-00/data/ceres_data/9ca0_45378/01_2025/9ca0_45378_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ca0_45378/01_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-5571/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: 4.79, per 1000 atoms: 0.76 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: 1.72 Conformation dependent library (CDL) restraints added in 931.2 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: 1.93 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: 1.83 Time building geometry restraints manager: 1.90 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: 0.000 Normalize map: mean=0, sd=1: 1.810 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: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 20.030 Find NCS groups from input model: 0.060 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:3.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.160 ------------------------------------------------------------------------------- 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 : 0.683 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: 0.2379 time to fit residues: 57.3897 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 : 0.724 ------------------------------------------------------------------------------- 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 = 10057.183| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 2.15 r_work: 0.3138 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 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 : 0.724 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: 0.7891 (ttp80) REVERT: A 171 ASP cc_start: 0.7472 (m-30) cc_final: 0.7250 (m-30) REVERT: A 240 TYR cc_start: 0.7789 (m-10) cc_final: 0.7537 (m-10) REVERT: A 272 MET cc_start: 0.7465 (tmm) cc_final: 0.7215 (tmm) REVERT: A 285 VAL cc_start: 0.8918 (t) cc_final: 0.8571 (p) REVERT: A 349 ASP cc_start: 0.7779 (t0) cc_final: 0.7346 (t0) REVERT: A 393 MET cc_start: 0.8283 (mmm) cc_final: 0.7899 (mtt) REVERT: A 482 LYS cc_start: 0.7917 (ptmt) cc_final: 0.7569 (ptmt) REVERT: A 483 MET cc_start: 0.7955 (mpp) cc_final: 0.7410 (mpp) REVERT: A 551 ILE cc_start: 0.8522 (mm) cc_final: 0.8293 (mm) REVERT: A 552 ASP cc_start: 0.8041 (t0) cc_final: 0.7781 (t0) REVERT: A 597 VAL cc_start: 0.8880 (p) cc_final: 0.8653 (p) REVERT: B 22 GLU cc_start: 0.8054 (mp0) cc_final: 0.7234 (mp0) outliers start: 6 outliers final: 2 residues processed: 185 average time/residue: 0.2166 time to fit residues: 50.5989 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 : 0.701 ------------------------------------------------------------------------------- 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: 0.9980 chunk 32 optimal weight: 0.8980 chunk 40 optimal weight: 0.5980 chunk 58 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3429 r_free = 0.3429 target = 0.111544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.099246 restraints weight = 10012.891| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 2.15 r_work: 0.3121 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 6411 Z= 0.301 Angle : 0.538 7.308 8715 Z= 0.280 Chirality : 0.042 0.140 977 Planarity : 0.004 0.034 1092 Dihedral : 11.267 62.456 950 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % 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: -0.54 (0.30), residues: 766 helix: 0.69 (0.30), residues: 301 sheet: -0.17 (0.46), residues: 137 loop : -1.41 (0.32), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 458 HIS 0.005 0.001 HIS A 320 PHE 0.017 0.002 PHE A 265 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 : 0.690 Fit side-chains revert: symmetry clash REVERT: A 7 VAL cc_start: 0.8546 (OUTLIER) cc_final: 0.8260 (m) REVERT: A 30 LYS cc_start: 0.8556 (mppt) cc_final: 0.8331 (mppt) REVERT: A 171 ASP cc_start: 0.7465 (m-30) cc_final: 0.7246 (m-30) REVERT: A 240 TYR cc_start: 0.7878 (m-10) cc_final: 0.7541 (m-10) REVERT: A 258 ASP cc_start: 0.7688 (OUTLIER) cc_final: 0.7310 (m-30) REVERT: A 285 VAL cc_start: 0.8914 (t) cc_final: 0.8580 (p) REVERT: A 349 ASP cc_start: 0.7770 (t0) cc_final: 0.7336 (t0) REVERT: A 393 MET cc_start: 0.8295 (mmm) cc_final: 0.7939 (mtt) REVERT: A 482 LYS cc_start: 0.7918 (ptmt) cc_final: 0.7553 (ptmt) REVERT: A 483 MET cc_start: 0.7954 (mpp) cc_final: 0.7449 (mpp) REVERT: A 552 ASP cc_start: 0.8062 (t0) cc_final: 0.7814 (t0) REVERT: A 597 VAL cc_start: 0.8870 (p) cc_final: 0.8631 (p) REVERT: B 22 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7306 (mp0) REVERT: B 120 ASN cc_start: 0.8022 (p0) cc_final: 0.7760 (p0) REVERT: B 136 LYS cc_start: 0.7969 (mmmt) cc_final: 0.7716 (mmmt) outliers start: 19 outliers final: 9 residues processed: 183 average time/residue: 0.2256 time to fit residues: 52.8315 Evaluate side-chains 183 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 171 time to evaluate : 0.776 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain B residue 22 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 26 optimal weight: 0.9980 chunk 63 optimal weight: 0.7980 chunk 75 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 chunk 74 optimal weight: 0.0470 chunk 43 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 34 optimal weight: 0.2980 chunk 54 optimal weight: 0.0980 overall best weight: 0.3878 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.112879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.100440 restraints weight = 10143.837| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 2.19 r_work: 0.3133 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.1552 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= 0.195 Angle : 0.492 7.653 8715 Z= 0.257 Chirality : 0.039 0.130 977 Planarity : 0.004 0.031 1092 Dihedral : 10.795 61.596 950 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.70 % Allowed : 16.04 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.46 (0.30), residues: 766 helix: 0.78 (0.30), residues: 304 sheet: -0.19 (0.47), residues: 129 loop : -1.35 (0.31), residues: 333 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 0.014 0.001 PHE A 66 TYR 0.012 0.001 TYR A 411 ARG 0.006 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 195 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 177 time to evaluate : 0.681 Fit side-chains revert: symmetry clash REVERT: A 30 LYS cc_start: 0.8543 (mppt) cc_final: 0.8330 (mppt) REVERT: A 171 ASP cc_start: 0.7469 (m-30) cc_final: 0.7228 (m-30) REVERT: A 240 TYR cc_start: 0.7713 (m-10) cc_final: 0.7440 (m-10) REVERT: A 258 ASP cc_start: 0.7695 (OUTLIER) cc_final: 0.7329 (m-30) REVERT: A 272 MET cc_start: 0.7451 (tmm) cc_final: 0.7192 (tmm) REVERT: A 349 ASP cc_start: 0.7782 (t0) cc_final: 0.7345 (t0) REVERT: A 393 MET cc_start: 0.8289 (mmm) cc_final: 0.7930 (mtt) REVERT: A 482 LYS cc_start: 0.7900 (ptmt) cc_final: 0.7522 (ptmt) REVERT: A 483 MET cc_start: 0.7945 (mpp) cc_final: 0.7451 (mpp) REVERT: A 498 GLU cc_start: 0.7963 (tt0) cc_final: 0.7735 (mt-10) REVERT: A 552 ASP cc_start: 0.8011 (t0) cc_final: 0.7798 (t0) REVERT: A 597 VAL cc_start: 0.8875 (p) cc_final: 0.8644 (p) REVERT: B 120 ASN cc_start: 0.8003 (p0) cc_final: 0.7746 (p0) outliers start: 18 outliers final: 10 residues processed: 181 average time/residue: 0.2151 time to fit residues: 49.4068 Evaluate side-chains 186 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 175 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU 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 387 HIS Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 453 THR 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: 1.9990 chunk 38 optimal weight: 5.9990 chunk 52 optimal weight: 0.4980 chunk 41 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 29 optimal weight: 0.4980 chunk 55 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.3409 r_free = 0.3409 target = 0.110484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.098051 restraints weight = 10087.096| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 2.16 r_work: 0.3097 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 6411 Z= 0.342 Angle : 0.566 11.479 8715 Z= 0.290 Chirality : 0.043 0.147 977 Planarity : 0.004 0.038 1092 Dihedral : 10.805 61.941 950 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 2.70 % Allowed : 18.29 % Favored : 79.01 % 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: -0.53 (0.30), residues: 766 helix: 0.73 (0.30), residues: 302 sheet: -0.22 (0.46), residues: 136 loop : -1.42 (0.32), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 458 HIS 0.005 0.001 HIS A 320 PHE 0.020 0.002 PHE A 265 TYR 0.018 0.002 TYR A 578 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 196 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 178 time to evaluate : 0.686 Fit side-chains revert: symmetry clash REVERT: A 7 VAL cc_start: 0.8553 (OUTLIER) cc_final: 0.8292 (m) REVERT: A 9 GLU cc_start: 0.7444 (tt0) cc_final: 0.7186 (tt0) REVERT: A 30 LYS cc_start: 0.8594 (mppt) cc_final: 0.8381 (mppt) REVERT: A 98 MET cc_start: 0.7950 (mmm) cc_final: 0.7612 (tmm) REVERT: A 134 LEU cc_start: 0.8178 (mt) cc_final: 0.7898 (mt) REVERT: A 171 ASP cc_start: 0.7515 (m-30) cc_final: 0.7293 (m-30) REVERT: A 240 TYR cc_start: 0.7966 (m-10) cc_final: 0.7587 (m-10) REVERT: A 258 ASP cc_start: 0.7721 (OUTLIER) cc_final: 0.7336 (m-30) REVERT: A 349 ASP cc_start: 0.7809 (t0) cc_final: 0.7399 (t0) REVERT: A 393 MET cc_start: 0.8329 (mmm) cc_final: 0.7988 (mtt) REVERT: A 482 LYS cc_start: 0.7935 (ptmt) cc_final: 0.7540 (ptmt) REVERT: A 483 MET cc_start: 0.7927 (mpp) cc_final: 0.7453 (mpp) REVERT: A 498 GLU cc_start: 0.7988 (tt0) cc_final: 0.7771 (mt-10) REVERT: A 552 ASP cc_start: 0.8095 (t0) cc_final: 0.7850 (t0) REVERT: A 597 VAL cc_start: 0.8883 (OUTLIER) cc_final: 0.8650 (p) REVERT: B 22 GLU cc_start: 0.8157 (mm-30) cc_final: 0.7455 (mp0) REVERT: B 120 ASN cc_start: 0.8032 (p0) cc_final: 0.7778 (p0) REVERT: B 136 LYS cc_start: 0.7919 (mmmt) cc_final: 0.7625 (mmmt) outliers start: 18 outliers final: 9 residues processed: 184 average time/residue: 0.2173 time to fit residues: 50.5486 Evaluate side-chains 185 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 173 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL 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 453 THR Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 598 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 11 optimal weight: 0.5980 chunk 75 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 50 optimal weight: 0.5980 chunk 54 optimal weight: 0.5980 chunk 47 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 59 optimal weight: 0.3980 chunk 12 optimal weight: 0.2980 chunk 42 optimal weight: 0.5980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.3431 r_free = 0.3431 target = 0.111928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.099590 restraints weight = 10070.638| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.15 r_work: 0.3123 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.1743 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 : 0.516 9.650 8715 Z= 0.265 Chirality : 0.040 0.126 977 Planarity : 0.004 0.035 1092 Dihedral : 10.683 60.686 950 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.15 % Allowed : 18.44 % Favored : 78.41 % 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: -0.50 (0.30), residues: 766 helix: 0.77 (0.30), residues: 305 sheet: -0.30 (0.46), residues: 130 loop : -1.36 (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 0.016 0.002 PHE A 66 TYR 0.012 0.001 TYR A 578 ARG 0.008 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 193 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 172 time to evaluate : 0.687 Fit side-chains revert: symmetry clash REVERT: A 7 VAL cc_start: 0.8533 (OUTLIER) cc_final: 0.8302 (m) REVERT: A 30 LYS cc_start: 0.8579 (mppt) cc_final: 0.8357 (mppt) REVERT: A 171 ASP cc_start: 0.7450 (m-30) cc_final: 0.7222 (m-30) REVERT: A 240 TYR cc_start: 0.7769 (m-10) cc_final: 0.7458 (m-10) REVERT: A 258 ASP cc_start: 0.7659 (OUTLIER) cc_final: 0.7292 (m-30) REVERT: A 272 MET cc_start: 0.7459 (tmm) cc_final: 0.7183 (tmm) REVERT: A 349 ASP cc_start: 0.7789 (t0) cc_final: 0.7382 (t0) REVERT: A 393 MET cc_start: 0.8284 (mmm) cc_final: 0.7935 (mtt) REVERT: A 482 LYS cc_start: 0.7902 (ptmt) cc_final: 0.7510 (ptmt) REVERT: A 483 MET cc_start: 0.7921 (mpp) cc_final: 0.7416 (mpp) REVERT: A 498 GLU cc_start: 0.7955 (tt0) cc_final: 0.7702 (mt-10) REVERT: A 552 ASP cc_start: 0.8047 (t0) cc_final: 0.7819 (t0) REVERT: A 597 VAL cc_start: 0.8854 (p) cc_final: 0.8619 (p) REVERT: B 22 GLU cc_start: 0.8173 (mm-30) cc_final: 0.7511 (mp0) REVERT: B 120 ASN cc_start: 0.8009 (p0) cc_final: 0.7750 (p0) outliers start: 21 outliers final: 16 residues processed: 180 average time/residue: 0.2120 time to fit residues: 48.5519 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 : 0.662 ------------------------------------------------------------------------------- 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 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 258 ASP Chi-restraints excluded: chain A residue 387 HIS 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 598 ASP Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 145 SER 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: 0.7980 chunk 2 optimal weight: 0.8980 chunk 50 optimal weight: 0.7980 chunk 60 optimal weight: 3.9990 chunk 3 optimal weight: 0.3980 chunk 21 optimal weight: 0.1980 chunk 20 optimal weight: 0.7980 chunk 4 optimal weight: 0.6980 chunk 58 optimal weight: 0.7980 chunk 63 optimal weight: 0.9980 chunk 38 optimal weight: 0.5980 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 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 = 0.111749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.099409 restraints weight = 10050.117| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.15 r_work: 0.3121 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6411 Z= 0.248 Angle : 0.534 9.150 8715 Z= 0.271 Chirality : 0.041 0.244 977 Planarity : 0.004 0.035 1092 Dihedral : 10.664 61.714 950 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 3.15 % Allowed : 19.34 % Favored : 77.51 % 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: -0.53 (0.30), residues: 766 helix: 0.75 (0.30), residues: 305 sheet: -0.32 (0.46), residues: 130 loop : -1.40 (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 0.016 0.002 PHE A 66 TYR 0.013 0.001 TYR A 578 ARG 0.007 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: 21 poor density : 173 time to evaluate : 0.687 Fit side-chains REVERT: A 7 VAL cc_start: 0.8519 (OUTLIER) cc_final: 0.8309 (m) REVERT: A 30 LYS cc_start: 0.8576 (mppt) cc_final: 0.8346 (mppt) REVERT: A 171 ASP cc_start: 0.7480 (m-30) cc_final: 0.7253 (m-30) REVERT: A 240 TYR cc_start: 0.7802 (m-10) cc_final: 0.7467 (m-10) REVERT: A 258 ASP cc_start: 0.7701 (OUTLIER) cc_final: 0.7340 (m-30) REVERT: A 272 MET cc_start: 0.7429 (tmm) cc_final: 0.7157 (tmm) REVERT: A 349 ASP cc_start: 0.7788 (t0) cc_final: 0.7383 (t0) REVERT: A 393 MET cc_start: 0.8284 (mmm) cc_final: 0.7939 (mtt) REVERT: A 482 LYS cc_start: 0.7905 (ptmt) cc_final: 0.7519 (ptmt) REVERT: A 483 MET cc_start: 0.7936 (mpp) cc_final: 0.7449 (mpp) REVERT: A 498 GLU cc_start: 0.7939 (tt0) cc_final: 0.7730 (mt-10) REVERT: A 552 ASP cc_start: 0.8062 (t0) cc_final: 0.7826 (t0) REVERT: A 597 VAL cc_start: 0.8875 (OUTLIER) cc_final: 0.8643 (p) REVERT: B 22 GLU cc_start: 0.8197 (mm-30) cc_final: 0.7553 (mp0) REVERT: B 120 ASN cc_start: 0.8034 (p0) cc_final: 0.7768 (p0) outliers start: 21 outliers final: 15 residues processed: 179 average time/residue: 0.2210 time to fit residues: 50.5163 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 : 0.665 ------------------------------------------------------------------------------- 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 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 258 ASP 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 A residue 598 ASP Chi-restraints excluded: chain B residue 141 LEU 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: 1.9990 chunk 21 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 71 optimal weight: 0.1980 chunk 64 optimal weight: 0.1980 chunk 38 optimal weight: 0.9980 chunk 67 optimal weight: 3.9990 chunk 32 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3428 r_free = 0.3428 target = 0.111704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.099379 restraints weight = 10068.343| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 2.15 r_work: 0.3122 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.1833 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= 0.255 Angle : 0.533 8.195 8715 Z= 0.272 Chirality : 0.041 0.136 977 Planarity : 0.004 0.048 1092 Dihedral : 10.666 62.375 950 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 3.45 % Allowed : 19.04 % Favored : 77.51 % 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: 0.71 (0.30), residues: 305 sheet: -0.34 (0.46), residues: 130 loop : -1.42 (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 0.016 0.002 PHE A 66 TYR 0.013 0.001 TYR A 578 ARG 0.011 0.000 ARG A 524 *********************** 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 201 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 178 time to evaluate : 0.734 Fit side-chains REVERT: A 7 VAL cc_start: 0.8521 (OUTLIER) cc_final: 0.8316 (m) REVERT: A 30 LYS cc_start: 0.8592 (mppt) cc_final: 0.8357 (mppt) REVERT: A 171 ASP cc_start: 0.7495 (m-30) cc_final: 0.7262 (m-30) REVERT: A 240 TYR cc_start: 0.7811 (m-10) cc_final: 0.7481 (m-10) REVERT: A 258 ASP cc_start: 0.7753 (OUTLIER) cc_final: 0.7381 (m-30) REVERT: A 272 MET cc_start: 0.7456 (tmm) cc_final: 0.7183 (tmm) REVERT: A 349 ASP cc_start: 0.7794 (t0) cc_final: 0.7392 (t0) REVERT: A 393 MET cc_start: 0.8284 (mmm) cc_final: 0.7960 (mtt) REVERT: A 424 CYS cc_start: 0.8487 (t) cc_final: 0.8257 (t) REVERT: A 482 LYS cc_start: 0.7900 (ptmt) cc_final: 0.7515 (ptmt) REVERT: A 483 MET cc_start: 0.7935 (mpp) cc_final: 0.7457 (mpp) REVERT: A 498 GLU cc_start: 0.7931 (tt0) cc_final: 0.7723 (mt-10) REVERT: A 552 ASP cc_start: 0.8044 (t0) cc_final: 0.7810 (t0) REVERT: A 597 VAL cc_start: 0.8873 (OUTLIER) cc_final: 0.8639 (p) REVERT: B 22 GLU cc_start: 0.8219 (mm-30) cc_final: 0.7561 (mp0) REVERT: B 120 ASN cc_start: 0.8037 (p0) cc_final: 0.7776 (p0) outliers start: 23 outliers final: 14 residues processed: 187 average time/residue: 0.2123 time to fit residues: 50.5419 Evaluate side-chains 190 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 173 time to evaluate : 0.661 ------------------------------------------------------------------------------- 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 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 258 ASP Chi-restraints excluded: chain A residue 421 SER 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 A residue 598 ASP Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 158 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 54 optimal weight: 0.5980 chunk 20 optimal weight: 0.0030 chunk 5 optimal weight: 0.2980 chunk 33 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 72 optimal weight: 0.0770 chunk 18 optimal weight: 0.5980 chunk 75 optimal weight: 1.9990 chunk 34 optimal weight: 0.1980 chunk 50 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 overall best weight: 0.2348 ------------------------------------------------------------------------------- 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 = 0.3459 r_free = 0.3459 target = 0.113616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.101290 restraints weight = 10130.370| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 2.17 r_work: 0.3154 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6411 Z= 0.155 Angle : 0.501 8.495 8715 Z= 0.255 Chirality : 0.039 0.125 977 Planarity : 0.004 0.042 1092 Dihedral : 10.556 62.751 950 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 3.15 % Allowed : 21.14 % Favored : 75.71 % 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: -0.47 (0.30), residues: 766 helix: 0.76 (0.30), residues: 305 sheet: -0.33 (0.47), residues: 126 loop : -1.29 (0.32), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 458 HIS 0.002 0.000 HIS A 39 PHE 0.012 0.001 PHE A 66 TYR 0.013 0.001 TYR A 41 ARG 0.009 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 193 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 172 time to evaluate : 0.660 Fit side-chains REVERT: A 30 LYS cc_start: 0.8568 (mppt) cc_final: 0.8342 (mppt) REVERT: A 171 ASP cc_start: 0.7386 (m-30) cc_final: 0.7134 (m-30) REVERT: A 240 TYR cc_start: 0.7578 (m-10) cc_final: 0.7304 (m-10) REVERT: A 258 ASP cc_start: 0.7728 (OUTLIER) cc_final: 0.7396 (m-30) REVERT: A 272 MET cc_start: 0.7391 (tmm) cc_final: 0.7152 (tmm) REVERT: A 349 ASP cc_start: 0.7780 (t0) cc_final: 0.7405 (t0) REVERT: A 393 MET cc_start: 0.8264 (mmm) cc_final: 0.7899 (mtt) REVERT: A 482 LYS cc_start: 0.7900 (ptmt) cc_final: 0.7531 (ptmt) REVERT: A 483 MET cc_start: 0.7963 (mpp) cc_final: 0.7463 (mpp) REVERT: A 498 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7654 (mt-10) REVERT: A 552 ASP cc_start: 0.8005 (t0) cc_final: 0.7781 (t0) REVERT: A 597 VAL cc_start: 0.8849 (OUTLIER) cc_final: 0.8610 (p) REVERT: B 22 GLU cc_start: 0.8206 (mm-30) cc_final: 0.7540 (mp0) REVERT: B 120 ASN cc_start: 0.8003 (p0) cc_final: 0.7731 (p0) REVERT: B 141 LEU cc_start: 0.8511 (mt) cc_final: 0.8299 (mm) outliers start: 21 outliers final: 14 residues processed: 177 average time/residue: 0.2314 time to fit residues: 51.5408 Evaluate side-chains 188 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 171 time to evaluate : 0.639 ------------------------------------------------------------------------------- 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 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 498 GLU Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 598 ASP 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: 1.9990 chunk 21 optimal weight: 0.5980 chunk 17 optimal weight: 0.0670 chunk 61 optimal weight: 6.9990 chunk 9 optimal weight: 0.4980 chunk 15 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 70 optimal weight: 0.4980 chunk 44 optimal weight: 0.7980 chunk 20 optimal weight: 0.0970 chunk 60 optimal weight: 2.9990 overall best weight: 0.3516 ------------------------------------------------------------------------------- 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 = 0.3454 r_free = 0.3454 target = 0.113244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.100807 restraints weight = 10187.034| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 2.19 r_work: 0.3145 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.1999 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= 0.186 Angle : 0.501 8.403 8715 Z= 0.255 Chirality : 0.040 0.128 977 Planarity : 0.004 0.031 1092 Dihedral : 10.542 63.772 950 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.70 % Allowed : 21.14 % Favored : 76.16 % 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: -0.39 (0.30), residues: 766 helix: 0.84 (0.30), residues: 305 sheet: -0.28 (0.48), residues: 126 loop : -1.25 (0.32), residues: 335 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 0.014 0.001 PHE A 52 TYR 0.011 0.001 TYR A 578 ARG 0.004 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 191 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 173 time to evaluate : 0.657 Fit side-chains revert: symmetry clash REVERT: A 30 LYS cc_start: 0.8591 (mppt) cc_final: 0.8340 (mppt) REVERT: A 171 ASP cc_start: 0.7413 (m-30) cc_final: 0.7160 (m-30) REVERT: A 240 TYR cc_start: 0.7617 (m-10) cc_final: 0.7408 (m-10) REVERT: A 258 ASP cc_start: 0.7690 (OUTLIER) cc_final: 0.7386 (m-30) REVERT: A 272 MET cc_start: 0.7401 (tmm) cc_final: 0.7171 (tmm) REVERT: A 349 ASP cc_start: 0.7791 (t0) cc_final: 0.7406 (t0) REVERT: A 393 MET cc_start: 0.8278 (mmm) cc_final: 0.7924 (mtt) REVERT: A 482 LYS cc_start: 0.7942 (ptmt) cc_final: 0.7557 (ptmt) REVERT: A 483 MET cc_start: 0.7978 (mpp) cc_final: 0.7477 (mpp) REVERT: A 485 GLU cc_start: 0.8114 (tt0) cc_final: 0.7783 (mm-30) REVERT: A 498 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.7697 (mt-10) REVERT: A 552 ASP cc_start: 0.8023 (t0) cc_final: 0.7788 (t0) REVERT: A 597 VAL cc_start: 0.8855 (OUTLIER) cc_final: 0.8612 (p) REVERT: B 120 ASN cc_start: 0.8029 (p0) cc_final: 0.7759 (p0) outliers start: 18 outliers final: 14 residues processed: 177 average time/residue: 0.2193 time to fit residues: 48.8870 Evaluate side-chains 188 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 171 time to evaluate : 0.710 ------------------------------------------------------------------------------- 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 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 498 GLU Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 598 ASP 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: 3.9990 chunk 21 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 26 optimal weight: 0.0970 chunk 64 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 13 optimal weight: 0.0470 chunk 1 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 overall best weight: 0.6076 ------------------------------------------------------------------------------- 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 = 0.3432 r_free = 0.3432 target = 0.111855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.099532 restraints weight = 10185.036| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 2.17 r_work: 0.3126 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.1994 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= 0.271 Angle : 0.540 8.383 8715 Z= 0.274 Chirality : 0.041 0.131 977 Planarity : 0.004 0.035 1092 Dihedral : 10.624 64.561 950 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.55 % Allowed : 21.59 % Favored : 75.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.74 (0.30), residues: 305 sheet: -0.39 (0.46), residues: 129 loop : -1.31 (0.32), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 115 HIS 0.003 0.001 HIS A 320 PHE 0.018 0.002 PHE A 66 TYR 0.014 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: 3397.09 seconds wall clock time: 61 minutes 13.14 seconds (3673.14 seconds total)