Starting phenix.real_space_refine on Thu Nov 14 12:31:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ca0_45378/11_2024/9ca0_45378_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ca0_45378/11_2024/9ca0_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ca0_45378/11_2024/9ca0_45378.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ca0_45378/11_2024/9ca0_45378.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ca0_45378/11_2024/9ca0_45378_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ca0_45378/11_2024/9ca0_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-5513/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: 5.05, per 1000 atoms: 0.81 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: 1.76 Conformation dependent library (CDL) restraints added in 907.5 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: 2.00 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: 1.82 Time building geometry restraints manager: 2.01 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: 2.580 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 20.860 Find NCS groups from input model: 0.230 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: 0.010 Load rotamer database and sin/cos tables:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.630 ------------------------------------------------------------------------------- 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 : 0.775 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: 0.2194 time to fit residues: 52.5529 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 : 0.677 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 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 : 0.738 Fit side-chains revert: symmetry clash REVERT: A 30 LYS cc_start: 0.8189 (mppt) cc_final: 0.7967 (mppt) REVERT: A 51 ARG cc_start: 0.7401 (ttp-170) cc_final: 0.7161 (ttp80) REVERT: A 56 SER cc_start: 0.7986 (p) cc_final: 0.7758 (p) REVERT: A 171 ASP cc_start: 0.6890 (m-30) cc_final: 0.6674 (m-30) REVERT: A 214 PHE cc_start: 0.8582 (t80) cc_final: 0.8370 (t80) REVERT: A 240 TYR cc_start: 0.7216 (m-10) cc_final: 0.6930 (m-10) REVERT: A 272 MET cc_start: 0.7064 (tmm) cc_final: 0.6776 (tmm) REVERT: A 285 VAL cc_start: 0.8762 (t) cc_final: 0.8370 (p) REVERT: A 349 ASP cc_start: 0.7337 (t0) cc_final: 0.6941 (t0) REVERT: A 393 MET cc_start: 0.7763 (mmm) cc_final: 0.7294 (mtt) REVERT: A 482 LYS cc_start: 0.7613 (ptmt) cc_final: 0.7274 (ptmt) REVERT: A 483 MET cc_start: 0.7194 (mpp) cc_final: 0.6569 (mpp) REVERT: A 551 ILE cc_start: 0.8404 (mm) cc_final: 0.8173 (mm) REVERT: A 552 ASP cc_start: 0.7554 (t0) cc_final: 0.7354 (t0) REVERT: A 597 VAL cc_start: 0.8809 (p) cc_final: 0.8584 (p) REVERT: A 608 GLU cc_start: 0.7924 (mm-30) cc_final: 0.7711 (mm-30) REVERT: B 22 GLU cc_start: 0.7838 (mp0) cc_final: 0.7010 (mp0) outliers start: 6 outliers final: 2 residues processed: 185 average time/residue: 0.2242 time to fit residues: 52.3455 Evaluate side-chains 176 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 174 time to evaluate : 1.101 ------------------------------------------------------------------------------- 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 38 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 58 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 75 optimal weight: 0.6980 chunk 62 optimal weight: 0.9980 chunk 69 optimal weight: 0.0770 chunk 23 optimal weight: 0.9980 chunk 56 optimal weight: 0.6980 overall best weight: 0.6138 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.1388 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= 0.273 Angle : 0.526 7.288 8715 Z= 0.274 Chirality : 0.041 0.138 977 Planarity : 0.004 0.033 1092 Dihedral : 11.205 62.379 950 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.55 % Allowed : 13.94 % Favored : 83.51 % 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: -0.49 (0.30), residues: 766 helix: 0.74 (0.30), residues: 301 sheet: -0.13 (0.47), residues: 136 loop : -1.40 (0.32), 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 0.016 0.002 PHE A 66 TYR 0.015 0.001 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: 17 poor density : 180 time to evaluate : 0.751 Fit side-chains revert: symmetry clash REVERT: A 7 VAL cc_start: 0.8088 (OUTLIER) cc_final: 0.7841 (m) REVERT: A 30 LYS cc_start: 0.8199 (mppt) cc_final: 0.7991 (mppt) REVERT: A 171 ASP cc_start: 0.6898 (m-30) cc_final: 0.6680 (m-30) REVERT: A 240 TYR cc_start: 0.7246 (m-10) cc_final: 0.6881 (m-10) REVERT: A 258 ASP cc_start: 0.7231 (OUTLIER) cc_final: 0.6872 (m-30) REVERT: A 285 VAL cc_start: 0.8748 (t) cc_final: 0.8368 (p) REVERT: A 349 ASP cc_start: 0.7339 (t0) cc_final: 0.6940 (t0) REVERT: A 393 MET cc_start: 0.7765 (mmm) cc_final: 0.7301 (mtt) REVERT: A 482 LYS cc_start: 0.7602 (ptmt) cc_final: 0.7235 (ptmt) REVERT: A 483 MET cc_start: 0.7135 (mpp) cc_final: 0.6538 (mpp) REVERT: A 597 VAL cc_start: 0.8798 (p) cc_final: 0.8570 (p) REVERT: B 120 ASN cc_start: 0.7861 (p0) cc_final: 0.7617 (p0) REVERT: B 136 LYS cc_start: 0.7652 (mmmt) cc_final: 0.7327 (mmmt) outliers start: 17 outliers final: 7 residues processed: 183 average time/residue: 0.2169 time to fit residues: 50.3849 Evaluate side-chains 181 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 172 time to evaluate : 0.737 ------------------------------------------------------------------------------- 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 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 598 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 69 optimal weight: 0.0570 chunk 52 optimal weight: 0.5980 chunk 36 optimal weight: 0.8980 chunk 7 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 70 optimal weight: 0.2980 chunk 74 optimal weight: 1.9990 chunk 66 optimal weight: 0.0040 chunk 20 optimal weight: 0.1980 chunk 61 optimal weight: 5.9990 overall best weight: 0.2310 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6411 Z= 0.150 Angle : 0.476 7.664 8715 Z= 0.249 Chirality : 0.039 0.131 977 Planarity : 0.004 0.028 1092 Dihedral : 10.710 61.344 950 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.85 % Allowed : 15.74 % Favored : 81.41 % 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: -0.36 (0.30), residues: 766 helix: 0.87 (0.30), residues: 303 sheet: -0.15 (0.49), residues: 126 loop : -1.27 (0.31), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 458 HIS 0.002 0.000 HIS A 60 PHE 0.013 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 202 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 183 time to evaluate : 0.735 Fit side-chains revert: symmetry clash REVERT: A 171 ASP cc_start: 0.6802 (m-30) cc_final: 0.6566 (m-30) REVERT: A 240 TYR cc_start: 0.7016 (m-10) cc_final: 0.6783 (m-10) REVERT: A 258 ASP cc_start: 0.7224 (OUTLIER) cc_final: 0.6874 (m-30) REVERT: A 272 MET cc_start: 0.7039 (tmm) cc_final: 0.6753 (tmm) REVERT: A 349 ASP cc_start: 0.7325 (t0) cc_final: 0.6926 (t0) REVERT: A 393 MET cc_start: 0.7747 (mmm) cc_final: 0.7259 (mtt) REVERT: A 482 LYS cc_start: 0.7628 (ptmt) cc_final: 0.7252 (ptmt) REVERT: A 483 MET cc_start: 0.7158 (mpp) cc_final: 0.6557 (mpp) REVERT: A 498 GLU cc_start: 0.7269 (tt0) cc_final: 0.7050 (mt-10) REVERT: A 597 VAL cc_start: 0.8798 (p) cc_final: 0.8578 (p) REVERT: B 22 GLU cc_start: 0.7952 (mm-30) cc_final: 0.7230 (mp0) REVERT: B 120 ASN cc_start: 0.7832 (p0) cc_final: 0.7590 (p0) outliers start: 19 outliers final: 12 residues processed: 187 average time/residue: 0.2121 time to fit residues: 50.6842 Evaluate side-chains 191 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 178 time to evaluate : 0.743 ------------------------------------------------------------------------------- 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 188 ILE 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 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 42 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 51 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 38 optimal weight: 0.0870 chunk 66 optimal weight: 0.0000 chunk 18 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 overall best weight: 0.4762 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 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 : 0.003 0.032 6411 Z= 0.229 Angle : 0.521 11.202 8715 Z= 0.265 Chirality : 0.040 0.127 977 Planarity : 0.004 0.047 1092 Dihedral : 10.627 61.706 950 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.85 % Allowed : 17.09 % Favored : 80.06 % 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: -0.35 (0.30), residues: 766 helix: 0.88 (0.30), residues: 303 sheet: -0.19 (0.47), residues: 130 loop : -1.26 (0.32), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 458 HIS 0.003 0.001 HIS A 320 PHE 0.015 0.002 PHE A 66 TYR 0.013 0.001 TYR A 578 ARG 0.010 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 197 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 178 time to evaluate : 0.672 Fit side-chains revert: symmetry clash REVERT: A 171 ASP cc_start: 0.6861 (m-30) cc_final: 0.6608 (m-30) REVERT: A 240 TYR cc_start: 0.7125 (m-10) cc_final: 0.6856 (m-10) REVERT: A 258 ASP cc_start: 0.7281 (OUTLIER) cc_final: 0.6919 (m-30) REVERT: A 272 MET cc_start: 0.7080 (tmm) cc_final: 0.6766 (tmm) REVERT: A 349 ASP cc_start: 0.7330 (t0) cc_final: 0.6961 (t0) REVERT: A 393 MET cc_start: 0.7757 (mmm) cc_final: 0.7281 (mtt) REVERT: A 482 LYS cc_start: 0.7650 (ptmt) cc_final: 0.7272 (ptmt) REVERT: A 483 MET cc_start: 0.7132 (mpp) cc_final: 0.6565 (mpp) REVERT: A 492 ASP cc_start: 0.7279 (t0) cc_final: 0.7066 (t0) REVERT: A 498 GLU cc_start: 0.7282 (tt0) cc_final: 0.7047 (mt-10) REVERT: A 523 GLN cc_start: 0.8115 (tt0) cc_final: 0.7883 (tt0) REVERT: A 597 VAL cc_start: 0.8826 (p) cc_final: 0.8594 (p) REVERT: B 22 GLU cc_start: 0.7984 (mm-30) cc_final: 0.7349 (mp0) REVERT: B 120 ASN cc_start: 0.7836 (p0) cc_final: 0.7586 (p0) outliers start: 19 outliers final: 11 residues processed: 183 average time/residue: 0.2121 time to fit residues: 49.5427 Evaluate side-chains 188 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 176 time to evaluate : 0.765 ------------------------------------------------------------------------------- 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 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 494 LEU Chi-restraints excluded: chain B residue 141 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 67 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 18 optimal weight: 0.2980 chunk 74 optimal weight: 0.6980 chunk 61 optimal weight: 5.9990 chunk 34 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.1773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 6411 Z= 0.319 Angle : 0.556 9.463 8715 Z= 0.286 Chirality : 0.042 0.139 977 Planarity : 0.004 0.033 1092 Dihedral : 10.703 60.498 950 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.45 % Allowed : 17.09 % 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: 0.83 (0.30), residues: 303 sheet: -0.23 (0.46), residues: 136 loop : -1.33 (0.33), 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 0.021 0.002 PHE A 66 TYR 0.017 0.002 TYR A 578 ARG 0.005 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 201 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 178 time to evaluate : 0.756 Fit side-chains REVERT: A 52 PHE cc_start: 0.8122 (m-10) cc_final: 0.7772 (m-10) REVERT: A 171 ASP cc_start: 0.6873 (m-30) cc_final: 0.6655 (m-30) REVERT: A 240 TYR cc_start: 0.7266 (m-10) cc_final: 0.6896 (m-10) REVERT: A 258 ASP cc_start: 0.7283 (OUTLIER) cc_final: 0.6923 (m-30) REVERT: A 349 ASP cc_start: 0.7350 (t0) cc_final: 0.6986 (t0) REVERT: A 393 MET cc_start: 0.7790 (mmm) cc_final: 0.7322 (mtt) REVERT: A 482 LYS cc_start: 0.7646 (ptmt) cc_final: 0.7259 (ptmt) REVERT: A 483 MET cc_start: 0.7069 (mpp) cc_final: 0.6513 (mpp) REVERT: A 492 ASP cc_start: 0.7272 (t0) cc_final: 0.7065 (t0) REVERT: A 498 GLU cc_start: 0.7325 (tt0) cc_final: 0.7075 (mt-10) REVERT: A 597 VAL cc_start: 0.8815 (OUTLIER) cc_final: 0.8613 (p) REVERT: A 608 GLU cc_start: 0.7974 (mm-30) cc_final: 0.7756 (mm-30) REVERT: B 22 GLU cc_start: 0.8019 (mm-30) cc_final: 0.7405 (mp0) REVERT: B 120 ASN cc_start: 0.7822 (p0) cc_final: 0.7583 (p0) outliers start: 23 outliers final: 15 residues processed: 185 average time/residue: 0.2160 time to fit residues: 50.6414 Evaluate side-chains 193 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 176 time to evaluate : 0.787 ------------------------------------------------------------------------------- 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 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 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 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 8 optimal weight: 0.8980 chunk 42 optimal weight: 0.5980 chunk 54 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 chunk 41 optimal weight: 0.3980 chunk 74 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 45 optimal weight: 0.0370 chunk 34 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 overall best weight: 0.4458 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6411 Z= 0.225 Angle : 0.544 9.659 8715 Z= 0.275 Chirality : 0.041 0.289 977 Planarity : 0.004 0.031 1092 Dihedral : 10.643 61.344 950 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.70 % Allowed : 18.89 % 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: -0.49 (0.30), residues: 766 helix: 0.77 (0.30), residues: 305 sheet: -0.30 (0.47), residues: 130 loop : -1.35 (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 0.002 PHE A 66 TYR 0.012 0.001 TYR A 578 ARG 0.004 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 191 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 173 time to evaluate : 0.799 Fit side-chains REVERT: A 7 VAL cc_start: 0.8047 (OUTLIER) cc_final: 0.7808 (m) REVERT: A 171 ASP cc_start: 0.6863 (m-30) cc_final: 0.6628 (m-30) REVERT: A 240 TYR cc_start: 0.7174 (m-10) cc_final: 0.6841 (m-10) REVERT: A 258 ASP cc_start: 0.7266 (OUTLIER) cc_final: 0.6909 (m-30) REVERT: A 349 ASP cc_start: 0.7346 (t0) cc_final: 0.6979 (t0) REVERT: A 393 MET cc_start: 0.7760 (mmm) cc_final: 0.7284 (mtt) REVERT: A 482 LYS cc_start: 0.7620 (ptmt) cc_final: 0.7239 (ptmt) REVERT: A 483 MET cc_start: 0.7065 (mpp) cc_final: 0.6496 (mpp) REVERT: A 492 ASP cc_start: 0.7263 (t0) cc_final: 0.7059 (t0) REVERT: A 498 GLU cc_start: 0.7277 (tt0) cc_final: 0.7055 (mt-10) REVERT: A 597 VAL cc_start: 0.8805 (OUTLIER) cc_final: 0.8585 (p) REVERT: B 120 ASN cc_start: 0.7823 (p0) cc_final: 0.7575 (p0) outliers start: 18 outliers final: 11 residues processed: 178 average time/residue: 0.2068 time to fit residues: 46.7282 Evaluate side-chains 184 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 170 time to evaluate : 0.793 ------------------------------------------------------------------------------- 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 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 B residue 145 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 22 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 47 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 chunk 67 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 6411 Z= 0.368 Angle : 0.582 8.042 8715 Z= 0.299 Chirality : 0.043 0.181 977 Planarity : 0.004 0.034 1092 Dihedral : 10.762 61.802 950 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.25 % Allowed : 20.24 % 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: -0.62 (0.30), residues: 766 helix: 0.65 (0.30), residues: 305 sheet: -0.29 (0.45), residues: 136 loop : -1.47 (0.32), residues: 325 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 0.021 0.002 PHE A 66 TYR 0.018 0.002 TYR A 578 ARG 0.006 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 186 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 171 time to evaluate : 0.614 Fit side-chains revert: symmetry clash REVERT: A 98 MET cc_start: 0.7335 (mmm) cc_final: 0.6965 (mmm) REVERT: A 171 ASP cc_start: 0.6886 (m-30) cc_final: 0.6666 (m-30) REVERT: A 240 TYR cc_start: 0.7296 (m-10) cc_final: 0.6869 (m-10) REVERT: A 258 ASP cc_start: 0.7327 (OUTLIER) cc_final: 0.6955 (m-30) REVERT: A 349 ASP cc_start: 0.7363 (t0) cc_final: 0.6985 (t0) REVERT: A 393 MET cc_start: 0.7777 (mmm) cc_final: 0.7348 (mtt) REVERT: A 482 LYS cc_start: 0.7664 (ptmt) cc_final: 0.7273 (ptmt) REVERT: A 483 MET cc_start: 0.7063 (mpp) cc_final: 0.6538 (mpp) REVERT: A 492 ASP cc_start: 0.7265 (t0) cc_final: 0.7058 (t0) REVERT: A 498 GLU cc_start: 0.7384 (tt0) cc_final: 0.7153 (mt-10) REVERT: A 597 VAL cc_start: 0.8804 (OUTLIER) cc_final: 0.8588 (p) REVERT: B 22 GLU cc_start: 0.7952 (mm-30) cc_final: 0.7214 (mp0) REVERT: B 120 ASN cc_start: 0.7830 (p0) cc_final: 0.7583 (p0) outliers start: 15 outliers final: 12 residues processed: 176 average time/residue: 0.1975 time to fit residues: 43.8123 Evaluate side-chains 186 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 172 time to evaluate : 0.760 ------------------------------------------------------------------------------- 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 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 B residue 158 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 71 optimal weight: 2.9990 chunk 41 optimal weight: 0.1980 chunk 30 optimal weight: 0.9980 chunk 54 optimal weight: 0.5980 chunk 21 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 68 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6411 Z= 0.276 Angle : 0.553 8.349 8715 Z= 0.283 Chirality : 0.041 0.151 977 Planarity : 0.004 0.033 1092 Dihedral : 10.717 61.261 950 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.70 % Allowed : 20.54 % Favored : 76.76 % 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: -0.62 (0.30), residues: 766 helix: 0.65 (0.30), residues: 304 sheet: -0.34 (0.45), residues: 136 loop : -1.44 (0.32), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 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 0.005 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 192 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 174 time to evaluate : 0.739 Fit side-chains revert: symmetry clash REVERT: A 7 VAL cc_start: 0.8089 (OUTLIER) cc_final: 0.7869 (m) REVERT: A 171 ASP cc_start: 0.6843 (m-30) cc_final: 0.6616 (m-30) REVERT: A 240 TYR cc_start: 0.7206 (m-10) cc_final: 0.6843 (m-10) REVERT: A 258 ASP cc_start: 0.7282 (OUTLIER) cc_final: 0.6917 (m-30) REVERT: A 349 ASP cc_start: 0.7360 (t0) cc_final: 0.6986 (t0) REVERT: A 393 MET cc_start: 0.7765 (mmm) cc_final: 0.7333 (mtt) REVERT: A 482 LYS cc_start: 0.7636 (ptmt) cc_final: 0.7251 (ptmt) REVERT: A 483 MET cc_start: 0.7062 (mpp) cc_final: 0.6538 (mpp) REVERT: A 498 GLU cc_start: 0.7297 (tt0) cc_final: 0.7074 (mt-10) REVERT: A 597 VAL cc_start: 0.8792 (OUTLIER) cc_final: 0.8574 (p) REVERT: B 22 GLU cc_start: 0.7969 (mm-30) cc_final: 0.7228 (mp0) outliers start: 18 outliers final: 12 residues processed: 179 average time/residue: 0.1804 time to fit residues: 41.0481 Evaluate side-chains 188 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 173 time to evaluate : 0.546 ------------------------------------------------------------------------------- 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 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 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 34 optimal weight: 0.5980 chunk 50 optimal weight: 2.9990 chunk 76 optimal weight: 0.0770 chunk 70 optimal weight: 0.6980 chunk 61 optimal weight: 6.9990 chunk 6 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 37 optimal weight: 0.5980 chunk 48 optimal weight: 0.3980 chunk 65 optimal weight: 0.0070 chunk 18 optimal weight: 0.5980 overall best weight: 0.3356 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6411 Z= 0.189 Angle : 0.523 8.554 8715 Z= 0.266 Chirality : 0.040 0.142 977 Planarity : 0.004 0.031 1092 Dihedral : 10.591 61.873 950 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.10 % Allowed : 20.84 % Favored : 77.06 % 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: 0.78 (0.30), residues: 304 sheet: -0.40 (0.47), residues: 126 loop : -1.32 (0.32), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 458 HIS 0.002 0.001 HIS A 387 PHE 0.013 0.001 PHE A 66 TYR 0.012 0.001 TYR A 411 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 188 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 174 time to evaluate : 0.765 Fit side-chains revert: symmetry clash REVERT: A 171 ASP cc_start: 0.6809 (m-30) cc_final: 0.6569 (m-30) REVERT: A 240 TYR cc_start: 0.7061 (m-10) cc_final: 0.6772 (m-10) REVERT: A 258 ASP cc_start: 0.7267 (OUTLIER) cc_final: 0.6935 (m-30) REVERT: A 349 ASP cc_start: 0.7342 (t0) cc_final: 0.7003 (t0) REVERT: A 393 MET cc_start: 0.7755 (mmm) cc_final: 0.7303 (mtt) REVERT: A 482 LYS cc_start: 0.7656 (ptmt) cc_final: 0.7277 (ptmt) REVERT: A 483 MET cc_start: 0.7109 (mpp) cc_final: 0.6561 (mpp) REVERT: A 498 GLU cc_start: 0.7274 (tt0) cc_final: 0.7059 (mt-10) REVERT: A 597 VAL cc_start: 0.8758 (OUTLIER) cc_final: 0.8542 (p) REVERT: B 22 GLU cc_start: 0.7960 (mm-30) cc_final: 0.7248 (mp0) REVERT: B 120 ASN cc_start: 0.7833 (p0) cc_final: 0.7574 (p0) REVERT: B 141 LEU cc_start: 0.8302 (mt) cc_final: 0.8090 (mm) outliers start: 14 outliers final: 11 residues processed: 177 average time/residue: 0.2186 time to fit residues: 49.3488 Evaluate side-chains 186 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 173 time to evaluate : 0.697 ------------------------------------------------------------------------------- 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 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 B residue 145 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 56 optimal weight: 0.8980 chunk 9 optimal weight: 0.4980 chunk 16 optimal weight: 0.5980 chunk 61 optimal weight: 6.9990 chunk 25 optimal weight: 0.4980 chunk 62 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3406 r_free = 0.3406 target = 0.110856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.097841 restraints weight = 9992.690| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 2.29 r_work: 0.3080 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6411 Z= 0.282 Angle : 0.551 8.400 8715 Z= 0.282 Chirality : 0.041 0.130 977 Planarity : 0.004 0.033 1092 Dihedral : 10.649 62.479 950 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.25 % Allowed : 20.39 % Favored : 77.36 % 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: -0.55 (0.30), residues: 766 helix: 0.72 (0.30), residues: 305 sheet: -0.39 (0.46), residues: 129 loop : -1.36 (0.32), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 458 HIS 0.004 0.001 HIS A 320 PHE 0.018 0.002 PHE A 66 TYR 0.014 0.002 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: 2069.70 seconds wall clock time: 49 minutes 30.50 seconds (2970.50 seconds total)