Starting phenix.real_space_refine on Fri Aug 2 23:05:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q75_18204/08_2024/8q75_18204.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q75_18204/08_2024/8q75_18204.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q75_18204/08_2024/8q75_18204.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q75_18204/08_2024/8q75_18204.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q75_18204/08_2024/8q75_18204.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q75_18204/08_2024/8q75_18204.cif" } resolution = 3.2 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= -0.002 sd= 0.047 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: 7 Type Number sf(0) Gaussians Al 1 5.89 5 Mg 1 5.21 5 S 34 5.16 5 C 3760 2.51 5 N 975 2.21 5 O 1095 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 272": "OE1" <-> "OE2" Residue "A TYR 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 364": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 754": "OE1" <-> "OE2" Residue "A ASP 766": "OD1" <-> "OD2" Residue "A ASP 777": "OD1" <-> "OD2" Residue "A ASP 835": "OD1" <-> "OD2" Residue "A GLU 886": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 5870 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 774, 5864 Classifications: {'peptide': 774} Link IDs: {'PCIS': 2, 'PTRANS': 33, 'TRANS': 738} Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 6 Unusual residues: {' MG': 1, 'ALF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.13, per 1000 atoms: 0.70 Number of scatterers: 5870 At special positions: 0 Unit cell: (78.208, 84.864, 135.616, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 34 16.00 Al 1 13.00 Mg 1 11.99 F 4 9.00 O 1095 8.00 N 975 7.00 C 3760 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.64 Conformation dependent library (CDL) restraints added in 1.1 seconds 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1430 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 6 sheets defined 51.7% alpha, 6.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'A' and resid 197 through 210 removed outlier: 3.692A pdb=" N ILE A 201 " --> pdb=" O SER A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 246 removed outlier: 4.465A pdb=" N LEU A 240 " --> pdb=" O GLY A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 293 removed outlier: 3.547A pdb=" N PHE A 286 " --> pdb=" O TRP A 282 " (cutoff:3.500A) Proline residue: A 289 - end of helix Processing helix chain 'A' and resid 296 through 300 Processing helix chain 'A' and resid 302 through 309 Processing helix chain 'A' and resid 316 through 332 Proline residue: A 328 - end of helix Processing helix chain 'A' and resid 334 through 345 Processing helix chain 'A' and resid 351 through 377 removed outlier: 3.708A pdb=" N LEU A 355 " --> pdb=" O ASN A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 406 removed outlier: 3.634A pdb=" N SER A 389 " --> pdb=" O PHE A 385 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE A 393 " --> pdb=" O SER A 389 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER A 394 " --> pdb=" O ALA A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 421 removed outlier: 3.905A pdb=" N ALA A 421 " --> pdb=" O LEU A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 515 Processing helix chain 'A' and resid 516 through 531 Processing helix chain 'A' and resid 537 through 562 removed outlier: 3.680A pdb=" N PHE A 545 " --> pdb=" O ARG A 541 " (cutoff:3.500A) Proline residue: A 548 - end of helix removed outlier: 3.798A pdb=" N LEU A 556 " --> pdb=" O VAL A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 567 Processing helix chain 'A' and resid 571 through 575 Processing helix chain 'A' and resid 580 through 597 removed outlier: 3.640A pdb=" N LEU A 593 " --> pdb=" O GLY A 589 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N CYS A 597 " --> pdb=" O LEU A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 609 Processing helix chain 'A' and resid 611 through 620 removed outlier: 6.266A pdb=" N ALA A 617 " --> pdb=" O THR A 613 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 633 removed outlier: 4.030A pdb=" N HIS A 633 " --> pdb=" O LEU A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 675 Processing helix chain 'A' and resid 680 through 697 Processing helix chain 'A' and resid 721 through 725 Processing helix chain 'A' and resid 731 through 738 removed outlier: 3.722A pdb=" N PHE A 738 " --> pdb=" O LEU A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 through 793 Processing helix chain 'A' and resid 804 through 816 Processing helix chain 'A' and resid 825 through 839 Processing helix chain 'A' and resid 851 through 859 removed outlier: 4.615A pdb=" N ALA A 855 " --> pdb=" O ASN A 851 " (cutoff:3.500A) Processing helix chain 'A' and resid 869 through 876 Processing helix chain 'A' and resid 885 through 897 removed outlier: 3.937A pdb=" N ILE A 889 " --> pdb=" O LEU A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 906 through 915 removed outlier: 4.551A pdb=" N TYR A 912 " --> pdb=" O TRP A 908 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ASN A 913 " --> pdb=" O ALA A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 922 Processing helix chain 'A' and resid 923 through 929 removed outlier: 4.444A pdb=" N PHE A 927 " --> pdb=" O VAL A 923 " (cutoff:3.500A) Processing helix chain 'A' and resid 939 through 948 removed outlier: 3.996A pdb=" N ALA A 943 " --> pdb=" O ALA A 939 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 216 through 218 Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 453 removed outlier: 3.706A pdb=" N VAL A 507 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ILE A 506 " --> pdb=" O ILE A 468 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 472 through 474 Processing sheet with id=AA4, first strand: chain 'A' and resid 621 through 623 removed outlier: 6.856A pdb=" N ALA A 864 " --> pdb=" O LEU A 880 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N LEU A 863 " --> pdb=" O VAL A 843 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N MET A 845 " --> pdb=" O LEU A 863 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N ILE A 865 " --> pdb=" O MET A 845 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N GLY A 847 " --> pdb=" O ILE A 865 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N THR A 842 " --> pdb=" O VAL A 635 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA A 637 " --> pdb=" O THR A 842 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N LYS A 636 " --> pdb=" O SER A 796 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N ILE A 798 " --> pdb=" O LYS A 636 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ILE A 638 " --> pdb=" O ILE A 798 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 652 through 653 Processing sheet with id=AA6, first strand: chain 'A' and resid 717 through 720 274 hydrogen bonds defined for protein. 774 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.69 Time building geometry restraints manager: 2.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 999 1.32 - 1.44: 1434 1.44 - 1.56: 3489 1.56 - 1.69: 0 1.69 - 1.81: 58 Bond restraints: 5980 Sorted by residual: bond pdb=" CA LYS A 642 " pdb=" C LYS A 642 " ideal model delta sigma weight residual 1.526 1.450 0.076 9.20e-03 1.18e+04 6.81e+01 bond pdb=" CA ASP A 641 " pdb=" C ASP A 641 " ideal model delta sigma weight residual 1.524 1.458 0.066 1.31e-02 5.83e+03 2.51e+01 bond pdb=" F1 ALF A1001 " pdb="AL ALF A1001 " ideal model delta sigma weight residual 1.684 1.783 -0.099 2.00e-02 2.50e+03 2.44e+01 bond pdb=" F3 ALF A1001 " pdb="AL ALF A1001 " ideal model delta sigma weight residual 1.685 1.783 -0.098 2.00e-02 2.50e+03 2.39e+01 bond pdb=" F2 ALF A1001 " pdb="AL ALF A1001 " ideal model delta sigma weight residual 1.685 1.783 -0.098 2.00e-02 2.50e+03 2.39e+01 ... (remaining 5975 not shown) Histogram of bond angle deviations from ideal: 89.93 - 107.90: 269 107.90 - 125.86: 7758 125.86 - 143.82: 94 143.82 - 161.78: 0 161.78 - 179.75: 2 Bond angle restraints: 8123 Sorted by residual: angle pdb=" F1 ALF A1001 " pdb="AL ALF A1001 " pdb=" F2 ALF A1001 " ideal model delta sigma weight residual 108.68 179.62 -70.94 3.00e+00 1.11e-01 5.59e+02 angle pdb=" F3 ALF A1001 " pdb="AL ALF A1001 " pdb=" F4 ALF A1001 " ideal model delta sigma weight residual 109.63 179.75 -70.12 3.00e+00 1.11e-01 5.46e+02 angle pdb=" N ILE A 902 " pdb=" CA ILE A 902 " pdb=" C ILE A 902 " ideal model delta sigma weight residual 113.71 105.97 7.74 9.50e-01 1.11e+00 6.64e+01 angle pdb=" N THR A 753 " pdb=" CA THR A 753 " pdb=" C THR A 753 " ideal model delta sigma weight residual 114.62 106.58 8.04 1.14e+00 7.69e-01 4.98e+01 angle pdb=" F2 ALF A1001 " pdb="AL ALF A1001 " pdb=" F4 ALF A1001 " ideal model delta sigma weight residual 110.21 89.95 20.26 3.00e+00 1.11e-01 4.56e+01 ... (remaining 8118 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 3234 17.92 - 35.84: 301 35.84 - 53.76: 43 53.76 - 71.69: 16 71.69 - 89.61: 7 Dihedral angle restraints: 3601 sinusoidal: 1380 harmonic: 2221 Sorted by residual: dihedral pdb=" CA PHE A 293 " pdb=" C PHE A 293 " pdb=" N SER A 294 " pdb=" CA SER A 294 " ideal model delta harmonic sigma weight residual 180.00 -140.20 -39.80 0 5.00e+00 4.00e-02 6.34e+01 dihedral pdb=" CA ARG A 758 " pdb=" C ARG A 758 " pdb=" N THR A 759 " pdb=" CA THR A 759 " ideal model delta harmonic sigma weight residual 180.00 145.31 34.69 0 5.00e+00 4.00e-02 4.81e+01 dihedral pdb=" CA GLU A 752 " pdb=" C GLU A 752 " pdb=" N THR A 753 " pdb=" CA THR A 753 " ideal model delta harmonic sigma weight residual 180.00 148.27 31.73 0 5.00e+00 4.00e-02 4.03e+01 ... (remaining 3598 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 747 0.056 - 0.113: 180 0.113 - 0.169: 27 0.169 - 0.225: 8 0.225 - 0.282: 1 Chirality restraints: 963 Sorted by residual: chirality pdb=" CA ARG A 758 " pdb=" N ARG A 758 " pdb=" C ARG A 758 " pdb=" CB ARG A 758 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.98e+00 chirality pdb=" CA VAL A 311 " pdb=" N VAL A 311 " pdb=" C VAL A 311 " pdb=" CB VAL A 311 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 8.96e-01 chirality pdb=" CG LEU A 954 " pdb=" CB LEU A 954 " pdb=" CD1 LEU A 954 " pdb=" CD2 LEU A 954 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.72e-01 ... (remaining 960 not shown) Planarity restraints: 1028 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 265 " 0.248 9.50e-02 1.11e+02 1.12e-01 9.01e+00 pdb=" NE ARG A 265 " -0.022 2.00e-02 2.50e+03 pdb=" CZ ARG A 265 " 0.018 2.00e-02 2.50e+03 pdb=" NH1 ARG A 265 " -0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG A 265 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 288 " -0.045 5.00e-02 4.00e+02 6.78e-02 7.37e+00 pdb=" N PRO A 289 " 0.117 5.00e-02 4.00e+02 pdb=" CA PRO A 289 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 289 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 680 " 0.043 5.00e-02 4.00e+02 6.47e-02 6.70e+00 pdb=" N PRO A 681 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO A 681 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 681 " 0.036 5.00e-02 4.00e+02 ... (remaining 1025 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.44: 50 2.44 - 3.06: 4287 3.06 - 3.67: 9621 3.67 - 4.29: 13723 4.29 - 4.90: 21542 Nonbonded interactions: 49223 Sorted by model distance: nonbonded pdb=" OD2 ASP A 641 " pdb=" F2 ALF A1001 " model vdw 1.828 2.990 nonbonded pdb=" F2 ALF A1001 " pdb="MG MG A1002 " model vdw 1.895 2.120 nonbonded pdb=" OD2 ASP A 641 " pdb="MG MG A1002 " model vdw 1.913 2.170 nonbonded pdb=" OD2 ASP A 848 " pdb="MG MG A1002 " model vdw 2.029 2.170 nonbonded pdb=" O THR A 643 " pdb="MG MG A1002 " model vdw 2.030 2.170 ... (remaining 49218 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 1.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 20.560 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 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 : 0.006 0.099 5980 Z= 0.374 Angle : 1.557 70.940 8123 Z= 0.722 Chirality : 0.051 0.282 963 Planarity : 0.008 0.112 1028 Dihedral : 14.765 89.606 2171 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 20.97 Ramachandran Plot: Outliers : 1.55 % Allowed : 12.31 % Favored : 86.14 % Rotamer: Outliers : 0.62 % Allowed : 0.62 % Favored : 98.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.41 % 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: -2.02 (0.31), residues: 772 helix: 0.19 (0.28), residues: 383 sheet: -2.68 (0.65), residues: 53 loop : -3.02 (0.32), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 935 HIS 0.004 0.001 HIS A 633 PHE 0.019 0.001 PHE A 710 TYR 0.009 0.001 TYR A 689 ARG 0.021 0.002 ARG A 265 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 123 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 271 HIS cc_start: 0.9504 (m-70) cc_final: 0.9288 (m-70) REVERT: A 299 MET cc_start: 0.6834 (tmm) cc_final: 0.6553 (tmm) REVERT: A 300 ILE cc_start: 0.8149 (tp) cc_final: 0.7888 (mm) REVERT: A 403 GLU cc_start: 0.9030 (tp30) cc_final: 0.8812 (tp30) REVERT: A 446 LEU cc_start: 0.9507 (mt) cc_final: 0.9241 (mm) REVERT: A 613 THR cc_start: 0.9447 (m) cc_final: 0.9087 (p) REVERT: A 630 GLU cc_start: 0.8728 (tm-30) cc_final: 0.8178 (tm-30) REVERT: A 642 LYS cc_start: 0.9480 (OUTLIER) cc_final: 0.8974 (ttpp) REVERT: A 659 PHE cc_start: 0.8873 (p90) cc_final: 0.8284 (p90) REVERT: A 705 MET cc_start: 0.7363 (ppp) cc_final: 0.6989 (ppp) REVERT: A 766 ASP cc_start: 0.8177 (t70) cc_final: 0.7856 (t0) REVERT: A 860 ASP cc_start: 0.9382 (m-30) cc_final: 0.9060 (m-30) outliers start: 4 outliers final: 0 residues processed: 126 average time/residue: 0.1905 time to fit residues: 31.0865 Evaluate side-chains 82 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 81 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 642 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 65 optimal weight: 1.9990 chunk 58 optimal weight: 20.0000 chunk 32 optimal weight: 9.9990 chunk 19 optimal weight: 4.9990 chunk 39 optimal weight: 0.7980 chunk 31 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 36 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 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 : 0.004 0.042 5980 Z= 0.290 Angle : 0.851 11.979 8123 Z= 0.429 Chirality : 0.049 0.172 963 Planarity : 0.007 0.070 1028 Dihedral : 6.516 43.642 820 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 17.10 Ramachandran Plot: Outliers : 1.55 % Allowed : 11.66 % Favored : 86.79 % Rotamer: Outliers : 2.19 % Allowed : 11.88 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.54 % 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: -2.06 (0.30), residues: 772 helix: 0.02 (0.26), residues: 384 sheet: -2.12 (0.67), residues: 53 loop : -2.99 (0.32), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 935 HIS 0.009 0.002 HIS A 749 PHE 0.017 0.002 PHE A 710 TYR 0.011 0.001 TYR A 906 ARG 0.010 0.001 ARG A 931 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 90 time to evaluate : 0.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 299 MET cc_start: 0.6680 (tmm) cc_final: 0.6367 (tmm) REVERT: A 300 ILE cc_start: 0.8039 (tp) cc_final: 0.7678 (mm) REVERT: A 319 MET cc_start: 0.9175 (mtt) cc_final: 0.8868 (mtp) REVERT: A 446 LEU cc_start: 0.9489 (mt) cc_final: 0.9218 (mm) REVERT: A 558 TRP cc_start: 0.8538 (t60) cc_final: 0.8322 (t60) REVERT: A 610 MET cc_start: 0.7737 (mmt) cc_final: 0.7479 (mmp) REVERT: A 613 THR cc_start: 0.9432 (m) cc_final: 0.9141 (p) REVERT: A 630 GLU cc_start: 0.8712 (tm-30) cc_final: 0.8085 (tm-30) REVERT: A 659 PHE cc_start: 0.8794 (p90) cc_final: 0.8100 (p90) REVERT: A 705 MET cc_start: 0.7206 (ppp) cc_final: 0.6835 (ppp) REVERT: A 860 ASP cc_start: 0.9324 (m-30) cc_final: 0.9075 (m-30) REVERT: A 903 ARG cc_start: 0.6007 (tpt170) cc_final: 0.5416 (mmm160) outliers start: 14 outliers final: 9 residues processed: 99 average time/residue: 0.1672 time to fit residues: 22.0567 Evaluate side-chains 85 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 76 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 SER Chi-restraints excluded: chain A residue 303 PHE Chi-restraints excluded: chain A residue 335 TRP Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 523 GLN Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 935 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 38 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 58 optimal weight: 10.0000 chunk 47 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 chunk 75 optimal weight: 0.9990 chunk 62 optimal weight: 5.9990 chunk 69 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 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 913 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5980 Z= 0.236 Angle : 0.787 11.338 8123 Z= 0.393 Chirality : 0.047 0.161 963 Planarity : 0.006 0.064 1028 Dihedral : 6.247 47.890 816 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 1.30 % Allowed : 11.53 % Favored : 87.18 % Rotamer: Outliers : 3.44 % Allowed : 15.47 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.54 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.30), residues: 772 helix: 0.23 (0.26), residues: 387 sheet: -1.83 (0.69), residues: 49 loop : -2.91 (0.32), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 335 HIS 0.004 0.001 HIS A 680 PHE 0.014 0.001 PHE A 710 TYR 0.016 0.001 TYR A 906 ARG 0.004 0.001 ARG A 694 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 84 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 266 GLU cc_start: 0.8877 (tm-30) cc_final: 0.8605 (tm-30) REVERT: A 299 MET cc_start: 0.6696 (tmm) cc_final: 0.6252 (tmm) REVERT: A 300 ILE cc_start: 0.7933 (tp) cc_final: 0.7421 (mm) REVERT: A 319 MET cc_start: 0.9181 (mtt) cc_final: 0.8850 (mtp) REVERT: A 403 GLU cc_start: 0.9112 (tp30) cc_final: 0.8692 (tp30) REVERT: A 446 LEU cc_start: 0.9459 (mt) cc_final: 0.9194 (mm) REVERT: A 558 TRP cc_start: 0.8533 (t60) cc_final: 0.8060 (t60) REVERT: A 610 MET cc_start: 0.7700 (mmt) cc_final: 0.7365 (mmp) REVERT: A 613 THR cc_start: 0.9381 (m) cc_final: 0.9139 (p) REVERT: A 630 GLU cc_start: 0.8701 (tm-30) cc_final: 0.8056 (tm-30) REVERT: A 650 LYS cc_start: 0.8648 (tptt) cc_final: 0.8343 (tptt) REVERT: A 655 GLN cc_start: 0.8850 (tm-30) cc_final: 0.8649 (tm-30) REVERT: A 705 MET cc_start: 0.7030 (ppp) cc_final: 0.6651 (ppp) REVERT: A 860 ASP cc_start: 0.9298 (m-30) cc_final: 0.9084 (m-30) REVERT: A 903 ARG cc_start: 0.5999 (tpt170) cc_final: 0.5373 (mmm160) outliers start: 22 outliers final: 13 residues processed: 99 average time/residue: 0.1513 time to fit residues: 20.5359 Evaluate side-chains 89 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 76 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 SER Chi-restraints excluded: chain A residue 303 PHE Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 335 TRP Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 523 GLN Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 881 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 69 optimal weight: 0.7980 chunk 52 optimal weight: 20.0000 chunk 36 optimal weight: 0.7980 chunk 7 optimal weight: 0.0030 chunk 33 optimal weight: 0.0870 chunk 47 optimal weight: 3.9990 chunk 70 optimal weight: 0.8980 chunk 74 optimal weight: 0.5980 chunk 66 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 chunk 61 optimal weight: 4.9990 overall best weight: 0.4168 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.2871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5980 Z= 0.185 Angle : 0.759 11.137 8123 Z= 0.375 Chirality : 0.046 0.157 963 Planarity : 0.005 0.058 1028 Dihedral : 6.036 45.088 816 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 1.04 % Allowed : 11.01 % Favored : 87.95 % Rotamer: Outliers : 2.97 % Allowed : 16.56 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.41 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.30), residues: 772 helix: 0.35 (0.26), residues: 389 sheet: -1.23 (0.72), residues: 44 loop : -2.78 (0.32), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 335 HIS 0.003 0.001 HIS A 189 PHE 0.011 0.001 PHE A 710 TYR 0.022 0.001 TYR A 906 ARG 0.004 0.000 ARG A 694 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 88 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 299 MET cc_start: 0.6533 (tmm) cc_final: 0.6274 (tmm) REVERT: A 319 MET cc_start: 0.9195 (mtt) cc_final: 0.8877 (mtp) REVERT: A 403 GLU cc_start: 0.9056 (tp30) cc_final: 0.8618 (tp30) REVERT: A 446 LEU cc_start: 0.9445 (mt) cc_final: 0.9176 (mm) REVERT: A 558 TRP cc_start: 0.8488 (t60) cc_final: 0.8071 (t60) REVERT: A 610 MET cc_start: 0.7334 (mmt) cc_final: 0.7127 (mmp) REVERT: A 630 GLU cc_start: 0.8690 (tm-30) cc_final: 0.8045 (tm-30) REVERT: A 650 LYS cc_start: 0.8667 (tptt) cc_final: 0.8463 (tptt) REVERT: A 705 MET cc_start: 0.7013 (ppp) cc_final: 0.6624 (ppp) REVERT: A 903 ARG cc_start: 0.6049 (tpt170) cc_final: 0.5405 (mmm160) outliers start: 19 outliers final: 10 residues processed: 101 average time/residue: 0.1756 time to fit residues: 23.4561 Evaluate side-chains 83 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 73 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 335 TRP Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 523 GLN Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 881 MET Chi-restraints excluded: chain A residue 906 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 42 optimal weight: 0.0570 chunk 1 optimal weight: 30.0000 chunk 55 optimal weight: 0.0070 chunk 30 optimal weight: 10.0000 chunk 63 optimal weight: 0.9990 chunk 51 optimal weight: 9.9990 chunk 0 optimal weight: 30.0000 chunk 38 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 overall best weight: 0.5516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 361 ASN A 587 GLN A 913 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.3192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5980 Z= 0.188 Angle : 0.753 10.755 8123 Z= 0.370 Chirality : 0.045 0.153 963 Planarity : 0.005 0.063 1028 Dihedral : 5.863 43.851 816 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 1.04 % Allowed : 10.49 % Favored : 88.47 % Rotamer: Outliers : 3.75 % Allowed : 16.72 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.41 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.30), residues: 772 helix: 0.55 (0.27), residues: 386 sheet: -1.39 (0.70), residues: 47 loop : -2.65 (0.32), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 335 HIS 0.003 0.001 HIS A 189 PHE 0.009 0.001 PHE A 710 TYR 0.023 0.002 TYR A 906 ARG 0.003 0.001 ARG A 694 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 77 time to evaluate : 0.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 299 MET cc_start: 0.6324 (tmm) cc_final: 0.6060 (tmm) REVERT: A 319 MET cc_start: 0.9215 (mtt) cc_final: 0.8912 (mtp) REVERT: A 403 GLU cc_start: 0.9063 (tp30) cc_final: 0.8576 (tp30) REVERT: A 446 LEU cc_start: 0.9437 (mt) cc_final: 0.9173 (mm) REVERT: A 558 TRP cc_start: 0.8487 (t60) cc_final: 0.8036 (t60) REVERT: A 630 GLU cc_start: 0.8670 (tm-30) cc_final: 0.8022 (tm-30) REVERT: A 705 MET cc_start: 0.6915 (ppp) cc_final: 0.6492 (ppp) REVERT: A 903 ARG cc_start: 0.6115 (tpt170) cc_final: 0.5488 (mmm160) outliers start: 24 outliers final: 16 residues processed: 92 average time/residue: 0.1661 time to fit residues: 20.7522 Evaluate side-chains 90 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 74 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 SER Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 335 TRP Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 511 HIS Chi-restraints excluded: chain A residue 523 GLN Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 881 MET Chi-restraints excluded: chain A residue 906 TYR Chi-restraints excluded: chain A residue 908 TRP Chi-restraints excluded: chain A residue 932 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 67 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 6 optimal weight: 8.9990 chunk 24 optimal weight: 0.0980 chunk 39 optimal weight: 0.8980 chunk 71 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.3389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5980 Z= 0.204 Angle : 0.752 10.478 8123 Z= 0.369 Chirality : 0.045 0.193 963 Planarity : 0.005 0.065 1028 Dihedral : 5.794 43.166 816 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.91 % Allowed : 10.62 % Favored : 88.47 % Rotamer: Outliers : 3.12 % Allowed : 18.44 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.30), residues: 772 helix: 0.56 (0.27), residues: 391 sheet: -1.22 (0.80), residues: 36 loop : -2.48 (0.32), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 335 HIS 0.002 0.000 HIS A 749 PHE 0.010 0.001 PHE A 293 TYR 0.020 0.001 TYR A 906 ARG 0.002 0.000 ARG A 532 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 79 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 299 MET cc_start: 0.6287 (tmm) cc_final: 0.5977 (tmm) REVERT: A 319 MET cc_start: 0.9198 (mtt) cc_final: 0.8919 (mtp) REVERT: A 353 ASP cc_start: 0.9103 (m-30) cc_final: 0.8829 (m-30) REVERT: A 403 GLU cc_start: 0.9056 (tp30) cc_final: 0.8569 (tp30) REVERT: A 446 LEU cc_start: 0.9434 (mt) cc_final: 0.9168 (mm) REVERT: A 558 TRP cc_start: 0.8505 (t60) cc_final: 0.8030 (t60) REVERT: A 630 GLU cc_start: 0.8691 (tm-30) cc_final: 0.8048 (tm-30) REVERT: A 650 LYS cc_start: 0.8660 (tptt) cc_final: 0.8454 (tptt) REVERT: A 705 MET cc_start: 0.6878 (ppp) cc_final: 0.6417 (ppp) REVERT: A 903 ARG cc_start: 0.6067 (tpt170) cc_final: 0.5423 (mmm160) outliers start: 20 outliers final: 16 residues processed: 93 average time/residue: 0.1763 time to fit residues: 22.3570 Evaluate side-chains 91 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 75 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 SER Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 335 TRP Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 511 HIS Chi-restraints excluded: chain A residue 523 GLN Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 881 MET Chi-restraints excluded: chain A residue 902 ILE Chi-restraints excluded: chain A residue 906 TYR Chi-restraints excluded: chain A residue 908 TRP Chi-restraints excluded: chain A residue 932 LEU 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: 0.9990 chunk 54 optimal weight: 9.9990 chunk 62 optimal weight: 6.9990 chunk 41 optimal weight: 0.2980 chunk 74 optimal weight: 0.9980 chunk 46 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 29 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 GLN A 361 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.3544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5980 Z= 0.209 Angle : 0.768 11.797 8123 Z= 0.371 Chirality : 0.045 0.184 963 Planarity : 0.005 0.068 1028 Dihedral : 5.721 41.607 816 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.91 % Allowed : 10.62 % Favored : 88.47 % Rotamer: Outliers : 3.59 % Allowed : 18.44 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.31), residues: 772 helix: 0.75 (0.27), residues: 383 sheet: -1.15 (0.82), residues: 37 loop : -2.31 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 335 HIS 0.002 0.000 HIS A 749 PHE 0.010 0.001 PHE A 293 TYR 0.015 0.001 TYR A 906 ARG 0.004 0.000 ARG A 758 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 80 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 299 MET cc_start: 0.6271 (tmm) cc_final: 0.6012 (tmm) REVERT: A 300 ILE cc_start: 0.7620 (tp) cc_final: 0.7252 (tp) REVERT: A 319 MET cc_start: 0.9197 (mtt) cc_final: 0.8924 (mtp) REVERT: A 353 ASP cc_start: 0.9116 (m-30) cc_final: 0.8846 (m-30) REVERT: A 403 GLU cc_start: 0.9057 (tp30) cc_final: 0.8571 (tp30) REVERT: A 446 LEU cc_start: 0.9439 (mt) cc_final: 0.9177 (mm) REVERT: A 558 TRP cc_start: 0.8520 (t60) cc_final: 0.8031 (t60) REVERT: A 630 GLU cc_start: 0.8707 (tm-30) cc_final: 0.8071 (tm-30) REVERT: A 659 PHE cc_start: 0.8982 (OUTLIER) cc_final: 0.8217 (p90) REVERT: A 705 MET cc_start: 0.6921 (ppp) cc_final: 0.6418 (ppp) REVERT: A 903 ARG cc_start: 0.6000 (tpt170) cc_final: 0.5365 (mmm160) outliers start: 23 outliers final: 16 residues processed: 93 average time/residue: 0.1881 time to fit residues: 23.6178 Evaluate side-chains 91 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 74 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 SER Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 335 TRP Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 511 HIS Chi-restraints excluded: chain A residue 523 GLN Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 881 MET Chi-restraints excluded: chain A residue 902 ILE Chi-restraints excluded: chain A residue 906 TYR Chi-restraints excluded: chain A residue 908 TRP Chi-restraints excluded: chain A residue 932 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 22 optimal weight: 6.9990 chunk 14 optimal weight: 0.5980 chunk 47 optimal weight: 2.9990 chunk 50 optimal weight: 6.9990 chunk 36 optimal weight: 0.2980 chunk 6 optimal weight: 30.0000 chunk 58 optimal weight: 0.0270 chunk 67 optimal weight: 0.1980 chunk 71 optimal weight: 0.3980 chunk 64 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 overall best weight: 0.3038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.3855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5980 Z= 0.174 Angle : 0.769 12.192 8123 Z= 0.373 Chirality : 0.045 0.192 963 Planarity : 0.005 0.070 1028 Dihedral : 5.717 43.016 816 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.78 % Allowed : 10.36 % Favored : 88.86 % Rotamer: Outliers : 3.28 % Allowed : 19.22 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: -0.94 (0.31), residues: 772 helix: 0.83 (0.27), residues: 384 sheet: -1.38 (0.75), residues: 44 loop : -2.30 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 335 HIS 0.002 0.000 HIS A 749 PHE 0.012 0.001 PHE A 293 TYR 0.014 0.001 TYR A 906 ARG 0.003 0.000 ARG A 758 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 88 time to evaluate : 0.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 299 MET cc_start: 0.6190 (tmm) cc_final: 0.5911 (tmm) REVERT: A 300 ILE cc_start: 0.7408 (tp) cc_final: 0.6955 (tp) REVERT: A 319 MET cc_start: 0.9186 (mtt) cc_final: 0.8910 (mtp) REVERT: A 353 ASP cc_start: 0.9070 (m-30) cc_final: 0.8781 (m-30) REVERT: A 403 GLU cc_start: 0.9036 (tp30) cc_final: 0.8533 (tp30) REVERT: A 446 LEU cc_start: 0.9428 (mt) cc_final: 0.9169 (mm) REVERT: A 558 TRP cc_start: 0.8512 (t60) cc_final: 0.8039 (t60) REVERT: A 630 GLU cc_start: 0.8691 (tm-30) cc_final: 0.8040 (tm-30) REVERT: A 659 PHE cc_start: 0.8952 (OUTLIER) cc_final: 0.8293 (p90) REVERT: A 705 MET cc_start: 0.6896 (ppp) cc_final: 0.6388 (ppp) REVERT: A 903 ARG cc_start: 0.5960 (tpt170) cc_final: 0.5419 (mmm160) outliers start: 21 outliers final: 15 residues processed: 102 average time/residue: 0.1621 time to fit residues: 22.4563 Evaluate side-chains 94 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 78 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 335 TRP Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 511 HIS Chi-restraints excluded: chain A residue 523 GLN Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 902 ILE Chi-restraints excluded: chain A residue 906 TYR Chi-restraints excluded: chain A residue 907 VAL Chi-restraints excluded: chain A residue 908 TRP Chi-restraints excluded: chain A residue 912 TYR Chi-restraints excluded: chain A residue 932 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 71 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 30 optimal weight: 3.9990 chunk 54 optimal weight: 20.0000 chunk 21 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 73 optimal weight: 0.0970 chunk 44 optimal weight: 0.9980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.3918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5980 Z= 0.254 Angle : 0.797 16.454 8123 Z= 0.387 Chirality : 0.047 0.183 963 Planarity : 0.005 0.069 1028 Dihedral : 5.670 39.081 816 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.78 % Allowed : 10.75 % Favored : 88.47 % Rotamer: Outliers : 3.28 % Allowed : 19.69 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: -0.95 (0.31), residues: 772 helix: 0.80 (0.27), residues: 386 sheet: -1.30 (0.75), residues: 44 loop : -2.30 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 935 HIS 0.002 0.000 HIS A 749 PHE 0.015 0.001 PHE A 337 TYR 0.022 0.002 TYR A 906 ARG 0.003 0.000 ARG A 758 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 79 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 299 MET cc_start: 0.6224 (tmm) cc_final: 0.5917 (tmm) REVERT: A 300 ILE cc_start: 0.7358 (tp) cc_final: 0.6974 (tp) REVERT: A 319 MET cc_start: 0.9204 (mtt) cc_final: 0.8933 (mtp) REVERT: A 353 ASP cc_start: 0.9099 (m-30) cc_final: 0.8834 (m-30) REVERT: A 403 GLU cc_start: 0.9043 (tp30) cc_final: 0.8555 (tp30) REVERT: A 441 GLU cc_start: 0.9172 (tp30) cc_final: 0.8868 (tp30) REVERT: A 446 LEU cc_start: 0.9437 (mt) cc_final: 0.9171 (mm) REVERT: A 630 GLU cc_start: 0.8721 (tm-30) cc_final: 0.8065 (tm-30) REVERT: A 650 LYS cc_start: 0.9241 (ttpp) cc_final: 0.8929 (tptt) REVERT: A 659 PHE cc_start: 0.9087 (OUTLIER) cc_final: 0.8450 (p90) REVERT: A 705 MET cc_start: 0.6808 (ppp) cc_final: 0.6283 (ppp) REVERT: A 752 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7336 (tp30) REVERT: A 903 ARG cc_start: 0.5883 (tpt170) cc_final: 0.5230 (mmm160) outliers start: 21 outliers final: 15 residues processed: 90 average time/residue: 0.1704 time to fit residues: 20.7237 Evaluate side-chains 93 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 76 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 335 TRP Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 511 HIS Chi-restraints excluded: chain A residue 523 GLN Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain A residue 752 GLU Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 902 ILE Chi-restraints excluded: chain A residue 906 TYR Chi-restraints excluded: chain A residue 907 VAL Chi-restraints excluded: chain A residue 908 TRP Chi-restraints excluded: chain A residue 912 TYR Chi-restraints excluded: chain A residue 932 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 34 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 chunk 70 optimal weight: 0.7980 chunk 61 optimal weight: 0.7980 chunk 6 optimal weight: 40.0000 chunk 47 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 18 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.4048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5980 Z= 0.214 Angle : 0.810 13.738 8123 Z= 0.395 Chirality : 0.046 0.189 963 Planarity : 0.005 0.068 1028 Dihedral : 5.703 39.951 816 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.78 % Allowed : 10.62 % Favored : 88.60 % Rotamer: Outliers : 2.66 % Allowed : 20.62 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -0.96 (0.31), residues: 772 helix: 0.77 (0.27), residues: 386 sheet: -1.24 (0.75), residues: 44 loop : -2.28 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 335 HIS 0.002 0.000 HIS A 749 PHE 0.013 0.001 PHE A 337 TYR 0.018 0.001 TYR A 906 ARG 0.002 0.000 ARG A 694 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 77 time to evaluate : 0.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 299 MET cc_start: 0.6096 (tmm) cc_final: 0.5818 (tmm) REVERT: A 300 ILE cc_start: 0.7284 (tp) cc_final: 0.6911 (tp) REVERT: A 319 MET cc_start: 0.9203 (mtt) cc_final: 0.8929 (mtp) REVERT: A 353 ASP cc_start: 0.9089 (m-30) cc_final: 0.8816 (m-30) REVERT: A 403 GLU cc_start: 0.9020 (tp30) cc_final: 0.8524 (tp30) REVERT: A 441 GLU cc_start: 0.9118 (tp30) cc_final: 0.8828 (tp30) REVERT: A 446 LEU cc_start: 0.9448 (mt) cc_final: 0.9181 (mm) REVERT: A 558 TRP cc_start: 0.8535 (t60) cc_final: 0.8042 (t60) REVERT: A 630 GLU cc_start: 0.8711 (tm-30) cc_final: 0.8047 (tm-30) REVERT: A 659 PHE cc_start: 0.9093 (OUTLIER) cc_final: 0.8470 (p90) REVERT: A 705 MET cc_start: 0.6909 (ppp) cc_final: 0.6381 (ppp) REVERT: A 799 MET cc_start: 0.8921 (ttp) cc_final: 0.8640 (ttm) REVERT: A 903 ARG cc_start: 0.5841 (tpt170) cc_final: 0.5205 (mmm160) outliers start: 17 outliers final: 14 residues processed: 87 average time/residue: 0.1645 time to fit residues: 19.6818 Evaluate side-chains 87 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 72 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 335 TRP Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 511 HIS Chi-restraints excluded: chain A residue 523 GLN Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 902 ILE Chi-restraints excluded: chain A residue 906 TYR Chi-restraints excluded: chain A residue 907 VAL Chi-restraints excluded: chain A residue 908 TRP Chi-restraints excluded: chain A residue 912 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 56 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 16 optimal weight: 6.9990 chunk 61 optimal weight: 0.6980 chunk 25 optimal weight: 9.9990 chunk 62 optimal weight: 0.9990 chunk 7 optimal weight: 5.9990 chunk 11 optimal weight: 0.0060 chunk 53 optimal weight: 2.9990 chunk 3 optimal weight: 20.0000 chunk 44 optimal weight: 4.9990 overall best weight: 1.3402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.120577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.080027 restraints weight = 15888.480| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 4.37 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.4064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 5980 Z= 0.273 Angle : 0.807 12.836 8123 Z= 0.397 Chirality : 0.047 0.184 963 Planarity : 0.005 0.068 1028 Dihedral : 5.736 38.783 816 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.78 % Allowed : 11.01 % Favored : 88.21 % Rotamer: Outliers : 2.19 % Allowed : 20.94 % Favored : 76.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -0.97 (0.31), residues: 772 helix: 0.76 (0.27), residues: 384 sheet: -1.67 (0.68), residues: 51 loop : -2.21 (0.35), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 335 HIS 0.002 0.000 HIS A 189 PHE 0.013 0.001 PHE A 337 TYR 0.024 0.002 TYR A 906 ARG 0.003 0.000 ARG A 758 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1719.44 seconds wall clock time: 31 minutes 21.40 seconds (1881.40 seconds total)