Starting phenix.real_space_refine on Wed Aug 5 04:38:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wru_37790/08_2026/8wru_37790.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wru_37790/08_2026/8wru_37790.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8wru_37790/08_2026/8wru_37790.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wru_37790/08_2026/8wru_37790.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wru_37790/08_2026/8wru_37790.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wru_37790/08_2026/8wru_37790.map" } resolution = 3.14 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 90 5.49 5 S 25 5.16 5 C 5133 2.51 5 N 1594 2.21 5 O 1844 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8686 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 831, 6794 Classifications: {'peptide': 831} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 29, 'TRANS': 801} Chain breaks: 4 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 1188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 1188 Classifications: {'RNA': 56} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 2, 'rna3p_pur': 21, 'rna3p_pyr': 27} Link IDs: {'rna2p': 8, 'rna3p': 47} Chain: "C" Number of atoms: 538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 538 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "D" Number of atoms: 166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 166 Classifications: {'DNA': 8} Link IDs: {'rna3p': 7} Time building chain proxies: 1.93, per 1000 atoms: 0.22 Number of scatterers: 8686 At special positions: 0 Unit cell: (91.08, 103.62, 111.54, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 25 16.00 P 90 15.00 O 1844 8.00 N 1594 7.00 C 5133 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.63 Conformation dependent library (CDL) restraints added in 165.8 milliseconds 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1568 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 8 sheets defined 48.7% alpha, 16.8% beta 25 base pairs and 57 stacking pairs defined. Time for finding SS restraints: 1.24 Creating SS restraints... Processing helix chain 'A' and resid 15 through 41 Processing helix chain 'A' and resid 57 through 69 Processing helix chain 'A' and resid 77 through 88 Processing helix chain 'A' and resid 100 through 103 Processing helix chain 'A' and resid 104 through 110 removed outlier: 3.665A pdb=" N LEU A 110 " --> pdb=" O SER A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 136 removed outlier: 3.793A pdb=" N GLU A 134 " --> pdb=" O LYS A 130 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU A 135 " --> pdb=" O ALA A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 150 removed outlier: 3.798A pdb=" N ALA A 143 " --> pdb=" O ASP A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 171 removed outlier: 3.611A pdb=" N ARG A 167 " --> pdb=" O GLU A 163 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA A 171 " --> pdb=" O ARG A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 185 Processing helix chain 'A' and resid 187 through 199 Processing helix chain 'A' and resid 211 through 253 Processing helix chain 'A' and resid 256 through 259 removed outlier: 3.634A pdb=" N TYR A 259 " --> pdb=" O PRO A 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 256 through 259' Processing helix chain 'A' and resid 260 through 273 removed outlier: 4.451A pdb=" N LYS A 264 " --> pdb=" O ALA A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 331 removed outlier: 3.551A pdb=" N ARG A 331 " --> pdb=" O LYS A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 459 removed outlier: 3.531A pdb=" N LYS A 451 " --> pdb=" O SER A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 552 removed outlier: 3.574A pdb=" N HIS A 526 " --> pdb=" O SER A 522 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER A 533 " --> pdb=" O MET A 529 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA A 540 " --> pdb=" O CYS A 536 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG A 541 " --> pdb=" O PHE A 537 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LYS A 548 " --> pdb=" O ARG A 544 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG A 550 " --> pdb=" O SER A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 565 Processing helix chain 'A' and resid 567 through 572 Processing helix chain 'A' and resid 579 through 606 removed outlier: 3.699A pdb=" N ARG A 583 " --> pdb=" O ALA A 579 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ARG A 584 " --> pdb=" O ASP A 580 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR A 585 " --> pdb=" O GLU A 581 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N THR A 589 " --> pdb=" O THR A 585 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ARG A 599 " --> pdb=" O GLN A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 614 removed outlier: 3.964A pdb=" N ASP A 614 " --> pdb=" O SER A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 642 removed outlier: 3.650A pdb=" N LEU A 627 " --> pdb=" O TYR A 623 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG A 642 " --> pdb=" O LYS A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 689 removed outlier: 3.689A pdb=" N HIS A 689 " --> pdb=" O THR A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 736 Processing helix chain 'A' and resid 782 through 796 Processing helix chain 'A' and resid 820 through 831 removed outlier: 3.527A pdb=" N GLU A 828 " --> pdb=" O ARG A 824 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN A 830 " --> pdb=" O TYR A 826 " (cutoff:3.500A) Processing helix chain 'A' and resid 881 through 899 removed outlier: 3.583A pdb=" N GLN A 894 " --> pdb=" O GLU A 890 " (cutoff:3.500A) Processing helix chain 'A' and resid 900 through 903 Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 10 removed outlier: 3.627A pdb=" N SER A 7 " --> pdb=" O ILE A 437 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ASP A 438 " --> pdb=" O GLU A 423 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N GLU A 423 " --> pdb=" O ASP A 438 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N ASN A 440 " --> pdb=" O VAL A 421 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N VAL A 421 " --> pdb=" O ASN A 440 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 4 through 10 removed outlier: 3.627A pdb=" N SER A 7 " --> pdb=" O ILE A 437 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ASP A 438 " --> pdb=" O GLU A 423 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N GLU A 423 " --> pdb=" O ASP A 438 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N ASN A 440 " --> pdb=" O VAL A 421 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N VAL A 421 " --> pdb=" O ASN A 440 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N THR A 408 " --> pdb=" O ASN A 392 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N ASN A 392 " --> pdb=" O THR A 408 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 56 removed outlier: 3.925A pdb=" N TYR A 44 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N SER A 45 " --> pdb=" O VAL A 337 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 363 through 365 Processing sheet with id=AA5, first strand: chain 'A' and resid 511 through 517 removed outlier: 7.128A pdb=" N PHE A 511 " --> pdb=" O THR A 491 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N THR A 491 " --> pdb=" O PHE A 511 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N SER A 513 " --> pdb=" O VAL A 489 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N PHE A 485 " --> pdb=" O ARG A 517 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU A 697 " --> pdb=" O ILE A 477 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N LEU A 479 " --> pdb=" O GLU A 697 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N VAL A 694 " --> pdb=" O TRP A 741 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N VAL A 743 " --> pdb=" O VAL A 694 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N MET A 696 " --> pdb=" O VAL A 743 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 501 through 503 removed outlier: 4.126A pdb=" N VAL A 503 " --> pdb=" O GLU A 507 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N GLU A 507 " --> pdb=" O VAL A 503 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 760 through 761 Processing sheet with id=AA8, first strand: chain 'A' and resid 846 through 848 354 hydrogen bonds defined for protein. 1011 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 59 hydrogen bonds 108 hydrogen bond angles 0 basepair planarities 25 basepair parallelities 57 stacking parallelities Total time for adding SS restraints: 2.27 Time building geometry restraints manager: 0.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2023 1.33 - 1.45: 2312 1.45 - 1.57: 4492 1.57 - 1.69: 177 1.69 - 1.81: 39 Bond restraints: 9043 Sorted by residual: bond pdb=" C TYR A 643 " pdb=" N HIS A 644 " ideal model delta sigma weight residual 1.334 1.285 0.049 1.49e-02 4.50e+03 1.08e+01 bond pdb=" C3' DG C -7 " pdb=" C2' DG C -7 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.05e+00 bond pdb=" C3' DT C 5 " pdb=" C2' DT C 5 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.79e+00 bond pdb=" CA GLU A 659 " pdb=" CB GLU A 659 " ideal model delta sigma weight residual 1.527 1.491 0.036 1.38e-02 5.25e+03 6.82e+00 bond pdb=" C3' DG C 7 " pdb=" C2' DG C 7 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 6.67e+00 ... (remaining 9038 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.24: 12284 2.24 - 4.47: 298 4.47 - 6.71: 17 6.71 - 8.95: 5 8.95 - 11.19: 2 Bond angle restraints: 12606 Sorted by residual: angle pdb=" N TYR A 4 " pdb=" CA TYR A 4 " pdb=" C TYR A 4 " ideal model delta sigma weight residual 108.69 118.92 -10.23 1.77e+00 3.19e-01 3.34e+01 angle pdb=" O4' DA C -2 " pdb=" C4' DA C -2 " pdb=" C3' DA C -2 " ideal model delta sigma weight residual 106.00 103.20 2.80 6.00e-01 2.78e+00 2.18e+01 angle pdb=" O5' G B -20 " pdb=" C5' G B -20 " pdb=" C4' G B -20 " ideal model delta sigma weight residual 109.40 112.81 -3.41 8.00e-01 1.56e+00 1.81e+01 angle pdb=" N3 DT C 3 " pdb=" C4 DT C 3 " pdb=" O4 DT C 3 " ideal model delta sigma weight residual 119.90 122.41 -2.51 6.00e-01 2.78e+00 1.75e+01 angle pdb=" N3 DT D 5 " pdb=" C4 DT D 5 " pdb=" O4 DT D 5 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.72e+01 ... (remaining 12601 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.00: 5124 35.00 - 69.99: 307 69.99 - 104.99: 29 104.99 - 139.99: 2 139.99 - 174.98: 1 Dihedral angle restraints: 5463 sinusoidal: 3038 harmonic: 2425 Sorted by residual: dihedral pdb=" O4' U B -32 " pdb=" C1' U B -32 " pdb=" N1 U B -32 " pdb=" C2 U B -32 " ideal model delta sinusoidal sigma weight residual -128.00 46.98 -174.98 1 1.70e+01 3.46e-03 6.63e+01 dihedral pdb=" O4' A B -21 " pdb=" C1' A B -21 " pdb=" N9 A B -21 " pdb=" C4 A B -21 " ideal model delta sinusoidal sigma weight residual 70.00 -2.73 72.73 1 2.00e+01 2.50e-03 1.69e+01 dihedral pdb=" CA GLU A 559 " pdb=" C GLU A 559 " pdb=" N ALA A 560 " pdb=" CA ALA A 560 " ideal model delta harmonic sigma weight residual -180.00 -162.11 -17.89 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 5460 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 1285 0.091 - 0.181: 114 0.181 - 0.272: 5 0.272 - 0.362: 1 0.362 - 0.453: 1 Chirality restraints: 1406 Sorted by residual: chirality pdb=" CA GLU A 659 " pdb=" N GLU A 659 " pdb=" C GLU A 659 " pdb=" CB GLU A 659 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.13e+00 chirality pdb=" CA HIS A 747 " pdb=" N HIS A 747 " pdb=" C HIS A 747 " pdb=" CB HIS A 747 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" CA TRP A 645 " pdb=" N TRP A 645 " pdb=" C TRP A 645 " pdb=" CB TRP A 645 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.51e+00 ... (remaining 1403 not shown) Planarity restraints: 1311 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR A 643 " -0.013 2.00e-02 2.50e+03 2.66e-02 7.06e+00 pdb=" C TYR A 643 " 0.046 2.00e-02 2.50e+03 pdb=" O TYR A 643 " -0.017 2.00e-02 2.50e+03 pdb=" N HIS A 644 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 487 " -0.009 2.00e-02 2.50e+03 1.09e-02 2.06e+00 pdb=" CG PHE A 487 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 PHE A 487 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE A 487 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE A 487 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 487 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 487 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 903 " -0.023 5.00e-02 4.00e+02 3.45e-02 1.91e+00 pdb=" N PRO A 904 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO A 904 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 904 " -0.019 5.00e-02 4.00e+02 ... (remaining 1308 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 998 2.74 - 3.28: 8256 3.28 - 3.82: 15135 3.82 - 4.36: 18189 4.36 - 4.90: 28557 Nonbonded interactions: 71135 Sorted by model distance: nonbonded pdb=" OG1 THR A 338 " pdb=" OP1 A B 5 " model vdw 2.204 3.040 nonbonded pdb=" O LEU A 146 " pdb=" OG1 THR A 150 " model vdw 2.205 3.040 nonbonded pdb=" NZ LYS A 591 " pdb=" OP1 G B -17 " model vdw 2.216 3.120 nonbonded pdb=" OD1 ASP A 164 " pdb=" NH2 ARG A 167 " model vdw 2.251 3.120 nonbonded pdb=" OE2 GLU A 463 " pdb=" NE2 GLN A 821 " model vdw 2.256 3.120 ... (remaining 71130 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: 5.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 10.520 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 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:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 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 : 0.005 0.049 9043 Z= 0.332 Angle : 0.747 11.186 12606 Z= 0.515 Chirality : 0.052 0.453 1406 Planarity : 0.004 0.035 1311 Dihedral : 19.201 174.985 3895 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 0.56 % Allowed : 1.12 % Favored : 98.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.29), residues: 821 helix: 0.18 (0.26), residues: 378 sheet: -1.28 (0.43), residues: 136 loop : -1.88 (0.35), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 561 TYR 0.019 0.002 TYR A 798 PHE 0.025 0.002 PHE A 487 TRP 0.016 0.002 TRP A 720 HIS 0.010 0.002 HIS A 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.33 ( 9043) covalent geometry : angle 0.74712 / 0.51 (12606) hydrogen bonds : bond 0.24449 / 16.47 ( 402) hydrogen bonds : angle 8.35854 / 6.13 ( 1119) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 214 time to evaluate : 0.179 Fit side-chains REVERT: A 79 ASP cc_start: 0.7135 (m-30) cc_final: 0.6912 (m-30) REVERT: A 99 LEU cc_start: 0.7770 (tt) cc_final: 0.7320 (tt) REVERT: A 391 TRP cc_start: 0.7462 (t-100) cc_final: 0.6127 (t-100) REVERT: A 564 GLU cc_start: 0.7281 (tp30) cc_final: 0.7033 (tp30) REVERT: A 568 ILE cc_start: 0.8275 (mm) cc_final: 0.8041 (mt) REVERT: A 613 ARG cc_start: 0.7557 (ttm110) cc_final: 0.7245 (ttm110) REVERT: A 688 GLU cc_start: 0.7114 (tm-30) cc_final: 0.6778 (tm-30) REVERT: A 697 GLU cc_start: 0.6096 (pt0) cc_final: 0.5857 (pt0) REVERT: A 760 TYR cc_start: 0.6908 (t80) cc_final: 0.6194 (t80) REVERT: A 783 ASP cc_start: 0.6897 (m-30) cc_final: 0.6593 (m-30) REVERT: A 823 GLU cc_start: 0.7940 (mt-10) cc_final: 0.7035 (tt0) outliers start: 4 outliers final: 2 residues processed: 218 average time/residue: 0.1116 time to fit residues: 30.5565 Evaluate side-chains 203 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 201 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 615 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.0470 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 overall best weight: 0.8682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 641 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.150995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.127074 restraints weight = 12820.797| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 1.74 r_work: 0.3423 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.1391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9043 Z= 0.214 Angle : 0.667 9.069 12606 Z= 0.363 Chirality : 0.045 0.171 1406 Planarity : 0.005 0.052 1311 Dihedral : 21.075 179.526 2196 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 1.53 % Allowed : 9.62 % Favored : 88.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.30), residues: 821 helix: 0.92 (0.27), residues: 385 sheet: -1.06 (0.43), residues: 138 loop : -1.66 (0.37), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 642 TYR 0.022 0.002 TYR A 4 PHE 0.021 0.002 PHE A 435 TRP 0.018 0.002 TRP A 645 HIS 0.008 0.002 HIS A 526 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.21 ( 9043) covalent geometry : angle 0.66702 / 0.36 (12606) hydrogen bonds : bond 0.07161 / 4.95 ( 402) hydrogen bonds : angle 4.85292 / 3.57 ( 1119) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 220 time to evaluate : 0.173 Fit side-chains REVERT: A 55 GLU cc_start: 0.7307 (mm-30) cc_final: 0.7091 (mm-30) REVERT: A 99 LEU cc_start: 0.8093 (tt) cc_final: 0.7726 (tt) REVERT: A 100 GLU cc_start: 0.7960 (mm-30) cc_final: 0.7161 (mm-30) REVERT: A 230 LEU cc_start: 0.8401 (tp) cc_final: 0.8102 (tp) REVERT: A 235 ARG cc_start: 0.7758 (ttp-170) cc_final: 0.7144 (ttp-170) REVERT: A 391 TRP cc_start: 0.7887 (t-100) cc_final: 0.6407 (t-100) REVERT: A 463 GLU cc_start: 0.7682 (mm-30) cc_final: 0.7469 (mm-30) REVERT: A 538 TYR cc_start: 0.8162 (m-80) cc_final: 0.7684 (m-80) REVERT: A 559 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.7452 (pp20) REVERT: A 564 GLU cc_start: 0.8137 (tp30) cc_final: 0.7915 (tp30) REVERT: A 613 ARG cc_start: 0.7770 (ttm110) cc_final: 0.7529 (ttm110) REVERT: A 650 ARG cc_start: 0.7605 (mtp85) cc_final: 0.7191 (mtp180) REVERT: A 760 TYR cc_start: 0.7143 (t80) cc_final: 0.6581 (t80) REVERT: A 783 ASP cc_start: 0.7344 (m-30) cc_final: 0.7110 (m-30) REVERT: A 823 GLU cc_start: 0.8313 (mt-10) cc_final: 0.7691 (mt-10) REVERT: A 882 GLU cc_start: 0.7217 (mp0) cc_final: 0.6906 (mp0) outliers start: 11 outliers final: 6 residues processed: 224 average time/residue: 0.1015 time to fit residues: 29.2457 Evaluate side-chains 216 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 209 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 167 ARG Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 559 GLU Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 886 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 13 optimal weight: 5.9990 chunk 24 optimal weight: 0.0980 chunk 77 optimal weight: 2.9990 chunk 65 optimal weight: 0.0040 chunk 71 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 73 optimal weight: 0.7980 chunk 56 optimal weight: 0.0060 chunk 33 optimal weight: 0.5980 overall best weight: 0.2808 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 735 ASN A 894 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.152813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.128932 restraints weight = 12784.513| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 1.73 r_work: 0.3427 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3275 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9043 Z= 0.133 Angle : 0.567 9.601 12606 Z= 0.311 Chirality : 0.039 0.163 1406 Planarity : 0.004 0.057 1311 Dihedral : 20.964 175.390 2192 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 3.35 % Allowed : 11.99 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.31), residues: 821 helix: 1.44 (0.27), residues: 382 sheet: -1.09 (0.42), residues: 138 loop : -1.39 (0.38), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.000 ARG A 582 TYR 0.011 0.001 TYR A 22 PHE 0.015 0.001 PHE A 262 TRP 0.011 0.001 TRP A 328 HIS 0.006 0.001 HIS A 526 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.13 ( 9043) covalent geometry : angle 0.56663 / 0.31 (12606) hydrogen bonds : bond 0.06188 / 4.39 ( 402) hydrogen bonds : angle 4.43268 / 3.25 ( 1119) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 214 time to evaluate : 0.210 Fit side-chains REVERT: A 55 GLU cc_start: 0.7274 (mm-30) cc_final: 0.7008 (mm-30) REVERT: A 99 LEU cc_start: 0.8010 (tt) cc_final: 0.7330 (tt) REVERT: A 100 GLU cc_start: 0.8096 (mm-30) cc_final: 0.7173 (mm-30) REVERT: A 230 LEU cc_start: 0.8349 (tp) cc_final: 0.8126 (tp) REVERT: A 391 TRP cc_start: 0.7829 (t-100) cc_final: 0.6306 (t-100) REVERT: A 463 GLU cc_start: 0.7609 (mm-30) cc_final: 0.7337 (mm-30) REVERT: A 559 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.7377 (pt0) REVERT: A 564 GLU cc_start: 0.8141 (tp30) cc_final: 0.7897 (tp30) REVERT: A 578 ASP cc_start: 0.7746 (t0) cc_final: 0.7488 (t0) REVERT: A 608 TYR cc_start: 0.7641 (m-10) cc_final: 0.7390 (m-10) REVERT: A 618 LEU cc_start: 0.7787 (OUTLIER) cc_final: 0.7453 (tt) REVERT: A 760 TYR cc_start: 0.7124 (t80) cc_final: 0.6462 (t80) REVERT: A 783 ASP cc_start: 0.7392 (m-30) cc_final: 0.7109 (m-30) REVERT: A 823 GLU cc_start: 0.8318 (mt-10) cc_final: 0.7427 (tt0) REVERT: A 882 GLU cc_start: 0.7144 (mp0) cc_final: 0.6830 (mp0) outliers start: 24 outliers final: 10 residues processed: 219 average time/residue: 0.1197 time to fit residues: 32.8790 Evaluate side-chains 222 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 210 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 167 ARG Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 559 GLU Chi-restraints excluded: chain A residue 618 LEU Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 820 ARG Chi-restraints excluded: chain A residue 886 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 12 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 87 optimal weight: 7.9990 chunk 16 optimal weight: 6.9990 chunk 7 optimal weight: 3.9990 chunk 26 optimal weight: 9.9990 chunk 4 optimal weight: 0.0980 chunk 22 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 60 optimal weight: 0.7980 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 575 HIS A 731 GLN A 735 ASN A 894 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.151315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.127437 restraints weight = 12923.681| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 1.73 r_work: 0.3425 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9043 Z= 0.185 Angle : 0.587 8.672 12606 Z= 0.322 Chirality : 0.041 0.183 1406 Planarity : 0.004 0.038 1311 Dihedral : 21.007 179.118 2192 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 3.21 % Allowed : 14.09 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.31), residues: 821 helix: 1.43 (0.27), residues: 387 sheet: -1.05 (0.43), residues: 138 loop : -1.43 (0.38), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 701 TYR 0.020 0.002 TYR A 605 PHE 0.031 0.002 PHE A 31 TRP 0.009 0.001 TRP A 741 HIS 0.007 0.002 HIS A 874 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.19 ( 9043) covalent geometry : angle 0.58679 / 0.32 (12606) hydrogen bonds : bond 0.05880 / 4.16 ( 402) hydrogen bonds : angle 4.29918 / 3.16 ( 1119) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 206 time to evaluate : 0.165 Fit side-chains REVERT: A 55 GLU cc_start: 0.7319 (mm-30) cc_final: 0.7086 (mm-30) REVERT: A 100 GLU cc_start: 0.8135 (mm-30) cc_final: 0.7257 (mm-30) REVERT: A 230 LEU cc_start: 0.8327 (tp) cc_final: 0.8093 (tp) REVERT: A 391 TRP cc_start: 0.7879 (t-100) cc_final: 0.6344 (t-100) REVERT: A 559 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7512 (pt0) REVERT: A 564 GLU cc_start: 0.8152 (tp30) cc_final: 0.7913 (tp30) REVERT: A 578 ASP cc_start: 0.7778 (t0) cc_final: 0.7569 (t0) REVERT: A 613 ARG cc_start: 0.7619 (ttm-80) cc_final: 0.7240 (ttm110) REVERT: A 618 LEU cc_start: 0.7812 (OUTLIER) cc_final: 0.7487 (tt) REVERT: A 688 GLU cc_start: 0.7773 (tm-30) cc_final: 0.7271 (tm-30) REVERT: A 760 TYR cc_start: 0.7148 (t80) cc_final: 0.6429 (t80) REVERT: A 783 ASP cc_start: 0.7358 (m-30) cc_final: 0.7056 (m-30) REVERT: A 823 GLU cc_start: 0.8360 (mt-10) cc_final: 0.7483 (tt0) REVERT: A 882 GLU cc_start: 0.7310 (mp0) cc_final: 0.6985 (mp0) outliers start: 23 outliers final: 15 residues processed: 214 average time/residue: 0.1150 time to fit residues: 30.8287 Evaluate side-chains 219 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 202 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 167 ARG Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 559 GLU Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 618 LEU Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 807 SER Chi-restraints excluded: chain A residue 820 ARG Chi-restraints excluded: chain A residue 886 GLU Chi-restraints excluded: chain A residue 896 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 89 optimal weight: 4.9990 chunk 70 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 72 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 chunk 71 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 60 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 575 HIS A 735 ASN A 894 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.151228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.127374 restraints weight = 12796.758| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 1.72 r_work: 0.3424 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3269 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9043 Z= 0.172 Angle : 0.570 10.072 12606 Z= 0.313 Chirality : 0.040 0.156 1406 Planarity : 0.004 0.054 1311 Dihedral : 21.032 177.134 2192 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 4.18 % Allowed : 14.78 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.31), residues: 821 helix: 1.48 (0.27), residues: 387 sheet: -1.09 (0.42), residues: 140 loop : -1.40 (0.39), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 465 TYR 0.017 0.002 TYR A 605 PHE 0.028 0.002 PHE A 31 TRP 0.008 0.001 TRP A 328 HIS 0.006 0.001 HIS A 747 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.17 ( 9043) covalent geometry : angle 0.56962 / 0.31 (12606) hydrogen bonds : bond 0.05623 / 4.01 ( 402) hydrogen bonds : angle 4.22668 / 3.10 ( 1119) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 202 time to evaluate : 0.288 Fit side-chains REVERT: A 55 GLU cc_start: 0.7311 (mm-30) cc_final: 0.7068 (mm-30) REVERT: A 230 LEU cc_start: 0.8331 (tp) cc_final: 0.8089 (tp) REVERT: A 391 TRP cc_start: 0.7889 (t-100) cc_final: 0.6338 (t-100) REVERT: A 410 ARG cc_start: 0.7701 (mtm-85) cc_final: 0.6921 (mtm180) REVERT: A 559 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7550 (pt0) REVERT: A 564 GLU cc_start: 0.8157 (tp30) cc_final: 0.7903 (tp30) REVERT: A 578 ASP cc_start: 0.7805 (t0) cc_final: 0.7583 (t0) REVERT: A 618 LEU cc_start: 0.7816 (OUTLIER) cc_final: 0.7516 (tp) REVERT: A 760 TYR cc_start: 0.7121 (t80) cc_final: 0.6395 (t80) REVERT: A 783 ASP cc_start: 0.7314 (m-30) cc_final: 0.7084 (m-30) REVERT: A 823 GLU cc_start: 0.8340 (mt-10) cc_final: 0.7522 (tt0) REVERT: A 882 GLU cc_start: 0.7351 (mp0) cc_final: 0.7022 (mp0) outliers start: 30 outliers final: 17 residues processed: 213 average time/residue: 0.1195 time to fit residues: 32.0837 Evaluate side-chains 217 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 198 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 167 ARG Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 559 GLU Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 618 LEU Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 807 SER Chi-restraints excluded: chain A residue 820 ARG Chi-restraints excluded: chain A residue 883 LYS Chi-restraints excluded: chain A residue 886 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 87 optimal weight: 7.9990 chunk 6 optimal weight: 0.7980 chunk 72 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 53 optimal weight: 0.6980 chunk 14 optimal weight: 0.7980 chunk 16 optimal weight: 0.0010 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 575 HIS A 894 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.151782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.127961 restraints weight = 12793.391| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 1.73 r_work: 0.3431 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3278 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9043 Z= 0.153 Angle : 0.557 9.648 12606 Z= 0.305 Chirality : 0.039 0.146 1406 Planarity : 0.004 0.048 1311 Dihedral : 21.027 177.206 2192 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 4.46 % Allowed : 15.76 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.31), residues: 821 helix: 1.55 (0.27), residues: 387 sheet: -1.09 (0.42), residues: 140 loop : -1.33 (0.39), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 12 TYR 0.014 0.001 TYR A 605 PHE 0.024 0.002 PHE A 31 TRP 0.008 0.001 TRP A 645 HIS 0.006 0.001 HIS A 747 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.15 ( 9043) covalent geometry : angle 0.55733 / 0.31 (12606) hydrogen bonds : bond 0.05415 / 3.89 ( 402) hydrogen bonds : angle 4.12822 / 3.03 ( 1119) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 204 time to evaluate : 0.192 Fit side-chains REVERT: A 26 HIS cc_start: 0.8139 (OUTLIER) cc_final: 0.7931 (m90) REVERT: A 55 GLU cc_start: 0.7292 (mm-30) cc_final: 0.7044 (mm-30) REVERT: A 230 LEU cc_start: 0.8336 (tp) cc_final: 0.8089 (tp) REVERT: A 391 TRP cc_start: 0.7893 (t-100) cc_final: 0.6318 (t-100) REVERT: A 410 ARG cc_start: 0.7687 (mtm-85) cc_final: 0.6922 (mtm180) REVERT: A 434 TYR cc_start: 0.8021 (m-80) cc_final: 0.7579 (m-80) REVERT: A 564 GLU cc_start: 0.8146 (tp30) cc_final: 0.7888 (tp30) REVERT: A 578 ASP cc_start: 0.7840 (t0) cc_final: 0.7622 (t0) REVERT: A 613 ARG cc_start: 0.7589 (ttm-80) cc_final: 0.7250 (ttm110) REVERT: A 618 LEU cc_start: 0.7805 (OUTLIER) cc_final: 0.7494 (tp) REVERT: A 760 TYR cc_start: 0.7116 (t80) cc_final: 0.6393 (t80) REVERT: A 823 GLU cc_start: 0.8347 (mt-10) cc_final: 0.7520 (tt0) REVERT: A 869 GLU cc_start: 0.6913 (mp0) cc_final: 0.6580 (mp0) REVERT: A 882 GLU cc_start: 0.7330 (mp0) cc_final: 0.7011 (mp0) outliers start: 32 outliers final: 21 residues processed: 215 average time/residue: 0.1044 time to fit residues: 28.4042 Evaluate side-chains 222 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 199 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 16 GLU Chi-restraints excluded: chain A residue 26 HIS Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 167 ARG Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 618 LEU Chi-restraints excluded: chain A residue 724 MET Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 820 ARG Chi-restraints excluded: chain A residue 883 LYS Chi-restraints excluded: chain A residue 886 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 57 optimal weight: 0.5980 chunk 76 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 75 optimal weight: 0.5980 chunk 4 optimal weight: 0.1980 chunk 56 optimal weight: 0.8980 chunk 89 optimal weight: 4.9990 chunk 28 optimal weight: 0.2980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 92 ASN A 575 HIS A 894 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.152354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.128473 restraints weight = 12849.128| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 1.73 r_work: 0.3436 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9043 Z= 0.142 Angle : 0.545 8.888 12606 Z= 0.299 Chirality : 0.039 0.148 1406 Planarity : 0.004 0.049 1311 Dihedral : 21.002 176.990 2192 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 4.74 % Allowed : 15.76 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.31), residues: 821 helix: 1.61 (0.27), residues: 387 sheet: -1.02 (0.43), residues: 138 loop : -1.29 (0.39), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 465 TYR 0.013 0.001 TYR A 605 PHE 0.021 0.001 PHE A 31 TRP 0.009 0.001 TRP A 645 HIS 0.005 0.001 HIS A 747 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.14 ( 9043) covalent geometry : angle 0.54476 / 0.30 (12606) hydrogen bonds : bond 0.05286 / 3.81 ( 402) hydrogen bonds : angle 4.06841 / 2.99 ( 1119) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 195 time to evaluate : 0.184 Fit side-chains REVERT: A 55 GLU cc_start: 0.7297 (mm-30) cc_final: 0.7029 (mm-30) REVERT: A 230 LEU cc_start: 0.8335 (tp) cc_final: 0.8094 (tp) REVERT: A 391 TRP cc_start: 0.7901 (t-100) cc_final: 0.6314 (t-100) REVERT: A 410 ARG cc_start: 0.7675 (mtm-85) cc_final: 0.6867 (mtm180) REVERT: A 434 TYR cc_start: 0.8023 (m-80) cc_final: 0.7595 (m-80) REVERT: A 564 GLU cc_start: 0.8142 (tp30) cc_final: 0.7847 (tp30) REVERT: A 578 ASP cc_start: 0.7862 (t0) cc_final: 0.7644 (t0) REVERT: A 613 ARG cc_start: 0.7584 (ttm-80) cc_final: 0.7278 (ttm110) REVERT: A 618 LEU cc_start: 0.7803 (OUTLIER) cc_final: 0.7495 (tt) REVERT: A 760 TYR cc_start: 0.7114 (t80) cc_final: 0.6377 (t80) REVERT: A 817 ASN cc_start: 0.7743 (t0) cc_final: 0.7515 (t0) REVERT: A 823 GLU cc_start: 0.8350 (mt-10) cc_final: 0.7565 (tt0) REVERT: A 882 GLU cc_start: 0.7389 (mp0) cc_final: 0.7067 (mp0) outliers start: 34 outliers final: 24 residues processed: 209 average time/residue: 0.1109 time to fit residues: 29.4554 Evaluate side-chains 219 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 194 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 16 GLU Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain A residue 167 ARG Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 618 LEU Chi-restraints excluded: chain A residue 697 GLU Chi-restraints excluded: chain A residue 724 MET Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 807 SER Chi-restraints excluded: chain A residue 820 ARG Chi-restraints excluded: chain A residue 883 LYS Chi-restraints excluded: chain A residue 886 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 67 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 87 optimal weight: 6.9990 chunk 22 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 chunk 63 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 72 optimal weight: 0.5980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 26 HIS A 575 HIS A 894 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.150351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.126390 restraints weight = 12668.367| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 1.72 r_work: 0.3409 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 9043 Z= 0.243 Angle : 0.607 8.919 12606 Z= 0.332 Chirality : 0.043 0.160 1406 Planarity : 0.004 0.051 1311 Dihedral : 21.074 178.776 2192 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 3.91 % Allowed : 17.02 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.30), residues: 821 helix: 1.41 (0.27), residues: 387 sheet: -1.18 (0.44), residues: 132 loop : -1.41 (0.37), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 465 TYR 0.026 0.002 TYR A 605 PHE 0.019 0.002 PHE A 31 TRP 0.011 0.002 TRP A 645 HIS 0.007 0.002 HIS A 874 Details of bonding type rmsd/Z covalent geometry : bond 0.00510 / 0.24 ( 9043) covalent geometry : angle 0.60671 / 0.33 (12606) hydrogen bonds : bond 0.05663 / 4.04 ( 402) hydrogen bonds : angle 4.16835 / 3.06 ( 1119) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 207 time to evaluate : 0.184 Fit side-chains REVERT: A 55 GLU cc_start: 0.7346 (mm-30) cc_final: 0.7089 (mm-30) REVERT: A 213 ASP cc_start: 0.7556 (m-30) cc_final: 0.7116 (m-30) REVERT: A 230 LEU cc_start: 0.8356 (tp) cc_final: 0.8132 (tp) REVERT: A 410 ARG cc_start: 0.7690 (mtm-85) cc_final: 0.6873 (mtm180) REVERT: A 524 LYS cc_start: 0.8235 (tttt) cc_final: 0.7970 (ttpt) REVERT: A 528 GLU cc_start: 0.7424 (mt-10) cc_final: 0.7094 (mt-10) REVERT: A 564 GLU cc_start: 0.8154 (tp30) cc_final: 0.7888 (tp30) REVERT: A 578 ASP cc_start: 0.7844 (t0) cc_final: 0.7637 (t0) REVERT: A 599 ARG cc_start: 0.8050 (ttp80) cc_final: 0.7721 (ptm-80) REVERT: A 618 LEU cc_start: 0.7799 (OUTLIER) cc_final: 0.7497 (tt) REVERT: A 760 TYR cc_start: 0.7124 (t80) cc_final: 0.6394 (t80) REVERT: A 817 ASN cc_start: 0.7782 (t0) cc_final: 0.7560 (t0) REVERT: A 823 GLU cc_start: 0.8375 (mt-10) cc_final: 0.7550 (tt0) REVERT: A 882 GLU cc_start: 0.7392 (mp0) cc_final: 0.7078 (mp0) outliers start: 28 outliers final: 20 residues processed: 216 average time/residue: 0.1100 time to fit residues: 30.3152 Evaluate side-chains 226 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 205 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 167 ARG Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 618 LEU Chi-restraints excluded: chain A residue 697 GLU Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 807 SER Chi-restraints excluded: chain A residue 883 LYS Chi-restraints excluded: chain A residue 886 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 19 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 88 optimal weight: 10.0000 chunk 43 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 chunk 40 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 26 HIS A 575 HIS A 894 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.151111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.127214 restraints weight = 12679.697| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 1.71 r_work: 0.3417 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3266 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9043 Z= 0.190 Angle : 0.586 8.801 12606 Z= 0.321 Chirality : 0.041 0.161 1406 Planarity : 0.004 0.049 1311 Dihedral : 21.098 177.277 2192 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 3.35 % Allowed : 18.41 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.00 (0.31), residues: 821 helix: 1.42 (0.27), residues: 387 sheet: -1.07 (0.43), residues: 138 loop : -1.34 (0.38), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 465 TYR 0.019 0.002 TYR A 605 PHE 0.020 0.002 PHE A 31 TRP 0.012 0.001 TRP A 645 HIS 0.007 0.001 HIS A 874 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.19 ( 9043) covalent geometry : angle 0.58614 / 0.32 (12606) hydrogen bonds : bond 0.05434 / 3.90 ( 402) hydrogen bonds : angle 4.16317 / 3.05 ( 1119) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 198 time to evaluate : 0.188 Fit side-chains REVERT: A 55 GLU cc_start: 0.7316 (mm-30) cc_final: 0.7056 (mm-30) REVERT: A 213 ASP cc_start: 0.7546 (m-30) cc_final: 0.7101 (m-30) REVERT: A 230 LEU cc_start: 0.8363 (tp) cc_final: 0.8128 (tp) REVERT: A 410 ARG cc_start: 0.7669 (mtm-85) cc_final: 0.6833 (mtm180) REVERT: A 524 LYS cc_start: 0.8265 (tttt) cc_final: 0.7987 (ttpt) REVERT: A 564 GLU cc_start: 0.8129 (tp30) cc_final: 0.7870 (tp30) REVERT: A 599 ARG cc_start: 0.8035 (ttp80) cc_final: 0.7666 (ptm-80) REVERT: A 618 LEU cc_start: 0.7792 (OUTLIER) cc_final: 0.7492 (tt) REVERT: A 688 GLU cc_start: 0.7824 (tm-30) cc_final: 0.7308 (tm-30) REVERT: A 739 LEU cc_start: 0.8024 (mt) cc_final: 0.7716 (mt) REVERT: A 760 TYR cc_start: 0.7117 (t80) cc_final: 0.6379 (t80) REVERT: A 817 ASN cc_start: 0.7771 (t0) cc_final: 0.7557 (t0) REVERT: A 823 GLU cc_start: 0.8362 (mt-10) cc_final: 0.7558 (tt0) REVERT: A 882 GLU cc_start: 0.7335 (mp0) cc_final: 0.7015 (mp0) outliers start: 24 outliers final: 21 residues processed: 207 average time/residue: 0.1145 time to fit residues: 29.7884 Evaluate side-chains 217 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 195 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 167 ARG Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 618 LEU Chi-restraints excluded: chain A residue 697 GLU Chi-restraints excluded: chain A residue 762 SER Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 807 SER Chi-restraints excluded: chain A residue 883 LYS Chi-restraints excluded: chain A residue 886 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 73 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 48 optimal weight: 0.3980 chunk 33 optimal weight: 0.5980 chunk 5 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 76 optimal weight: 0.9990 chunk 16 optimal weight: 5.9990 chunk 18 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 26 HIS A 575 HIS A 894 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.151614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.127721 restraints weight = 12677.349| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 1.71 r_work: 0.3421 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9043 Z= 0.170 Angle : 0.574 8.565 12606 Z= 0.314 Chirality : 0.040 0.160 1406 Planarity : 0.004 0.047 1311 Dihedral : 21.082 177.175 2192 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 3.35 % Allowed : 18.27 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.31), residues: 821 helix: 1.50 (0.27), residues: 387 sheet: -1.08 (0.43), residues: 138 loop : -1.33 (0.38), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 12 TYR 0.017 0.002 TYR A 605 PHE 0.020 0.002 PHE A 31 TRP 0.012 0.001 TRP A 645 HIS 0.006 0.001 HIS A 874 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.17 ( 9043) covalent geometry : angle 0.57360 / 0.31 (12606) hydrogen bonds : bond 0.05336 / 3.84 ( 402) hydrogen bonds : angle 4.13833 / 3.04 ( 1119) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 198 time to evaluate : 0.225 Fit side-chains REVERT: A 55 GLU cc_start: 0.7341 (mm-30) cc_final: 0.7072 (mm-30) REVERT: A 230 LEU cc_start: 0.8348 (tp) cc_final: 0.8121 (tp) REVERT: A 410 ARG cc_start: 0.7647 (mtm-85) cc_final: 0.6832 (mtm180) REVERT: A 564 GLU cc_start: 0.8138 (tp30) cc_final: 0.7887 (tp30) REVERT: A 599 ARG cc_start: 0.8010 (ttp80) cc_final: 0.7771 (ptm-80) REVERT: A 618 LEU cc_start: 0.7787 (OUTLIER) cc_final: 0.7488 (tt) REVERT: A 650 ARG cc_start: 0.7538 (mtp85) cc_final: 0.6812 (mtp180) REVERT: A 688 GLU cc_start: 0.7806 (tm-30) cc_final: 0.7315 (tm-30) REVERT: A 739 LEU cc_start: 0.8025 (mt) cc_final: 0.7707 (mt) REVERT: A 760 TYR cc_start: 0.7101 (t80) cc_final: 0.6367 (t80) REVERT: A 817 ASN cc_start: 0.7760 (t0) cc_final: 0.7550 (t0) REVERT: A 823 GLU cc_start: 0.8348 (mt-10) cc_final: 0.7555 (tt0) REVERT: A 869 GLU cc_start: 0.6914 (mp0) cc_final: 0.6592 (mp0) REVERT: A 882 GLU cc_start: 0.7361 (mp0) cc_final: 0.7036 (mp0) outliers start: 24 outliers final: 18 residues processed: 208 average time/residue: 0.1130 time to fit residues: 29.8049 Evaluate side-chains 216 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 197 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 167 ARG Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 618 LEU Chi-restraints excluded: chain A residue 762 SER Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 807 SER Chi-restraints excluded: chain A residue 886 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 72 optimal weight: 0.5980 chunk 63 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 chunk 51 optimal weight: 0.0060 chunk 44 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 43 optimal weight: 0.3980 chunk 11 optimal weight: 1.9990 chunk 33 optimal weight: 0.2980 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 26 HIS A 575 HIS A 894 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.152808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.128944 restraints weight = 12604.502| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 1.72 r_work: 0.3446 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3293 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9043 Z= 0.132 Angle : 0.558 8.760 12606 Z= 0.304 Chirality : 0.038 0.142 1406 Planarity : 0.004 0.044 1311 Dihedral : 21.037 176.132 2192 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 2.79 % Allowed : 19.11 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.31), residues: 821 helix: 1.59 (0.27), residues: 389 sheet: -1.04 (0.43), residues: 140 loop : -1.37 (0.38), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 561 TYR 0.010 0.001 TYR A 605 PHE 0.020 0.001 PHE A 31 TRP 0.011 0.001 TRP A 645 HIS 0.004 0.001 HIS A 526 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.13 ( 9043) covalent geometry : angle 0.55765 / 0.30 (12606) hydrogen bonds : bond 0.05180 / 3.76 ( 402) hydrogen bonds : angle 4.13585 / 3.05 ( 1119) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2185.68 seconds wall clock time: 37 minutes 55.05 seconds (2275.05 seconds total)