Starting phenix.real_space_refine on Fri Oct 10 19:07:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wru_37790/10_2025/8wru_37790.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wru_37790/10_2025/8wru_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8wru_37790/10_2025/8wru_37790.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wru_37790/10_2025/8wru_37790.map" model { file = "/net/cci-nas-00/data/ceres_data/8wru_37790/10_2025/8wru_37790.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wru_37790/10_2025/8wru_37790.cif" } 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-2.0-5842/lib/python3.9/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: 2.31, per 1000 atoms: 0.27 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: 0.92 Conformation dependent library (CDL) restraints added in 256.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 1.25 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: 1.87 Time building geometry restraints manager: 1.19 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=" 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=" C GLU A 659 " pdb=" N LEU A 660 " ideal model delta sigma weight residual 1.333 1.296 0.037 1.45e-02 4.76e+03 6.49e+00 bond pdb=" N GLU A 659 " pdb=" CA GLU A 659 " ideal model delta sigma weight residual 1.458 1.428 0.030 1.24e-02 6.50e+03 5.66e+00 bond pdb=" N HIS A 644 " pdb=" CA HIS A 644 " ideal model delta sigma weight residual 1.457 1.432 0.025 1.33e-02 5.65e+03 3.61e+00 ... (remaining 9038 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.24: 12412 2.24 - 4.47: 170 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=" N TRP A 645 " pdb=" CA TRP A 645 " pdb=" C TRP A 645 " ideal model delta sigma weight residual 110.80 102.26 8.54 2.13e+00 2.20e-01 1.61e+01 angle pdb=" C TYR A 4 " pdb=" CA TYR A 4 " pdb=" CB TYR A 4 " ideal model delta sigma weight residual 109.65 102.69 6.96 1.75e+00 3.27e-01 1.58e+01 angle pdb=" CA PRO A 483 " pdb=" C PRO A 483 " pdb=" O PRO A 483 " ideal model delta sigma weight residual 123.07 117.70 5.37 1.38e+00 5.25e-01 1.51e+01 angle pdb=" CA THR A 646 " pdb=" C THR A 646 " pdb=" O THR A 646 " ideal model delta sigma weight residual 121.58 117.12 4.46 1.16e+00 7.43e-01 1.48e+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: 1344 0.091 - 0.181: 55 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: 4.850 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.230 Find NCS groups from input model: 0.030 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:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7036 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9043 Z= 0.218 Angle : 0.666 11.186 12606 Z= 0.368 Chirality : 0.044 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 aren 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 covalent geometry : bond 0.00437 ( 9043) covalent geometry : angle 0.66649 (12606) hydrogen bonds : bond 0.24449 ( 402) hydrogen bonds : angle 8.35854 ( 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 : 0.260 Fit side-chains REVERT: A 79 ASP cc_start: 0.7135 (m-30) cc_final: 0.6911 (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: 0.8040 (mt) REVERT: A 613 ARG cc_start: 0.7557 (ttm110) cc_final: 0.7249 (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: 0.5856 (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: 0.6592 (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: 0.1533 time to fit residues: 41.5559 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 : 0.294 ------------------------------------------------------------------------------- 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: 3.9990 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: 0.9980 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 overall best weight: 0.8680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 530 HIS A 641 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.150708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.126783 restraints weight = 12830.686| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 1.74 r_work: 0.3415 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3263 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 9043 Z= 0.220 Angle : 0.652 10.120 12606 Z= 0.342 Chirality : 0.042 0.186 1406 Planarity : 0.005 0.052 1311 Dihedral : 21.104 177.600 2196 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 1.95 % Allowed : 9.48 % Favored : 88.56 % 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 aren not related in a simple way. whole: -0.47 (0.30), residues: 821 helix: 1.00 (0.27), residues: 386 sheet: -1.10 (0.43), residues: 140 loop : -1.64 (0.37), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 12 TYR 0.024 0.002 TYR A 4 PHE 0.017 0.002 PHE A 435 TRP 0.014 0.002 TRP A 645 HIS 0.008 0.002 HIS A 874 Details of bonding type rmsd covalent geometry : bond 0.00470 ( 9043) covalent geometry : angle 0.65221 (12606) hydrogen bonds : bond 0.06571 ( 402) hydrogen bonds : angle 4.73542 ( 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 233 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 219 time to evaluate : 0.277 Fit side-chains REVERT: A 99 LEU cc_start: 0.8088 (tt) cc_final: 0.7647 (tt) REVERT: A 100 GLU cc_start: 0.8027 (mm-30) cc_final: 0.7176 (mm-30) REVERT: A 167 ARG cc_start: 0.7843 (OUTLIER) cc_final: 0.7563 (mpp80) REVERT: A 230 LEU cc_start: 0.8403 (tp) cc_final: 0.8118 (tp) REVERT: A 235 ARG cc_start: 0.7775 (ttp-170) cc_final: 0.7147 (ttp-170) REVERT: A 391 TRP cc_start: 0.7901 (t-100) cc_final: 0.6387 (t-100) REVERT: A 559 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.7334 (pt0) REVERT: A 564 GLU cc_start: 0.8145 (tp30) cc_final: 0.7919 (tp30) REVERT: A 613 ARG cc_start: 0.7777 (ttm110) cc_final: 0.7531 (ttm110) REVERT: A 650 ARG cc_start: 0.7613 (mtp85) cc_final: 0.7207 (mtp180) REVERT: A 760 TYR cc_start: 0.7158 (t80) cc_final: 0.6606 (t80) REVERT: A 783 ASP cc_start: 0.7365 (m-30) cc_final: 0.7130 (m-30) REVERT: A 823 GLU cc_start: 0.8320 (mt-10) cc_final: 0.7392 (tt0) REVERT: A 882 GLU cc_start: 0.7277 (mp0) cc_final: 0.6966 (mp0) outliers start: 14 outliers final: 7 residues processed: 224 average time/residue: 0.1504 time to fit residues: 42.1897 Evaluate side-chains 227 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 218 time to evaluate : 0.287 ------------------------------------------------------------------------------- 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 489 VAL 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: 6.9990 chunk 24 optimal weight: 0.0570 chunk 77 optimal weight: 2.9990 chunk 65 optimal weight: 0.3980 chunk 71 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 73 optimal weight: 0.2980 chunk 56 optimal weight: 0.1980 chunk 33 optimal weight: 0.9990 overall best weight: 0.3098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 440 ASN A 641 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 = 0.3908 r_free = 0.3908 target = 0.153296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.129317 restraints weight = 12816.940| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 1.75 r_work: 0.3456 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3303 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9043 Z= 0.125 Angle : 0.560 7.440 12606 Z= 0.294 Chirality : 0.037 0.156 1406 Planarity : 0.005 0.079 1311 Dihedral : 20.943 174.804 2192 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 3.21 % Allowed : 12.41 % Favored : 84.38 % 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 aren not related in a simple way. whole: 0.07 (0.31), residues: 821 helix: 1.54 (0.27), residues: 382 sheet: -0.97 (0.43), residues: 140 loop : -1.39 (0.38), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 582 TYR 0.012 0.001 TYR A 4 PHE 0.017 0.001 PHE A 64 TRP 0.010 0.001 TRP A 328 HIS 0.005 0.001 HIS A 526 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 9043) covalent geometry : angle 0.55965 (12606) hydrogen bonds : bond 0.05249 ( 402) hydrogen bonds : angle 4.20720 ( 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 241 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 218 time to evaluate : 0.236 Fit side-chains REVERT: A 100 GLU cc_start: 0.8170 (mm-30) cc_final: 0.7233 (mm-30) REVERT: A 177 LEU cc_start: 0.8143 (tp) cc_final: 0.7940 (tp) REVERT: A 190 MET cc_start: 0.8235 (tpp) cc_final: 0.7985 (mmt) REVERT: A 230 LEU cc_start: 0.8326 (tp) cc_final: 0.8118 (tp) REVERT: A 391 TRP cc_start: 0.7835 (t-100) cc_final: 0.6288 (t-100) REVERT: A 434 TYR cc_start: 0.8025 (m-80) cc_final: 0.7550 (m-80) REVERT: A 559 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7458 (pt0) REVERT: A 564 GLU cc_start: 0.8120 (tp30) cc_final: 0.7863 (tp30) REVERT: A 578 ASP cc_start: 0.7755 (t0) cc_final: 0.7519 (t0) REVERT: A 608 TYR cc_start: 0.7640 (m-10) cc_final: 0.7367 (m-10) REVERT: A 618 LEU cc_start: 0.7810 (OUTLIER) cc_final: 0.7514 (tt) REVERT: A 650 ARG cc_start: 0.7479 (mtp85) cc_final: 0.7074 (mtp180) REVERT: A 736 GLU cc_start: 0.7015 (mm-30) cc_final: 0.6813 (mm-30) REVERT: A 760 TYR cc_start: 0.7146 (t80) cc_final: 0.6419 (t80) REVERT: A 783 ASP cc_start: 0.7398 (m-30) cc_final: 0.7094 (m-30) REVERT: A 817 ASN cc_start: 0.7648 (t0) cc_final: 0.7411 (t0) REVERT: A 823 GLU cc_start: 0.8333 (mt-10) cc_final: 0.7487 (tt0) REVERT: A 882 GLU cc_start: 0.7195 (mp0) cc_final: 0.6856 (mp0) outliers start: 23 outliers final: 11 residues processed: 224 average time/residue: 0.1502 time to fit residues: 41.9104 Evaluate side-chains 225 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 212 time to evaluate : 0.292 ------------------------------------------------------------------------------- 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 211 ASP Chi-restraints excluded: chain A residue 224 GLU 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 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: 4.9990 chunk 45 optimal weight: 0.5980 chunk 87 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 26 optimal weight: 0.0060 chunk 4 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 71 optimal weight: 0.4980 chunk 60 optimal weight: 0.8980 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 641 ASN A 731 GLN A 894 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.152063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.127919 restraints weight = 12942.782| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 1.77 r_work: 0.3434 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3279 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9043 Z= 0.155 Angle : 0.559 8.250 12606 Z= 0.294 Chirality : 0.038 0.153 1406 Planarity : 0.004 0.036 1311 Dihedral : 20.913 177.109 2192 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 2.65 % Allowed : 16.04 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.17 (0.31), residues: 821 helix: 1.63 (0.27), residues: 384 sheet: -1.01 (0.43), residues: 138 loop : -1.33 (0.39), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 642 TYR 0.016 0.001 TYR A 605 PHE 0.024 0.002 PHE A 31 TRP 0.008 0.001 TRP A 645 HIS 0.005 0.001 HIS A 874 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 9043) covalent geometry : angle 0.55885 (12606) hydrogen bonds : bond 0.05002 ( 402) hydrogen bonds : angle 4.10870 ( 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 230 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 211 time to evaluate : 0.301 Fit side-chains REVERT: A 34 ARG cc_start: 0.8278 (mtt90) cc_final: 0.7860 (mtt-85) REVERT: A 164 ASP cc_start: 0.7465 (m-30) cc_final: 0.6992 (m-30) REVERT: A 167 ARG cc_start: 0.7950 (OUTLIER) cc_final: 0.7587 (mtm-85) REVERT: A 230 LEU cc_start: 0.8301 (tp) cc_final: 0.8069 (tp) REVERT: A 391 TRP cc_start: 0.7864 (t-100) cc_final: 0.6293 (t-100) REVERT: A 410 ARG cc_start: 0.7671 (mtm180) cc_final: 0.6637 (mtm180) REVERT: A 564 GLU cc_start: 0.8151 (tp30) cc_final: 0.7873 (tp30) REVERT: A 578 ASP cc_start: 0.7812 (t0) cc_final: 0.7514 (t0) REVERT: A 608 TYR cc_start: 0.7675 (m-10) cc_final: 0.7452 (m-10) REVERT: A 613 ARG cc_start: 0.7594 (ttm-80) cc_final: 0.7267 (ttm110) REVERT: A 618 LEU cc_start: 0.7811 (OUTLIER) cc_final: 0.7498 (tp) REVERT: A 643 TYR cc_start: 0.8126 (t80) cc_final: 0.7558 (t80) REVERT: A 650 ARG cc_start: 0.7491 (mtp85) cc_final: 0.6976 (mtp180) REVERT: A 736 GLU cc_start: 0.7050 (mm-30) cc_final: 0.6848 (mm-30) REVERT: A 760 TYR cc_start: 0.7145 (t80) cc_final: 0.6418 (t80) REVERT: A 783 ASP cc_start: 0.7322 (m-30) cc_final: 0.7079 (m-30) REVERT: A 823 GLU cc_start: 0.8351 (mt-10) cc_final: 0.7563 (tt0) REVERT: A 882 GLU cc_start: 0.7290 (mp0) cc_final: 0.6964 (mp0) outliers start: 19 outliers final: 11 residues processed: 217 average time/residue: 0.1544 time to fit residues: 41.4869 Evaluate side-chains 217 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 204 time to evaluate : 0.305 ------------------------------------------------------------------------------- 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 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 763 LEU Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 886 GLU Chi-restraints excluded: chain A residue 890 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 89 optimal weight: 1.9990 chunk 70 optimal weight: 0.2980 chunk 32 optimal weight: 0.0570 chunk 69 optimal weight: 0.8980 chunk 72 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 641 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 = 0.3893 r_free = 0.3893 target = 0.152427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.128410 restraints weight = 12814.644| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 1.75 r_work: 0.3437 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.2355 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= 0.148 Angle : 0.551 6.557 12606 Z= 0.290 Chirality : 0.038 0.151 1406 Planarity : 0.004 0.032 1311 Dihedral : 20.894 176.173 2192 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 3.77 % Allowed : 16.32 % Favored : 79.92 % 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 aren not related in a simple way. whole: 0.25 (0.31), residues: 821 helix: 1.72 (0.27), residues: 384 sheet: -1.00 (0.43), residues: 140 loop : -1.29 (0.39), residues: 297 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 0.024 0.001 PHE A 31 TRP 0.008 0.001 TRP A 645 HIS 0.005 0.001 HIS A 526 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 9043) covalent geometry : angle 0.55086 (12606) hydrogen bonds : bond 0.04846 ( 402) hydrogen bonds : angle 4.01240 ( 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 234 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 207 time to evaluate : 0.315 Fit side-chains REVERT: A 164 ASP cc_start: 0.7501 (m-30) cc_final: 0.7010 (m-30) REVERT: A 167 ARG cc_start: 0.7953 (OUTLIER) cc_final: 0.7593 (mtm-85) REVERT: A 230 LEU cc_start: 0.8317 (tp) cc_final: 0.8084 (tp) REVERT: A 391 TRP cc_start: 0.7878 (t-100) cc_final: 0.6305 (t-100) REVERT: A 410 ARG cc_start: 0.7621 (mtm180) cc_final: 0.7017 (mtm180) REVERT: A 434 TYR cc_start: 0.8012 (m-80) cc_final: 0.7566 (m-80) REVERT: A 564 GLU cc_start: 0.8128 (tp30) cc_final: 0.7810 (tp30) REVERT: A 578 ASP cc_start: 0.7758 (t0) cc_final: 0.7441 (t0) REVERT: A 582 ARG cc_start: 0.8216 (mtp-110) cc_final: 0.7921 (ttm110) REVERT: A 608 TYR cc_start: 0.7698 (m-10) cc_final: 0.7467 (m-10) REVERT: A 613 ARG cc_start: 0.7588 (ttm-80) cc_final: 0.7290 (ttm110) REVERT: A 618 LEU cc_start: 0.7799 (OUTLIER) cc_final: 0.7483 (tp) REVERT: A 650 ARG cc_start: 0.7512 (mtp85) cc_final: 0.6987 (mtp180) REVERT: A 760 TYR cc_start: 0.7112 (t80) cc_final: 0.6381 (t80) REVERT: A 783 ASP cc_start: 0.7313 (m-30) cc_final: 0.7112 (m-30) REVERT: A 823 GLU cc_start: 0.8362 (mt-10) cc_final: 0.7584 (tt0) REVERT: A 848 LEU cc_start: 0.7754 (mt) cc_final: 0.7553 (mt) REVERT: A 882 GLU cc_start: 0.7298 (mp0) cc_final: 0.6964 (mp0) outliers start: 27 outliers final: 12 residues processed: 216 average time/residue: 0.1494 time to fit residues: 40.2377 Evaluate side-chains 218 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 204 time to evaluate : 0.292 ------------------------------------------------------------------------------- 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 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 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 Chi-restraints excluded: chain A residue 896 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 87 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 36 optimal weight: 0.5980 chunk 1 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 51 optimal weight: 0.2980 chunk 53 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 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 = 0.3880 r_free = 0.3880 target = 0.151376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.127350 restraints weight = 12784.445| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 1.75 r_work: 0.3425 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.2378 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= 0.191 Angle : 0.586 9.226 12606 Z= 0.307 Chirality : 0.039 0.183 1406 Planarity : 0.004 0.035 1311 Dihedral : 20.960 177.655 2192 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 3.07 % Allowed : 17.71 % Favored : 79.22 % 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 aren not related in a simple way. whole: 0.16 (0.31), residues: 821 helix: 1.62 (0.27), residues: 384 sheet: -1.06 (0.43), residues: 140 loop : -1.30 (0.39), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 8 TYR 0.020 0.002 TYR A 605 PHE 0.020 0.002 PHE A 31 TRP 0.010 0.001 TRP A 645 HIS 0.006 0.001 HIS A 874 Details of bonding type rmsd covalent geometry : bond 0.00410 ( 9043) covalent geometry : angle 0.58576 (12606) hydrogen bonds : bond 0.05012 ( 402) hydrogen bonds : angle 4.06079 ( 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 230 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 208 time to evaluate : 0.362 Fit side-chains revert: symmetry clash REVERT: A 48 MET cc_start: 0.6800 (OUTLIER) cc_final: 0.6503 (mpt) REVERT: A 162 MET cc_start: 0.6720 (ptp) cc_final: 0.6498 (ptp) REVERT: A 167 ARG cc_start: 0.7975 (OUTLIER) cc_final: 0.7607 (mtm-85) REVERT: A 230 LEU cc_start: 0.8341 (tp) cc_final: 0.8095 (tp) REVERT: A 409 LYS cc_start: 0.7533 (mtpt) cc_final: 0.7325 (mtpt) REVERT: A 564 GLU cc_start: 0.8152 (tp30) cc_final: 0.7851 (tp30) REVERT: A 578 ASP cc_start: 0.7778 (t0) cc_final: 0.7463 (t0) REVERT: A 582 ARG cc_start: 0.8290 (mtp-110) cc_final: 0.7943 (ttm110) REVERT: A 608 TYR cc_start: 0.7741 (m-80) cc_final: 0.7519 (m-10) REVERT: A 618 LEU cc_start: 0.7785 (OUTLIER) cc_final: 0.7457 (tt) REVERT: A 643 TYR cc_start: 0.8134 (t80) cc_final: 0.7708 (t80) REVERT: A 650 ARG cc_start: 0.7500 (mtp85) cc_final: 0.7005 (mtp180) REVERT: A 760 TYR cc_start: 0.7130 (t80) cc_final: 0.6401 (t80) REVERT: A 823 GLU cc_start: 0.8374 (mt-10) cc_final: 0.7626 (tt0) REVERT: A 882 GLU cc_start: 0.7284 (mp0) cc_final: 0.6969 (mp0) outliers start: 22 outliers final: 11 residues processed: 215 average time/residue: 0.1581 time to fit residues: 42.1436 Evaluate side-chains 225 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 211 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 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 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 886 GLU Chi-restraints excluded: chain A residue 896 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 57 optimal weight: 0.8980 chunk 76 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 75 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 28 optimal weight: 0.4980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 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 = 0.3877 r_free = 0.3877 target = 0.151131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.127041 restraints weight = 12849.587| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 1.76 r_work: 0.3416 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.2443 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= 0.201 Angle : 0.595 8.215 12606 Z= 0.312 Chirality : 0.040 0.203 1406 Planarity : 0.004 0.036 1311 Dihedral : 20.993 177.199 2192 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 3.77 % Allowed : 17.43 % Favored : 78.80 % 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 aren not related in a simple way. whole: 0.07 (0.31), residues: 821 helix: 1.54 (0.27), residues: 386 sheet: -1.03 (0.43), residues: 140 loop : -1.40 (0.39), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 416 TYR 0.020 0.002 TYR A 605 PHE 0.017 0.002 PHE A 31 TRP 0.011 0.001 TRP A 645 HIS 0.006 0.002 HIS A 874 Details of bonding type rmsd covalent geometry : bond 0.00433 ( 9043) covalent geometry : angle 0.59481 (12606) hydrogen bonds : bond 0.05036 ( 402) hydrogen bonds : angle 4.05759 ( 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 226 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 199 time to evaluate : 0.298 Fit side-chains REVERT: A 230 LEU cc_start: 0.8350 (tp) cc_final: 0.8117 (tp) REVERT: A 410 ARG cc_start: 0.7661 (mtm180) cc_final: 0.7062 (mtt180) REVERT: A 564 GLU cc_start: 0.8167 (tp30) cc_final: 0.7895 (tp30) REVERT: A 578 ASP cc_start: 0.7812 (t0) cc_final: 0.7506 (t0) REVERT: A 582 ARG cc_start: 0.8302 (mtp-110) cc_final: 0.7767 (mtp-110) REVERT: A 608 TYR cc_start: 0.7782 (m-80) cc_final: 0.7524 (m-10) REVERT: A 618 LEU cc_start: 0.7773 (OUTLIER) cc_final: 0.7464 (tp) REVERT: A 643 TYR cc_start: 0.8133 (t80) cc_final: 0.7733 (t80) REVERT: A 650 ARG cc_start: 0.7485 (mtp85) cc_final: 0.6958 (mtp180) REVERT: A 760 TYR cc_start: 0.7143 (t80) cc_final: 0.6405 (t80) REVERT: A 823 GLU cc_start: 0.8362 (mt-10) cc_final: 0.7559 (tt0) REVERT: A 882 GLU cc_start: 0.7297 (mp0) cc_final: 0.6975 (mp0) outliers start: 27 outliers final: 17 residues processed: 208 average time/residue: 0.1464 time to fit residues: 38.0530 Evaluate side-chains 226 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 208 time to evaluate : 0.217 ------------------------------------------------------------------------------- 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 167 ARG Chi-restraints excluded: chain A residue 211 ASP 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 489 VAL 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 816 VAL Chi-restraints excluded: chain A residue 886 GLU Chi-restraints excluded: chain A residue 890 GLU Chi-restraints excluded: chain A residue 896 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 67 optimal weight: 0.7980 chunk 45 optimal weight: 0.5980 chunk 86 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 89 optimal weight: 0.9990 chunk 63 optimal weight: 0.5980 chunk 34 optimal weight: 0.5980 chunk 60 optimal weight: 0.0770 chunk 72 optimal weight: 0.3980 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 HIS A 92 ASN 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 = 0.3897 r_free = 0.3897 target = 0.152729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.128691 restraints weight = 12680.607| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 1.73 r_work: 0.3442 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3289 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.2612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9043 Z= 0.141 Angle : 0.563 6.792 12606 Z= 0.296 Chirality : 0.037 0.152 1406 Planarity : 0.004 0.035 1311 Dihedral : 20.927 175.563 2192 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 3.21 % Allowed : 18.13 % Favored : 78.66 % 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 aren not related in a simple way. whole: 0.19 (0.31), residues: 821 helix: 1.69 (0.27), residues: 385 sheet: -0.99 (0.43), residues: 140 loop : -1.40 (0.38), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 8 TYR 0.011 0.001 TYR A 605 PHE 0.018 0.001 PHE A 31 TRP 0.010 0.001 TRP A 645 HIS 0.004 0.001 HIS A 526 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 9043) covalent geometry : angle 0.56298 (12606) hydrogen bonds : bond 0.04804 ( 402) hydrogen bonds : angle 3.98069 ( 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 222 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 199 time to evaluate : 0.247 Fit side-chains revert: symmetry clash REVERT: A 188 GLU cc_start: 0.6629 (tp30) cc_final: 0.6403 (tp30) REVERT: A 230 LEU cc_start: 0.8324 (tp) cc_final: 0.8103 (tp) REVERT: A 564 GLU cc_start: 0.8138 (tp30) cc_final: 0.7835 (tp30) REVERT: A 578 ASP cc_start: 0.7778 (t0) cc_final: 0.7464 (t70) REVERT: A 582 ARG cc_start: 0.8269 (mtp-110) cc_final: 0.7923 (ttm110) REVERT: A 608 TYR cc_start: 0.7737 (m-80) cc_final: 0.7479 (m-10) REVERT: A 618 LEU cc_start: 0.7756 (OUTLIER) cc_final: 0.7454 (tt) REVERT: A 643 TYR cc_start: 0.8109 (t80) cc_final: 0.7737 (t80) REVERT: A 650 ARG cc_start: 0.7482 (mtp85) cc_final: 0.6973 (mtp180) REVERT: A 744 ASP cc_start: 0.7617 (t0) cc_final: 0.7257 (t0) REVERT: A 760 TYR cc_start: 0.7110 (t80) cc_final: 0.6375 (t80) REVERT: A 823 GLU cc_start: 0.8353 (mt-10) cc_final: 0.7641 (tt0) REVERT: A 869 GLU cc_start: 0.6892 (mp0) cc_final: 0.6564 (mp0) REVERT: A 882 GLU cc_start: 0.7293 (mp0) cc_final: 0.6965 (mp0) outliers start: 23 outliers final: 16 residues processed: 208 average time/residue: 0.1559 time to fit residues: 40.2779 Evaluate side-chains 216 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 199 time to evaluate : 0.343 ------------------------------------------------------------------------------- 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 92 ASN 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 254 VAL Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 489 VAL 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 816 VAL Chi-restraints excluded: chain A residue 886 GLU Chi-restraints excluded: chain A residue 890 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 19 optimal weight: 0.0030 chunk 55 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 23 optimal weight: 6.9990 chunk 74 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 HIS A 89 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 = 0.3885 r_free = 0.3885 target = 0.151734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.127685 restraints weight = 12682.418| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 1.75 r_work: 0.3424 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3271 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.2618 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= 0.179 Angle : 0.585 7.049 12606 Z= 0.306 Chirality : 0.039 0.164 1406 Planarity : 0.004 0.057 1311 Dihedral : 20.944 176.996 2192 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 2.65 % Allowed : 18.69 % Favored : 78.66 % 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 aren not related in a simple way. whole: 0.12 (0.31), residues: 821 helix: 1.61 (0.27), residues: 385 sheet: -1.03 (0.43), residues: 140 loop : -1.41 (0.38), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 12 TYR 0.018 0.002 TYR A 605 PHE 0.017 0.002 PHE A 31 TRP 0.010 0.001 TRP A 645 HIS 0.006 0.001 HIS A 874 Details of bonding type rmsd covalent geometry : bond 0.00386 ( 9043) covalent geometry : angle 0.58486 (12606) hydrogen bonds : bond 0.04896 ( 402) hydrogen bonds : angle 4.03072 ( 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 213 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 194 time to evaluate : 0.314 Fit side-chains revert: symmetry clash REVERT: A 230 LEU cc_start: 0.8331 (tp) cc_final: 0.8113 (tp) REVERT: A 564 GLU cc_start: 0.8127 (tp30) cc_final: 0.7838 (tp30) REVERT: A 578 ASP cc_start: 0.7767 (t0) cc_final: 0.7466 (t70) REVERT: A 582 ARG cc_start: 0.8293 (mtp-110) cc_final: 0.7728 (mtp-110) REVERT: A 613 ARG cc_start: 0.7614 (ttm-80) cc_final: 0.7173 (ttm110) REVERT: A 618 LEU cc_start: 0.7755 (OUTLIER) cc_final: 0.7442 (tt) REVERT: A 643 TYR cc_start: 0.8117 (t80) cc_final: 0.7749 (t80) REVERT: A 650 ARG cc_start: 0.7472 (mtp85) cc_final: 0.6956 (mtp180) REVERT: A 760 TYR cc_start: 0.7110 (t80) cc_final: 0.6378 (t80) REVERT: A 823 GLU cc_start: 0.8356 (mt-10) cc_final: 0.7631 (tt0) REVERT: A 869 GLU cc_start: 0.6884 (mp0) cc_final: 0.6561 (mp0) REVERT: A 882 GLU cc_start: 0.7315 (mp0) cc_final: 0.6985 (mp0) outliers start: 19 outliers final: 16 residues processed: 203 average time/residue: 0.1488 time to fit residues: 37.6366 Evaluate side-chains 218 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 201 time to evaluate : 0.312 ------------------------------------------------------------------------------- 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 167 ARG Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 489 VAL 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 816 VAL Chi-restraints excluded: chain A residue 886 GLU Chi-restraints excluded: chain A residue 890 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 73 optimal weight: 0.1980 chunk 71 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 76 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 50 optimal weight: 0.3980 chunk 69 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 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 = 0.3889 r_free = 0.3889 target = 0.152180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.128440 restraints weight = 12672.481| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 1.70 r_work: 0.3437 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.2692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9043 Z= 0.162 Angle : 0.590 11.443 12606 Z= 0.306 Chirality : 0.039 0.158 1406 Planarity : 0.004 0.054 1311 Dihedral : 20.948 176.040 2192 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 2.65 % Allowed : 18.69 % Favored : 78.66 % 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 aren not related in a simple way. whole: 0.15 (0.31), residues: 821 helix: 1.67 (0.27), residues: 385 sheet: -1.03 (0.43), residues: 140 loop : -1.42 (0.38), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 8 TYR 0.017 0.002 TYR A 605 PHE 0.016 0.001 PHE A 31 TRP 0.010 0.001 TRP A 645 HIS 0.005 0.001 HIS A 874 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 9043) covalent geometry : angle 0.59001 (12606) hydrogen bonds : bond 0.04830 ( 402) hydrogen bonds : angle 4.02682 ( 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 221 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 202 time to evaluate : 0.267 Fit side-chains revert: symmetry clash REVERT: A 230 LEU cc_start: 0.8329 (tp) cc_final: 0.8101 (tp) REVERT: A 564 GLU cc_start: 0.8126 (tp30) cc_final: 0.7824 (tp30) REVERT: A 578 ASP cc_start: 0.7757 (t0) cc_final: 0.7450 (t70) REVERT: A 582 ARG cc_start: 0.8257 (mtp-110) cc_final: 0.7913 (ttm110) REVERT: A 613 ARG cc_start: 0.7610 (ttm-80) cc_final: 0.7184 (ttm110) REVERT: A 618 LEU cc_start: 0.7739 (OUTLIER) cc_final: 0.7429 (tt) REVERT: A 643 TYR cc_start: 0.8134 (t80) cc_final: 0.7782 (t80) REVERT: A 650 ARG cc_start: 0.7488 (mtp85) cc_final: 0.6979 (mtp180) REVERT: A 760 TYR cc_start: 0.7104 (t80) cc_final: 0.6371 (t80) REVERT: A 823 GLU cc_start: 0.8356 (mt-10) cc_final: 0.7645 (tt0) REVERT: A 869 GLU cc_start: 0.6867 (mp0) cc_final: 0.6552 (mp0) REVERT: A 882 GLU cc_start: 0.7294 (mp0) cc_final: 0.6968 (mp0) outliers start: 19 outliers final: 16 residues processed: 210 average time/residue: 0.1582 time to fit residues: 41.0268 Evaluate side-chains 220 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 203 time to evaluate : 0.281 ------------------------------------------------------------------------------- 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 167 ARG Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 489 VAL 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 816 VAL Chi-restraints excluded: chain A residue 886 GLU Chi-restraints excluded: chain A residue 890 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 72 optimal weight: 0.7980 chunk 63 optimal weight: 0.6980 chunk 62 optimal weight: 0.7980 chunk 60 optimal weight: 0.4980 chunk 50 optimal weight: 0.4980 chunk 51 optimal weight: 0.6980 chunk 44 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 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 = 0.3889 r_free = 0.3889 target = 0.152116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.128315 restraints weight = 12602.828| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 1.71 r_work: 0.3439 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3285 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9043 Z= 0.170 Angle : 0.600 11.021 12606 Z= 0.309 Chirality : 0.039 0.161 1406 Planarity : 0.004 0.050 1311 Dihedral : 20.956 176.367 2192 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 2.79 % Allowed : 18.97 % 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 aren not related in a simple way. whole: 0.12 (0.31), residues: 821 helix: 1.61 (0.27), residues: 385 sheet: -1.02 (0.43), residues: 140 loop : -1.40 (0.38), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 8 TYR 0.019 0.002 TYR A 608 PHE 0.015 0.001 PHE A 64 TRP 0.011 0.001 TRP A 645 HIS 0.005 0.001 HIS A 874 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 9043) covalent geometry : angle 0.59953 (12606) hydrogen bonds : bond 0.04862 ( 402) hydrogen bonds : angle 4.04574 ( 1119) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2948.88 seconds wall clock time: 51 minutes 2.40 seconds (3062.40 seconds total)