Starting phenix.real_space_refine on Wed Aug 5 06:33:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y9n_39084/08_2026/8y9n_39084.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y9n_39084/08_2026/8y9n_39084.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8y9n_39084/08_2026/8y9n_39084.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y9n_39084/08_2026/8y9n_39084.map" model { file = "/net/cci-nas-00/data/ceres_data/8y9n_39084/08_2026/8y9n_39084.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y9n_39084/08_2026/8y9n_39084.cif" } resolution = 3.0 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= 0.051 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 99 5.49 5 Mg 1 5.21 5 S 27 5.16 5 C 5344 2.51 5 N 1580 2.21 5 O 1910 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 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: 8961 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 6883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 851, 6883 Classifications: {'peptide': 851} Link IDs: {'PTRANS': 33, 'TRANS': 817} Chain breaks: 2 Chain: "B" Number of atoms: 1158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 1158 Classifications: {'RNA': 54} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 2, 'rna3p_pur': 28, 'rna3p_pyr': 21} Link IDs: {'rna2p': 4, 'rna3p': 49} Chain: "C" Number of atoms: 527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 527 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "D" Number of atoms: 392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 392 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Chain breaks: 2 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.85, per 1000 atoms: 0.21 Number of scatterers: 8961 At special positions: 0 Unit cell: (88.065, 101.745, 123.975, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 27 16.00 P 99 15.00 Mg 1 11.99 O 1910 8.00 N 1580 7.00 C 5344 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: 0.74 Conformation dependent library (CDL) restraints added in 246.6 milliseconds 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1596 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 7 sheets defined 50.2% alpha, 12.7% beta 29 base pairs and 72 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'A' and resid 20 through 43 Processing helix chain 'A' and resid 59 through 72 Processing helix chain 'A' and resid 74 through 88 Processing helix chain 'A' and resid 89 through 93 Processing helix chain 'A' and resid 94 through 99 removed outlier: 3.659A pdb=" N SER A 97 " --> pdb=" O SER A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 121 removed outlier: 3.557A pdb=" N PHE A 118 " --> pdb=" O ALA A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 134 Processing helix chain 'A' and resid 139 through 143 Processing helix chain 'A' and resid 144 through 155 Processing helix chain 'A' and resid 156 through 165 removed outlier: 3.689A pdb=" N GLU A 162 " --> pdb=" O GLU A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 169 removed outlier: 3.947A pdb=" N VAL A 169 " --> pdb=" O PRO A 166 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 166 through 169' Processing helix chain 'A' and resid 174 through 184 removed outlier: 3.614A pdb=" N GLN A 178 " --> pdb=" O SER A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 230 removed outlier: 3.674A pdb=" N HIS A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 248 Processing helix chain 'A' and resid 254 through 267 removed outlier: 3.853A pdb=" N LEU A 266 " --> pdb=" O VAL A 262 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N LYS A 267 " --> pdb=" O LYS A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 283 Processing helix chain 'A' and resid 284 through 286 No H-bonds generated for 'chain 'A' and resid 284 through 286' Processing helix chain 'A' and resid 287 through 292 removed outlier: 3.833A pdb=" N LEU A 291 " --> pdb=" O PHE A 287 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N THR A 292 " --> pdb=" O ALA A 288 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 287 through 292' Processing helix chain 'A' and resid 294 through 314 removed outlier: 3.723A pdb=" N ARG A 314 " --> pdb=" O ARG A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 441 removed outlier: 3.564A pdb=" N ALA A 438 " --> pdb=" O ASN A 434 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS A 439 " --> pdb=" O PHE A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 454 removed outlier: 3.500A pdb=" N GLY A 454 " --> pdb=" O GLU A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 511 Processing helix chain 'A' and resid 512 through 537 removed outlier: 3.801A pdb=" N LYS A 518 " --> pdb=" O LEU A 514 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA A 533 " --> pdb=" O LYS A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 550 Processing helix chain 'A' and resid 558 through 585 removed outlier: 3.685A pdb=" N ARG A 573 " --> pdb=" O ASP A 569 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU A 574 " --> pdb=" O THR A 570 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER A 576 " --> pdb=" O ARG A 572 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU A 584 " --> pdb=" O GLN A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 611 removed outlier: 3.870A pdb=" N ARG A 611 " --> pdb=" O GLU A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 649 removed outlier: 3.689A pdb=" N ASP A 635 " --> pdb=" O ALA A 631 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU A 636 " --> pdb=" O SER A 632 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG A 638 " --> pdb=" O ARG A 634 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE A 645 " --> pdb=" O VAL A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 678 removed outlier: 3.802A pdb=" N LEU A 676 " --> pdb=" O ALA A 672 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU A 677 " --> pdb=" O LEU A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 692 removed outlier: 3.701A pdb=" N LEU A 682 " --> pdb=" O SER A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 740 through 753 Processing helix chain 'A' and resid 779 through 790 Processing helix chain 'A' and resid 831 through 847 Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 8 removed outlier: 5.208A pdb=" N SER A 429 " --> pdb=" O GLU A 404 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N GLU A 404 " --> pdb=" O SER A 429 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N ARG A 383 " --> pdb=" O ASP A 368 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N ASP A 368 " --> pdb=" O ARG A 383 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 329 through 331 removed outlier: 5.162A pdb=" N PHE A 420 " --> pdb=" O ILE A 14 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 48 Processing sheet with id=AA4, first strand: chain 'A' and resid 487 through 489 removed outlier: 3.698A pdb=" N TYR A 494 " --> pdb=" O GLY A 480 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LYS A 476 " --> pdb=" O ILE A 498 " (cutoff:3.500A) removed outlier: 9.199A pdb=" N ILE A 654 " --> pdb=" O GLU A 458 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N VAL A 460 " --> pdb=" O ILE A 654 " (cutoff:3.500A) removed outlier: 8.656A pdb=" N PHE A 656 " --> pdb=" O VAL A 460 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N GLY A 462 " --> pdb=" O PHE A 656 " (cutoff:3.500A) removed outlier: 8.943A pdb=" N GLU A 658 " --> pdb=" O GLY A 462 " (cutoff:3.500A) removed outlier: 8.867A pdb=" N ALA A 464 " --> pdb=" O GLU A 658 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N VAL A 655 " --> pdb=" O VAL A 698 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N VAL A 700 " --> pdb=" O VAL A 655 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N PHE A 657 " --> pdb=" O VAL A 700 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 717 through 718 Processing sheet with id=AA6, first strand: chain 'A' and resid 760 through 762 removed outlier: 3.596A pdb=" N GLU A 827 " --> pdb=" O HIS A 824 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 796 through 800 removed outlier: 3.664A pdb=" N LEU A 798 " --> pdb=" O THR A 806 " (cutoff:3.500A) 352 hydrogen bonds defined for protein. 990 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 73 hydrogen bonds 138 hydrogen bond angles 0 basepair planarities 29 basepair parallelities 72 stacking parallelities Total time for adding SS restraints: 1.51 Time building geometry restraints manager: 0.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.26: 1238 1.26 - 1.40: 2530 1.40 - 1.53: 5179 1.53 - 1.67: 360 1.67 - 1.81: 43 Bond restraints: 9350 Sorted by residual: bond pdb=" C SER A 678 " pdb=" N PRO A 679 " ideal model delta sigma weight residual 1.336 1.502 -0.166 1.20e-02 6.94e+03 1.92e+02 bond pdb=" O3' DG D 11 " pdb=" P DT D 12 " ideal model delta sigma weight residual 1.607 1.475 0.132 1.20e-02 6.94e+03 1.21e+02 bond pdb=" O3' DG D -3 " pdb=" P DA D -2 " ideal model delta sigma weight residual 1.607 1.492 0.115 1.20e-02 6.94e+03 9.25e+01 bond pdb=" C ALA A 642 " pdb=" O ALA A 642 " ideal model delta sigma weight residual 1.237 1.129 0.108 1.17e-02 7.31e+03 8.52e+01 bond pdb=" C LEU A 636 " pdb=" O LEU A 636 " ideal model delta sigma weight residual 1.237 1.134 0.103 1.17e-02 7.31e+03 7.76e+01 ... (remaining 9345 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.32: 12710 3.32 - 6.65: 308 6.65 - 9.97: 29 9.97 - 13.30: 6 13.30 - 16.62: 7 Bond angle restraints: 13060 Sorted by residual: angle pdb=" C SER A 678 " pdb=" N PRO A 679 " pdb=" CA PRO A 679 " ideal model delta sigma weight residual 118.85 132.87 -14.02 1.09e+00 8.42e-01 1.66e+02 angle pdb=" C ARG A 820 " pdb=" CA ARG A 820 " pdb=" CB ARG A 820 " ideal model delta sigma weight residual 109.65 93.98 15.67 1.71e+00 3.42e-01 8.40e+01 angle pdb=" C GLN A 564 " pdb=" CA GLN A 564 " pdb=" CB GLN A 564 " ideal model delta sigma weight residual 110.67 126.18 -15.51 1.92e+00 2.71e-01 6.53e+01 angle pdb=" CB ARG A 638 " pdb=" CG ARG A 638 " pdb=" CD ARG A 638 " ideal model delta sigma weight residual 111.30 95.22 16.08 2.30e+00 1.89e-01 4.89e+01 angle pdb=" O4' DA C -5 " pdb=" C4' DA C -5 " pdb=" C3' DA C -5 " ideal model delta sigma weight residual 106.00 101.96 4.04 6.00e-01 2.78e+00 4.54e+01 ... (remaining 13055 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.25: 5114 31.25 - 62.51: 430 62.51 - 93.76: 57 93.76 - 125.01: 1 125.01 - 156.27: 2 Dihedral angle restraints: 5604 sinusoidal: 3123 harmonic: 2481 Sorted by residual: dihedral pdb=" C GLN A 564 " pdb=" N GLN A 564 " pdb=" CA GLN A 564 " pdb=" CB GLN A 564 " ideal model delta harmonic sigma weight residual -122.60 -147.21 24.61 0 2.50e+00 1.60e-01 9.69e+01 dihedral pdb=" O4' U B -18 " pdb=" C1' U B -18 " pdb=" N1 U B -18 " pdb=" C2 U B -18 " ideal model delta sinusoidal sigma weight residual 200.00 51.40 148.60 1 1.50e+01 4.44e-03 7.91e+01 dihedral pdb=" C ARG A 820 " pdb=" N ARG A 820 " pdb=" CA ARG A 820 " pdb=" CB ARG A 820 " ideal model delta harmonic sigma weight residual -122.60 -100.90 -21.70 0 2.50e+00 1.60e-01 7.54e+01 ... (remaining 5601 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.184: 1408 0.184 - 0.367: 53 0.367 - 0.551: 5 0.551 - 0.734: 0 0.734 - 0.918: 1 Chirality restraints: 1467 Sorted by residual: chirality pdb=" CA GLN A 564 " pdb=" N GLN A 564 " pdb=" C GLN A 564 " pdb=" CB GLN A 564 " both_signs ideal model delta sigma weight residual False 2.51 1.59 0.92 2.00e-01 2.50e+01 2.11e+01 chirality pdb=" CA ARG A 820 " pdb=" N ARG A 820 " pdb=" C ARG A 820 " pdb=" CB ARG A 820 " both_signs ideal model delta sigma weight residual False 2.51 3.00 -0.49 2.00e-01 2.50e+01 5.93e+00 chirality pdb=" C3' DT D 5 " pdb=" C4' DT D 5 " pdb=" O3' DT D 5 " pdb=" C2' DT D 5 " both_signs ideal model delta sigma weight residual False -2.73 -2.26 -0.47 2.00e-01 2.50e+01 5.63e+00 ... (remaining 1464 not shown) Planarity restraints: 1315 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 106 " -0.799 9.50e-02 1.11e+02 3.58e-01 7.83e+01 pdb=" NE ARG A 106 " 0.051 2.00e-02 2.50e+03 pdb=" CZ ARG A 106 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG A 106 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A 106 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 639 " 0.022 2.00e-02 2.50e+03 4.61e-02 2.13e+01 pdb=" C ARG A 639 " -0.080 2.00e-02 2.50e+03 pdb=" O ARG A 639 " 0.030 2.00e-02 2.50e+03 pdb=" N ARG A 640 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG D 0 " -0.059 2.00e-02 2.50e+03 2.65e-02 2.10e+01 pdb=" N9 DG D 0 " 0.059 2.00e-02 2.50e+03 pdb=" C8 DG D 0 " 0.005 2.00e-02 2.50e+03 pdb=" N7 DG D 0 " 0.017 2.00e-02 2.50e+03 pdb=" C5 DG D 0 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DG D 0 " -0.019 2.00e-02 2.50e+03 pdb=" O6 DG D 0 " -0.019 2.00e-02 2.50e+03 pdb=" N1 DG D 0 " -0.005 2.00e-02 2.50e+03 pdb=" C2 DG D 0 " 0.008 2.00e-02 2.50e+03 pdb=" N2 DG D 0 " 0.016 2.00e-02 2.50e+03 pdb=" N3 DG D 0 " -0.005 2.00e-02 2.50e+03 pdb=" C4 DG D 0 " 0.000 2.00e-02 2.50e+03 ... (remaining 1312 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1333 2.75 - 3.29: 7438 3.29 - 3.83: 14761 3.83 - 4.36: 18628 4.36 - 4.90: 30034 Nonbonded interactions: 72194 Sorted by model distance: nonbonded pdb=" O SER A 678 " pdb=" OG SER A 678 " model vdw 2.214 3.040 nonbonded pdb=" O2' C B -19 " pdb=" OP2 A B -17 " model vdw 2.234 3.040 nonbonded pdb=" O ASN A 709 " pdb=" OG SER A 866 " model vdw 2.244 3.040 nonbonded pdb=" OH TYR A 96 " pdb=" OP2 DA D -2 " model vdw 2.254 3.040 nonbonded pdb=" O SER A 94 " pdb=" OG SER A 94 " model vdw 2.290 3.040 ... (remaining 72189 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.290 Find NCS groups from input model: 0.040 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:6.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 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 : 0.012 0.166 9350 Z= 0.845 Angle : 1.181 16.620 13060 Z= 0.793 Chirality : 0.083 0.918 1467 Planarity : 0.015 0.358 1315 Dihedral : 20.092 156.268 4008 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.11 % Allowed : 2.16 % Favored : 94.73 % Cbeta Deviations : 1.38 % 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: 0.40 (0.28), residues: 845 helix: 1.24 (0.26), residues: 398 sheet: 0.48 (0.49), residues: 113 loop : -0.97 (0.30), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG A 639 TYR 0.023 0.002 TYR A 822 PHE 0.014 0.002 PHE A 103 TRP 0.014 0.002 TRP A 323 HIS 0.008 0.001 HIS A 831 Details of bonding type rmsd/Z covalent geometry : bond 0.01156 / 0.84 ( 9350) covalent geometry : angle 1.18123 / 0.79 (13060) hydrogen bonds : bond 0.19999 / 13.37 ( 425) hydrogen bonds : angle 5.93964 / 4.21 ( 1128) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 85 time to evaluate : 0.301 Fit side-chains REVERT: A 118 PHE cc_start: 0.8390 (t80) cc_final: 0.8135 (t80) REVERT: A 669 ARG cc_start: 0.7949 (mtp180) cc_final: 0.7541 (mmt180) REVERT: A 796 ARG cc_start: 0.8079 (OUTLIER) cc_final: 0.7210 (mpp-170) outliers start: 23 outliers final: 13 residues processed: 104 average time/residue: 0.6205 time to fit residues: 67.7429 Evaluate side-chains 79 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 ASN Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain A residue 634 ARG Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain A residue 796 ARG Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 802 MET Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain A residue 820 ARG Chi-restraints excluded: chain A residue 830 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.0870 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 overall best weight: 0.7758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 281 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.113345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.084966 restraints weight = 11729.985| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 2.00 r_work: 0.2595 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2454 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9158 moved from start: 0.1089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9350 Z= 0.145 Angle : 0.612 7.934 13060 Z= 0.357 Chirality : 0.045 0.327 1467 Planarity : 0.005 0.047 1315 Dihedral : 21.074 162.602 2301 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.16 % Allowed : 9.05 % Favored : 88.78 % 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: 0.65 (0.28), residues: 845 helix: 1.45 (0.26), residues: 406 sheet: 0.49 (0.47), residues: 124 loop : -0.93 (0.31), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 116 TYR 0.018 0.001 TYR A 214 PHE 0.009 0.001 PHE A 633 TRP 0.012 0.001 TRP A 323 HIS 0.004 0.001 HIS A 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.15 ( 9350) covalent geometry : angle 0.61190 / 0.36 (13060) hydrogen bonds : bond 0.06284 / 4.11 ( 425) hydrogen bonds : angle 4.18843 / 3.04 ( 1128) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 70 time to evaluate : 0.197 Fit side-chains REVERT: A 138 GLU cc_start: 0.7502 (tp30) cc_final: 0.6818 (tm-30) REVERT: A 182 ARG cc_start: 0.8752 (OUTLIER) cc_final: 0.8534 (ttp-170) REVERT: A 394 ARG cc_start: 0.8675 (mmm160) cc_final: 0.8278 (mpp-170) REVERT: A 669 ARG cc_start: 0.8585 (mtp180) cc_final: 0.7892 (mmt180) REVERT: A 673 LEU cc_start: 0.9284 (tp) cc_final: 0.9017 (tp) outliers start: 16 outliers final: 9 residues processed: 81 average time/residue: 0.6460 time to fit residues: 55.1019 Evaluate side-chains 70 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 60 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 ARG Chi-restraints excluded: chain A residue 201 GLU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain A residue 634 ARG Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain A residue 830 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 71 optimal weight: 7.9990 chunk 31 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 58 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 34 optimal weight: 0.1980 chunk 4 optimal weight: 0.5980 chunk 17 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.112488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.083281 restraints weight = 11701.290| |-----------------------------------------------------------------------------| r_work (start): 0.2882 rms_B_bonded: 1.95 r_work: 0.2581 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2439 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9182 moved from start: 0.1235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9350 Z= 0.160 Angle : 0.566 6.472 13060 Z= 0.330 Chirality : 0.043 0.228 1467 Planarity : 0.004 0.047 1315 Dihedral : 20.698 164.716 2283 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.03 % Allowed : 11.49 % Favored : 86.49 % 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: 0.86 (0.28), residues: 845 helix: 1.69 (0.26), residues: 406 sheet: 0.60 (0.47), residues: 124 loop : -0.92 (0.31), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 383 TYR 0.017 0.001 TYR A 214 PHE 0.009 0.001 PHE A 35 TRP 0.013 0.001 TRP A 323 HIS 0.005 0.001 HIS A 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.16 ( 9350) covalent geometry : angle 0.56598 / 0.33 (13060) hydrogen bonds : bond 0.06134 / 4.00 ( 425) hydrogen bonds : angle 3.93226 / 2.85 ( 1128) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 65 time to evaluate : 0.281 Fit side-chains REVERT: A 87 LYS cc_start: 0.8902 (ttmp) cc_final: 0.8644 (tttm) REVERT: A 138 GLU cc_start: 0.7418 (tp30) cc_final: 0.6703 (tm-30) REVERT: A 182 ARG cc_start: 0.8781 (OUTLIER) cc_final: 0.8556 (ttp-170) REVERT: A 394 ARG cc_start: 0.8668 (mmm160) cc_final: 0.8312 (mpp-170) REVERT: A 669 ARG cc_start: 0.8643 (mtp180) cc_final: 0.7910 (mtt-85) REVERT: A 673 LEU cc_start: 0.9307 (tp) cc_final: 0.9069 (tp) outliers start: 15 outliers final: 10 residues processed: 77 average time/residue: 0.6605 time to fit residues: 53.6130 Evaluate side-chains 71 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 60 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 ARG Chi-restraints excluded: chain A residue 201 GLU Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 526 SER Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain A residue 634 ARG Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain A residue 830 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 64 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 31 optimal weight: 0.0010 chunk 92 optimal weight: 9.9990 chunk 42 optimal weight: 0.4980 chunk 62 optimal weight: 0.0980 chunk 15 optimal weight: 6.9990 chunk 70 optimal weight: 0.8980 chunk 76 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 overall best weight: 0.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.116397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.087698 restraints weight = 11802.267| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 1.86 r_work: 0.2682 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2543 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9096 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9350 Z= 0.117 Angle : 0.494 6.302 13060 Z= 0.292 Chirality : 0.038 0.164 1467 Planarity : 0.004 0.045 1315 Dihedral : 20.580 166.408 2280 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.62 % Allowed : 12.30 % Favored : 86.08 % 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: 1.20 (0.29), residues: 845 helix: 1.94 (0.27), residues: 410 sheet: 0.68 (0.47), residues: 124 loop : -0.72 (0.32), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 383 TYR 0.015 0.001 TYR A 214 PHE 0.006 0.001 PHE A 35 TRP 0.011 0.001 TRP A 24 HIS 0.003 0.000 HIS A 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00206 / 0.12 ( 9350) covalent geometry : angle 0.49414 / 0.29 (13060) hydrogen bonds : bond 0.04714 / 3.09 ( 425) hydrogen bonds : angle 3.72533 / 2.71 ( 1128) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 0.299 Fit side-chains REVERT: A 87 LYS cc_start: 0.8732 (ttmp) cc_final: 0.8477 (tptp) REVERT: A 182 ARG cc_start: 0.8691 (OUTLIER) cc_final: 0.8490 (ttp-170) REVERT: A 394 ARG cc_start: 0.8590 (mmm160) cc_final: 0.8245 (mpp-170) REVERT: A 669 ARG cc_start: 0.8606 (mtp180) cc_final: 0.7878 (mtt180) REVERT: A 673 LEU cc_start: 0.9245 (tp) cc_final: 0.9005 (tp) outliers start: 12 outliers final: 6 residues processed: 71 average time/residue: 0.6353 time to fit residues: 47.4151 Evaluate side-chains 67 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 60 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 ARG Chi-restraints excluded: chain A residue 201 GLU Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain A residue 634 ARG Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain A residue 830 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 57 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 36 optimal weight: 6.9990 chunk 43 optimal weight: 4.9990 chunk 91 optimal weight: 7.9990 chunk 64 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 86 optimal weight: 10.0000 chunk 60 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.111285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.081713 restraints weight = 11690.026| |-----------------------------------------------------------------------------| r_work (start): 0.2853 rms_B_bonded: 1.85 r_work: 0.2581 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2439 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9171 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 9350 Z= 0.217 Angle : 0.590 6.578 13060 Z= 0.337 Chirality : 0.045 0.231 1467 Planarity : 0.005 0.049 1315 Dihedral : 20.596 165.405 2280 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.30 % Allowed : 12.84 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.01 (0.29), residues: 845 helix: 1.82 (0.26), residues: 406 sheet: 0.69 (0.48), residues: 124 loop : -0.87 (0.31), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 383 TYR 0.017 0.001 TYR A 214 PHE 0.011 0.002 PHE A 35 TRP 0.015 0.002 TRP A 323 HIS 0.006 0.001 HIS A 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.22 ( 9350) covalent geometry : angle 0.59027 / 0.34 (13060) hydrogen bonds : bond 0.06510 / 4.21 ( 425) hydrogen bonds : angle 3.84370 / 2.78 ( 1128) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 62 time to evaluate : 0.277 Fit side-chains REVERT: A 87 LYS cc_start: 0.8856 (ttmp) cc_final: 0.8631 (tttm) REVERT: A 182 ARG cc_start: 0.8764 (OUTLIER) cc_final: 0.8421 (ttp-170) REVERT: A 394 ARG cc_start: 0.8661 (mmm160) cc_final: 0.8296 (mpp-170) REVERT: A 669 ARG cc_start: 0.8611 (mtp180) cc_final: 0.7895 (mtt180) REVERT: A 673 LEU cc_start: 0.9312 (tp) cc_final: 0.9049 (tp) REVERT: A 847 LYS cc_start: 0.7987 (mptm) cc_final: 0.7774 (mttt) outliers start: 17 outliers final: 12 residues processed: 76 average time/residue: 0.5980 time to fit residues: 48.0752 Evaluate side-chains 71 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 58 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 182 ARG Chi-restraints excluded: chain A residue 201 GLU Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain A residue 634 ARG Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain A residue 830 THR Chi-restraints excluded: chain A residue 866 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 21 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.111616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.082154 restraints weight = 11699.994| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 1.85 r_work: 0.2580 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2439 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9180 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9350 Z= 0.183 Angle : 0.571 6.545 13060 Z= 0.328 Chirality : 0.042 0.230 1467 Planarity : 0.004 0.049 1315 Dihedral : 20.598 165.419 2280 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.62 % Allowed : 13.92 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.97 (0.29), residues: 845 helix: 1.77 (0.26), residues: 407 sheet: 0.65 (0.48), residues: 124 loop : -0.87 (0.31), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 383 TYR 0.016 0.001 TYR A 214 PHE 0.011 0.001 PHE A 35 TRP 0.016 0.001 TRP A 323 HIS 0.005 0.001 HIS A 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.18 ( 9350) covalent geometry : angle 0.57104 / 0.33 (13060) hydrogen bonds : bond 0.06254 / 4.05 ( 425) hydrogen bonds : angle 3.84206 / 2.78 ( 1128) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 0.211 Fit side-chains REVERT: A 87 LYS cc_start: 0.8885 (ttmp) cc_final: 0.8658 (tttm) REVERT: A 182 ARG cc_start: 0.8748 (OUTLIER) cc_final: 0.8494 (ttp-170) REVERT: A 394 ARG cc_start: 0.8678 (mmm160) cc_final: 0.8304 (mpp-170) REVERT: A 669 ARG cc_start: 0.8630 (mtp180) cc_final: 0.7925 (mtt180) REVERT: A 847 LYS cc_start: 0.8028 (mptm) cc_final: 0.7798 (mttt) outliers start: 12 outliers final: 10 residues processed: 70 average time/residue: 0.6816 time to fit residues: 50.1576 Evaluate side-chains 69 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 182 ARG Chi-restraints excluded: chain A residue 201 GLU Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain A residue 634 ARG Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain A residue 830 THR Chi-restraints excluded: chain A residue 866 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 30 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 73 optimal weight: 0.6980 chunk 58 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 49 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 88 optimal weight: 6.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.112518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.083148 restraints weight = 11825.583| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 1.94 r_work: 0.2591 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2450 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9168 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9350 Z= 0.151 Angle : 0.541 6.577 13060 Z= 0.314 Chirality : 0.041 0.222 1467 Planarity : 0.004 0.048 1315 Dihedral : 20.574 165.865 2280 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.76 % Allowed : 14.46 % Favored : 83.78 % 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: 1.05 (0.29), residues: 845 helix: 1.85 (0.26), residues: 407 sheet: 0.65 (0.48), residues: 124 loop : -0.83 (0.32), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 116 TYR 0.016 0.001 TYR A 214 PHE 0.009 0.001 PHE A 35 TRP 0.015 0.001 TRP A 323 HIS 0.005 0.001 HIS A 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.15 ( 9350) covalent geometry : angle 0.54148 / 0.31 (13060) hydrogen bonds : bond 0.05803 / 3.77 ( 425) hydrogen bonds : angle 3.79658 / 2.74 ( 1128) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 0.298 Fit side-chains REVERT: A 87 LYS cc_start: 0.8844 (ttmp) cc_final: 0.8621 (tttm) REVERT: A 182 ARG cc_start: 0.8736 (OUTLIER) cc_final: 0.8501 (ttp-170) REVERT: A 394 ARG cc_start: 0.8691 (mmm160) cc_final: 0.8304 (mpp-170) REVERT: A 669 ARG cc_start: 0.8623 (mtp180) cc_final: 0.7919 (mtt180) REVERT: A 847 LYS cc_start: 0.8022 (mptm) cc_final: 0.7808 (mttt) outliers start: 13 outliers final: 12 residues processed: 73 average time/residue: 0.6245 time to fit residues: 48.1539 Evaluate side-chains 73 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 60 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 182 ARG Chi-restraints excluded: chain A residue 201 GLU Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain A residue 634 ARG Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain A residue 830 THR Chi-restraints excluded: chain A residue 866 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 72 optimal weight: 5.9990 chunk 23 optimal weight: 8.9990 chunk 65 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 91 optimal weight: 7.9990 chunk 63 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.112536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.083233 restraints weight = 11669.809| |-----------------------------------------------------------------------------| r_work (start): 0.2881 rms_B_bonded: 1.93 r_work: 0.2594 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2452 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9167 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9350 Z= 0.156 Angle : 0.543 6.620 13060 Z= 0.314 Chirality : 0.041 0.218 1467 Planarity : 0.004 0.048 1315 Dihedral : 20.553 166.040 2280 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.76 % Allowed : 14.73 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.07 (0.29), residues: 845 helix: 1.83 (0.26), residues: 411 sheet: 0.63 (0.48), residues: 124 loop : -0.79 (0.32), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 383 TYR 0.016 0.001 TYR A 214 PHE 0.009 0.001 PHE A 35 TRP 0.014 0.001 TRP A 323 HIS 0.005 0.001 HIS A 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.16 ( 9350) covalent geometry : angle 0.54295 / 0.31 (13060) hydrogen bonds : bond 0.05770 / 3.75 ( 425) hydrogen bonds : angle 3.78072 / 2.73 ( 1128) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 0.230 Fit side-chains REVERT: A 87 LYS cc_start: 0.8854 (ttmp) cc_final: 0.8629 (tttm) REVERT: A 182 ARG cc_start: 0.8736 (OUTLIER) cc_final: 0.8503 (ttp-170) REVERT: A 394 ARG cc_start: 0.8677 (mmm160) cc_final: 0.8309 (mpp-170) REVERT: A 669 ARG cc_start: 0.8627 (mtp180) cc_final: 0.7923 (mtt180) REVERT: A 847 LYS cc_start: 0.8033 (mptm) cc_final: 0.7818 (mttt) outliers start: 13 outliers final: 11 residues processed: 73 average time/residue: 0.5962 time to fit residues: 45.8803 Evaluate side-chains 74 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 182 ARG Chi-restraints excluded: chain A residue 201 GLU Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain A residue 634 ARG Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain A residue 830 THR Chi-restraints excluded: chain A residue 866 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 77 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 chunk 88 optimal weight: 8.9990 chunk 49 optimal weight: 0.7980 chunk 14 optimal weight: 6.9990 chunk 29 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.110270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.080894 restraints weight = 11702.161| |-----------------------------------------------------------------------------| r_work (start): 0.2842 rms_B_bonded: 1.92 r_work: 0.2548 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2406 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9201 moved from start: 0.1498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 9350 Z= 0.258 Angle : 0.630 6.625 13060 Z= 0.355 Chirality : 0.046 0.242 1467 Planarity : 0.005 0.049 1315 Dihedral : 20.608 164.893 2279 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.89 % Allowed : 14.86 % Favored : 83.24 % 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: 0.85 (0.28), residues: 845 helix: 1.76 (0.26), residues: 400 sheet: 0.54 (0.49), residues: 117 loop : -0.94 (0.30), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 383 TYR 0.017 0.002 TYR A 214 PHE 0.013 0.002 PHE A 35 TRP 0.016 0.002 TRP A 323 HIS 0.005 0.001 HIS A 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00585 / 0.26 ( 9350) covalent geometry : angle 0.63011 / 0.35 (13060) hydrogen bonds : bond 0.06981 / 4.50 ( 425) hydrogen bonds : angle 3.89376 / 2.81 ( 1128) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 63 time to evaluate : 0.217 Fit side-chains REVERT: A 87 LYS cc_start: 0.8898 (ttmp) cc_final: 0.8696 (tptt) REVERT: A 182 ARG cc_start: 0.8791 (OUTLIER) cc_final: 0.8416 (ttp-170) REVERT: A 394 ARG cc_start: 0.8716 (mmm160) cc_final: 0.8323 (mpp-170) REVERT: A 669 ARG cc_start: 0.8633 (mtp180) cc_final: 0.7940 (mtt180) outliers start: 14 outliers final: 11 residues processed: 74 average time/residue: 0.6365 time to fit residues: 49.6958 Evaluate side-chains 72 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 182 ARG Chi-restraints excluded: chain A residue 201 GLU Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain A residue 634 ARG Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain A residue 830 THR Chi-restraints excluded: chain A residue 866 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 21 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 50 optimal weight: 0.5980 chunk 54 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 73 optimal weight: 0.8980 chunk 71 optimal weight: 0.5980 chunk 60 optimal weight: 0.8980 chunk 82 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.113722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.084452 restraints weight = 11641.657| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 1.91 r_work: 0.2621 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2480 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9145 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9350 Z= 0.128 Angle : 0.525 6.625 13060 Z= 0.307 Chirality : 0.039 0.204 1467 Planarity : 0.004 0.047 1315 Dihedral : 20.563 166.257 2279 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.35 % Allowed : 15.41 % Favored : 83.24 % 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: 1.06 (0.29), residues: 845 helix: 1.86 (0.26), residues: 411 sheet: 0.63 (0.48), residues: 124 loop : -0.84 (0.32), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 638 TYR 0.015 0.001 TYR A 214 PHE 0.009 0.001 PHE A 339 TRP 0.014 0.001 TRP A 323 HIS 0.004 0.001 HIS A 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.13 ( 9350) covalent geometry : angle 0.52491 / 0.31 (13060) hydrogen bonds : bond 0.05287 / 3.47 ( 425) hydrogen bonds : angle 3.74740 / 2.71 ( 1128) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.265 Fit side-chains REVERT: A 87 LYS cc_start: 0.8790 (ttmp) cc_final: 0.8570 (tttm) REVERT: A 182 ARG cc_start: 0.8713 (OUTLIER) cc_final: 0.8473 (ttp-170) REVERT: A 394 ARG cc_start: 0.8663 (mmm160) cc_final: 0.8303 (mpp-170) REVERT: A 669 ARG cc_start: 0.8598 (mtp180) cc_final: 0.7882 (mtt180) outliers start: 10 outliers final: 10 residues processed: 72 average time/residue: 0.6234 time to fit residues: 47.4046 Evaluate side-chains 73 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 62 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain A residue 182 ARG Chi-restraints excluded: chain A residue 201 GLU Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain A residue 634 ARG Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain A residue 830 THR Chi-restraints excluded: chain A residue 866 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 1 optimal weight: 0.6980 chunk 25 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 77 optimal weight: 4.9990 chunk 88 optimal weight: 8.9990 chunk 30 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.113146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.083419 restraints weight = 11548.953| |-----------------------------------------------------------------------------| r_work (start): 0.2879 rms_B_bonded: 1.89 r_work: 0.2600 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2456 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9157 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9350 Z= 0.139 Angle : 0.521 6.676 13060 Z= 0.303 Chirality : 0.039 0.207 1467 Planarity : 0.004 0.049 1315 Dihedral : 20.526 166.432 2279 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.49 % Allowed : 15.41 % Favored : 83.11 % 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: 1.10 (0.29), residues: 845 helix: 1.89 (0.26), residues: 411 sheet: 0.69 (0.48), residues: 124 loop : -0.83 (0.32), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 638 TYR 0.016 0.001 TYR A 214 PHE 0.010 0.001 PHE A 339 TRP 0.013 0.001 TRP A 323 HIS 0.005 0.001 HIS A 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.14 ( 9350) covalent geometry : angle 0.52072 / 0.30 (13060) hydrogen bonds : bond 0.05410 / 3.52 ( 425) hydrogen bonds : angle 3.71795 / 2.69 ( 1128) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2474.36 seconds wall clock time: 42 minutes 48.40 seconds (2568.40 seconds total)