Starting phenix.real_space_refine on Thu Jul 2 13:43:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y9n_39084/07_2026/8y9n_39084.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y9n_39084/07_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_39084/07_2026/8y9n_39084.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y9n_39084/07_2026/8y9n_39084.map" model { file = "/net/cci-nas-00/data/ceres_data/8y9n_39084/07_2026/8y9n_39084.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y9n_39084/07_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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/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: 1.65, per 1000 atoms: 0.18 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: 0.86 Conformation dependent library (CDL) restraints added in 228.2 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: 1.08 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: 1.74 Time building geometry restraints manager: 1.07 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=" 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 bond pdb=" O3' DG D 11 " pdb=" P DT D 12 " ideal model delta sigma weight residual 1.607 1.475 0.132 1.50e-02 4.44e+03 7.75e+01 bond pdb=" C ARG A 630 " pdb=" O ARG A 630 " ideal model delta sigma weight residual 1.237 1.132 0.105 1.19e-02 7.06e+03 7.72e+01 ... (remaining 9345 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.32: 12712 3.32 - 6.65: 306 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: 2.170 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: 0.020 Extract box with map and model: 0.110 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 9.590 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.950 ------------------------------------------------------------------------------- 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= 0.823 Angle : 1.146 16.620 13060 Z= 0.754 Chirality : 0.079 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 0.01155 / 0.82 ( 9350) covalent geometry : angle 1.14570 / 0.75 (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: 0.7219 time to fit residues: 78.9048 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 : 0.266 ------------------------------------------------------------------------------- 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: 0.1980 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3344 r_free = 0.3344 target = 0.113380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.083281 restraints weight = 11732.408| |-----------------------------------------------------------------------------| r_work (start): 0.2879 rms_B_bonded: 2.11 r_work: 0.2591 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2450 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9166 moved from start: 0.1106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9350 Z= 0.149 Angle : 0.604 7.848 13060 Z= 0.353 Chirality : 0.044 0.314 1467 Planarity : 0.005 0.047 1315 Dihedral : 21.072 162.454 2301 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.16 % Allowed : 9.46 % Favored : 88.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.28), residues: 845 helix: 1.45 (0.26), residues: 405 sheet: 0.50 (0.47), residues: 124 loop : -0.95 (0.31), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 116 TYR 0.018 0.001 TYR A 214 PHE 0.008 0.001 PHE A 35 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 0.00281 / 0.15 ( 9350) covalent geometry : angle 0.60398 / 0.35 (13060) hydrogen bonds : bond 0.06210 / 4.07 ( 425) hydrogen bonds : angle 4.17032 / 3.03 ( 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 88 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 72 time to evaluate : 0.294 Fit side-chains REVERT: A 138 GLU cc_start: 0.7501 (tp30) cc_final: 0.6721 (tm-30) REVERT: A 182 ARG cc_start: 0.8762 (OUTLIER) cc_final: 0.8544 (ttp-170) REVERT: A 394 ARG cc_start: 0.8677 (mmm160) cc_final: 0.8289 (mpp-170) REVERT: A 669 ARG cc_start: 0.8586 (mtp180) cc_final: 0.7915 (mmt180) REVERT: A 673 LEU cc_start: 0.9292 (tp) cc_final: 0.9038 (tp) outliers start: 16 outliers final: 10 residues processed: 83 average time/residue: 0.7024 time to fit residues: 61.5292 Evaluate side-chains 72 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 61 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 ILE 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: 0.0270 chunk 21 optimal weight: 0.9990 chunk 58 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 17 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 overall best weight: 2.0044 ------------------------------------------------------------------------------- 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 = 0.3311 r_free = 0.3311 target = 0.111040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.081760 restraints weight = 11711.252| |-----------------------------------------------------------------------------| r_work (start): 0.2855 rms_B_bonded: 1.95 r_work: 0.2564 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2423 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9192 moved from start: 0.1159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9350 Z= 0.203 Angle : 0.599 6.188 13060 Z= 0.348 Chirality : 0.045 0.277 1467 Planarity : 0.005 0.048 1315 Dihedral : 20.774 163.566 2283 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.03 % Allowed : 12.03 % Favored : 85.95 % 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: 0.71 (0.28), residues: 845 helix: 1.54 (0.26), residues: 406 sheet: 0.56 (0.47), residues: 124 loop : -0.97 (0.30), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 383 TYR 0.017 0.001 TYR A 214 PHE 0.011 0.001 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 0.00435 / 0.20 ( 9350) covalent geometry : angle 0.59902 / 0.35 (13060) hydrogen bonds : bond 0.06829 / 4.44 ( 425) hydrogen bonds : angle 4.03091 / 2.92 ( 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 77 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 62 time to evaluate : 0.307 Fit side-chains REVERT: A 87 LYS cc_start: 0.8941 (ttmp) cc_final: 0.8663 (tttm) REVERT: A 138 GLU cc_start: 0.7461 (tp30) cc_final: 0.6666 (tm-30) REVERT: A 182 ARG cc_start: 0.8772 (OUTLIER) cc_final: 0.8521 (ttp-170) REVERT: A 394 ARG cc_start: 0.8674 (mmm160) cc_final: 0.8303 (mpp-170) REVERT: A 669 ARG cc_start: 0.8643 (mtp180) cc_final: 0.7895 (mtt-85) REVERT: A 673 LEU cc_start: 0.9320 (tp) cc_final: 0.9053 (tp) outliers start: 15 outliers final: 11 residues processed: 74 average time/residue: 0.7860 time to fit residues: 61.1262 Evaluate side-chains 71 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 150 ILE 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 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: 0.0170 chunk 31 optimal weight: 0.0000 chunk 92 optimal weight: 9.9990 chunk 42 optimal weight: 1.9990 chunk 62 optimal weight: 0.0050 chunk 15 optimal weight: 7.9990 chunk 70 optimal weight: 6.9990 chunk 76 optimal weight: 5.9990 chunk 65 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 overall best weight: 0.5238 ------------------------------------------------------------------------------- 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 = 0.3368 r_free = 0.3368 target = 0.115018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.086151 restraints weight = 11814.633| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 1.79 r_work: 0.2647 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2507 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9141 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9350 Z= 0.119 Angle : 0.505 5.951 13060 Z= 0.300 Chirality : 0.040 0.236 1467 Planarity : 0.004 0.046 1315 Dihedral : 20.602 165.059 2280 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.76 % Allowed : 12.57 % Favored : 85.68 % 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: 0.65 (0.48), residues: 124 loop : -0.85 (0.31), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 116 TYR 0.016 0.001 TYR A 214 PHE 0.007 0.001 PHE A 633 TRP 0.011 0.001 TRP A 323 HIS 0.003 0.001 HIS A 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.12 ( 9350) covalent geometry : angle 0.50464 / 0.30 (13060) hydrogen bonds : bond 0.05005 / 3.29 ( 425) hydrogen bonds : angle 3.81138 / 2.77 ( 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 77 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 0.313 Fit side-chains REVERT: A 87 LYS cc_start: 0.8801 (ttmp) cc_final: 0.8555 (tptp) REVERT: A 182 ARG cc_start: 0.8704 (OUTLIER) cc_final: 0.8477 (ttp-170) REVERT: A 394 ARG cc_start: 0.8608 (mmm160) cc_final: 0.8286 (mpp-170) REVERT: A 669 ARG cc_start: 0.8599 (mtp180) cc_final: 0.7901 (mtt180) REVERT: A 673 LEU cc_start: 0.9307 (tp) cc_final: 0.9071 (tp) outliers start: 13 outliers final: 7 residues processed: 72 average time/residue: 0.7866 time to fit residues: 59.6919 Evaluate side-chains 67 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 59 time to evaluate : 0.303 ------------------------------------------------------------------------------- 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 526 SER 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: 4.9990 chunk 54 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 91 optimal weight: 7.9990 chunk 64 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 86 optimal weight: 10.0000 chunk 60 optimal weight: 3.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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 = 0.3298 r_free = 0.3298 target = 0.110170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.080602 restraints weight = 11711.390| |-----------------------------------------------------------------------------| r_work (start): 0.2835 rms_B_bonded: 1.90 r_work: 0.2553 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2412 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9210 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 9350 Z= 0.251 Angle : 0.613 6.293 13060 Z= 0.351 Chirality : 0.046 0.292 1467 Planarity : 0.005 0.051 1315 Dihedral : 20.649 163.758 2280 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.43 % Allowed : 12.84 % Favored : 84.73 % 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: 0.81 (0.28), residues: 845 helix: 1.67 (0.26), residues: 405 sheet: 0.59 (0.48), residues: 124 loop : -0.99 (0.31), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 383 TYR 0.018 0.002 TYR A 214 PHE 0.011 0.002 PHE A 339 TRP 0.017 0.002 TRP A 323 HIS 0.006 0.001 HIS A 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00559 / 0.25 ( 9350) covalent geometry : angle 0.61298 / 0.35 (13060) hydrogen bonds : bond 0.07023 / 4.54 ( 425) hydrogen bonds : angle 3.94914 / 2.86 ( 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 75 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 57 time to evaluate : 0.320 Fit side-chains REVERT: A 87 LYS cc_start: 0.8927 (ttmp) cc_final: 0.8697 (tttm) REVERT: A 182 ARG cc_start: 0.8799 (OUTLIER) cc_final: 0.8432 (ttp-170) REVERT: A 394 ARG cc_start: 0.8667 (mmm160) cc_final: 0.8303 (mpp-170) REVERT: A 669 ARG cc_start: 0.8624 (mtp180) cc_final: 0.7938 (mtt180) REVERT: A 674 VAL cc_start: 0.9068 (OUTLIER) cc_final: 0.8838 (t) REVERT: A 847 LYS cc_start: 0.8026 (OUTLIER) cc_final: 0.7800 (mttt) outliers start: 18 outliers final: 11 residues processed: 72 average time/residue: 0.7687 time to fit residues: 58.4244 Evaluate side-chains 70 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 56 time to evaluate : 0.320 ------------------------------------------------------------------------------- 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 674 VAL 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 847 LYS 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: 0.8980 chunk 17 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 72 optimal weight: 5.9990 chunk 15 optimal weight: 0.5980 chunk 43 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.112914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.083748 restraints weight = 11701.224| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 1.82 r_work: 0.2608 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2466 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9161 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9350 Z= 0.131 Angle : 0.526 6.214 13060 Z= 0.309 Chirality : 0.040 0.262 1467 Planarity : 0.004 0.048 1315 Dihedral : 20.598 164.778 2280 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.03 % Allowed : 14.05 % Favored : 83.92 % 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 are not related in a simple way. whole: 0.99 (0.29), residues: 845 helix: 1.83 (0.26), residues: 406 sheet: 0.61 (0.48), residues: 124 loop : -0.89 (0.31), residues: 315 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 35 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 0.00254 / 0.13 ( 9350) covalent geometry : angle 0.52623 / 0.31 (13060) hydrogen bonds : bond 0.05554 / 3.62 ( 425) hydrogen bonds : angle 3.84054 / 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 78 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 63 time to evaluate : 0.307 Fit side-chains REVERT: A 87 LYS cc_start: 0.8824 (ttmp) cc_final: 0.8611 (tttm) REVERT: A 182 ARG cc_start: 0.8722 (OUTLIER) cc_final: 0.8485 (ttp-170) REVERT: A 394 ARG cc_start: 0.8654 (mmm160) cc_final: 0.8312 (mpp-170) REVERT: A 669 ARG cc_start: 0.8607 (mtp180) cc_final: 0.7900 (mtt180) REVERT: A 673 LEU cc_start: 0.9323 (tp) cc_final: 0.9054 (tp) REVERT: A 847 LYS cc_start: 0.8028 (OUTLIER) cc_final: 0.7762 (mttt) outliers start: 15 outliers final: 11 residues processed: 73 average time/residue: 0.7592 time to fit residues: 58.5768 Evaluate side-chains 72 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 59 time to evaluate : 0.299 ------------------------------------------------------------------------------- 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 234 ASN 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 847 LYS 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: 5.9990 chunk 1 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 2 optimal weight: 4.9990 chunk 73 optimal weight: 7.9990 chunk 58 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 49 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 88 optimal weight: 6.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- 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 = 0.3321 r_free = 0.3321 target = 0.111595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.082254 restraints weight = 11847.778| |-----------------------------------------------------------------------------| r_work (start): 0.2865 rms_B_bonded: 1.95 r_work: 0.2574 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2432 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9183 moved from start: 0.1456 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= 0.186 Angle : 0.562 6.335 13060 Z= 0.326 Chirality : 0.043 0.279 1467 Planarity : 0.004 0.049 1315 Dihedral : 20.575 164.453 2280 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.16 % Allowed : 14.46 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.29), residues: 845 helix: 1.80 (0.26), residues: 406 sheet: 0.61 (0.48), residues: 124 loop : -0.92 (0.31), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 383 TYR 0.017 0.001 TYR A 214 PHE 0.010 0.001 PHE A 35 TRP 0.015 0.002 TRP A 323 HIS 0.005 0.001 HIS A 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.19 ( 9350) covalent geometry : angle 0.56164 / 0.33 (13060) hydrogen bonds : bond 0.06104 / 3.97 ( 425) hydrogen bonds : angle 3.84417 / 2.79 ( 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 76 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 60 time to evaluate : 0.236 Fit side-chains REVERT: A 87 LYS cc_start: 0.8883 (ttmp) cc_final: 0.8656 (tttm) REVERT: A 182 ARG cc_start: 0.8772 (OUTLIER) cc_final: 0.8519 (ttp-170) REVERT: A 394 ARG cc_start: 0.8694 (mmm160) cc_final: 0.8309 (mpp-170) REVERT: A 669 ARG cc_start: 0.8630 (mtp180) cc_final: 0.7924 (mtt180) REVERT: A 847 LYS cc_start: 0.8047 (OUTLIER) cc_final: 0.7793 (mttt) outliers start: 16 outliers final: 13 residues processed: 72 average time/residue: 0.7676 time to fit residues: 58.4549 Evaluate side-chains 74 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 59 time to evaluate : 0.321 ------------------------------------------------------------------------------- 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 234 ASN 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 847 LYS 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: 10.0000 chunk 65 optimal weight: 4.9990 chunk 69 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 91 optimal weight: 7.9990 chunk 63 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 = 0.3329 r_free = 0.3329 target = 0.112144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.082918 restraints weight = 11669.607| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 1.91 r_work: 0.2585 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2444 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9175 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9350 Z= 0.158 Angle : 0.543 6.335 13060 Z= 0.317 Chirality : 0.041 0.274 1467 Planarity : 0.004 0.049 1315 Dihedral : 20.562 164.625 2280 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.03 % Allowed : 14.73 % 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: 0.98 (0.29), residues: 845 helix: 1.83 (0.26), residues: 406 sheet: 0.60 (0.48), residues: 124 loop : -0.90 (0.31), residues: 315 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 0.010 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 0.00330 / 0.16 ( 9350) covalent geometry : angle 0.54288 / 0.32 (13060) hydrogen bonds : bond 0.05813 / 3.78 ( 425) hydrogen bonds : angle 3.81646 / 2.76 ( 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 76 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 61 time to evaluate : 0.325 Fit side-chains REVERT: A 87 LYS cc_start: 0.8862 (ttmp) cc_final: 0.8637 (tttm) REVERT: A 182 ARG cc_start: 0.8744 (OUTLIER) cc_final: 0.8510 (ttp-170) REVERT: A 394 ARG cc_start: 0.8692 (mmm160) cc_final: 0.8310 (mpp-170) REVERT: A 669 ARG cc_start: 0.8618 (mtp180) cc_final: 0.7921 (mtt180) REVERT: A 847 LYS cc_start: 0.8047 (OUTLIER) cc_final: 0.7791 (mttt) outliers start: 15 outliers final: 14 residues processed: 73 average time/residue: 0.7683 time to fit residues: 59.1628 Evaluate side-chains 76 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 60 time to evaluate : 0.293 ------------------------------------------------------------------------------- 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 234 ASN 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 778 TYR Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain A residue 830 THR Chi-restraints excluded: chain A residue 847 LYS 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: 5.9990 chunk 48 optimal weight: 6.9990 chunk 69 optimal weight: 0.0970 chunk 80 optimal weight: 2.9990 chunk 88 optimal weight: 7.9990 chunk 49 optimal weight: 2.9990 chunk 14 optimal weight: 6.9990 chunk 29 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- 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 = 0.3310 r_free = 0.3310 target = 0.110811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.081371 restraints weight = 11682.736| |-----------------------------------------------------------------------------| r_work (start): 0.2851 rms_B_bonded: 1.95 r_work: 0.2559 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2417 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9194 moved from start: 0.1485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 9350 Z= 0.217 Angle : 0.587 6.375 13060 Z= 0.338 Chirality : 0.044 0.294 1467 Planarity : 0.004 0.049 1315 Dihedral : 20.586 163.934 2280 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.16 % Allowed : 15.00 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.28), residues: 845 helix: 1.74 (0.26), residues: 406 sheet: 0.54 (0.48), residues: 124 loop : -0.95 (0.31), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 383 TYR 0.017 0.001 TYR A 214 PHE 0.011 0.001 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 0.00483 / 0.22 ( 9350) covalent geometry : angle 0.58714 / 0.34 (13060) hydrogen bonds : bond 0.06490 / 4.20 ( 425) hydrogen bonds : angle 3.86814 / 2.79 ( 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 78 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 62 time to evaluate : 0.320 Fit side-chains REVERT: A 87 LYS cc_start: 0.8887 (ttmp) cc_final: 0.8654 (tttm) REVERT: A 182 ARG cc_start: 0.8781 (OUTLIER) cc_final: 0.8426 (ttp-170) REVERT: A 394 ARG cc_start: 0.8715 (mmm160) cc_final: 0.8322 (mpp-170) REVERT: A 669 ARG cc_start: 0.8638 (mtp180) cc_final: 0.7933 (mtt180) REVERT: A 847 LYS cc_start: 0.8105 (OUTLIER) cc_final: 0.7841 (mttt) outliers start: 16 outliers final: 12 residues processed: 75 average time/residue: 0.7581 time to fit residues: 60.1027 Evaluate side-chains 75 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 61 time to evaluate : 0.310 ------------------------------------------------------------------------------- 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 847 LYS 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: 1.9990 chunk 1 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 73 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 82 optimal weight: 0.0270 overall best weight: 1.1442 ------------------------------------------------------------------------------- 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 = 0.3331 r_free = 0.3331 target = 0.112267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.082880 restraints weight = 11632.459| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 1.85 r_work: 0.2592 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2449 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9172 moved from start: 0.1552 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 : 0.540 6.369 13060 Z= 0.316 Chirality : 0.041 0.274 1467 Planarity : 0.004 0.049 1315 Dihedral : 20.563 164.411 2280 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.76 % Allowed : 15.41 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.29), residues: 845 helix: 1.84 (0.26), residues: 406 sheet: 0.58 (0.48), residues: 124 loop : -0.93 (0.31), residues: 315 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 0.015 0.001 TRP A 323 HIS 0.005 0.001 HIS A 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.15 ( 9350) covalent geometry : angle 0.53954 / 0.32 (13060) hydrogen bonds : bond 0.05722 / 3.73 ( 425) hydrogen bonds : angle 3.81385 / 2.75 ( 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 75 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 0.376 Fit side-chains REVERT: A 87 LYS cc_start: 0.8858 (ttmp) cc_final: 0.8633 (tttm) REVERT: A 182 ARG cc_start: 0.8749 (OUTLIER) cc_final: 0.8514 (ttp-170) REVERT: A 394 ARG cc_start: 0.8680 (mmm160) cc_final: 0.8323 (mpp-170) REVERT: A 669 ARG cc_start: 0.8610 (mtp180) cc_final: 0.7913 (mtt180) REVERT: A 847 LYS cc_start: 0.8086 (OUTLIER) cc_final: 0.7819 (mttt) outliers start: 13 outliers final: 12 residues processed: 72 average time/residue: 0.7753 time to fit residues: 58.8767 Evaluate side-chains 74 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 60 time to evaluate : 0.306 ------------------------------------------------------------------------------- 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 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 847 LYS 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: 0.0970 chunk 25 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 16 optimal weight: 8.9990 chunk 77 optimal weight: 4.9990 chunk 88 optimal weight: 7.9990 chunk 30 optimal weight: 0.9980 chunk 84 optimal weight: 0.0670 chunk 73 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 overall best weight: 1.4320 ------------------------------------------------------------------------------- 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 = 0.3321 r_free = 0.3321 target = 0.111846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.081643 restraints weight = 11557.699| |-----------------------------------------------------------------------------| r_work (start): 0.2852 rms_B_bonded: 1.89 r_work: 0.2578 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2435 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9177 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9350 Z= 0.161 Angle : 0.542 6.388 13060 Z= 0.316 Chirality : 0.041 0.278 1467 Planarity : 0.004 0.049 1315 Dihedral : 20.544 164.342 2279 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.76 % Allowed : 15.54 % Favored : 82.70 % 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: 1.84 (0.26), residues: 406 sheet: 0.59 (0.48), residues: 124 loop : -0.94 (0.31), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 383 TYR 0.016 0.001 TYR A 214 PHE 0.010 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 0.00340 / 0.16 ( 9350) covalent geometry : angle 0.54205 / 0.32 (13060) hydrogen bonds : bond 0.05816 / 3.78 ( 425) hydrogen bonds : angle 3.80239 / 2.74 ( 1128) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2941.58 seconds wall clock time: 51 minutes 1.10 seconds (3061.10 seconds total)