Starting phenix.real_space_refine on Wed Sep 17 13:27:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y9n_39084/09_2025/8y9n_39084.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y9n_39084/09_2025/8y9n_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 { model { file = "/net/cci-nas-00/data/ceres_data/8y9n_39084/09_2025/8y9n_39084.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y9n_39084/09_2025/8y9n_39084.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8y9n_39084/09_2025/8y9n_39084.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y9n_39084/09_2025/8y9n_39084.map" } 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-2.0-5805/lib/python3.9/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: 2.54, per 1000 atoms: 0.28 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: 0.97 Conformation dependent library (CDL) restraints added in 253.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 1.32 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: 2.01 Time building geometry restraints manager: 1.26 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 - 3.74: 12814 3.74 - 7.49: 214 7.49 - 11.23: 22 11.23 - 14.98: 5 14.98 - 18.72: 5 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=" O3' DA D 1 " pdb=" C3' DA D 1 " pdb=" C2' DA D 1 " ideal model delta sigma weight residual 111.50 92.78 18.72 1.50e+00 4.44e-01 1.56e+02 angle pdb=" O3' DG D 0 " pdb=" C3' DG D 0 " pdb=" C2' DG D 0 " ideal model delta sigma weight residual 111.50 93.32 18.18 1.50e+00 4.44e-01 1.47e+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=" C4' DG D 0 " pdb=" C3' DG D 0 " pdb=" O3' DG D 0 " ideal model delta sigma weight residual 110.00 96.34 13.66 1.50e+00 4.44e-01 8.29e+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: 1399 0.184 - 0.367: 62 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=" C1' DT D -1 " pdb=" O4' DT D -1 " pdb=" C2' DT D -1 " pdb=" N1 DT D -1 " both_signs ideal model delta sigma weight residual False 2.47 1.96 0.51 2.00e-01 2.50e+01 6.52e+00 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 ... (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: 2.740 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 11.840 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:10.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 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= 0.752 Angle : 1.172 18.720 13060 Z= 0.742 Chirality : 0.081 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 aren 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 covalent geometry : bond 0.01170 ( 9350) covalent geometry : angle 1.17235 (13060) hydrogen bonds : bond 0.19999 ( 425) hydrogen bonds : angle 5.93964 ( 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 : 0.272 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: 0.7845 time to fit residues: 85.5080 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 : 0.350 ------------------------------------------------------------------------------- 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: 0.8980 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: 0.0020 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 overall best weight: 0.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 281 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.114712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.086470 restraints weight = 11750.243| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 1.88 r_work: 0.2635 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2494 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8977 moved from start: 0.1355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9350 Z= 0.138 Angle : 0.542 7.503 13060 Z= 0.306 Chirality : 0.038 0.206 1467 Planarity : 0.004 0.044 1315 Dihedral : 20.642 164.229 2301 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.76 % Allowed : 9.46 % 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 aren not related in a simple way. whole: 0.79 (0.28), residues: 845 helix: 1.64 (0.26), residues: 405 sheet: 0.56 (0.47), residues: 124 loop : -0.96 (0.31), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 116 TYR 0.018 0.001 TYR A 214 PHE 0.008 0.001 PHE A 339 TRP 0.012 0.001 TRP A 323 HIS 0.004 0.001 HIS A 210 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 9350) covalent geometry : angle 0.54229 (13060) hydrogen bonds : bond 0.05284 ( 425) hydrogen bonds : angle 3.90538 ( 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 83 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 70 time to evaluate : 0.252 Fit side-chains REVERT: A 87 LYS cc_start: 0.8811 (ttmp) cc_final: 0.8544 (tptp) REVERT: A 394 ARG cc_start: 0.8632 (mmm160) cc_final: 0.8301 (mpp-170) REVERT: A 669 ARG cc_start: 0.8600 (mtp180) cc_final: 0.7907 (mtt-85) REVERT: A 673 LEU cc_start: 0.9292 (tp) cc_final: 0.9043 (tp) outliers start: 13 outliers final: 8 residues processed: 78 average time/residue: 0.7845 time to fit residues: 64.2882 Evaluate side-chains 68 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 GLU 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 720 LYS 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: 3.9990 chunk 31 optimal weight: 0.4980 chunk 21 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 34 optimal weight: 0.0980 chunk 4 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.114710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.085332 restraints weight = 11674.095| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 1.94 r_work: 0.2634 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2494 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8964 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9350 Z= 0.135 Angle : 0.510 6.396 13060 Z= 0.285 Chirality : 0.037 0.177 1467 Planarity : 0.004 0.045 1315 Dihedral : 20.305 165.921 2280 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.49 % Allowed : 11.76 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.07 (0.29), residues: 845 helix: 1.89 (0.26), residues: 405 sheet: 0.63 (0.47), residues: 124 loop : -0.82 (0.31), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 116 TYR 0.017 0.001 TYR A 214 PHE 0.008 0.001 PHE A 35 TRP 0.011 0.001 TRP A 323 HIS 0.004 0.001 HIS A 210 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 9350) covalent geometry : angle 0.50992 (13060) hydrogen bonds : bond 0.05020 ( 425) hydrogen bonds : angle 3.67486 ( 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 79 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 68 time to evaluate : 0.304 Fit side-chains REVERT: A 87 LYS cc_start: 0.8785 (ttmp) cc_final: 0.8247 (ttpt) REVERT: A 394 ARG cc_start: 0.8652 (mmm160) cc_final: 0.8299 (mpp-170) REVERT: A 669 ARG cc_start: 0.8634 (mtp180) cc_final: 0.7931 (mtt180) REVERT: A 673 LEU cc_start: 0.9270 (tp) cc_final: 0.9036 (tp) outliers start: 11 outliers final: 8 residues processed: 77 average time/residue: 0.7935 time to fit residues: 64.2328 Evaluate side-chains 71 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 1.9990 chunk 28 optimal weight: 0.0370 chunk 31 optimal weight: 0.0970 chunk 92 optimal weight: 4.9990 chunk 42 optimal weight: 0.8980 chunk 62 optimal weight: 4.9990 chunk 15 optimal weight: 0.0970 chunk 70 optimal weight: 7.9990 chunk 76 optimal weight: 5.9990 chunk 65 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 overall best weight: 0.4054 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 GLN A 564 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.118456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.088972 restraints weight = 11782.371| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 1.95 r_work: 0.2711 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2572 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8888 moved from start: 0.2013 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= 0.106 Angle : 0.468 7.287 13060 Z= 0.262 Chirality : 0.035 0.149 1467 Planarity : 0.003 0.045 1315 Dihedral : 20.149 169.421 2279 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.08 % Allowed : 13.24 % 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 aren not related in a simple way. whole: 1.38 (0.29), residues: 845 helix: 2.09 (0.26), residues: 411 sheet: 0.80 (0.47), residues: 124 loop : -0.65 (0.32), residues: 310 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 0.008 0.001 PHE A 657 TRP 0.012 0.001 TRP A 24 HIS 0.003 0.001 HIS A 210 Details of bonding type rmsd covalent geometry : bond 0.00221 ( 9350) covalent geometry : angle 0.46825 (13060) hydrogen bonds : bond 0.03828 ( 425) hydrogen bonds : angle 3.45463 ( 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: 8 poor density : 69 time to evaluate : 0.317 Fit side-chains REVERT: A 87 LYS cc_start: 0.8659 (ttmp) cc_final: 0.8129 (ttpt) REVERT: A 241 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7829 (mp0) REVERT: A 394 ARG cc_start: 0.8615 (mmm160) cc_final: 0.8333 (mpp-170) REVERT: A 669 ARG cc_start: 0.8612 (mtp180) cc_final: 0.7952 (mtt180) REVERT: A 673 LEU cc_start: 0.9233 (tp) cc_final: 0.9004 (tp) outliers start: 8 outliers final: 4 residues processed: 74 average time/residue: 0.7676 time to fit residues: 59.7025 Evaluate side-chains 66 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 61 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 634 ARG 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: 2.9990 chunk 58 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 43 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 86 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 GLN A 281 GLN A 564 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.110810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.080666 restraints weight = 11688.435| |-----------------------------------------------------------------------------| r_work (start): 0.2833 rms_B_bonded: 1.96 r_work: 0.2552 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2409 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9027 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 9350 Z= 0.237 Angle : 0.605 7.096 13060 Z= 0.334 Chirality : 0.042 0.268 1467 Planarity : 0.005 0.048 1315 Dihedral : 20.422 166.468 2278 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.76 % Allowed : 13.38 % 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 aren not related in a simple way. whole: 1.06 (0.29), residues: 845 helix: 1.87 (0.26), residues: 407 sheet: 0.56 (0.47), residues: 129 loop : -0.81 (0.31), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 383 TYR 0.014 0.001 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 covalent geometry : bond 0.00539 ( 9350) covalent geometry : angle 0.60548 (13060) hydrogen bonds : bond 0.06802 ( 425) hydrogen bonds : angle 3.86802 ( 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 78 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 65 time to evaluate : 0.210 Fit side-chains REVERT: A 87 LYS cc_start: 0.8936 (ttmp) cc_final: 0.8387 (ttpt) REVERT: A 138 GLU cc_start: 0.7397 (tp30) cc_final: 0.6731 (tm-30) REVERT: A 294 LYS cc_start: 0.7675 (tmtt) cc_final: 0.7447 (tptt) REVERT: A 394 ARG cc_start: 0.8710 (mmm160) cc_final: 0.8356 (mpp-170) REVERT: A 669 ARG cc_start: 0.8633 (mtp180) cc_final: 0.7932 (mtt180) REVERT: A 671 ASN cc_start: 0.8671 (OUTLIER) cc_final: 0.8453 (p0) outliers start: 13 outliers final: 7 residues processed: 74 average time/residue: 0.8849 time to fit residues: 68.7340 Evaluate side-chains 70 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 62 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 634 ARG Chi-restraints excluded: chain A residue 671 ASN 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: 0.8980 chunk 17 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 72 optimal weight: 5.9990 chunk 15 optimal weight: 9.9990 chunk 43 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.111885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.082581 restraints weight = 11656.442| |-----------------------------------------------------------------------------| r_work (start): 0.2869 rms_B_bonded: 1.91 r_work: 0.2580 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2439 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9005 moved from start: 0.1612 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= 0.184 Angle : 0.555 7.043 13060 Z= 0.310 Chirality : 0.040 0.252 1467 Planarity : 0.004 0.047 1315 Dihedral : 20.327 166.860 2278 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.89 % Allowed : 14.05 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.05 (0.29), residues: 845 helix: 1.91 (0.26), residues: 405 sheet: 0.64 (0.48), residues: 124 loop : -0.90 (0.31), residues: 316 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 0.011 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 covalent geometry : bond 0.00412 ( 9350) covalent geometry : angle 0.55490 (13060) hydrogen bonds : bond 0.05927 ( 425) hydrogen bonds : angle 3.78785 ( 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: 14 poor density : 64 time to evaluate : 0.192 Fit side-chains REVERT: A 87 LYS cc_start: 0.8865 (ttmp) cc_final: 0.8317 (ttpt) REVERT: A 241 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7847 (mp0) REVERT: A 394 ARG cc_start: 0.8672 (mmm160) cc_final: 0.8343 (mpp-170) REVERT: A 669 ARG cc_start: 0.8616 (mtp180) cc_final: 0.7935 (mtt180) outliers start: 14 outliers final: 8 residues processed: 75 average time/residue: 0.7775 time to fit residues: 61.3820 Evaluate side-chains 71 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 62 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 241 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 30 optimal weight: 4.9990 chunk 1 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 73 optimal weight: 0.6980 chunk 58 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 49 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.112528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.082843 restraints weight = 11794.692| |-----------------------------------------------------------------------------| r_work (start): 0.2869 rms_B_bonded: 2.00 r_work: 0.2586 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2444 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9003 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9350 Z= 0.164 Angle : 0.538 6.938 13060 Z= 0.300 Chirality : 0.039 0.239 1467 Planarity : 0.004 0.048 1315 Dihedral : 20.265 167.620 2278 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.49 % Allowed : 15.00 % 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 aren not related in a simple way. whole: 1.13 (0.29), residues: 845 helix: 1.95 (0.26), residues: 409 sheet: 0.64 (0.48), residues: 124 loop : -0.83 (0.32), residues: 312 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 0.013 0.001 TRP A 323 HIS 0.005 0.001 HIS A 210 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 9350) covalent geometry : angle 0.53777 (13060) hydrogen bonds : bond 0.05530 ( 425) hydrogen bonds : angle 3.70948 ( 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: 11 poor density : 65 time to evaluate : 0.343 Fit side-chains REVERT: A 87 LYS cc_start: 0.8834 (ttmp) cc_final: 0.8293 (ttpt) REVERT: A 241 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7880 (mp0) REVERT: A 248 GLU cc_start: 0.8072 (mt-10) cc_final: 0.7793 (mp0) REVERT: A 394 ARG cc_start: 0.8680 (mmm160) cc_final: 0.8365 (mpp-170) REVERT: A 669 ARG cc_start: 0.8611 (mtp180) cc_final: 0.7919 (mtt180) outliers start: 11 outliers final: 9 residues processed: 76 average time/residue: 0.8468 time to fit residues: 67.8438 Evaluate side-chains 75 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 241 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 634 ARG 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 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: 9.9990 chunk 65 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 48 optimal weight: 6.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.112081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.082219 restraints weight = 11620.233| |-----------------------------------------------------------------------------| r_work (start): 0.2860 rms_B_bonded: 1.95 r_work: 0.2584 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2442 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9007 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9350 Z= 0.179 Angle : 0.549 6.836 13060 Z= 0.306 Chirality : 0.039 0.245 1467 Planarity : 0.004 0.048 1315 Dihedral : 20.275 167.753 2278 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.03 % Allowed : 15.14 % 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 aren not related in a simple way. whole: 1.11 (0.29), residues: 845 helix: 1.98 (0.26), residues: 405 sheet: 0.66 (0.48), residues: 124 loop : -0.89 (0.31), residues: 316 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 0.014 0.001 TRP A 323 HIS 0.005 0.001 HIS A 210 Details of bonding type rmsd covalent geometry : bond 0.00401 ( 9350) covalent geometry : angle 0.54867 (13060) hydrogen bonds : bond 0.05740 ( 425) hydrogen bonds : angle 3.72384 ( 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 81 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 66 time to evaluate : 0.328 Fit side-chains REVERT: A 87 LYS cc_start: 0.8831 (ttmp) cc_final: 0.8308 (ttpt) REVERT: A 241 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7851 (mp0) REVERT: A 248 GLU cc_start: 0.8065 (mt-10) cc_final: 0.7792 (mp0) REVERT: A 394 ARG cc_start: 0.8685 (mmm160) cc_final: 0.8363 (mpp-170) REVERT: A 669 ARG cc_start: 0.8618 (mtp180) cc_final: 0.7924 (mtt180) outliers start: 15 outliers final: 10 residues processed: 79 average time/residue: 0.8118 time to fit residues: 67.7414 Evaluate side-chains 75 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 241 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 778 TYR 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: 7.9990 chunk 69 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 31 optimal weight: 0.4980 chunk 35 optimal weight: 3.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.112111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.083031 restraints weight = 11637.829| |-----------------------------------------------------------------------------| r_work (start): 0.2877 rms_B_bonded: 1.88 r_work: 0.2588 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2447 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9000 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9350 Z= 0.178 Angle : 0.549 6.745 13060 Z= 0.306 Chirality : 0.039 0.247 1467 Planarity : 0.004 0.048 1315 Dihedral : 20.270 167.995 2278 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.49 % Allowed : 16.08 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.15 (0.29), residues: 845 helix: 2.04 (0.26), residues: 398 sheet: 0.66 (0.48), residues: 124 loop : -0.84 (0.31), residues: 323 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 0.014 0.001 TRP A 323 HIS 0.005 0.001 HIS A 210 Details of bonding type rmsd covalent geometry : bond 0.00398 ( 9350) covalent geometry : angle 0.54870 (13060) hydrogen bonds : bond 0.05723 ( 425) hydrogen bonds : angle 3.71843 ( 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 76 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.267 Fit side-chains REVERT: A 87 LYS cc_start: 0.8825 (ttmp) cc_final: 0.8292 (ttpt) REVERT: A 241 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7838 (mp0) REVERT: A 248 GLU cc_start: 0.8059 (mt-10) cc_final: 0.7791 (mp0) REVERT: A 394 ARG cc_start: 0.8667 (mmm160) cc_final: 0.8358 (mpp-170) REVERT: A 669 ARG cc_start: 0.8607 (mtp180) cc_final: 0.7912 (mtt180) outliers start: 11 outliers final: 10 residues processed: 76 average time/residue: 0.7748 time to fit residues: 61.9783 Evaluate side-chains 75 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 241 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 778 TYR 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: 2.9990 chunk 1 optimal weight: 0.0040 chunk 63 optimal weight: 3.9990 chunk 50 optimal weight: 0.0980 chunk 54 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 chunk 71 optimal weight: 0.0870 chunk 60 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 overall best weight: 0.6172 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 564 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.115719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.086728 restraints weight = 11615.586| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 1.88 r_work: 0.2665 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2525 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8932 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9350 Z= 0.117 Angle : 0.491 6.571 13060 Z= 0.274 Chirality : 0.036 0.177 1467 Planarity : 0.004 0.048 1315 Dihedral : 20.127 171.124 2278 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.35 % Allowed : 16.49 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.34 (0.29), residues: 845 helix: 2.12 (0.26), residues: 410 sheet: 0.75 (0.47), residues: 124 loop : -0.74 (0.32), residues: 311 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 0.011 0.001 PHE A 86 TRP 0.012 0.001 TRP A 24 HIS 0.004 0.001 HIS A 210 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 9350) covalent geometry : angle 0.49086 (13060) hydrogen bonds : bond 0.04355 ( 425) hydrogen bonds : angle 3.52810 ( 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 77 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 0.346 Fit side-chains REVERT: A 87 LYS cc_start: 0.8717 (ttmp) cc_final: 0.8197 (ttpt) REVERT: A 241 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7832 (mp0) REVERT: A 394 ARG cc_start: 0.8613 (mmm160) cc_final: 0.8374 (mpp-170) REVERT: A 669 ARG cc_start: 0.8612 (mtp180) cc_final: 0.7912 (mtt180) outliers start: 10 outliers final: 6 residues processed: 75 average time/residue: 0.8250 time to fit residues: 65.1833 Evaluate side-chains 71 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 64 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 241 GLU 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: 0.9980 chunk 25 optimal weight: 0.0870 chunk 4 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 77 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 84 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 overall best weight: 0.9960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.114115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.084756 restraints weight = 11523.275| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 1.96 r_work: 0.2619 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2476 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8978 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9350 Z= 0.139 Angle : 0.505 6.463 13060 Z= 0.281 Chirality : 0.037 0.185 1467 Planarity : 0.004 0.048 1315 Dihedral : 20.158 171.651 2278 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.35 % Allowed : 16.49 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.36 (0.29), residues: 845 helix: 2.12 (0.26), residues: 411 sheet: 0.76 (0.47), residues: 124 loop : -0.73 (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 45 TRP 0.012 0.001 TRP A 323 HIS 0.005 0.001 HIS A 210 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 9350) covalent geometry : angle 0.50481 (13060) hydrogen bonds : bond 0.04865 ( 425) hydrogen bonds : angle 3.55970 ( 1128) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3015.25 seconds wall clock time: 52 minutes 7.44 seconds (3127.44 seconds total)