Starting phenix.real_space_refine on Thu Jul 2 01:37:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8e4y_27898/07_2026/8e4y_27898_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e4y_27898/07_2026/8e4y_27898.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8e4y_27898/07_2026/8e4y_27898_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e4y_27898/07_2026/8e4y_27898_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8e4y_27898/07_2026/8e4y_27898.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e4y_27898/07_2026/8e4y_27898.map" } resolution = 3.4 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= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 24 5.16 5 C 3410 2.51 5 N 905 2.21 5 O 951 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s 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: 5294 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 651, 5202 Classifications: {'peptide': 651} Link IDs: {'PTRANS': 21, 'TRANS': 629} Chain breaks: 5 Chain: "A" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 92 Unusual residues: {'NKO': 1, 'UKL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.40, per 1000 atoms: 0.26 Number of scatterers: 5294 At special positions: 0 Unit cell: (70.56, 94.08, 97.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 24 16.00 P 4 15.00 O 951 8.00 N 905 7.00 C 3410 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: 0.73 Conformation dependent library (CDL) restraints added in 193.8 milliseconds 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1242 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 5 sheets defined 61.3% alpha, 10.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'A' and resid 103 through 109 removed outlier: 3.713A pdb=" N ARG A 108 " --> pdb=" O TRP A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 116 Processing helix chain 'A' and resid 128 through 135 Processing helix chain 'A' and resid 136 through 151 removed outlier: 3.776A pdb=" N LEU A 150 " --> pdb=" O VAL A 146 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ASN A 151 " --> pdb=" O ALA A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 176 removed outlier: 3.518A pdb=" N LEU A 174 " --> pdb=" O ALA A 170 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLU A 176 " --> pdb=" O ARG A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 201 removed outlier: 3.594A pdb=" N LEU A 188 " --> pdb=" O ALA A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 220 removed outlier: 3.702A pdb=" N MET A 213 " --> pdb=" O GLY A 209 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR A 220 " --> pdb=" O ALA A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 245 removed outlier: 3.741A pdb=" N LEU A 239 " --> pdb=" O ASP A 235 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N THR A 240 " --> pdb=" O TYR A 236 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU A 243 " --> pdb=" O LEU A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 260 No H-bonds generated for 'chain 'A' and resid 258 through 260' Processing helix chain 'A' and resid 263 through 271 removed outlier: 3.892A pdb=" N LEU A 267 " --> pdb=" O ILE A 263 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU A 271 " --> pdb=" O LEU A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 306 Processing helix chain 'A' and resid 331 through 341 removed outlier: 3.603A pdb=" N THR A 341 " --> pdb=" O ASP A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 370 Processing helix chain 'A' and resid 380 through 391 removed outlier: 3.580A pdb=" N GLY A 384 " --> pdb=" O SER A 380 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LYS A 391 " --> pdb=" O ARG A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 416 removed outlier: 3.533A pdb=" N LYS A 416 " --> pdb=" O SER A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 433 Proline residue: A 430 - end of helix Processing helix chain 'A' and resid 457 through 480 removed outlier: 4.118A pdb=" N ARG A 461 " --> pdb=" O ASP A 457 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N CYS A 480 " --> pdb=" O ALA A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 495 Processing helix chain 'A' and resid 502 through 519 removed outlier: 3.511A pdb=" N VAL A 511 " --> pdb=" O GLU A 507 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG A 519 " --> pdb=" O GLU A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 528 through 540 removed outlier: 3.761A pdb=" N VAL A 533 " --> pdb=" O SER A 529 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N MET A 534 " --> pdb=" O GLU A 530 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN A 538 " --> pdb=" O MET A 534 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU A 539 " --> pdb=" O HIS A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 574 removed outlier: 4.050A pdb=" N PHE A 567 " --> pdb=" O VAL A 563 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N GLU A 568 " --> pdb=" O PRO A 564 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU A 569 " --> pdb=" O SER A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 595 removed outlier: 3.795A pdb=" N PHE A 580 " --> pdb=" O VAL A 576 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N MET A 582 " --> pdb=" O HIS A 578 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N GLU A 583 " --> pdb=" O VAL A 579 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N TYR A 591 " --> pdb=" O ALA A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 626 removed outlier: 3.520A pdb=" N TYR A 624 " --> pdb=" O ALA A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 653 Processing helix chain 'A' and resid 711 through 725 removed outlier: 3.897A pdb=" N GLN A 716 " --> pdb=" O LYS A 712 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N PHE A 717 " --> pdb=" O GLU A 713 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU A 725 " --> pdb=" O LEU A 721 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 739 removed outlier: 3.719A pdb=" N TYR A 732 " --> pdb=" O LEU A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 740 through 742 No H-bonds generated for 'chain 'A' and resid 740 through 742' Processing helix chain 'A' and resid 748 through 765 removed outlier: 3.695A pdb=" N GLN A 753 " --> pdb=" O PRO A 749 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR A 763 " --> pdb=" O LEU A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 775 removed outlier: 3.565A pdb=" N SER A 773 " --> pdb=" O TYR A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 776 through 790 removed outlier: 3.517A pdb=" N ASP A 788 " --> pdb=" O LYS A 784 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 824 removed outlier: 4.081A pdb=" N ARG A 815 " --> pdb=" O PRO A 811 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN A 816 " --> pdb=" O GLN A 812 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 88 through 90 removed outlier: 6.339A pdb=" N GLN A 205 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N PHE A 400 " --> pdb=" O GLN A 205 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N HIS A 207 " --> pdb=" O PHE A 400 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N TYR A 252 " --> pdb=" O GLU A 311 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N ILE A 253 " --> pdb=" O PHE A 274 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ILE A 276 " --> pdb=" O ILE A 253 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N SER A 255 " --> pdb=" O ILE A 276 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 88 through 90 removed outlier: 6.339A pdb=" N GLN A 205 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N PHE A 400 " --> pdb=" O GLN A 205 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N HIS A 207 " --> pdb=" O PHE A 400 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 500 through 501 Processing sheet with id=AA4, first strand: chain 'A' and resid 610 through 611 Processing sheet with id=AA5, first strand: chain 'A' and resid 746 through 747 removed outlier: 3.888A pdb=" N THR A 795 " --> pdb=" O VAL A 802 " (cutoff:3.500A) 267 hydrogen bonds defined for protein. 780 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.84 Time building geometry restraints manager: 0.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 989 1.33 - 1.45: 1266 1.45 - 1.58: 3100 1.58 - 1.70: 6 1.70 - 1.82: 35 Bond restraints: 5396 Sorted by residual: bond pdb=" N ILE A 350 " pdb=" CA ILE A 350 " ideal model delta sigma weight residual 1.456 1.496 -0.041 8.60e-03 1.35e+04 2.22e+01 bond pdb=" OAF NKO A1002 " pdb=" PAC NKO A1002 " ideal model delta sigma weight residual 1.709 1.617 0.092 2.00e-02 2.50e+03 2.14e+01 bond pdb=" O65 UKL A1001 " pdb=" P66 UKL A1001 " ideal model delta sigma weight residual 1.687 1.609 0.078 2.00e-02 2.50e+03 1.50e+01 bond pdb=" N ILE A 261 " pdb=" CA ILE A 261 " ideal model delta sigma weight residual 1.462 1.497 -0.034 9.10e-03 1.21e+04 1.43e+01 bond pdb=" N LEU A 429 " pdb=" CA LEU A 429 " ideal model delta sigma weight residual 1.462 1.497 -0.035 9.50e-03 1.11e+04 1.36e+01 ... (remaining 5391 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 4842 1.61 - 3.21: 1872 3.21 - 4.82: 485 4.82 - 6.42: 99 6.42 - 8.03: 2 Bond angle restraints: 7300 Sorted by residual: angle pdb=" C THR A 562 " pdb=" N VAL A 563 " pdb=" CA VAL A 563 " ideal model delta sigma weight residual 120.24 125.60 -5.36 6.30e-01 2.52e+00 7.24e+01 angle pdb=" C ASN A 365 " pdb=" N GLY A 366 " pdb=" CA GLY A 366 " ideal model delta sigma weight residual 119.94 125.68 -5.74 1.11e+00 8.12e-01 2.67e+01 angle pdb=" C LYS A 208 " pdb=" N GLY A 209 " pdb=" CA GLY A 209 " ideal model delta sigma weight residual 120.03 125.49 -5.46 1.12e+00 7.97e-01 2.37e+01 angle pdb=" C ARG A 383 " pdb=" N GLY A 384 " pdb=" CA GLY A 384 " ideal model delta sigma weight residual 120.00 125.12 -5.12 1.10e+00 8.26e-01 2.17e+01 angle pdb=" C THR A 189 " pdb=" N GLY A 190 " pdb=" CA GLY A 190 " ideal model delta sigma weight residual 120.03 125.22 -5.19 1.12e+00 7.97e-01 2.15e+01 ... (remaining 7295 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.38: 2935 16.38 - 32.75: 251 32.75 - 49.13: 71 49.13 - 65.50: 22 65.50 - 81.88: 7 Dihedral angle restraints: 3286 sinusoidal: 1377 harmonic: 1909 Sorted by residual: dihedral pdb=" CA GLU A 794 " pdb=" C GLU A 794 " pdb=" N THR A 795 " pdb=" CA THR A 795 " ideal model delta harmonic sigma weight residual 180.00 158.71 21.29 0 5.00e+00 4.00e-02 1.81e+01 dihedral pdb=" CA HIS A 121 " pdb=" C HIS A 121 " pdb=" N LYS A 122 " pdb=" CA LYS A 122 " ideal model delta harmonic sigma weight residual 180.00 159.54 20.46 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CA LEU A 493 " pdb=" C LEU A 493 " pdb=" N TYR A 494 " pdb=" CA TYR A 494 " ideal model delta harmonic sigma weight residual 180.00 -162.65 -17.35 0 5.00e+00 4.00e-02 1.20e+01 ... (remaining 3283 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 363 0.059 - 0.119: 341 0.119 - 0.178: 126 0.178 - 0.237: 17 0.237 - 0.297: 2 Chirality restraints: 849 Sorted by residual: chirality pdb=" CA ARG A 799 " pdb=" N ARG A 799 " pdb=" C ARG A 799 " pdb=" CB ARG A 799 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" CA ILE A 248 " pdb=" N ILE A 248 " pdb=" C ILE A 248 " pdb=" CB ILE A 248 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CA GLN A 797 " pdb=" N GLN A 797 " pdb=" C GLN A 797 " pdb=" CB GLN A 797 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.40e+00 ... (remaining 846 not shown) Planarity restraints: 905 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C20 UKL A1001 " -0.199 2.00e-02 2.50e+03 1.65e-01 3.41e+02 pdb=" C22 UKL A1001 " 0.057 2.00e-02 2.50e+03 pdb=" C24 UKL A1001 " -0.144 2.00e-02 2.50e+03 pdb=" N21 UKL A1001 " 0.270 2.00e-02 2.50e+03 pdb=" O23 UKL A1001 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C25 UKL A1001 " -0.070 2.00e-02 2.50e+03 5.77e-02 4.16e+01 pdb=" C27 UKL A1001 " 0.013 2.00e-02 2.50e+03 pdb=" C29 UKL A1001 " -0.051 2.00e-02 2.50e+03 pdb=" N26 UKL A1001 " 0.094 2.00e-02 2.50e+03 pdb=" O28 UKL A1001 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 292 " 0.020 2.00e-02 2.50e+03 1.14e-02 2.62e+00 pdb=" CG TYR A 292 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 TYR A 292 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR A 292 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR A 292 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR A 292 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR A 292 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR A 292 " 0.006 2.00e-02 2.50e+03 ... (remaining 902 not shown) Histogram of nonbonded interaction distances: 2.41 - 2.91: 1567 2.91 - 3.41: 5299 3.41 - 3.90: 8304 3.90 - 4.40: 8957 4.40 - 4.90: 15853 Nonbonded interactions: 39980 Sorted by model distance: nonbonded pdb=" NH1 ARG A 278 " pdb=" O37 UKL A1001 " model vdw 2.412 3.120 nonbonded pdb=" O ILE A 760 " pdb=" OG1 THR A 763 " model vdw 2.443 3.040 nonbonded pdb=" OD2 ASP A 346 " pdb=" OG SER A 405 " model vdw 2.516 3.040 nonbonded pdb=" OE1 GLU A 361 " pdb=" OH TYR A 364 " model vdw 2.524 3.040 nonbonded pdb=" O GLU A 515 " pdb=" NH1 ARG A 519 " model vdw 2.562 3.120 ... (remaining 39975 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.160 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:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 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 : 0.014 0.092 5396 Z= 1.068 Angle : 1.798 8.027 7300 Z= 1.366 Chirality : 0.087 0.297 849 Planarity : 0.006 0.165 905 Dihedral : 14.559 81.880 2044 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 0.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % 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: -2.41 (0.27), residues: 639 helix: -1.30 (0.23), residues: 356 sheet: -1.33 (0.53), residues: 65 loop : -1.91 (0.36), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 397 TYR 0.024 0.002 TYR A 292 PHE 0.022 0.002 PHE A 200 TRP 0.010 0.002 TRP A 202 HIS 0.007 0.002 HIS A 496 Details of bonding type rmsd/Z covalent geometry : bond 0.01378 / 1.07 ( 5396) covalent geometry : angle 1.79770 / 1.37 ( 7300) hydrogen bonds : bond 0.27092 / 18.60 ( 261) hydrogen bonds : angle 7.60835 / 5.48 ( 780) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.205 Fit side-chains REVERT: A 169 LYS cc_start: 0.7978 (tttm) cc_final: 0.7752 (tptm) REVERT: A 172 ARG cc_start: 0.7571 (ttp-170) cc_final: 0.7359 (tmm160) REVERT: A 315 GLU cc_start: 0.7729 (mt-10) cc_final: 0.7433 (mt-10) REVERT: A 347 ILE cc_start: 0.7876 (mt) cc_final: 0.7610 (tt) REVERT: A 357 ASP cc_start: 0.8033 (t0) cc_final: 0.7717 (t0) REVERT: A 426 GLN cc_start: 0.8146 (tp40) cc_final: 0.7629 (mt0) REVERT: A 470 GLU cc_start: 0.7623 (tt0) cc_final: 0.7224 (tt0) REVERT: A 520 ASP cc_start: 0.8492 (t70) cc_final: 0.8063 (m-30) REVERT: A 555 PHE cc_start: 0.7791 (m-80) cc_final: 0.7483 (m-10) REVERT: A 582 MET cc_start: 0.7753 (mmm) cc_final: 0.7440 (mmm) REVERT: A 705 TYR cc_start: 0.7678 (m-80) cc_final: 0.7467 (m-80) outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.0995 time to fit residues: 9.2094 Evaluate side-chains 42 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 64 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 198 ASN A 297 HIS ** A 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 595 ASN A 714 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.111321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.089544 restraints weight = 8056.935| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 2.58 r_work: 0.2907 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5396 Z= 0.139 Angle : 0.512 5.312 7300 Z= 0.278 Chirality : 0.039 0.179 849 Planarity : 0.004 0.037 905 Dihedral : 8.651 83.654 798 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.55 % Allowed : 8.29 % Favored : 90.16 % 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 are not related in a simple way. whole: 0.27 (0.32), residues: 639 helix: 1.15 (0.26), residues: 372 sheet: -0.59 (0.62), residues: 66 loop : -1.32 (0.40), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 390 TYR 0.013 0.002 TYR A 292 PHE 0.024 0.001 PHE A 200 TRP 0.008 0.001 TRP A 202 HIS 0.003 0.001 HIS A 535 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 ( 5396) covalent geometry : angle 0.51176 / 0.28 ( 7300) hydrogen bonds : bond 0.04266 / 2.96 ( 261) hydrogen bonds : angle 4.38256 / 3.10 ( 780) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 48 time to evaluate : 0.200 Fit side-chains REVERT: A 289 ASP cc_start: 0.6649 (t0) cc_final: 0.6290 (t0) REVERT: A 347 ILE cc_start: 0.8819 (mt) cc_final: 0.8585 (tt) REVERT: A 357 ASP cc_start: 0.8640 (t0) cc_final: 0.8312 (t0) REVERT: A 426 GLN cc_start: 0.8396 (tp40) cc_final: 0.8181 (mt0) REVERT: A 520 ASP cc_start: 0.8561 (t70) cc_final: 0.8306 (m-30) REVERT: A 531 ASP cc_start: 0.8562 (t0) cc_final: 0.8313 (t0) REVERT: A 555 PHE cc_start: 0.8662 (m-80) cc_final: 0.8380 (m-10) REVERT: A 566 VAL cc_start: 0.8548 (OUTLIER) cc_final: 0.8198 (t) outliers start: 9 outliers final: 6 residues processed: 57 average time/residue: 0.0847 time to fit residues: 6.2649 Evaluate side-chains 45 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 38 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 HIS Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 823 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 29 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 21 optimal weight: 0.5980 chunk 44 optimal weight: 0.0670 chunk 50 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 overall best weight: 0.6722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 233 HIS A 363 HIS A 365 ASN A 715 GLN A 756 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.111289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.089600 restraints weight = 8065.843| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 2.55 r_work: 0.2912 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.2848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5396 Z= 0.119 Angle : 0.443 4.722 7300 Z= 0.240 Chirality : 0.038 0.149 849 Planarity : 0.004 0.044 905 Dihedral : 7.776 73.730 798 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.42 % Allowed : 8.29 % Favored : 89.29 % 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 (0.33), residues: 639 helix: 1.81 (0.26), residues: 380 sheet: -0.14 (0.63), residues: 66 loop : -1.38 (0.41), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 138 TYR 0.010 0.001 TYR A 292 PHE 0.014 0.001 PHE A 274 TRP 0.005 0.001 TRP A 202 HIS 0.003 0.001 HIS A 230 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 ( 5396) covalent geometry : angle 0.44308 / 0.24 ( 7300) hydrogen bonds : bond 0.03538 / 2.42 ( 261) hydrogen bonds : angle 3.78935 / 2.66 ( 780) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 43 time to evaluate : 0.181 Fit side-chains REVERT: A 105 LEU cc_start: 0.8224 (tt) cc_final: 0.7893 (mm) REVERT: A 202 TRP cc_start: 0.8184 (OUTLIER) cc_final: 0.7829 (t60) REVERT: A 347 ILE cc_start: 0.8782 (mt) cc_final: 0.8540 (tt) REVERT: A 357 ASP cc_start: 0.8674 (t0) cc_final: 0.8332 (t0) REVERT: A 363 HIS cc_start: 0.8032 (p90) cc_final: 0.7783 (p90) REVERT: A 520 ASP cc_start: 0.8602 (t70) cc_final: 0.8322 (m-30) REVERT: A 531 ASP cc_start: 0.8563 (t0) cc_final: 0.8306 (t0) REVERT: A 555 PHE cc_start: 0.8748 (m-80) cc_final: 0.8431 (m-10) REVERT: A 805 LEU cc_start: 0.8850 (tp) cc_final: 0.8636 (tp) outliers start: 14 outliers final: 12 residues processed: 55 average time/residue: 0.0690 time to fit residues: 5.2651 Evaluate side-chains 53 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 40 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 TRP Chi-restraints excluded: chain A residue 230 HIS Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 365 ASN Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 546 ILE Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain A residue 826 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 26 optimal weight: 0.8980 chunk 31 optimal weight: 0.0000 chunk 5 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 28 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 63 optimal weight: 4.9990 overall best weight: 0.9188 ------------------------------------------------------------------------------- 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 = 0.3338 r_free = 0.3338 target = 0.109823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.088278 restraints weight = 7986.383| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 2.53 r_work: 0.2890 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.3035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 5396 Z= 0.141 Angle : 0.451 4.609 7300 Z= 0.242 Chirality : 0.039 0.184 849 Planarity : 0.004 0.045 905 Dihedral : 7.712 75.475 798 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.11 % Allowed : 7.94 % Favored : 88.95 % 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: 1.09 (0.33), residues: 639 helix: 1.98 (0.26), residues: 373 sheet: 0.05 (0.64), residues: 66 loop : -1.53 (0.40), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 278 TYR 0.012 0.001 TYR A 572 PHE 0.016 0.001 PHE A 200 TRP 0.006 0.001 TRP A 202 HIS 0.003 0.001 HIS A 230 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.14 ( 5396) covalent geometry : angle 0.45135 / 0.24 ( 7300) hydrogen bonds : bond 0.03563 / 2.42 ( 261) hydrogen bonds : angle 3.79163 / 2.66 ( 780) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 38 time to evaluate : 0.200 Fit side-chains REVERT: A 105 LEU cc_start: 0.8255 (tt) cc_final: 0.7904 (mm) REVERT: A 202 TRP cc_start: 0.8199 (OUTLIER) cc_final: 0.7807 (t60) REVERT: A 347 ILE cc_start: 0.8775 (mt) cc_final: 0.8515 (tt) REVERT: A 365 ASN cc_start: 0.8150 (OUTLIER) cc_final: 0.7757 (m-40) REVERT: A 520 ASP cc_start: 0.8702 (t70) cc_final: 0.8396 (m-30) REVERT: A 531 ASP cc_start: 0.8562 (t0) cc_final: 0.8322 (t0) REVERT: A 555 PHE cc_start: 0.8810 (m-80) cc_final: 0.8508 (m-10) outliers start: 18 outliers final: 10 residues processed: 54 average time/residue: 0.0695 time to fit residues: 5.2432 Evaluate side-chains 48 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 36 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 TRP Chi-restraints excluded: chain A residue 230 HIS Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 365 ASN Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 546 ILE Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain A residue 823 LEU Chi-restraints excluded: chain A residue 826 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 34 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 56 optimal weight: 0.3980 chunk 48 optimal weight: 0.7980 chunk 19 optimal weight: 0.0030 chunk 14 optimal weight: 0.3980 chunk 1 optimal weight: 0.7980 chunk 53 optimal weight: 4.9990 chunk 43 optimal weight: 0.0970 chunk 26 optimal weight: 0.6980 chunk 46 optimal weight: 0.8980 overall best weight: 0.3188 ------------------------------------------------------------------------------- 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 = 0.3380 r_free = 0.3380 target = 0.112963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.091444 restraints weight = 8147.306| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 2.58 r_work: 0.2938 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.3280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 5396 Z= 0.084 Angle : 0.396 4.806 7300 Z= 0.214 Chirality : 0.037 0.154 849 Planarity : 0.004 0.042 905 Dihedral : 7.154 71.207 798 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.25 % Allowed : 8.64 % Favored : 89.12 % 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: 1.48 (0.33), residues: 639 helix: 2.24 (0.27), residues: 373 sheet: 0.38 (0.64), residues: 64 loop : -1.31 (0.40), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 278 TYR 0.009 0.001 TYR A 292 PHE 0.010 0.001 PHE A 274 TRP 0.003 0.001 TRP A 202 HIS 0.002 0.001 HIS A 230 Details of bonding type rmsd/Z covalent geometry : bond 0.00180 / 0.08 ( 5396) covalent geometry : angle 0.39564 / 0.21 ( 7300) hydrogen bonds : bond 0.02754 / 1.87 ( 261) hydrogen bonds : angle 3.49688 / 2.43 ( 780) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 38 time to evaluate : 0.206 Fit side-chains REVERT: A 105 LEU cc_start: 0.8213 (tt) cc_final: 0.7922 (mm) REVERT: A 202 TRP cc_start: 0.8139 (OUTLIER) cc_final: 0.7768 (t60) REVERT: A 347 ILE cc_start: 0.8727 (mt) cc_final: 0.8525 (tt) REVERT: A 520 ASP cc_start: 0.8683 (t70) cc_final: 0.8381 (m-30) REVERT: A 531 ASP cc_start: 0.8529 (t0) cc_final: 0.8294 (t0) REVERT: A 555 PHE cc_start: 0.8808 (m-80) cc_final: 0.8477 (m-10) REVERT: A 823 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8450 (mm) outliers start: 13 outliers final: 8 residues processed: 49 average time/residue: 0.0712 time to fit residues: 4.8379 Evaluate side-chains 45 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 35 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 TRP Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 546 ILE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain A residue 819 LEU Chi-restraints excluded: chain A residue 823 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 18 optimal weight: 0.9980 chunk 64 optimal weight: 0.5980 chunk 22 optimal weight: 3.9990 chunk 63 optimal weight: 0.5980 chunk 20 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 19 optimal weight: 0.1980 chunk 11 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 230 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.109945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.088248 restraints weight = 8194.828| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 2.60 r_work: 0.2899 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.3343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5396 Z= 0.112 Angle : 0.418 4.889 7300 Z= 0.223 Chirality : 0.037 0.158 849 Planarity : 0.004 0.041 905 Dihedral : 7.154 72.740 798 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.07 % Allowed : 8.98 % Favored : 88.95 % 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: 1.43 (0.33), residues: 639 helix: 2.18 (0.26), residues: 374 sheet: 0.47 (0.64), residues: 64 loop : -1.33 (0.39), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 278 TYR 0.010 0.001 TYR A 572 PHE 0.015 0.001 PHE A 200 TRP 0.005 0.001 TRP A 202 HIS 0.003 0.001 HIS A 578 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.11 ( 5396) covalent geometry : angle 0.41836 / 0.22 ( 7300) hydrogen bonds : bond 0.03150 / 2.14 ( 261) hydrogen bonds : angle 3.52604 / 2.47 ( 780) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 36 time to evaluate : 0.183 Fit side-chains REVERT: A 105 LEU cc_start: 0.8183 (tt) cc_final: 0.7897 (mm) REVERT: A 347 ILE cc_start: 0.8762 (mt) cc_final: 0.8541 (tt) REVERT: A 520 ASP cc_start: 0.8714 (t70) cc_final: 0.8395 (m-30) REVERT: A 531 ASP cc_start: 0.8557 (t0) cc_final: 0.8303 (t0) REVERT: A 555 PHE cc_start: 0.8824 (m-80) cc_final: 0.8465 (m-10) REVERT: A 823 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8449 (mm) outliers start: 12 outliers final: 9 residues processed: 46 average time/residue: 0.0546 time to fit residues: 3.7224 Evaluate side-chains 44 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 34 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 HIS Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 546 ILE Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain A residue 819 LEU Chi-restraints excluded: chain A residue 823 LEU Chi-restraints excluded: chain A residue 826 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 26 optimal weight: 0.0770 chunk 9 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 35 optimal weight: 0.5980 chunk 63 optimal weight: 0.5980 chunk 55 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 overall best weight: 0.7940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 230 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.110698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.088732 restraints weight = 8236.696| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 2.64 r_work: 0.2888 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.3396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5396 Z= 0.123 Angle : 0.426 4.947 7300 Z= 0.226 Chirality : 0.038 0.159 849 Planarity : 0.004 0.041 905 Dihedral : 7.178 72.670 798 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.07 % Allowed : 8.98 % Favored : 88.95 % 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: 1.43 (0.33), residues: 639 helix: 2.15 (0.26), residues: 374 sheet: 0.49 (0.64), residues: 64 loop : -1.27 (0.40), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 278 TYR 0.010 0.001 TYR A 572 PHE 0.017 0.001 PHE A 200 TRP 0.004 0.001 TRP A 379 HIS 0.004 0.001 HIS A 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.12 ( 5396) covalent geometry : angle 0.42579 / 0.23 ( 7300) hydrogen bonds : bond 0.03192 / 2.16 ( 261) hydrogen bonds : angle 3.53790 / 2.47 ( 780) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 34 time to evaluate : 0.157 Fit side-chains REVERT: A 105 LEU cc_start: 0.8185 (tt) cc_final: 0.7888 (mm) REVERT: A 347 ILE cc_start: 0.8767 (mt) cc_final: 0.8535 (tt) REVERT: A 520 ASP cc_start: 0.8754 (t70) cc_final: 0.8412 (m-30) REVERT: A 531 ASP cc_start: 0.8559 (t0) cc_final: 0.8303 (t0) REVERT: A 555 PHE cc_start: 0.8850 (m-80) cc_final: 0.8496 (m-10) REVERT: A 823 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8447 (mm) outliers start: 12 outliers final: 11 residues processed: 45 average time/residue: 0.0520 time to fit residues: 3.4358 Evaluate side-chains 46 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 34 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 HIS Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 247 ASN Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 546 ILE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain A residue 819 LEU Chi-restraints excluded: chain A residue 823 LEU Chi-restraints excluded: chain A residue 826 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 2 optimal weight: 0.9990 chunk 49 optimal weight: 0.3980 chunk 14 optimal weight: 0.0010 chunk 44 optimal weight: 0.0070 chunk 21 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 15 optimal weight: 0.0170 chunk 10 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 overall best weight: 0.2442 ------------------------------------------------------------------------------- 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 = 0.3367 r_free = 0.3367 target = 0.112092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.090822 restraints weight = 8015.646| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 2.55 r_work: 0.2933 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.3503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 5396 Z= 0.079 Angle : 0.394 4.799 7300 Z= 0.211 Chirality : 0.036 0.145 849 Planarity : 0.004 0.042 905 Dihedral : 6.915 70.309 798 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.90 % Allowed : 9.33 % Favored : 88.77 % 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: 1.64 (0.33), residues: 639 helix: 2.31 (0.27), residues: 373 sheet: 0.70 (0.65), residues: 64 loop : -1.18 (0.40), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 278 TYR 0.009 0.001 TYR A 292 PHE 0.010 0.001 PHE A 200 TRP 0.003 0.000 TRP A 104 HIS 0.003 0.001 HIS A 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00162 / 0.08 ( 5396) covalent geometry : angle 0.39412 / 0.21 ( 7300) hydrogen bonds : bond 0.02702 / 1.84 ( 261) hydrogen bonds : angle 3.41457 / 2.37 ( 780) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 37 time to evaluate : 0.170 Fit side-chains REVERT: A 105 LEU cc_start: 0.8139 (tt) cc_final: 0.7872 (mm) REVERT: A 347 ILE cc_start: 0.8736 (mt) cc_final: 0.8512 (tt) REVERT: A 357 ASP cc_start: 0.8629 (t0) cc_final: 0.8354 (t0) REVERT: A 520 ASP cc_start: 0.8730 (t70) cc_final: 0.8417 (m-30) REVERT: A 531 ASP cc_start: 0.8515 (t0) cc_final: 0.8283 (t0) REVERT: A 555 PHE cc_start: 0.8854 (m-80) cc_final: 0.8522 (m-10) REVERT: A 823 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8434 (mm) outliers start: 11 outliers final: 10 residues processed: 46 average time/residue: 0.0606 time to fit residues: 4.0012 Evaluate side-chains 47 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 36 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 TRP Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 247 ASN Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 546 ILE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain A residue 819 LEU Chi-restraints excluded: chain A residue 823 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.0770 chunk 58 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 44 optimal weight: 0.0270 chunk 39 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 230 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.111114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.089737 restraints weight = 8212.855| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 2.60 r_work: 0.2907 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.3507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 5396 Z= 0.103 Angle : 0.412 5.475 7300 Z= 0.219 Chirality : 0.037 0.199 849 Planarity : 0.004 0.037 905 Dihedral : 6.893 71.393 798 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.25 % Allowed : 8.98 % Favored : 88.77 % 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: 1.60 (0.33), residues: 639 helix: 2.27 (0.26), residues: 374 sheet: 0.69 (0.65), residues: 64 loop : -1.22 (0.40), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 278 TYR 0.009 0.001 TYR A 572 PHE 0.010 0.001 PHE A 200 TRP 0.003 0.001 TRP A 379 HIS 0.004 0.001 HIS A 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.10 ( 5396) covalent geometry : angle 0.41223 / 0.22 ( 7300) hydrogen bonds : bond 0.02940 / 2.00 ( 261) hydrogen bonds : angle 3.43719 / 2.40 ( 780) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 35 time to evaluate : 0.207 Fit side-chains REVERT: A 105 LEU cc_start: 0.8172 (tt) cc_final: 0.7897 (mm) REVERT: A 347 ILE cc_start: 0.8754 (mt) cc_final: 0.8540 (tt) REVERT: A 520 ASP cc_start: 0.8736 (t70) cc_final: 0.8410 (m-30) REVERT: A 531 ASP cc_start: 0.8564 (t0) cc_final: 0.8323 (t0) REVERT: A 555 PHE cc_start: 0.8850 (m-80) cc_final: 0.8526 (m-10) REVERT: A 823 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8450 (mm) outliers start: 13 outliers final: 12 residues processed: 46 average time/residue: 0.0596 time to fit residues: 4.0158 Evaluate side-chains 48 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 35 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 TRP Chi-restraints excluded: chain A residue 230 HIS Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 247 ASN Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 546 ILE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain A residue 819 LEU Chi-restraints excluded: chain A residue 823 LEU Chi-restraints excluded: chain A residue 826 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 24 optimal weight: 2.9990 chunk 50 optimal weight: 0.0270 chunk 42 optimal weight: 0.0370 chunk 64 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 20 optimal weight: 0.5980 chunk 49 optimal weight: 0.5980 chunk 59 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 overall best weight: 0.4116 ------------------------------------------------------------------------------- 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 = 0.3366 r_free = 0.3366 target = 0.111982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.090667 restraints weight = 8100.309| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 2.58 r_work: 0.2918 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.3572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 5396 Z= 0.089 Angle : 0.404 6.042 7300 Z= 0.215 Chirality : 0.037 0.194 849 Planarity : 0.004 0.039 905 Dihedral : 6.802 70.499 798 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.07 % Allowed : 9.15 % Favored : 88.77 % 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: 1.66 (0.33), residues: 639 helix: 2.32 (0.26), residues: 374 sheet: 0.71 (0.65), residues: 64 loop : -1.18 (0.40), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 278 TYR 0.008 0.001 TYR A 292 PHE 0.010 0.001 PHE A 200 TRP 0.003 0.000 TRP A 104 HIS 0.004 0.001 HIS A 230 Details of bonding type rmsd/Z covalent geometry : bond 0.00198 / 0.09 ( 5396) covalent geometry : angle 0.40428 / 0.21 ( 7300) hydrogen bonds : bond 0.02784 / 1.89 ( 261) hydrogen bonds : angle 3.40649 / 2.38 ( 780) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 35 time to evaluate : 0.196 Fit side-chains REVERT: A 105 LEU cc_start: 0.8168 (tt) cc_final: 0.7900 (mm) REVERT: A 122 LYS cc_start: 0.7728 (tmmt) cc_final: 0.7476 (tttt) REVERT: A 347 ILE cc_start: 0.8748 (mt) cc_final: 0.8514 (tt) REVERT: A 520 ASP cc_start: 0.8744 (t70) cc_final: 0.8422 (m-30) REVERT: A 531 ASP cc_start: 0.8556 (t0) cc_final: 0.8321 (t0) REVERT: A 555 PHE cc_start: 0.8846 (m-80) cc_final: 0.8536 (m-10) REVERT: A 823 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8440 (mm) outliers start: 12 outliers final: 11 residues processed: 45 average time/residue: 0.0582 time to fit residues: 3.7680 Evaluate side-chains 47 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 35 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 TRP Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 247 ASN Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 546 ILE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain A residue 819 LEU Chi-restraints excluded: chain A residue 823 LEU Chi-restraints excluded: chain A residue 826 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( ^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( ^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 56.5995 > 50: distance: 14 - 20: 4.414 distance: 21 - 22: 6.121 distance: 22 - 23: 5.846 distance: 22 - 29: 10.063 distance: 24 - 25: 3.739 distance: 26 - 28: 7.044 distance: 29 - 30: 8.545 distance: 30 - 31: 7.623 distance: 30 - 33: 3.566 distance: 31 - 32: 24.939 distance: 31 - 36: 7.584 distance: 33 - 34: 10.455 distance: 33 - 35: 8.346 distance: 36 - 37: 6.330 distance: 37 - 38: 5.166 distance: 38 - 39: 6.268 distance: 38 - 46: 6.657 distance: 40 - 41: 9.297 distance: 41 - 43: 13.739 distance: 42 - 44: 12.603 distance: 43 - 45: 8.130 distance: 44 - 45: 9.367 distance: 47 - 48: 5.392 distance: 47 - 50: 5.740 distance: 48 - 49: 13.591 distance: 48 - 53: 13.346 distance: 50 - 51: 6.600 distance: 53 - 54: 8.674 distance: 54 - 55: 5.272 distance: 54 - 57: 5.713 distance: 55 - 56: 9.072 distance: 55 - 64: 5.679 distance: 57 - 58: 8.140 distance: 58 - 59: 3.483 distance: 59 - 60: 7.266 distance: 60 - 61: 3.447 distance: 61 - 62: 4.250 distance: 61 - 63: 3.258 distance: 64 - 65: 10.541 distance: 65 - 66: 6.504 distance: 65 - 68: 5.557 distance: 66 - 67: 23.192 distance: 66 - 74: 17.136 distance: 68 - 69: 5.138 distance: 69 - 71: 5.245 distance: 70 - 72: 6.917 distance: 71 - 73: 5.806 distance: 74 - 75: 17.922 distance: 75 - 76: 21.420 distance: 75 - 78: 7.655 distance: 76 - 77: 13.651 distance: 76 - 85: 24.257 distance: 78 - 79: 12.665 distance: 79 - 80: 19.385 distance: 80 - 81: 5.308 distance: 81 - 82: 3.745 distance: 82 - 83: 13.111 distance: 82 - 84: 12.367 distance: 85 - 86: 45.101 distance: 86 - 87: 19.414 distance: 87 - 88: 14.859 distance: 87 - 89: 24.890 distance: 88 - 116: 34.300 distance: 89 - 90: 16.982 distance: 90 - 91: 10.095 distance: 91 - 92: 5.835 distance: 91 - 103: 4.491 distance: 93 - 94: 11.758 distance: 94 - 95: 21.169 distance: 94 - 96: 11.223 distance: 95 - 97: 4.551 distance: 96 - 98: 7.379 distance: 96 - 99: 6.767 distance: 97 - 98: 5.554 distance: 98 - 100: 5.893 distance: 99 - 101: 5.841 distance: 100 - 102: 7.164 distance: 101 - 102: 8.213 distance: 103 - 104: 10.401 distance: 104 - 105: 4.801 distance: 104 - 107: 8.258 distance: 105 - 106: 4.036 distance: 105 - 111: 6.469 distance: 106 - 137: 8.278 distance: 107 - 108: 12.196 distance: 108 - 109: 8.225 distance: 108 - 110: 19.658