Starting phenix.real_space_refine on Wed Aug 5 12:18:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lgi_63066/08_2026/9lgi_63066_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lgi_63066/08_2026/9lgi_63066.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9lgi_63066/08_2026/9lgi_63066.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lgi_63066/08_2026/9lgi_63066.map" model { file = "/net/cci-nas-00/data/ceres_data/9lgi_63066/08_2026/9lgi_63066_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lgi_63066/08_2026/9lgi_63066_neut.cif" } resolution = 2.86 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= 0.013 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 Zn 2 6.06 5 P 212 5.49 5 S 23 5.16 5 C 5342 2.51 5 N 1776 2.21 5 O 2344 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9699 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 5232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 684, 5232 Classifications: {'peptide': 684} Incomplete info: {'truncation_to_alanine': 75} Link IDs: {'PTRANS': 17, 'TRANS': 666} Chain breaks: 2 Unresolved non-hydrogen bonds: 311 Unresolved non-hydrogen angles: 383 Unresolved non-hydrogen dihedrals: 261 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 30, 'ASP:plan': 11, 'TRP:plan': 2, 'GLN:plan1': 1, 'ASN:plan1': 2, 'ARG:plan': 4, 'TYR:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 221 Chain: "B" Number of atoms: 3220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 3220 Classifications: {'RNA': 151} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 7, 'rna3p_pur': 71, 'rna3p_pyr': 63} Link IDs: {'rna2p': 16, 'rna3p': 134} Chain: "C" Number of atoms: 733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 733 Classifications: {'DNA': 36} Link IDs: {'rna3p': 35} Chain: "D" Number of atoms: 506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 506 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain breaks: 2 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2351 SG CYS A 371 19.502 41.889 67.154 1.00 32.82 S ATOM 2377 SG CYS A 374 18.769 39.082 64.730 1.00 86.56 S ATOM 2609 SG CYS A 406 21.805 38.934 67.041 1.00 89.53 S ATOM 2628 SG CYS A 409 21.715 41.445 64.114 1.00 61.38 S ATOM 1272 SG CYS A 189 43.335 63.607 103.974 1.00101.69 S ATOM 1294 SG CYS A 192 46.493 62.906 106.034 1.00 98.77 S ATOM 1621 SG CYS A 276 43.728 60.894 106.775 1.00112.40 S Time building chain proxies: 2.43, per 1000 atoms: 0.25 Number of scatterers: 9699 At special positions: 0 Unit cell: (89.38, 113.98, 127.1, 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) Zn 2 29.99 S 23 16.00 P 212 15.00 O 2344 8.00 N 1776 7.00 C 5342 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: 0.84 Conformation dependent library (CDL) restraints added in 241.8 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 801 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 371 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 406 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 374 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 409 " pdb=" ZN A 802 " pdb="ZN ZN A 802 " - pdb=" ND1 HIS A 279 " pdb="ZN ZN A 802 " - pdb=" SG CYS A 192 " pdb="ZN ZN A 802 " - pdb=" SG CYS A 189 " pdb="ZN ZN A 802 " - pdb=" SG CYS A 276 " Number of angles added : 9 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1268 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 5 sheets defined 38.2% alpha, 11.0% beta 54 base pairs and 144 stacking pairs defined. Time for finding SS restraints: 1.38 Creating SS restraints... Processing helix chain 'A' and resid 39 through 74 Processing helix chain 'A' and resid 87 through 99 removed outlier: 3.823A pdb=" N HIS A 98 " --> pdb=" O TYR A 94 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N LYS A 99 " --> pdb=" O SER A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 158 Processing helix chain 'A' and resid 161 through 174 Processing helix chain 'A' and resid 198 through 201 Processing helix chain 'A' and resid 202 through 209 removed outlier: 3.666A pdb=" N GLU A 208 " --> pdb=" O GLU A 204 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASN A 209 " --> pdb=" O LEU A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 266 removed outlier: 3.699A pdb=" N ASP A 263 " --> pdb=" O LYS A 259 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ILE A 264 " --> pdb=" O ASN A 260 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ALA A 265 " --> pdb=" O LEU A 261 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG A 266 " --> pdb=" O ILE A 262 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 259 through 266' Processing helix chain 'A' and resid 297 through 319 removed outlier: 4.021A pdb=" N LEU A 316 " --> pdb=" O LYS A 312 " (cutoff:3.500A) Proline residue: A 317 - end of helix Processing helix chain 'A' and resid 332 through 337 Processing helix chain 'A' and resid 358 through 367 Processing helix chain 'A' and resid 398 through 402 removed outlier: 3.704A pdb=" N LEU A 402 " --> pdb=" O PHE A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 414 Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 429 through 433 Processing helix chain 'A' and resid 435 through 444 removed outlier: 3.622A pdb=" N LYS A 439 " --> pdb=" O ASN A 435 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS A 440 " --> pdb=" O ASP A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 451 removed outlier: 3.580A pdb=" N ILE A 448 " --> pdb=" O ALA A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 462 removed outlier: 4.280A pdb=" N SER A 458 " --> pdb=" O ASN A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 476 Processing helix chain 'A' and resid 486 through 498 removed outlier: 3.615A pdb=" N THR A 490 " --> pdb=" O SER A 486 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE A 493 " --> pdb=" O TYR A 489 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLY A 498 " --> pdb=" O ARG A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 518 removed outlier: 4.008A pdb=" N LEU A 511 " --> pdb=" O GLY A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 595 removed outlier: 4.130A pdb=" N VAL A 594 " --> pdb=" O LYS A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 612 Processing helix chain 'A' and resid 620 through 627 Processing helix chain 'A' and resid 649 through 651 No H-bonds generated for 'chain 'A' and resid 649 through 651' Processing helix chain 'A' and resid 688 through 691 removed outlier: 3.639A pdb=" N SER A 691 " --> pdb=" O PRO A 688 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 688 through 691' Processing helix chain 'A' and resid 740 through 744 removed outlier: 3.897A pdb=" N GLY A 743 " --> pdb=" O GLY A 740 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 35 removed outlier: 6.310A pdb=" N VAL A 28 " --> pdb=" O ASN A 22 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N ASN A 22 " --> pdb=" O VAL A 28 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N VAL A 324 " --> pdb=" O LYS A 483 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N GLN A 485 " --> pdb=" O VAL A 324 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N MET A 326 " --> pdb=" O GLN A 485 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 572 through 574 Processing sheet with id=AA3, first strand: chain 'A' and resid 653 through 656 Processing sheet with id=AA4, first strand: chain 'A' and resid 680 through 686 removed outlier: 3.924A pdb=" N GLY A 669 " --> pdb=" O LEU A 685 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N PHE A 707 " --> pdb=" O VAL A 672 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N LEU A 674 " --> pdb=" O VAL A 705 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N VAL A 705 " --> pdb=" O LEU A 674 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 746 through 747 removed outlier: 6.545A pdb=" N VAL A 734 " --> pdb=" O LYS A 727 " (cutoff:3.500A) 187 hydrogen bonds defined for protein. 516 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 125 hydrogen bonds 218 hydrogen bond angles 0 basepair planarities 54 basepair parallelities 144 stacking parallelities Total time for adding SS restraints: 2.49 Time building geometry restraints manager: 1.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2078 1.33 - 1.45: 3234 1.45 - 1.57: 4533 1.57 - 1.69: 419 1.69 - 1.81: 34 Bond restraints: 10298 Sorted by residual: bond pdb=" C ALA A 513 " pdb=" O ALA A 513 " ideal model delta sigma weight residual 1.237 1.276 -0.039 1.17e-02 7.31e+03 1.11e+01 bond pdb=" C3' DG C 8 " pdb=" C2' DG C 8 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.06e+01 bond pdb=" N HIS A 509 " pdb=" CA HIS A 509 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.30e-02 5.92e+03 8.25e+00 bond pdb=" C1' DT D 24 " pdb=" N1 DT D 24 " ideal model delta sigma weight residual 1.468 1.507 -0.039 1.40e-02 5.10e+03 7.75e+00 bond pdb=" N ILE A 515 " pdb=" CA ILE A 515 " ideal model delta sigma weight residual 1.459 1.494 -0.034 1.30e-02 5.92e+03 6.98e+00 ... (remaining 10293 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 14184 1.81 - 3.62: 670 3.62 - 5.43: 18 5.43 - 7.23: 3 7.23 - 9.04: 1 Bond angle restraints: 14876 Sorted by residual: angle pdb=" N VAL A 202 " pdb=" CA VAL A 202 " pdb=" C VAL A 202 " ideal model delta sigma weight residual 113.20 107.54 5.66 9.60e-01 1.09e+00 3.48e+01 angle pdb=" C ALA A 523 " pdb=" CA ALA A 523 " pdb=" CB ALA A 523 " ideal model delta sigma weight residual 115.79 110.31 5.48 1.19e+00 7.06e-01 2.12e+01 angle pdb=" C1' C B 64 " pdb=" N1 C B 64 " pdb=" C2 C B 64 " ideal model delta sigma weight residual 118.80 123.78 -4.98 1.10e+00 8.26e-01 2.05e+01 angle pdb=" N ILE A 388 " pdb=" CA ILE A 388 " pdb=" C ILE A 388 " ideal model delta sigma weight residual 110.62 105.59 5.03 1.14e+00 7.69e-01 1.94e+01 angle pdb=" N ASP A 512 " pdb=" CA ASP A 512 " pdb=" C ASP A 512 " ideal model delta sigma weight residual 111.28 106.61 4.67 1.09e+00 8.42e-01 1.84e+01 ... (remaining 14871 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.19: 5532 33.19 - 66.38: 670 66.38 - 99.57: 37 99.57 - 132.76: 0 132.76 - 165.95: 5 Dihedral angle restraints: 6244 sinusoidal: 4274 harmonic: 1970 Sorted by residual: dihedral pdb=" O4' C B 64 " pdb=" C1' C B 64 " pdb=" N1 C B 64 " pdb=" C2 C B 64 " ideal model delta sinusoidal sigma weight residual 200.00 48.10 151.90 1 1.50e+01 4.44e-03 8.03e+01 dihedral pdb=" O4' U B 97 " pdb=" C1' U B 97 " pdb=" N1 U B 97 " pdb=" C2 U B 97 " ideal model delta sinusoidal sigma weight residual 232.00 66.05 165.95 1 1.70e+01 3.46e-03 6.54e+01 dihedral pdb=" O4' A B 82 " pdb=" C1' A B 82 " pdb=" N9 A B 82 " pdb=" C4 A B 82 " ideal model delta sinusoidal sigma weight residual -106.00 -164.18 58.18 1 1.70e+01 3.46e-03 1.57e+01 ... (remaining 6241 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1385 0.042 - 0.083: 202 0.083 - 0.125: 84 0.125 - 0.167: 137 0.167 - 0.208: 5 Chirality restraints: 1813 Sorted by residual: chirality pdb=" CA ILE A 388 " pdb=" N ILE A 388 " pdb=" C ILE A 388 " pdb=" CB ILE A 388 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" C3' DT D 20 " pdb=" C4' DT D 20 " pdb=" O3' DT D 20 " pdb=" C2' DT D 20 " both_signs ideal model delta sigma weight residual False -2.73 -2.53 -0.20 2.00e-01 2.50e+01 1.00e+00 chirality pdb=" CB VAL A 514 " pdb=" CA VAL A 514 " pdb=" CG1 VAL A 514 " pdb=" CG2 VAL A 514 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 1.00e+00 ... (remaining 1810 not shown) Planarity restraints: 1123 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS A 508 " 0.013 2.00e-02 2.50e+03 2.56e-02 6.55e+00 pdb=" C HIS A 508 " -0.044 2.00e-02 2.50e+03 pdb=" O HIS A 508 " 0.016 2.00e-02 2.50e+03 pdb=" N HIS A 509 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 383 " -0.008 2.00e-02 2.50e+03 1.60e-02 2.55e+00 pdb=" C ALA A 383 " 0.028 2.00e-02 2.50e+03 pdb=" O ALA A 383 " -0.011 2.00e-02 2.50e+03 pdb=" N HIS A 384 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA D 21 " -0.019 2.00e-02 2.50e+03 8.52e-03 2.00e+00 pdb=" N9 DA D 21 " 0.019 2.00e-02 2.50e+03 pdb=" C8 DA D 21 " 0.004 2.00e-02 2.50e+03 pdb=" N7 DA D 21 " -0.002 2.00e-02 2.50e+03 pdb=" C5 DA D 21 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DA D 21 " -0.004 2.00e-02 2.50e+03 pdb=" N6 DA D 21 " -0.002 2.00e-02 2.50e+03 pdb=" N1 DA D 21 " -0.004 2.00e-02 2.50e+03 pdb=" C2 DA D 21 " 0.004 2.00e-02 2.50e+03 pdb=" N3 DA D 21 " 0.003 2.00e-02 2.50e+03 pdb=" C4 DA D 21 " 0.002 2.00e-02 2.50e+03 ... (remaining 1120 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2565 2.81 - 3.33: 7940 3.33 - 3.86: 18462 3.86 - 4.38: 22197 4.38 - 4.90: 31659 Nonbonded interactions: 82823 Sorted by model distance: nonbonded pdb=" O LEU A 565 " pdb=" OG1 THR A 663 " model vdw 2.290 3.040 nonbonded pdb=" O2' C B 66 " pdb=" OP1 U B 95 " model vdw 2.303 3.040 nonbonded pdb=" NH2 ARG A 295 " pdb=" O2 U B 13 " model vdw 2.306 3.120 nonbonded pdb=" OD2 ASP A 38 " pdb=" OH TYR A 456 " model vdw 2.322 3.040 nonbonded pdb=" NH2 ARG A 414 " pdb=" OG1 THR A 585 " model vdw 2.327 3.120 ... (remaining 82818 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: 2.060 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 13.480 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 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 : 0.003 0.061 10306 Z= 0.280 Angle : 0.661 15.841 14885 Z= 0.515 Chirality : 0.051 0.208 1813 Planarity : 0.002 0.033 1123 Dihedral : 22.215 165.954 4976 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 1.89 % Allowed : 35.98 % Favored : 62.12 % 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: 0.42 (0.33), residues: 678 helix: 1.23 (0.37), residues: 213 sheet: 1.37 (0.70), residues: 61 loop : -0.40 (0.32), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 370 TYR 0.012 0.001 TYR A 30 PHE 0.009 0.001 PHE A 181 TRP 0.013 0.001 TRP A 464 HIS 0.004 0.001 HIS A 384 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.28 (10298) covalent geometry : angle 0.64749 / 0.51 (14876) hydrogen bonds : bond 0.25269 / 16.66 ( 312) hydrogen bonds : angle 7.97597 / 5.94 ( 734) metal coordination : bond 0.02181 / 1.09 ( 8) metal coordination : angle 5.42065 / 3.19 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 89 time to evaluate : 0.315 Fit side-chains outliers start: 10 outliers final: 2 residues processed: 95 average time/residue: 0.4823 time to fit residues: 49.9529 Evaluate side-chains 66 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 64 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 630 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.0020 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 4.9990 chunk 45 optimal weight: 0.0770 chunk 74 optimal weight: 10.0000 overall best weight: 1.0148 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 159 ASN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 652 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.127670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.099066 restraints weight = 20570.233| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 2.11 r_work: 0.3430 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.1407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10306 Z= 0.152 Angle : 0.557 8.945 14885 Z= 0.319 Chirality : 0.040 0.255 1813 Planarity : 0.004 0.046 1123 Dihedral : 21.949 170.090 3749 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 6.25 % Allowed : 33.90 % Favored : 59.85 % 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: 0.33 (0.33), residues: 678 helix: 1.42 (0.37), residues: 215 sheet: 0.98 (0.64), residues: 61 loop : -0.57 (0.32), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 494 TYR 0.007 0.001 TYR A 30 PHE 0.018 0.001 PHE A 707 TRP 0.008 0.001 TRP A 464 HIS 0.002 0.001 HIS A 387 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.15 (10298) covalent geometry : angle 0.55287 / 0.32 (14876) hydrogen bonds : bond 0.07041 / 4.47 ( 312) hydrogen bonds : angle 4.19995 / 3.08 ( 734) metal coordination : bond 0.01148 / 0.64 ( 8) metal coordination : angle 2.76066 / 1.57 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 60 time to evaluate : 0.267 Fit side-chains REVERT: A 346 GLU cc_start: 0.7940 (mt-10) cc_final: 0.7406 (tp30) REVERT: A 376 LYS cc_start: 0.8046 (ptpt) cc_final: 0.7608 (ptmm) REVERT: A 543 ASP cc_start: 0.7890 (OUTLIER) cc_final: 0.7667 (m-30) REVERT: A 736 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.7571 (pp20) outliers start: 33 outliers final: 9 residues processed: 84 average time/residue: 0.4776 time to fit residues: 43.7500 Evaluate side-chains 65 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 54 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 543 ASP Chi-restraints excluded: chain A residue 568 ARG Chi-restraints excluded: chain A residue 630 TYR Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 736 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 8 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 86 optimal weight: 40.0000 chunk 39 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 43 optimal weight: 10.0000 chunk 16 optimal weight: 0.7980 chunk 54 optimal weight: 6.9990 chunk 14 optimal weight: 2.9990 chunk 27 optimal weight: 7.9990 chunk 13 optimal weight: 0.7980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.125508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.096561 restraints weight = 20519.972| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 2.02 r_work: 0.3408 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10306 Z= 0.143 Angle : 0.495 5.811 14885 Z= 0.294 Chirality : 0.037 0.275 1813 Planarity : 0.003 0.035 1123 Dihedral : 22.072 169.935 3749 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 5.68 % Allowed : 33.33 % Favored : 60.98 % 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: 0.21 (0.32), residues: 678 helix: 1.47 (0.37), residues: 216 sheet: 0.35 (0.59), residues: 61 loop : -0.64 (0.31), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 494 TYR 0.009 0.001 TYR A 30 PHE 0.011 0.001 PHE A 331 TRP 0.011 0.001 TRP A 464 HIS 0.002 0.001 HIS A 387 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.14 (10298) covalent geometry : angle 0.49306 / 0.29 (14876) hydrogen bonds : bond 0.05669 / 3.64 ( 312) hydrogen bonds : angle 3.90450 / 2.85 ( 734) metal coordination : bond 0.01456 / 0.82 ( 8) metal coordination : angle 1.74978 / 1.08 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 62 time to evaluate : 0.265 Fit side-chains REVERT: A 27 GLN cc_start: 0.8004 (OUTLIER) cc_final: 0.7525 (tp40) REVERT: A 346 GLU cc_start: 0.8044 (mt-10) cc_final: 0.7546 (tp30) REVERT: A 631 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8111 (pp) outliers start: 30 outliers final: 12 residues processed: 85 average time/residue: 0.4558 time to fit residues: 42.4746 Evaluate side-chains 65 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 51 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLN Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 562 SER Chi-restraints excluded: chain A residue 568 ARG Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 630 TYR Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 634 ASN Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 705 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 38 optimal weight: 5.9990 chunk 66 optimal weight: 6.9990 chunk 55 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 72 optimal weight: 50.0000 chunk 62 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 76 optimal weight: 10.0000 chunk 46 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 401 ASN A 410 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.120383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.090806 restraints weight = 20448.915| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 2.04 r_work: 0.3305 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 10306 Z= 0.253 Angle : 0.624 7.682 14885 Z= 0.347 Chirality : 0.042 0.285 1813 Planarity : 0.004 0.034 1123 Dihedral : 22.166 164.552 3749 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.75 % Favored : 94.10 % Rotamer: Outliers : 7.39 % Allowed : 32.01 % Favored : 60.61 % 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: -0.25 (0.31), residues: 678 helix: 1.07 (0.36), residues: 211 sheet: -0.09 (0.59), residues: 60 loop : -0.86 (0.30), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 266 TYR 0.014 0.002 TYR A 600 PHE 0.019 0.002 PHE A 90 TRP 0.015 0.002 TRP A 464 HIS 0.004 0.001 HIS A 666 Details of bonding type rmsd/Z covalent geometry : bond 0.00493 / 0.25 (10298) covalent geometry : angle 0.61937 / 0.35 (14876) hydrogen bonds : bond 0.05960 / 3.86 ( 312) hydrogen bonds : angle 4.11779 / 3.00 ( 734) metal coordination : bond 0.03002 / 1.53 ( 8) metal coordination : angle 3.29508 / 1.98 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 57 time to evaluate : 0.274 Fit side-chains revert: symmetry clash REVERT: A 27 GLN cc_start: 0.7990 (OUTLIER) cc_final: 0.7481 (tp40) REVERT: A 142 ARG cc_start: 0.7859 (OUTLIER) cc_final: 0.7378 (ptt180) REVERT: A 326 MET cc_start: 0.8659 (mtp) cc_final: 0.8409 (mtm) REVERT: A 376 LYS cc_start: 0.8257 (ptpt) cc_final: 0.7527 (ptmm) REVERT: A 401 ASN cc_start: 0.8047 (OUTLIER) cc_final: 0.7811 (t160) REVERT: A 467 MET cc_start: 0.9268 (ttt) cc_final: 0.8979 (ttt) REVERT: A 736 GLU cc_start: 0.8560 (OUTLIER) cc_final: 0.7784 (pp20) outliers start: 39 outliers final: 21 residues processed: 87 average time/residue: 0.4972 time to fit residues: 47.1212 Evaluate side-chains 78 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 53 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 27 GLN Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 142 ARG Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 562 SER Chi-restraints excluded: chain A residue 568 ARG Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 630 TYR Chi-restraints excluded: chain A residue 634 ASN Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 679 LYS Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 736 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 82 optimal weight: 10.0000 chunk 4 optimal weight: 0.9980 chunk 73 optimal weight: 10.0000 chunk 86 optimal weight: 40.0000 chunk 22 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 46 optimal weight: 0.6980 chunk 63 optimal weight: 4.9990 chunk 25 optimal weight: 7.9990 chunk 1 optimal weight: 4.9990 chunk 57 optimal weight: 0.6980 overall best weight: 2.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 401 ASN A 713 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.120530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.091016 restraints weight = 20486.403| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 2.02 r_work: 0.3309 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10306 Z= 0.211 Angle : 0.567 7.652 14885 Z= 0.322 Chirality : 0.040 0.285 1813 Planarity : 0.004 0.037 1123 Dihedral : 22.195 166.331 3749 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.46 % Favored : 94.40 % Rotamer: Outliers : 6.63 % Allowed : 32.95 % Favored : 60.42 % 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: -0.30 (0.31), residues: 678 helix: 1.04 (0.36), residues: 211 sheet: -0.47 (0.56), residues: 65 loop : -0.83 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 266 TYR 0.026 0.002 TYR A 78 PHE 0.014 0.002 PHE A 90 TRP 0.014 0.002 TRP A 464 HIS 0.003 0.001 HIS A 693 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.21 (10298) covalent geometry : angle 0.56362 / 0.32 (14876) hydrogen bonds : bond 0.05530 / 3.55 ( 312) hydrogen bonds : angle 4.02303 / 2.93 ( 734) metal coordination : bond 0.02037 / 1.04 ( 8) metal coordination : angle 2.43924 / 1.47 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 54 time to evaluate : 0.280 Fit side-chains revert: symmetry clash REVERT: A 142 ARG cc_start: 0.7782 (OUTLIER) cc_final: 0.7332 (ptt180) REVERT: A 326 MET cc_start: 0.8649 (mtp) cc_final: 0.8415 (mtm) REVERT: A 376 LYS cc_start: 0.8253 (ptpt) cc_final: 0.7748 (ptmm) REVERT: A 717 VAL cc_start: 0.8095 (t) cc_final: 0.7803 (p) REVERT: A 736 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.7747 (pp20) outliers start: 35 outliers final: 19 residues processed: 81 average time/residue: 0.4793 time to fit residues: 42.4798 Evaluate side-chains 75 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 54 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 142 ARG Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 352 HIS Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 562 SER Chi-restraints excluded: chain A residue 568 ARG Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 630 TYR Chi-restraints excluded: chain A residue 634 ASN Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 736 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 39 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 79 optimal weight: 10.0000 chunk 34 optimal weight: 4.9990 chunk 56 optimal weight: 0.9980 chunk 86 optimal weight: 40.0000 chunk 15 optimal weight: 2.9990 chunk 67 optimal weight: 0.3980 chunk 61 optimal weight: 0.9980 chunk 36 optimal weight: 5.9990 chunk 42 optimal weight: 7.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 401 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.121319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.091974 restraints weight = 20570.280| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 2.01 r_work: 0.3330 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.2810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10306 Z= 0.166 Angle : 0.531 7.165 14885 Z= 0.305 Chirality : 0.038 0.276 1813 Planarity : 0.004 0.038 1123 Dihedral : 22.169 168.643 3749 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.60 % Favored : 94.25 % Rotamer: Outliers : 5.30 % Allowed : 33.90 % Favored : 60.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.32), residues: 678 helix: 1.03 (0.36), residues: 217 sheet: -0.55 (0.55), residues: 65 loop : -0.80 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 266 TYR 0.024 0.002 TYR A 78 PHE 0.011 0.001 PHE A 661 TRP 0.011 0.002 TRP A 464 HIS 0.002 0.001 HIS A 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.17 (10298) covalent geometry : angle 0.52504 / 0.30 (14876) hydrogen bonds : bond 0.05012 / 3.20 ( 312) hydrogen bonds : angle 3.86801 / 2.81 ( 734) metal coordination : bond 0.01990 / 1.22 ( 8) metal coordination : angle 3.25856 / 1.89 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 58 time to evaluate : 0.275 Fit side-chains REVERT: A 27 GLN cc_start: 0.8051 (OUTLIER) cc_final: 0.7501 (tp40) REVERT: A 142 ARG cc_start: 0.7580 (OUTLIER) cc_final: 0.7147 (ptt180) REVERT: A 326 MET cc_start: 0.8643 (mtp) cc_final: 0.8409 (mtm) REVERT: A 492 TYR cc_start: 0.7346 (t80) cc_final: 0.7120 (t80) REVERT: A 717 VAL cc_start: 0.8169 (OUTLIER) cc_final: 0.7878 (p) REVERT: A 736 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.7725 (pp20) outliers start: 28 outliers final: 14 residues processed: 80 average time/residue: 0.4834 time to fit residues: 42.2515 Evaluate side-chains 69 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 51 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 27 GLN Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 142 ARG Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 562 SER Chi-restraints excluded: chain A residue 568 ARG Chi-restraints excluded: chain A residue 630 TYR Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 736 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 10 optimal weight: 5.9990 chunk 75 optimal weight: 10.0000 chunk 3 optimal weight: 6.9990 chunk 86 optimal weight: 40.0000 chunk 12 optimal weight: 3.9990 chunk 72 optimal weight: 50.0000 chunk 63 optimal weight: 0.9990 chunk 85 optimal weight: 10.0000 chunk 6 optimal weight: 0.7980 chunk 41 optimal weight: 0.8980 chunk 76 optimal weight: 10.0000 overall best weight: 2.5386 ------------------------------------------------------------------------------- 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 = 0.3903 r_free = 0.3903 target = 0.119695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.090265 restraints weight = 20417.003| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 1.99 r_work: 0.3298 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.2977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10306 Z= 0.220 Angle : 0.601 9.797 14885 Z= 0.334 Chirality : 0.040 0.286 1813 Planarity : 0.004 0.049 1123 Dihedral : 22.197 166.594 3747 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.90 % Favored : 93.95 % Rotamer: Outliers : 6.44 % Allowed : 32.58 % Favored : 60.98 % 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: -0.34 (0.32), residues: 678 helix: 1.25 (0.37), residues: 198 sheet: -0.88 (0.54), residues: 63 loop : -0.86 (0.30), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 266 TYR 0.023 0.002 TYR A 78 PHE 0.013 0.002 PHE A 90 TRP 0.008 0.002 TRP A 464 HIS 0.003 0.001 HIS A 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.22 (10298) covalent geometry : angle 0.58940 / 0.33 (14876) hydrogen bonds : bond 0.05407 / 3.48 ( 312) hydrogen bonds : angle 4.01182 / 2.91 ( 734) metal coordination : bond 0.02029 / 1.07 ( 8) metal coordination : angle 4.76624 / 2.81 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 53 time to evaluate : 0.273 Fit side-chains REVERT: A 27 GLN cc_start: 0.8096 (OUTLIER) cc_final: 0.7538 (tp40) REVERT: A 142 ARG cc_start: 0.7761 (OUTLIER) cc_final: 0.7303 (ptt180) REVERT: A 326 MET cc_start: 0.8690 (mtp) cc_final: 0.8478 (mtm) REVERT: A 370 ARG cc_start: 0.8238 (mtm110) cc_final: 0.7907 (ttp-110) REVERT: A 376 LYS cc_start: 0.8196 (ptmt) cc_final: 0.7952 (ptmt) REVERT: A 492 TYR cc_start: 0.7350 (t80) cc_final: 0.7147 (t80) REVERT: A 717 VAL cc_start: 0.8251 (OUTLIER) cc_final: 0.8008 (p) REVERT: A 736 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.7741 (pp20) outliers start: 34 outliers final: 18 residues processed: 79 average time/residue: 0.4759 time to fit residues: 41.1615 Evaluate side-chains 72 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 50 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 27 GLN Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 142 ARG Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 352 HIS Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 562 SER Chi-restraints excluded: chain A residue 568 ARG Chi-restraints excluded: chain A residue 630 TYR Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 736 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 43 optimal weight: 0.5980 chunk 50 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 48 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 78 optimal weight: 10.0000 chunk 63 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 56 optimal weight: 0.2980 chunk 15 optimal weight: 0.8980 chunk 57 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 435 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.122825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.093967 restraints weight = 20461.169| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 1.97 r_work: 0.3366 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.3022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10306 Z= 0.120 Angle : 0.510 8.431 14885 Z= 0.296 Chirality : 0.035 0.263 1813 Planarity : 0.003 0.037 1123 Dihedral : 22.159 171.687 3747 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.46 % Favored : 94.40 % Rotamer: Outliers : 4.55 % Allowed : 34.28 % Favored : 61.17 % 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: -0.24 (0.32), residues: 678 helix: 1.06 (0.36), residues: 216 sheet: -0.73 (0.55), residues: 63 loop : -0.74 (0.31), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 266 TYR 0.023 0.001 TYR A 78 PHE 0.012 0.001 PHE A 661 TRP 0.013 0.001 TRP A 464 HIS 0.003 0.001 HIS A 387 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.12 (10298) covalent geometry : angle 0.50548 / 0.30 (14876) hydrogen bonds : bond 0.04589 / 2.91 ( 312) hydrogen bonds : angle 3.84409 / 2.80 ( 734) metal coordination : bond 0.00850 / 0.47 ( 8) metal coordination : angle 2.89127 / 1.73 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 54 time to evaluate : 0.233 Fit side-chains REVERT: A 27 GLN cc_start: 0.8100 (OUTLIER) cc_final: 0.7550 (tp40) REVERT: A 326 MET cc_start: 0.8610 (mtp) cc_final: 0.8379 (mtm) REVERT: A 344 LEU cc_start: 0.8440 (mt) cc_final: 0.8212 (mp) REVERT: A 370 ARG cc_start: 0.8175 (mtm110) cc_final: 0.7896 (ttp-110) REVERT: A 376 LYS cc_start: 0.8189 (ptmt) cc_final: 0.7934 (ptmt) REVERT: A 405 CYS cc_start: 0.7881 (OUTLIER) cc_final: 0.7513 (m) REVERT: A 609 LYS cc_start: 0.8381 (OUTLIER) cc_final: 0.8105 (pmtt) REVERT: A 717 VAL cc_start: 0.8125 (OUTLIER) cc_final: 0.7842 (p) outliers start: 24 outliers final: 10 residues processed: 73 average time/residue: 0.4461 time to fit residues: 35.5588 Evaluate side-chains 65 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 51 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLN Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 405 CYS Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 562 SER Chi-restraints excluded: chain A residue 568 ARG Chi-restraints excluded: chain A residue 609 LYS Chi-restraints excluded: chain A residue 630 TYR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 717 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 28 optimal weight: 10.0000 chunk 6 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 68 optimal weight: 10.0000 chunk 71 optimal weight: 30.0000 chunk 0 optimal weight: 8.9990 chunk 85 optimal weight: 10.0000 chunk 16 optimal weight: 0.4980 chunk 50 optimal weight: 0.9990 chunk 77 optimal weight: 10.0000 overall best weight: 2.4988 ------------------------------------------------------------------------------- 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 = 0.3906 r_free = 0.3906 target = 0.119831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.090532 restraints weight = 20446.462| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 1.99 r_work: 0.3304 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10306 Z= 0.217 Angle : 0.576 7.600 14885 Z= 0.323 Chirality : 0.040 0.283 1813 Planarity : 0.004 0.036 1123 Dihedral : 22.193 167.171 3747 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.60 % Favored : 94.25 % Rotamer: Outliers : 3.79 % Allowed : 35.23 % Favored : 60.98 % 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: -0.35 (0.32), residues: 678 helix: 1.02 (0.36), residues: 204 sheet: -0.95 (0.54), residues: 63 loop : -0.76 (0.31), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 266 TYR 0.023 0.002 TYR A 78 PHE 0.013 0.002 PHE A 90 TRP 0.006 0.001 TRP A 464 HIS 0.003 0.001 HIS A 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.22 (10298) covalent geometry : angle 0.56974 / 0.32 (14876) hydrogen bonds : bond 0.05150 / 3.32 ( 312) hydrogen bonds : angle 3.98425 / 2.89 ( 734) metal coordination : bond 0.01768 / 0.92 ( 8) metal coordination : angle 3.39045 / 1.97 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 52 time to evaluate : 0.208 Fit side-chains revert: symmetry clash REVERT: A 27 GLN cc_start: 0.8119 (OUTLIER) cc_final: 0.7760 (tp40) REVERT: A 344 LEU cc_start: 0.8504 (mt) cc_final: 0.8217 (mp) REVERT: A 370 ARG cc_start: 0.8277 (mtm110) cc_final: 0.7788 (ttm110) REVERT: A 376 LYS cc_start: 0.8181 (ptmt) cc_final: 0.7896 (ptmt) REVERT: A 391 ARG cc_start: 0.8090 (OUTLIER) cc_final: 0.7446 (mtp85) REVERT: A 717 VAL cc_start: 0.8239 (OUTLIER) cc_final: 0.8013 (p) outliers start: 20 outliers final: 12 residues processed: 68 average time/residue: 0.4328 time to fit residues: 32.2322 Evaluate side-chains 63 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 48 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLN Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 391 ARG Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 412 GLU Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 562 SER Chi-restraints excluded: chain A residue 568 ARG Chi-restraints excluded: chain A residue 630 TYR Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 717 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 36 optimal weight: 0.2980 chunk 63 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 chunk 70 optimal weight: 10.0000 chunk 22 optimal weight: 3.9990 chunk 59 optimal weight: 0.1980 chunk 74 optimal weight: 9.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 435 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.122271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.093328 restraints weight = 20420.357| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 2.03 r_work: 0.3352 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.3161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10306 Z= 0.127 Angle : 0.513 6.692 14885 Z= 0.298 Chirality : 0.036 0.269 1813 Planarity : 0.004 0.038 1123 Dihedral : 22.177 170.957 3747 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.60 % Favored : 94.25 % Rotamer: Outliers : 4.55 % Allowed : 34.66 % Favored : 60.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.32), residues: 678 helix: 1.08 (0.37), residues: 210 sheet: -0.76 (0.55), residues: 63 loop : -0.71 (0.31), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 266 TYR 0.024 0.001 TYR A 78 PHE 0.013 0.001 PHE A 661 TRP 0.009 0.001 TRP A 464 HIS 0.003 0.001 HIS A 387 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.13 (10298) covalent geometry : angle 0.50815 / 0.30 (14876) hydrogen bonds : bond 0.04498 / 2.87 ( 312) hydrogen bonds : angle 3.86387 / 2.81 ( 734) metal coordination : bond 0.00948 / 0.50 ( 8) metal coordination : angle 2.83973 / 1.67 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 52 time to evaluate : 0.246 Fit side-chains revert: symmetry clash REVERT: A 27 GLN cc_start: 0.8127 (OUTLIER) cc_final: 0.7552 (tp40) REVERT: A 344 LEU cc_start: 0.8503 (mt) cc_final: 0.8221 (mp) REVERT: A 370 ARG cc_start: 0.8247 (mtm110) cc_final: 0.7887 (ttp-110) REVERT: A 376 LYS cc_start: 0.8180 (ptmt) cc_final: 0.7917 (ptmt) REVERT: A 391 ARG cc_start: 0.8083 (OUTLIER) cc_final: 0.7473 (mtp85) REVERT: A 405 CYS cc_start: 0.7842 (OUTLIER) cc_final: 0.7547 (m) REVERT: A 717 VAL cc_start: 0.8199 (OUTLIER) cc_final: 0.7949 (p) outliers start: 24 outliers final: 13 residues processed: 72 average time/residue: 0.4450 time to fit residues: 34.8881 Evaluate side-chains 69 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 52 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 27 GLN Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 391 ARG Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 405 CYS Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 412 GLU Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 562 SER Chi-restraints excluded: chain A residue 568 ARG Chi-restraints excluded: chain A residue 630 TYR Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 717 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 26 optimal weight: 0.0050 chunk 72 optimal weight: 50.0000 chunk 41 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 chunk 24 optimal weight: 0.0020 chunk 75 optimal weight: 10.0000 chunk 51 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 overall best weight: 1.2006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 435 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.121997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.093069 restraints weight = 20482.350| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 2.02 r_work: 0.3349 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.3184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10306 Z= 0.139 Angle : 0.524 7.606 14885 Z= 0.302 Chirality : 0.036 0.274 1813 Planarity : 0.004 0.038 1123 Dihedral : 22.151 169.994 3747 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.75 % Favored : 94.10 % Rotamer: Outliers : 4.17 % Allowed : 35.04 % Favored : 60.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.32), residues: 678 helix: 1.06 (0.37), residues: 210 sheet: -0.80 (0.54), residues: 63 loop : -0.69 (0.31), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 266 TYR 0.023 0.001 TYR A 78 PHE 0.010 0.001 PHE A 661 TRP 0.009 0.001 TRP A 464 HIS 0.002 0.001 HIS A 387 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.14 (10298) covalent geometry : angle 0.51912 / 0.30 (14876) hydrogen bonds : bond 0.04540 / 2.92 ( 312) hydrogen bonds : angle 3.85245 / 2.80 ( 734) metal coordination : bond 0.01080 / 0.57 ( 8) metal coordination : angle 2.91653 / 1.74 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2725.92 seconds wall clock time: 47 minutes 21.31 seconds (2841.31 seconds total)