Starting phenix.real_space_refine on Tue Feb 11 15:15:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cmp_45752/02_2025/9cmp_45752.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cmp_45752/02_2025/9cmp_45752.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9cmp_45752/02_2025/9cmp_45752.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cmp_45752/02_2025/9cmp_45752.map" model { file = "/net/cci-nas-00/data/ceres_data/9cmp_45752/02_2025/9cmp_45752.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cmp_45752/02_2025/9cmp_45752.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.005 sd= 0.094 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 42 5.49 5 Mg 1 5.21 5 S 24 5.16 5 C 3718 2.51 5 N 1141 2.21 5 O 1285 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 6211 Number of models: 1 Model: "" Number of chains: 4 Chain: "G" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 449 Classifications: {'RNA': 21} Modifications used: {'p5*END': 1, 'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 10, 'rna3p_pyr': 9} Link IDs: {'rna2p': 2, 'rna3p': 18} Chain: "T" Number of atoms: 458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 458 Classifications: {'RNA': 22} Modifications used: {'5*END': 1, 'rna2p_pur': 1, 'rna3p_pur': 9, 'rna3p_pyr': 12} Link IDs: {'rna3p': 21} Chain: "A" Number of atoms: 5303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 768, 5303 Classifications: {'peptide': 768} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 243} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 46, 'TRANS': 718} Chain breaks: 13 Unresolved chain link angles: 17 Unresolved non-hydrogen bonds: 890 Unresolved non-hydrogen angles: 1132 Unresolved non-hydrogen dihedrals: 750 Unresolved non-hydrogen chiralities: 80 Planarities with less than four sites: {'GLN:plan1': 12, 'ASP:plan': 12, 'TYR:plan': 8, 'ASN:plan1': 7, 'TRP:plan': 3, 'HIS:plan': 8, 'PHE:plan': 12, 'GLU:plan': 14, 'ARG:plan': 21} Unresolved non-hydrogen planarities: 461 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.74, per 1000 atoms: 0.76 Number of scatterers: 6211 At special positions: 0 Unit cell: (106.602, 82.404, 111.18, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 24 16.00 P 42 15.00 Mg 1 11.99 O 1285 8.00 N 1141 7.00 C 3718 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: 1.64 Conformation dependent library (CDL) restraints added in 871.4 milliseconds 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1454 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 8 sheets defined 35.0% alpha, 21.2% beta 18 base pairs and 24 stacking pairs defined. Time for finding SS restraints: 2.10 Creating SS restraints... Processing helix chain 'A' and resid 67 through 82 Processing helix chain 'A' and resid 140 through 148 removed outlier: 3.603A pdb=" N SER A 148 " --> pdb=" O HIS A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 167 removed outlier: 4.083A pdb=" N ARG A 167 " --> pdb=" O ASP A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 172 removed outlier: 3.869A pdb=" N MET A 172 " --> pdb=" O HIS A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 237 Processing helix chain 'A' and resid 251 through 259 removed outlier: 3.792A pdb=" N PHE A 258 " --> pdb=" O GLN A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 369 Processing helix chain 'A' and resid 372 through 387 removed outlier: 4.565A pdb=" N GLU A 378 " --> pdb=" O ASP A 374 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG A 384 " --> pdb=" O SER A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 391 Processing helix chain 'A' and resid 430 through 434 Processing helix chain 'A' and resid 463 through 481 Processing helix chain 'A' and resid 497 through 499 No H-bonds generated for 'chain 'A' and resid 497 through 499' Processing helix chain 'A' and resid 500 through 512 removed outlier: 3.816A pdb=" N MET A 504 " --> pdb=" O SER A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 537 removed outlier: 3.788A pdb=" N GLU A 531 " --> pdb=" O PRO A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 554 Processing helix chain 'A' and resid 556 through 571 removed outlier: 3.581A pdb=" N LYS A 566 " --> pdb=" O ASN A 562 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N VAL A 569 " --> pdb=" O LEU A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 589 removed outlier: 4.110A pdb=" N GLN A 589 " --> pdb=" O VAL A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 658 Processing helix chain 'A' and resid 672 through 674 No H-bonds generated for 'chain 'A' and resid 672 through 674' Processing helix chain 'A' and resid 675 through 695 removed outlier: 3.569A pdb=" N HIS A 681 " --> pdb=" O GLN A 677 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N LEU A 684 " --> pdb=" O LEU A 680 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LEU A 685 " --> pdb=" O HIS A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 723 removed outlier: 3.542A pdb=" N ARG A 723 " --> pdb=" O LYS A 720 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 786 Processing helix chain 'A' and resid 787 through 789 No H-bonds generated for 'chain 'A' and resid 787 through 789' Processing helix chain 'A' and resid 800 through 816 Processing helix chain 'A' and resid 819 through 824 removed outlier: 3.558A pdb=" N ASP A 823 " --> pdb=" O ASP A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 846 removed outlier: 3.812A pdb=" N ARG A 837 " --> pdb=" O GLN A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 854 Processing sheet with id=AA1, first strand: chain 'A' and resid 202 through 208 removed outlier: 7.300A pdb=" N MET A 213 " --> pdb=" O MET A 47 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N MET A 47 " --> pdb=" O MET A 213 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE A 217 " --> pdb=" O ASN A 43 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N ASN A 43 " --> pdb=" O ILE A 217 " (cutoff:3.500A) removed outlier: 12.740A pdb=" N VAL A 219 " --> pdb=" O GLN A 41 " (cutoff:3.500A) removed outlier: 17.368A pdb=" N GLN A 41 " --> pdb=" O VAL A 219 " (cutoff:3.500A) removed outlier: 8.534A pdb=" N ILE A 38 " --> pdb=" O VAL A 412 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N VAL A 412 " --> pdb=" O ILE A 38 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N LEU A 40 " --> pdb=" O GLY A 410 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N GLY A 410 " --> pdb=" O LEU A 40 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ALA A 42 " --> pdb=" O VAL A 408 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N VAL A 408 " --> pdb=" O ALA A 42 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N PHE A 44 " --> pdb=" O THR A 406 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N GLU A 46 " --> pdb=" O GLU A 404 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N GLU A 404 " --> pdb=" O GLU A 46 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N THR A 734 " --> pdb=" O CYS A 751 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N PHE A 704 " --> pdb=" O LEU A 768 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ASP A 770 " --> pdb=" O ILE A 702 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N ILE A 702 " --> pdb=" O ASP A 770 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ILE A 592 " --> pdb=" O ILE A 665 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N PHE A 593 " --> pdb=" O SER A 617 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N SER A 617 " --> pdb=" O PHE A 593 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER A 610 " --> pdb=" O GLN A 632 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 202 through 208 removed outlier: 7.300A pdb=" N MET A 213 " --> pdb=" O MET A 47 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N MET A 47 " --> pdb=" O MET A 213 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE A 217 " --> pdb=" O ASN A 43 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N ASN A 43 " --> pdb=" O ILE A 217 " (cutoff:3.500A) removed outlier: 12.740A pdb=" N VAL A 219 " --> pdb=" O GLN A 41 " (cutoff:3.500A) removed outlier: 17.368A pdb=" N GLN A 41 " --> pdb=" O VAL A 219 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 93 through 94 removed outlier: 5.832A pdb=" N ILE A 54 " --> pdb=" O CYS A 137 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N CYS A 137 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N HIS A 56 " --> pdb=" O VAL A 135 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N VAL A 113 " --> pdb=" O ILE A 132 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 196 through 197 Processing sheet with id=AA5, first strand: chain 'A' and resid 279 through 280 Processing sheet with id=AA6, first strand: chain 'A' and resid 283 through 288 removed outlier: 4.159A pdb=" N ASN A 283 " --> pdb=" O GLN A 329 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N CYS A 327 " --> pdb=" O THR A 285 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 427 through 428 Processing sheet with id=AA8, first strand: chain 'A' and resid 492 through 494 removed outlier: 3.830A pdb=" N LYS A 493 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ALA A 452 " --> pdb=" O VAL A 519 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N ILE A 521 " --> pdb=" O ALA A 452 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ALA A 454 " --> pdb=" O ILE A 521 " (cutoff:3.500A) 237 hydrogen bonds defined for protein. 672 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 42 hydrogen bonds 84 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 24 stacking parallelities Total time for adding SS restraints: 2.85 Time building geometry restraints manager: 1.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1733 1.34 - 1.45: 1224 1.45 - 1.57: 3324 1.57 - 1.69: 83 1.69 - 1.81: 36 Bond restraints: 6400 Sorted by residual: bond pdb=" O5' U G 1 " pdb=" C5' U G 1 " ideal model delta sigma weight residual 1.424 1.454 -0.030 1.50e-02 4.44e+03 3.95e+00 bond pdb=" C LEU A 522 " pdb=" N PRO A 523 " ideal model delta sigma weight residual 1.334 1.367 -0.033 2.34e-02 1.83e+03 1.97e+00 bond pdb=" CB PHE A 746 " pdb=" CG PHE A 746 " ideal model delta sigma weight residual 1.502 1.530 -0.028 2.30e-02 1.89e+03 1.48e+00 bond pdb=" C3' U G 1 " pdb=" O3' U G 1 " ideal model delta sigma weight residual 1.427 1.409 0.018 1.50e-02 4.44e+03 1.44e+00 bond pdb=" P U G 1 " pdb=" OP2 U G 1 " ideal model delta sigma weight residual 1.485 1.509 -0.024 2.00e-02 2.50e+03 1.42e+00 ... (remaining 6395 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.98: 8892 4.98 - 9.95: 14 9.95 - 14.93: 4 14.93 - 19.90: 0 19.90 - 24.88: 1 Bond angle restraints: 8911 Sorted by residual: angle pdb=" O3' U G 1 " pdb=" C3' U G 1 " pdb=" C2' U G 1 " ideal model delta sigma weight residual 109.50 95.51 13.99 1.50e+00 4.44e-01 8.70e+01 angle pdb=" O3' U G 1 " pdb=" P G G 2 " pdb=" OP1 G G 2 " ideal model delta sigma weight residual 108.00 83.12 24.88 3.00e+00 1.11e-01 6.88e+01 angle pdb=" O3' U G 1 " pdb=" P G G 2 " pdb=" O5' G G 2 " ideal model delta sigma weight residual 104.00 115.46 -11.46 1.50e+00 4.44e-01 5.83e+01 angle pdb=" C GLY A 109 " pdb=" N ARG A 110 " pdb=" CA ARG A 110 " ideal model delta sigma weight residual 121.70 132.54 -10.84 1.80e+00 3.09e-01 3.63e+01 angle pdb=" C3' U G 1 " pdb=" C2' U G 1 " pdb=" C1' U G 1 " ideal model delta sigma weight residual 101.50 95.95 5.55 1.00e+00 1.00e+00 3.08e+01 ... (remaining 8906 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 3612 17.96 - 35.93: 151 35.93 - 53.89: 47 53.89 - 71.85: 44 71.85 - 89.81: 13 Dihedral angle restraints: 3867 sinusoidal: 1642 harmonic: 2225 Sorted by residual: dihedral pdb=" C5' U G 1 " pdb=" C4' U G 1 " pdb=" C3' U G 1 " pdb=" O3' U G 1 " ideal model delta sinusoidal sigma weight residual 147.00 -176.22 -36.78 1 8.00e+00 1.56e-02 2.99e+01 dihedral pdb=" O4' U G 1 " pdb=" C1' U G 1 " pdb=" N1 U G 1 " pdb=" C2 U G 1 " ideal model delta sinusoidal sigma weight residual -128.00 -56.09 -71.91 1 1.70e+01 3.46e-03 2.29e+01 dihedral pdb=" CA THR A 538 " pdb=" C THR A 538 " pdb=" N VAL A 539 " pdb=" CA VAL A 539 " ideal model delta harmonic sigma weight residual -180.00 -162.64 -17.36 0 5.00e+00 4.00e-02 1.21e+01 ... (remaining 3864 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 1017 0.098 - 0.195: 62 0.195 - 0.293: 0 0.293 - 0.391: 0 0.391 - 0.488: 1 Chirality restraints: 1080 Sorted by residual: chirality pdb=" P U G 1 " pdb=" OP1 U G 1 " pdb=" OP2 U G 1 " pdb=" O5' U G 1 " both_signs ideal model delta sigma weight residual True 2.41 2.90 -0.49 2.00e-01 2.50e+01 5.96e+00 chirality pdb=" C2' U G 1 " pdb=" C3' U G 1 " pdb=" O2' U G 1 " pdb=" C1' U G 1 " both_signs ideal model delta sigma weight residual False -2.52 -2.71 0.19 2.00e-01 2.50e+01 8.85e-01 chirality pdb=" CA ILE A 705 " pdb=" N ILE A 705 " pdb=" C ILE A 705 " pdb=" CB ILE A 705 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.37e-01 ... (remaining 1077 not shown) Planarity restraints: 1020 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 429 " 0.033 5.00e-02 4.00e+02 5.04e-02 4.06e+00 pdb=" N PRO A 430 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO A 430 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 430 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 508 " -0.010 2.00e-02 2.50e+03 1.99e-02 3.97e+00 pdb=" C LEU A 508 " 0.034 2.00e-02 2.50e+03 pdb=" O LEU A 508 " -0.013 2.00e-02 2.50e+03 pdb=" N LYS A 509 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 506 " 0.008 2.00e-02 2.50e+03 1.69e-02 2.84e+00 pdb=" C ARG A 506 " -0.029 2.00e-02 2.50e+03 pdb=" O ARG A 506 " 0.011 2.00e-02 2.50e+03 pdb=" N HIS A 507 " 0.010 2.00e-02 2.50e+03 ... (remaining 1017 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 184 2.69 - 3.24: 5875 3.24 - 3.80: 9692 3.80 - 4.35: 12376 4.35 - 4.90: 20013 Nonbonded interactions: 48140 Sorted by model distance: nonbonded pdb=" OG SER A 610 " pdb=" O GLN A 633 " model vdw 2.141 3.040 nonbonded pdb=" O GLU A 637 " pdb=" NH2 ARG A 668 " model vdw 2.275 3.120 nonbonded pdb=" O2' G G 2 " pdb=" OD1 ASN A 562 " model vdw 2.318 3.040 nonbonded pdb=" O PRO A 661 " pdb=" OH TYR A 698 " model vdw 2.319 3.040 nonbonded pdb=" O ARG A 534 " pdb=" OG1 THR A 538 " model vdw 2.356 3.040 ... (remaining 48135 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: 1.380 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: 0.050 Set scattering table: 0.060 Process input model: 21.010 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 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:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6423 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 : 0.004 0.037 6400 Z= 0.233 Angle : 0.765 24.877 8911 Z= 0.397 Chirality : 0.046 0.488 1080 Planarity : 0.004 0.050 1020 Dihedral : 14.583 89.815 2413 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 1.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 0.46 % Allowed : 4.59 % Favored : 94.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.30), residues: 740 helix: 0.15 (0.35), residues: 207 sheet: -1.34 (0.38), residues: 173 loop : -0.90 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 435 HIS 0.003 0.001 HIS A 634 PHE 0.011 0.001 PHE A 811 TYR 0.010 0.001 TYR A 698 ARG 0.002 0.000 ARG A 837 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 132 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 388 PHE cc_start: 0.5178 (m-80) cc_final: 0.4867 (m-10) REVERT: A 555 THR cc_start: 0.7842 (p) cc_final: 0.7603 (p) REVERT: A 688 ARG cc_start: 0.7340 (tpp-160) cc_final: 0.6181 (tmm160) REVERT: A 796 SER cc_start: 0.8138 (t) cc_final: 0.7835 (p) outliers start: 2 outliers final: 1 residues processed: 134 average time/residue: 0.2303 time to fit residues: 38.9187 Evaluate side-chains 89 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 88 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 711 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 67 optimal weight: 3.9990 chunk 60 optimal weight: 0.7980 chunk 33 optimal weight: 0.0070 chunk 20 optimal weight: 40.0000 chunk 40 optimal weight: 9.9990 chunk 32 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 24 optimal weight: 40.0000 chunk 38 optimal weight: 3.9990 chunk 46 optimal weight: 0.6980 chunk 72 optimal weight: 0.2980 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 634 HIS A 766 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.170656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.136020 restraints weight = 13981.550| |-----------------------------------------------------------------------------| r_work (start): 0.3931 rms_B_bonded: 3.52 r_work: 0.3792 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6600 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6400 Z= 0.168 Angle : 0.563 9.656 8911 Z= 0.289 Chirality : 0.040 0.174 1080 Planarity : 0.004 0.042 1020 Dihedral : 14.622 150.521 1443 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.29 % Allowed : 11.01 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.30), residues: 740 helix: 0.39 (0.34), residues: 229 sheet: -1.16 (0.39), residues: 171 loop : -0.69 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 435 HIS 0.005 0.001 HIS A 634 PHE 0.009 0.001 PHE A 593 TYR 0.010 0.001 TYR A 804 ARG 0.005 0.001 ARG A 475 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 91 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 378 GLU cc_start: 0.7296 (mp0) cc_final: 0.7076 (mp0) REVERT: A 535 VAL cc_start: 0.8587 (t) cc_final: 0.8263 (m) REVERT: A 624 ARG cc_start: 0.7353 (mmm160) cc_final: 0.7082 (tpt170) REVERT: A 672 SER cc_start: 0.8081 (OUTLIER) cc_final: 0.7801 (p) REVERT: A 688 ARG cc_start: 0.7298 (tpp-160) cc_final: 0.5927 (tmm160) REVERT: A 796 SER cc_start: 0.8219 (t) cc_final: 0.7977 (p) REVERT: A 819 ASP cc_start: 0.3685 (p0) cc_final: 0.3194 (p0) outliers start: 10 outliers final: 6 residues processed: 93 average time/residue: 0.1876 time to fit residues: 23.0668 Evaluate side-chains 90 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 83 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 634 HIS Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain A residue 672 SER Chi-restraints excluded: chain A residue 711 HIS Chi-restraints excluded: chain A residue 756 ILE Chi-restraints excluded: chain A residue 842 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 72 optimal weight: 0.0670 chunk 17 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 10 optimal weight: 40.0000 chunk 60 optimal weight: 0.6980 chunk 30 optimal weight: 50.0000 chunk 44 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 19 optimal weight: 40.0000 chunk 46 optimal weight: 0.8980 overall best weight: 1.9322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 600 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 634 HIS ** A 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 807 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.165855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.128934 restraints weight = 13869.875| |-----------------------------------------------------------------------------| r_work (start): 0.3824 rms_B_bonded: 3.52 r_work: 0.3679 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6828 moved from start: 0.3177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6400 Z= 0.289 Angle : 0.594 8.098 8911 Z= 0.305 Chirality : 0.042 0.191 1080 Planarity : 0.004 0.038 1020 Dihedral : 14.933 157.536 1443 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.44 % Allowed : 11.93 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.30), residues: 740 helix: 0.42 (0.34), residues: 223 sheet: -1.07 (0.40), residues: 160 loop : -0.47 (0.33), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 451 HIS 0.026 0.002 HIS A 634 PHE 0.015 0.002 PHE A 397 TYR 0.012 0.002 TYR A 804 ARG 0.007 0.001 ARG A 635 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 83 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 ASP cc_start: 0.6370 (t0) cc_final: 0.6158 (t0) REVERT: A 672 SER cc_start: 0.8396 (OUTLIER) cc_final: 0.8082 (p) REVERT: A 688 ARG cc_start: 0.7419 (tpp-160) cc_final: 0.5758 (ttp80) REVERT: A 742 HIS cc_start: 0.7967 (OUTLIER) cc_final: 0.7622 (m-70) REVERT: A 796 SER cc_start: 0.8752 (t) cc_final: 0.8502 (p) outliers start: 15 outliers final: 8 residues processed: 93 average time/residue: 0.1817 time to fit residues: 23.3303 Evaluate side-chains 88 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 78 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 617 SER Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain A residue 672 SER Chi-restraints excluded: chain A residue 711 HIS Chi-restraints excluded: chain A residue 713 THR Chi-restraints excluded: chain A residue 727 SER Chi-restraints excluded: chain A residue 742 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 42 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 28 optimal weight: 50.0000 chunk 46 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 31 optimal weight: 50.0000 chunk 77 optimal weight: 0.0270 chunk 76 optimal weight: 0.5980 chunk 55 optimal weight: 2.9990 chunk 8 optimal weight: 50.0000 overall best weight: 0.8840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 553 GLN A 708 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.167844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.131420 restraints weight = 13902.688| |-----------------------------------------------------------------------------| r_work (start): 0.3867 rms_B_bonded: 3.55 r_work: 0.3725 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6759 moved from start: 0.3543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6400 Z= 0.177 Angle : 0.535 8.287 8911 Z= 0.270 Chirality : 0.040 0.181 1080 Planarity : 0.004 0.045 1020 Dihedral : 14.823 155.900 1443 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.52 % Allowed : 14.68 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.31), residues: 740 helix: 0.89 (0.35), residues: 217 sheet: -1.00 (0.39), residues: 160 loop : -0.44 (0.33), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 435 HIS 0.005 0.001 HIS A 600 PHE 0.011 0.001 PHE A 774 TYR 0.011 0.001 TYR A 790 ARG 0.009 0.001 ARG A 554 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 80 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 ASP cc_start: 0.6334 (t0) cc_final: 0.6089 (t0) REVERT: A 672 SER cc_start: 0.8351 (OUTLIER) cc_final: 0.8081 (p) REVERT: A 688 ARG cc_start: 0.7424 (tpp-160) cc_final: 0.5780 (ttp80) REVERT: A 742 HIS cc_start: 0.7941 (OUTLIER) cc_final: 0.7572 (m-70) REVERT: A 796 SER cc_start: 0.8680 (t) cc_final: 0.8446 (p) REVERT: A 804 TYR cc_start: 0.7194 (OUTLIER) cc_final: 0.6776 (t80) REVERT: A 842 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.8031 (tt) outliers start: 11 outliers final: 3 residues processed: 84 average time/residue: 0.1846 time to fit residues: 20.9339 Evaluate side-chains 85 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 78 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 634 HIS Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain A residue 672 SER Chi-restraints excluded: chain A residue 711 HIS Chi-restraints excluded: chain A residue 742 HIS Chi-restraints excluded: chain A residue 804 TYR Chi-restraints excluded: chain A residue 842 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 48 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 42 optimal weight: 0.2980 chunk 16 optimal weight: 30.0000 chunk 75 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 17 optimal weight: 8.9990 chunk 49 optimal weight: 4.9990 chunk 55 optimal weight: 0.4980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.167084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.131128 restraints weight = 13687.844| |-----------------------------------------------------------------------------| r_work (start): 0.3865 rms_B_bonded: 3.48 r_work: 0.3721 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6789 moved from start: 0.3830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6400 Z= 0.176 Angle : 0.514 8.334 8911 Z= 0.257 Chirality : 0.040 0.182 1080 Planarity : 0.004 0.033 1020 Dihedral : 14.748 155.384 1443 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.67 % Allowed : 12.84 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.31), residues: 740 helix: 1.03 (0.35), residues: 221 sheet: -0.94 (0.39), residues: 159 loop : -0.42 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 435 HIS 0.004 0.001 HIS A 600 PHE 0.008 0.001 PHE A 774 TYR 0.009 0.001 TYR A 790 ARG 0.003 0.000 ARG A 375 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 81 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 ASP cc_start: 0.6412 (t0) cc_final: 0.6180 (t0) REVERT: A 508 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8588 (tt) REVERT: A 672 SER cc_start: 0.8410 (OUTLIER) cc_final: 0.8141 (p) REVERT: A 688 ARG cc_start: 0.7491 (tpp-160) cc_final: 0.5644 (ttp80) REVERT: A 742 HIS cc_start: 0.7961 (OUTLIER) cc_final: 0.7589 (m-70) REVERT: A 796 SER cc_start: 0.8780 (t) cc_final: 0.8546 (p) REVERT: A 804 TYR cc_start: 0.7173 (OUTLIER) cc_final: 0.6805 (t80) REVERT: A 842 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.8038 (tt) outliers start: 16 outliers final: 5 residues processed: 90 average time/residue: 0.1786 time to fit residues: 21.6915 Evaluate side-chains 89 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain A residue 672 SER Chi-restraints excluded: chain A residue 711 HIS Chi-restraints excluded: chain A residue 713 THR Chi-restraints excluded: chain A residue 727 SER Chi-restraints excluded: chain A residue 742 HIS Chi-restraints excluded: chain A residue 804 TYR Chi-restraints excluded: chain A residue 842 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 51 optimal weight: 2.9990 chunk 4 optimal weight: 6.9990 chunk 69 optimal weight: 0.7980 chunk 63 optimal weight: 0.5980 chunk 44 optimal weight: 4.9990 chunk 35 optimal weight: 10.0000 chunk 65 optimal weight: 2.9990 chunk 14 optimal weight: 20.0000 chunk 17 optimal weight: 4.9990 chunk 32 optimal weight: 8.9990 chunk 27 optimal weight: 5.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.162670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.125738 restraints weight = 13602.223| |-----------------------------------------------------------------------------| r_work (start): 0.3782 rms_B_bonded: 3.41 r_work: 0.3633 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6966 moved from start: 0.4556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 6400 Z= 0.344 Angle : 0.627 9.275 8911 Z= 0.318 Chirality : 0.043 0.200 1080 Planarity : 0.005 0.064 1020 Dihedral : 15.251 158.480 1443 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.90 % Allowed : 13.07 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.30), residues: 740 helix: 0.41 (0.34), residues: 227 sheet: -1.06 (0.39), residues: 161 loop : -0.58 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 451 HIS 0.005 0.001 HIS A 681 PHE 0.016 0.002 PHE A 442 TYR 0.018 0.002 TYR A 667 ARG 0.004 0.001 ARG A 554 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 76 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 ASP cc_start: 0.6631 (t0) cc_final: 0.6357 (t0) REVERT: A 397 PHE cc_start: 0.7265 (t80) cc_final: 0.7063 (t80) REVERT: A 672 SER cc_start: 0.8517 (OUTLIER) cc_final: 0.8199 (p) REVERT: A 842 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8235 (tt) outliers start: 17 outliers final: 11 residues processed: 85 average time/residue: 0.1578 time to fit residues: 18.6898 Evaluate side-chains 83 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 70 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain A residue 672 SER Chi-restraints excluded: chain A residue 711 HIS Chi-restraints excluded: chain A residue 713 THR Chi-restraints excluded: chain A residue 727 SER Chi-restraints excluded: chain A residue 742 HIS Chi-restraints excluded: chain A residue 756 ILE Chi-restraints excluded: chain A residue 757 GLN Chi-restraints excluded: chain A residue 822 HIS Chi-restraints excluded: chain A residue 842 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 67 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 14 optimal weight: 10.0000 chunk 58 optimal weight: 5.9990 chunk 56 optimal weight: 5.9990 chunk 30 optimal weight: 0.0040 chunk 42 optimal weight: 0.9980 chunk 78 optimal weight: 10.0000 chunk 44 optimal weight: 3.9990 chunk 29 optimal weight: 50.0000 chunk 19 optimal weight: 40.0000 overall best weight: 2.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 558 GLN A 788 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.161213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.123610 restraints weight = 13736.223| |-----------------------------------------------------------------------------| r_work (start): 0.3752 rms_B_bonded: 3.45 r_work: 0.3607 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7021 moved from start: 0.5188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 6400 Z= 0.395 Angle : 0.654 9.542 8911 Z= 0.331 Chirality : 0.044 0.203 1080 Planarity : 0.005 0.034 1020 Dihedral : 15.588 158.529 1443 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 4.36 % Allowed : 15.83 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.31), residues: 740 helix: 0.58 (0.35), residues: 219 sheet: -1.16 (0.40), residues: 158 loop : -0.72 (0.33), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 435 HIS 0.005 0.001 HIS A 600 PHE 0.020 0.002 PHE A 593 TYR 0.016 0.002 TYR A 805 ARG 0.005 0.001 ARG A 554 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 70 time to evaluate : 0.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 ASP cc_start: 0.6684 (t0) cc_final: 0.6474 (t70) REVERT: A 562 ASN cc_start: 0.8078 (t0) cc_final: 0.7836 (t0) outliers start: 19 outliers final: 13 residues processed: 82 average time/residue: 0.1603 time to fit residues: 18.3581 Evaluate side-chains 80 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 67 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 617 SER Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain A residue 672 SER Chi-restraints excluded: chain A residue 711 HIS Chi-restraints excluded: chain A residue 713 THR Chi-restraints excluded: chain A residue 727 SER Chi-restraints excluded: chain A residue 742 HIS Chi-restraints excluded: chain A residue 799 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 35 optimal weight: 7.9990 chunk 34 optimal weight: 2.9990 chunk 1 optimal weight: 10.0000 chunk 33 optimal weight: 0.4980 chunk 14 optimal weight: 30.0000 chunk 54 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 16 optimal weight: 40.0000 chunk 9 optimal weight: 9.9990 chunk 43 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.163083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.125571 restraints weight = 13695.497| |-----------------------------------------------------------------------------| r_work (start): 0.3781 rms_B_bonded: 3.48 r_work: 0.3637 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6939 moved from start: 0.5282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6400 Z= 0.249 Angle : 0.577 9.804 8911 Z= 0.287 Chirality : 0.041 0.188 1080 Planarity : 0.004 0.035 1020 Dihedral : 15.211 155.010 1443 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.44 % Allowed : 17.20 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.31), residues: 740 helix: 0.75 (0.35), residues: 220 sheet: -1.14 (0.40), residues: 157 loop : -0.70 (0.33), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 435 HIS 0.004 0.001 HIS A 600 PHE 0.012 0.001 PHE A 858 TYR 0.010 0.001 TYR A 698 ARG 0.003 0.000 ARG A 375 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 68 time to evaluate : 0.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 ASP cc_start: 0.6514 (t0) cc_final: 0.6267 (t0) REVERT: A 562 ASN cc_start: 0.7978 (t0) cc_final: 0.7774 (t0) outliers start: 15 outliers final: 10 residues processed: 77 average time/residue: 0.1743 time to fit residues: 18.3644 Evaluate side-chains 78 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 68 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain A residue 672 SER Chi-restraints excluded: chain A residue 711 HIS Chi-restraints excluded: chain A residue 713 THR Chi-restraints excluded: chain A residue 727 SER Chi-restraints excluded: chain A residue 742 HIS Chi-restraints excluded: chain A residue 799 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 52 optimal weight: 2.9990 chunk 7 optimal weight: 10.0000 chunk 47 optimal weight: 0.3980 chunk 43 optimal weight: 3.9990 chunk 70 optimal weight: 6.9990 chunk 25 optimal weight: 40.0000 chunk 30 optimal weight: 40.0000 chunk 3 optimal weight: 7.9990 chunk 60 optimal weight: 0.9990 chunk 15 optimal weight: 10.0000 chunk 59 optimal weight: 0.8980 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 850 GLN ** 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 = 0.4371 r_free = 0.4371 target = 0.162558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.125095 restraints weight = 13881.052| |-----------------------------------------------------------------------------| r_work (start): 0.3776 rms_B_bonded: 3.46 r_work: 0.3632 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6979 moved from start: 0.5554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6400 Z= 0.270 Angle : 0.596 9.587 8911 Z= 0.295 Chirality : 0.041 0.189 1080 Planarity : 0.004 0.035 1020 Dihedral : 15.198 154.130 1443 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.52 % Allowed : 17.89 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.31), residues: 740 helix: 0.68 (0.35), residues: 221 sheet: -1.10 (0.40), residues: 156 loop : -0.67 (0.33), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 435 HIS 0.005 0.001 HIS A 600 PHE 0.013 0.002 PHE A 593 TYR 0.010 0.001 TYR A 698 ARG 0.004 0.000 ARG A 375 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 67 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 ASP cc_start: 0.6462 (t0) cc_final: 0.6233 (t0) REVERT: A 562 ASN cc_start: 0.8014 (t0) cc_final: 0.7793 (t0) outliers start: 11 outliers final: 11 residues processed: 72 average time/residue: 0.1701 time to fit residues: 17.0262 Evaluate side-chains 76 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain A residue 672 SER Chi-restraints excluded: chain A residue 711 HIS Chi-restraints excluded: chain A residue 713 THR Chi-restraints excluded: chain A residue 727 SER Chi-restraints excluded: chain A residue 742 HIS Chi-restraints excluded: chain A residue 757 GLN Chi-restraints excluded: chain A residue 799 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 34 optimal weight: 0.9980 chunk 35 optimal weight: 9.9990 chunk 4 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 8 optimal weight: 50.0000 chunk 16 optimal weight: 30.0000 chunk 0 optimal weight: 7.9990 chunk 46 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 68 optimal weight: 0.0870 overall best weight: 0.8160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 850 GLN ** 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 = 0.4398 r_free = 0.4398 target = 0.164466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.127576 restraints weight = 13940.398| |-----------------------------------------------------------------------------| r_work (start): 0.3819 rms_B_bonded: 3.46 r_work: 0.3674 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6897 moved from start: 0.5577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6400 Z= 0.172 Angle : 0.554 9.655 8911 Z= 0.272 Chirality : 0.040 0.190 1080 Planarity : 0.004 0.035 1020 Dihedral : 14.941 152.073 1443 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.29 % Allowed : 18.58 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.31), residues: 740 helix: 0.90 (0.36), residues: 222 sheet: -1.00 (0.39), residues: 156 loop : -0.57 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 435 HIS 0.005 0.001 HIS A 600 PHE 0.012 0.001 PHE A 858 TYR 0.008 0.001 TYR A 790 ARG 0.008 0.001 ARG A 554 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 68 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 ASP cc_start: 0.6280 (t0) cc_final: 0.6079 (t0) REVERT: A 562 ASN cc_start: 0.7875 (t0) cc_final: 0.7665 (t0) REVERT: A 858 PHE cc_start: 0.8210 (p90) cc_final: 0.8008 (p90) outliers start: 10 outliers final: 9 residues processed: 74 average time/residue: 0.1645 time to fit residues: 16.9740 Evaluate side-chains 77 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain A residue 672 SER Chi-restraints excluded: chain A residue 711 HIS Chi-restraints excluded: chain A residue 713 THR Chi-restraints excluded: chain A residue 727 SER Chi-restraints excluded: chain A residue 742 HIS Chi-restraints excluded: chain A residue 757 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 47 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 24 optimal weight: 0.4980 chunk 78 optimal weight: 0.2980 chunk 52 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 8 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 766 HIS ** A 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.165278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.128748 restraints weight = 14004.259| |-----------------------------------------------------------------------------| r_work (start): 0.3839 rms_B_bonded: 3.49 r_work: 0.3694 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6866 moved from start: 0.5697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6400 Z= 0.160 Angle : 0.529 9.225 8911 Z= 0.263 Chirality : 0.040 0.179 1080 Planarity : 0.004 0.034 1020 Dihedral : 14.721 150.998 1443 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.52 % Allowed : 17.89 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.31), residues: 740 helix: 1.03 (0.35), residues: 223 sheet: -0.96 (0.39), residues: 157 loop : -0.55 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 435 HIS 0.005 0.001 HIS A 600 PHE 0.013 0.001 PHE A 858 TYR 0.008 0.001 TYR A 420 ARG 0.005 0.000 ARG A 375 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3767.79 seconds wall clock time: 67 minutes 11.50 seconds (4031.50 seconds total)