Starting phenix.real_space_refine on Wed Sep 17 06:26:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cmp_45752/09_2025/9cmp_45752.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cmp_45752/09_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_45752/09_2025/9cmp_45752.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cmp_45752/09_2025/9cmp_45752.map" model { file = "/net/cci-nas-00/data/ceres_data/9cmp_45752/09_2025/9cmp_45752.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cmp_45752/09_2025/9cmp_45752.cif" } resolution = 3.3 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= 0.005 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-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'ASP:plan': 12, 'TYR:plan': 8, 'HIS:plan': 8, 'GLU:plan': 14, 'ARG:plan': 21, 'ASN:plan1': 7, 'GLN:plan1': 12, 'PHE:plan': 12, 'TRP:plan': 3} 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: 2.13, per 1000 atoms: 0.34 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: 0.46 Conformation dependent library (CDL) restraints added in 421.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.70 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: 1.20 Time building geometry restraints manager: 0.66 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: 2.730 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: 0.210 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 8.780 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.200 ------------------------------------------------------------------------------- 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= 0.166 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.15 (0.30), 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 ARG 0.002 0.000 ARG A 837 TYR 0.010 0.001 TYR A 698 PHE 0.011 0.001 PHE A 811 TRP 0.005 0.001 TRP A 435 HIS 0.003 0.001 HIS A 634 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 6400) covalent geometry : angle 0.76540 ( 8911) hydrogen bonds : bond 0.15822 ( 271) hydrogen bonds : angle 6.72657 ( 756) *********************** 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 : 0.225 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: 0.0925 time to fit residues: 15.7233 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 : 0.224 ------------------------------------------------------------------------------- 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 49 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 8.9990 chunk 74 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.4442 r_free = 0.4442 target = 0.169452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.134450 restraints weight = 14048.352| |-----------------------------------------------------------------------------| r_work (start): 0.3910 rms_B_bonded: 3.48 r_work: 0.3776 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6626 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6400 Z= 0.134 Angle : 0.573 9.007 8911 Z= 0.295 Chirality : 0.041 0.176 1080 Planarity : 0.004 0.041 1020 Dihedral : 14.658 150.134 1443 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.75 % Allowed : 10.55 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.75 (0.30), residues: 740 helix: 0.44 (0.34), residues: 223 sheet: -1.16 (0.39), residues: 171 loop : -0.63 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 630 TYR 0.011 0.001 TYR A 804 PHE 0.010 0.001 PHE A 593 TRP 0.008 0.001 TRP A 435 HIS 0.004 0.001 HIS A 634 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 6400) covalent geometry : angle 0.57320 ( 8911) hydrogen bonds : bond 0.04405 ( 271) hydrogen bonds : angle 5.01767 ( 756) *********************** 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 103 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 91 time to evaluate : 0.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 378 GLU cc_start: 0.7341 (mp0) cc_final: 0.7121 (mp0) REVERT: A 535 VAL cc_start: 0.8602 (t) cc_final: 0.8252 (m) REVERT: A 624 ARG cc_start: 0.7378 (mmm160) cc_final: 0.7143 (tpt170) REVERT: A 672 SER cc_start: 0.8182 (OUTLIER) cc_final: 0.7898 (p) REVERT: A 688 ARG cc_start: 0.7296 (tpp-160) cc_final: 0.5869 (tmm160) REVERT: A 796 SER cc_start: 0.8333 (t) cc_final: 0.8084 (p) REVERT: A 819 ASP cc_start: 0.3659 (p0) cc_final: 0.3179 (p0) outliers start: 12 outliers final: 8 residues processed: 95 average time/residue: 0.0860 time to fit residues: 10.7658 Evaluate side-chains 89 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 80 time to evaluate : 0.171 ------------------------------------------------------------------------------- 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 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 31 optimal weight: 50.0000 chunk 27 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 12 optimal weight: 0.0070 chunk 42 optimal weight: 0.8980 chunk 22 optimal weight: 10.0000 chunk 37 optimal weight: 0.6980 chunk 13 optimal weight: 40.0000 chunk 57 optimal weight: 2.9990 chunk 25 optimal weight: 6.9990 chunk 60 optimal weight: 0.7980 overall best weight: 0.8800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 600 HIS A 634 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.169126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.133362 restraints weight = 13911.042| |-----------------------------------------------------------------------------| r_work (start): 0.3888 rms_B_bonded: 3.49 r_work: 0.3747 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6694 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6400 Z= 0.121 Angle : 0.527 8.489 8911 Z= 0.269 Chirality : 0.040 0.182 1080 Planarity : 0.004 0.037 1020 Dihedral : 14.691 154.654 1443 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.48 (0.31), residues: 740 helix: 0.61 (0.34), residues: 223 sheet: -1.01 (0.40), residues: 160 loop : -0.45 (0.33), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 635 TYR 0.011 0.001 TYR A 804 PHE 0.007 0.001 PHE A 774 TRP 0.006 0.001 TRP A 435 HIS 0.015 0.001 HIS A 634 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 6400) covalent geometry : angle 0.52703 ( 8911) hydrogen bonds : bond 0.03606 ( 271) hydrogen bonds : angle 4.53346 ( 756) *********************** 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 99 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 84 time to evaluate : 0.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.5692 (mtp) cc_final: 0.5481 (mtm) REVERT: A 375 ARG cc_start: 0.5836 (ttm110) cc_final: 0.5382 (ttm110) REVERT: A 672 SER cc_start: 0.8229 (OUTLIER) cc_final: 0.7941 (p) REVERT: A 688 ARG cc_start: 0.7287 (tpp-160) cc_final: 0.5699 (tmm160) REVERT: A 742 HIS cc_start: 0.7879 (OUTLIER) cc_final: 0.7532 (m-70) REVERT: A 796 SER cc_start: 0.8434 (t) cc_final: 0.8207 (p) outliers start: 15 outliers final: 6 residues processed: 92 average time/residue: 0.0751 time to fit residues: 9.4215 Evaluate side-chains 85 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 77 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 569 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 727 SER Chi-restraints excluded: chain A residue 742 HIS Chi-restraints excluded: chain A residue 811 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 24 optimal weight: 50.0000 chunk 48 optimal weight: 1.9990 chunk 31 optimal weight: 50.0000 chunk 13 optimal weight: 0.0040 chunk 52 optimal weight: 5.9990 chunk 6 optimal weight: 5.9990 chunk 8 optimal weight: 50.0000 chunk 40 optimal weight: 6.9990 chunk 42 optimal weight: 0.4980 chunk 39 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 overall best weight: 0.8394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 708 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.168953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.133502 restraints weight = 13956.182| |-----------------------------------------------------------------------------| r_work (start): 0.3887 rms_B_bonded: 3.49 r_work: 0.3744 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6720 moved from start: 0.3285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6400 Z= 0.118 Angle : 0.524 8.152 8911 Z= 0.267 Chirality : 0.040 0.182 1080 Planarity : 0.004 0.046 1020 Dihedral : 14.706 156.582 1443 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.44 % Allowed : 12.61 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.32 (0.31), residues: 740 helix: 0.93 (0.36), residues: 218 sheet: -0.94 (0.40), residues: 160 loop : -0.47 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 554 TYR 0.010 0.001 TYR A 804 PHE 0.006 0.001 PHE A 774 TRP 0.007 0.001 TRP A 435 HIS 0.002 0.001 HIS A 764 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 6400) covalent geometry : angle 0.52444 ( 8911) hydrogen bonds : bond 0.03574 ( 271) hydrogen bonds : angle 4.43824 ( 756) *********************** 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 97 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 82 time to evaluate : 0.202 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 549 MET cc_start: 0.8084 (tpt) cc_final: 0.7859 (tpt) REVERT: A 672 SER cc_start: 0.8289 (OUTLIER) cc_final: 0.8017 (p) REVERT: A 688 ARG cc_start: 0.7326 (tpp-160) cc_final: 0.5931 (ttp80) REVERT: A 742 HIS cc_start: 0.7916 (OUTLIER) cc_final: 0.7554 (m-70) REVERT: A 796 SER cc_start: 0.8503 (t) cc_final: 0.8298 (p) REVERT: A 819 ASP cc_start: 0.2587 (p0) cc_final: 0.2150 (p0) outliers start: 15 outliers final: 7 residues processed: 91 average time/residue: 0.0775 time to fit residues: 9.4832 Evaluate side-chains 83 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 74 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 569 VAL 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 713 THR Chi-restraints excluded: chain A residue 727 SER Chi-restraints excluded: chain A residue 742 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 66 optimal weight: 4.9990 chunk 21 optimal weight: 20.0000 chunk 44 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 chunk 17 optimal weight: 6.9990 chunk 2 optimal weight: 10.9990 chunk 34 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 chunk 42 optimal weight: 0.6980 chunk 41 optimal weight: 0.9990 chunk 10 optimal weight: 50.0000 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 840 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.166178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.129957 restraints weight = 13958.948| |-----------------------------------------------------------------------------| r_work (start): 0.3839 rms_B_bonded: 3.52 r_work: 0.3694 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6836 moved from start: 0.3779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6400 Z= 0.170 Angle : 0.561 7.887 8911 Z= 0.282 Chirality : 0.041 0.191 1080 Planarity : 0.004 0.055 1020 Dihedral : 14.861 158.296 1443 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.44 % Allowed : 12.39 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.49 (0.31), residues: 740 helix: 0.66 (0.34), residues: 225 sheet: -1.01 (0.40), residues: 160 loop : -0.52 (0.33), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 375 TYR 0.011 0.002 TYR A 667 PHE 0.008 0.001 PHE A 774 TRP 0.006 0.001 TRP A 451 HIS 0.003 0.001 HIS A 681 Details of bonding type rmsd covalent geometry : bond 0.00388 ( 6400) covalent geometry : angle 0.56142 ( 8911) hydrogen bonds : bond 0.03813 ( 271) hydrogen bonds : angle 4.49145 ( 756) *********************** 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 95 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 0.222 Fit side-chains revert: symmetry clash REVERT: A 508 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8620 (tt) REVERT: A 549 MET cc_start: 0.8145 (tpt) cc_final: 0.7942 (tpt) REVERT: A 672 SER cc_start: 0.8424 (OUTLIER) cc_final: 0.8142 (p) REVERT: A 688 ARG cc_start: 0.7622 (tpp-160) cc_final: 0.5833 (ttp80) REVERT: A 742 HIS cc_start: 0.7970 (OUTLIER) cc_final: 0.7606 (m-70) REVERT: A 796 SER cc_start: 0.8783 (t) cc_final: 0.8545 (p) outliers start: 15 outliers final: 9 residues processed: 87 average time/residue: 0.0688 time to fit residues: 8.3945 Evaluate side-chains 87 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 75 time to evaluate : 0.203 ------------------------------------------------------------------------------- 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 542 MET Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 569 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 811 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 74 optimal weight: 0.8980 chunk 15 optimal weight: 7.9990 chunk 12 optimal weight: 40.0000 chunk 71 optimal weight: 5.9990 chunk 6 optimal weight: 6.9990 chunk 30 optimal weight: 0.3980 chunk 5 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 13 optimal weight: 50.0000 chunk 29 optimal weight: 30.0000 chunk 51 optimal weight: 8.9990 overall best weight: 3.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 807 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.161614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.124203 restraints weight = 13756.460| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 3.49 r_work: 0.3610 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7018 moved from start: 0.4778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 6400 Z= 0.276 Angle : 0.686 9.492 8911 Z= 0.351 Chirality : 0.045 0.203 1080 Planarity : 0.005 0.043 1020 Dihedral : 15.544 160.244 1443 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.67 % Allowed : 13.53 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.80 (0.30), residues: 740 helix: 0.28 (0.34), residues: 227 sheet: -1.11 (0.39), residues: 159 loop : -0.67 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 624 TYR 0.018 0.002 TYR A 667 PHE 0.023 0.002 PHE A 442 TRP 0.010 0.002 TRP A 451 HIS 0.007 0.002 HIS A 443 Details of bonding type rmsd covalent geometry : bond 0.00627 ( 6400) covalent geometry : angle 0.68648 ( 8911) hydrogen bonds : bond 0.04994 ( 271) hydrogen bonds : angle 4.98572 ( 756) *********************** 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 89 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 73 time to evaluate : 0.212 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 508 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8746 (tt) REVERT: A 672 SER cc_start: 0.8548 (OUTLIER) cc_final: 0.8226 (p) outliers start: 16 outliers final: 10 residues processed: 81 average time/residue: 0.0695 time to fit residues: 8.1571 Evaluate side-chains 77 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 65 time to evaluate : 0.207 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain A residue 822 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 35 optimal weight: 10.0000 chunk 14 optimal weight: 8.9990 chunk 34 optimal weight: 0.7980 chunk 66 optimal weight: 0.9990 chunk 12 optimal weight: 9.9990 chunk 2 optimal weight: 10.9990 chunk 9 optimal weight: 30.0000 chunk 6 optimal weight: 0.9980 chunk 17 optimal weight: 9.9990 chunk 48 optimal weight: 0.9990 chunk 67 optimal weight: 9.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 558 GLN A 753 HIS A 788 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.162336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.124906 restraints weight = 13767.663| |-----------------------------------------------------------------------------| r_work (start): 0.3772 rms_B_bonded: 3.46 r_work: 0.3625 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6995 moved from start: 0.5096 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= 0.224 Angle : 0.623 9.009 8911 Z= 0.315 Chirality : 0.043 0.194 1080 Planarity : 0.004 0.038 1020 Dihedral : 15.479 156.694 1443 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.90 % Allowed : 14.91 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.80 (0.31), residues: 740 helix: 0.57 (0.35), residues: 220 sheet: -1.21 (0.39), residues: 159 loop : -0.82 (0.33), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 795 TYR 0.012 0.002 TYR A 698 PHE 0.015 0.002 PHE A 593 TRP 0.009 0.001 TRP A 435 HIS 0.006 0.001 HIS A 753 Details of bonding type rmsd covalent geometry : bond 0.00516 ( 6400) covalent geometry : angle 0.62291 ( 8911) hydrogen bonds : bond 0.04298 ( 271) hydrogen bonds : angle 4.81215 ( 756) *********************** 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 86 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 69 time to evaluate : 0.223 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 688 ARG cc_start: 0.7913 (tpp-160) cc_final: 0.5717 (ttp80) REVERT: A 804 TYR cc_start: 0.7440 (t80) cc_final: 0.7170 (t80) REVERT: A 811 PHE cc_start: 0.7652 (OUTLIER) cc_final: 0.7342 (t80) REVERT: A 842 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8343 (tt) outliers start: 17 outliers final: 11 residues processed: 80 average time/residue: 0.0725 time to fit residues: 8.1334 Evaluate side-chains 79 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 0.261 ------------------------------------------------------------------------------- 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 542 MET 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 742 HIS Chi-restraints excluded: chain A residue 811 PHE Chi-restraints excluded: chain A residue 842 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 58 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 33 optimal weight: 0.4980 chunk 32 optimal weight: 7.9990 chunk 77 optimal weight: 30.0000 chunk 55 optimal weight: 0.8980 chunk 19 optimal weight: 30.0000 chunk 25 optimal weight: 10.0000 chunk 30 optimal weight: 20.0000 chunk 8 optimal weight: 50.0000 chunk 13 optimal weight: 50.0000 overall best weight: 2.8786 ------------------------------------------------------------------------------- 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 = 0.4349 r_free = 0.4349 target = 0.160986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.123213 restraints weight = 13938.323| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 3.48 r_work: 0.3599 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7041 moved from start: 0.5580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 6400 Z= 0.255 Angle : 0.670 9.561 8911 Z= 0.339 Chirality : 0.044 0.197 1080 Planarity : 0.005 0.038 1020 Dihedral : 15.469 156.757 1443 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 4.59 % Allowed : 15.37 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.95 (0.30), residues: 740 helix: 0.38 (0.34), residues: 225 sheet: -1.27 (0.39), residues: 156 loop : -0.90 (0.33), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 479 TYR 0.016 0.002 TYR A 805 PHE 0.018 0.002 PHE A 593 TRP 0.009 0.001 TRP A 451 HIS 0.005 0.001 HIS A 681 Details of bonding type rmsd covalent geometry : bond 0.00588 ( 6400) covalent geometry : angle 0.66999 ( 8911) hydrogen bonds : bond 0.04735 ( 271) hydrogen bonds : angle 4.90512 ( 756) *********************** 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 84 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 64 time to evaluate : 0.221 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 562 ASN cc_start: 0.8125 (t0) cc_final: 0.7881 (t0) REVERT: A 659 PHE cc_start: 0.7124 (m-10) cc_final: 0.6735 (m-80) REVERT: A 804 TYR cc_start: 0.7461 (t80) cc_final: 0.7171 (t80) REVERT: A 811 PHE cc_start: 0.7726 (OUTLIER) cc_final: 0.7407 (t80) REVERT: A 842 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8372 (tt) outliers start: 20 outliers final: 13 residues processed: 75 average time/residue: 0.0831 time to fit residues: 8.4711 Evaluate side-chains 78 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 63 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 466 HIS 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 757 GLN Chi-restraints excluded: chain A residue 811 PHE Chi-restraints excluded: chain A residue 822 HIS Chi-restraints excluded: chain A residue 842 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 59 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 70 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 47 optimal weight: 0.7980 chunk 76 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 28 optimal weight: 9.9990 chunk 50 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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 = 0.4401 r_free = 0.4401 target = 0.165021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.128083 restraints weight = 13882.104| |-----------------------------------------------------------------------------| r_work (start): 0.3822 rms_B_bonded: 3.46 r_work: 0.3677 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6905 moved from start: 0.5559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6400 Z= 0.121 Angle : 0.540 9.007 8911 Z= 0.272 Chirality : 0.040 0.175 1080 Planarity : 0.004 0.038 1020 Dihedral : 15.034 152.194 1443 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.83 % Allowed : 17.43 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.54 (0.31), residues: 740 helix: 0.85 (0.36), residues: 221 sheet: -1.11 (0.39), residues: 156 loop : -0.69 (0.33), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 375 TYR 0.008 0.001 TYR A 805 PHE 0.014 0.001 PHE A 456 TRP 0.012 0.001 TRP A 435 HIS 0.003 0.001 HIS A 681 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 6400) covalent geometry : angle 0.53982 ( 8911) hydrogen bonds : bond 0.03510 ( 271) hydrogen bonds : angle 4.45938 ( 756) *********************** 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 77 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 0.215 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.3723 (ptp) cc_final: 0.3444 (pmm) REVERT: A 562 ASN cc_start: 0.7941 (t0) cc_final: 0.7741 (t0) REVERT: A 688 ARG cc_start: 0.7930 (tpp-160) cc_final: 0.5658 (ttp80) outliers start: 8 outliers final: 8 residues processed: 74 average time/residue: 0.0917 time to fit residues: 8.9257 Evaluate side-chains 75 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 466 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 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 54 optimal weight: 1.9990 chunk 12 optimal weight: 30.0000 chunk 69 optimal weight: 0.8980 chunk 19 optimal weight: 40.0000 chunk 0 optimal weight: 7.9990 chunk 42 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 11 optimal weight: 20.0000 chunk 55 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 23 optimal weight: 40.0000 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 = 0.4384 r_free = 0.4384 target = 0.163463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.126264 restraints weight = 13811.104| |-----------------------------------------------------------------------------| r_work (start): 0.3800 rms_B_bonded: 3.46 r_work: 0.3659 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6944 moved from start: 0.5747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 6400 Z= 0.155 Angle : 0.570 8.899 8911 Z= 0.287 Chirality : 0.041 0.182 1080 Planarity : 0.004 0.038 1020 Dihedral : 15.040 151.994 1443 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.52 % Allowed : 16.97 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.52 (0.31), residues: 740 helix: 0.79 (0.35), residues: 222 sheet: -1.08 (0.39), residues: 156 loop : -0.63 (0.34), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 375 TYR 0.009 0.001 TYR A 698 PHE 0.017 0.001 PHE A 858 TRP 0.008 0.001 TRP A 435 HIS 0.003 0.001 HIS A 681 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 6400) covalent geometry : angle 0.57005 ( 8911) hydrogen bonds : bond 0.03768 ( 271) hydrogen bonds : angle 4.52180 ( 756) ********************** 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 79 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 68 time to evaluate : 0.194 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.4061 (ptp) cc_final: 0.3842 (pmm) REVERT: A 562 ASN cc_start: 0.8018 (t0) cc_final: 0.7808 (t0) REVERT: A 645 MET cc_start: 0.8310 (tmm) cc_final: 0.8059 (tmm) outliers start: 11 outliers final: 10 residues processed: 73 average time/residue: 0.0680 time to fit residues: 7.0020 Evaluate side-chains 75 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 466 HIS Chi-restraints excluded: chain A residue 569 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 822 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 23 optimal weight: 40.0000 chunk 57 optimal weight: 0.8980 chunk 77 optimal weight: 30.0000 chunk 11 optimal weight: 20.0000 chunk 4 optimal weight: 0.0570 chunk 27 optimal weight: 50.0000 chunk 36 optimal weight: 3.9990 chunk 12 optimal weight: 20.0000 chunk 78 optimal weight: 8.9990 chunk 56 optimal weight: 4.9990 chunk 24 optimal weight: 50.0000 overall best weight: 3.7904 ------------------------------------------------------------------------------- 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 = 0.4334 r_free = 0.4334 target = 0.159808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.122200 restraints weight = 13955.302| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 3.47 r_work: 0.3577 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7086 moved from start: 0.6226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 6400 Z= 0.320 Angle : 0.745 10.548 8911 Z= 0.378 Chirality : 0.046 0.201 1080 Planarity : 0.005 0.038 1020 Dihedral : 15.540 153.220 1443 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.52 % Allowed : 17.43 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.15 (0.31), residues: 740 helix: 0.17 (0.34), residues: 233 sheet: -1.44 (0.39), residues: 158 loop : -0.97 (0.34), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 375 TYR 0.017 0.002 TYR A 805 PHE 0.017 0.002 PHE A 593 TRP 0.012 0.002 TRP A 451 HIS 0.005 0.002 HIS A 681 Details of bonding type rmsd covalent geometry : bond 0.00734 ( 6400) covalent geometry : angle 0.74512 ( 8911) hydrogen bonds : bond 0.05363 ( 271) hydrogen bonds : angle 5.12885 ( 756) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1979.44 seconds wall clock time: 34 minutes 32.22 seconds (2072.22 seconds total)