Starting phenix.real_space_refine on Fri Oct 23 04:58:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ozv_13138/10_2026/7ozv_13138.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ozv_13138/10_2026/7ozv_13138.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7ozv_13138/10_2026/7ozv_13138.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ozv_13138/10_2026/7ozv_13138.cif" model { file = "/net/cci-nas-00/data/ceres_data/7ozv_13138/10_2026/7ozv_13138.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ozv_13138/10_2026/7ozv_13138.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ozv_13138/10_2026/7ozv_13138.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ozv_13138/10_2026/7ozv_13138.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 22 5.49 5 S 57 5.16 5 C 5284 2.51 5 N 1405 2.21 5 O 1639 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8409 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 814, 6565 Classifications: {'peptide': 814} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 786} Chain breaks: 3 Chain: "B" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 891 Classifications: {'peptide': 115} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 109} Chain: "C" Number of atoms: 478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 478 Classifications: {'peptide': 62} Link IDs: {'TRANS': 61} Chain: "P" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 213 Classifications: {'RNAv2': 10} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 4, 'rna3p_pyr': 5} Link IDs: {'rna3p': 9} Chain: "T" Number of atoms: 260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 260 Classifications: {'RNA': 1, 'RNAv2': 11} Modifications used: {'rna3p': 1, 'rna3p_pur': 7, 'rna3p_pyr': 4} Link IDs: {'rna3p': 11} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1692 SG CYS A 301 47.732 66.352 36.395 1.00 55.92 S ATOM 1733 SG CYS A 306 47.334 65.879 32.523 1.00 52.97 S ATOM 1765 SG CYS A 310 50.364 65.588 34.819 1.00 49.18 S ATOM 3132 SG CYS A 487 30.327 62.531 45.778 1.00 62.63 S ATOM 4385 SG CYS A 645 28.837 62.401 41.815 1.00 65.93 S ATOM 4391 SG CYS A 646 31.679 64.363 43.369 1.00 60.57 S Time building chain proxies: 1.41, per 1000 atoms: 0.17 Number of scatterers: 8409 At special positions: 0 Unit cell: (91.74, 93.408, 99.246, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 57 16.00 P 22 15.00 O 1639 8.00 N 1405 7.00 C 5284 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: 0.78 Conformation dependent library (CDL) restraints added in 156.7 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2000 " pdb="ZN ZN A2000 " - pdb=" ND1 HIS A 295 " pdb="ZN ZN A2000 " - pdb=" SG CYS A 301 " pdb="ZN ZN A2000 " - pdb=" SG CYS A 306 " pdb="ZN ZN A2000 " - pdb=" SG CYS A 310 " pdb=" ZN A2001 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 487 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 646 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 645 " pdb="ZN ZN A2001 " - pdb=" ND1 HIS A 642 " Number of angles added : 6 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1898 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 8 sheets defined 53.8% alpha, 11.1% beta 5 base pairs and 16 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'A' and resid 123 through 133 Processing helix chain 'A' and resid 139 through 149 removed outlier: 3.504A pdb=" N TYR A 149 " --> pdb=" O ILE A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 158 removed outlier: 3.529A pdb=" N ASN A 158 " --> pdb=" O ASP A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 199 removed outlier: 3.673A pdb=" N LEU A 178 " --> pdb=" O VAL A 174 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY A 179 " --> pdb=" O TYR A 175 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N GLU A 180 " --> pdb=" O ALA A 176 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N ARG A 181 " --> pdb=" O ASN A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 210 Processing helix chain 'A' and resid 234 through 248 Proline residue: A 243 - end of helix removed outlier: 4.032A pdb=" N THR A 246 " --> pdb=" O MET A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 256 removed outlier: 3.572A pdb=" N HIS A 256 " --> pdb=" O ALA A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 287 Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.581A pdb=" N LEU A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 377 Processing helix chain 'A' and resid 377 through 385 removed outlier: 4.736A pdb=" N HIS A 381 " --> pdb=" O ASP A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 426 Processing helix chain 'A' and resid 447 through 454 Processing helix chain 'A' and resid 455 through 459 Processing helix chain 'A' and resid 465 through 478 removed outlier: 3.718A pdb=" N LYS A 478 " --> pdb=" O GLU A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 481 No H-bonds generated for 'chain 'A' and resid 479 through 481' Processing helix chain 'A' and resid 489 through 493 Processing helix chain 'A' and resid 505 through 509 removed outlier: 3.533A pdb=" N TRP A 509 " --> pdb=" O PHE A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 519 removed outlier: 3.899A pdb=" N TYR A 515 " --> pdb=" O LYS A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 532 Processing helix chain 'A' and resid 561 through 581 removed outlier: 3.640A pdb=" N THR A 565 " --> pdb=" O SER A 561 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N LYS A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N LEU A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 607 Processing helix chain 'A' and resid 621 through 626 removed outlier: 3.607A pdb=" N MET A 626 " --> pdb=" O CYS A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 640 Processing helix chain 'A' and resid 647 through 662 Processing helix chain 'A' and resid 686 through 709 Processing helix chain 'A' and resid 717 through 733 Processing helix chain 'A' and resid 738 through 752 Processing helix chain 'A' and resid 768 through 774 Processing helix chain 'A' and resid 778 through 789 Processing helix chain 'A' and resid 833 through 842 removed outlier: 3.569A pdb=" N ILE A 837 " --> pdb=" O ASP A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 846 through 851 Processing helix chain 'A' and resid 853 through 864 removed outlier: 3.801A pdb=" N GLU A 857 " --> pdb=" O THR A 853 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 872 Processing helix chain 'A' and resid 874 through 896 removed outlier: 3.870A pdb=" N PHE A 881 " --> pdb=" O TYR A 877 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N HIS A 882 " --> pdb=" O ALA A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 916 Processing helix chain 'A' and resid 917 through 924 removed outlier: 4.267A pdb=" N TYR A 921 " --> pdb=" O GLU A 917 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N MET A 924 " --> pdb=" O PHE A 920 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 97 Processing helix chain 'B' and resid 100 through 109 removed outlier: 4.132A pdb=" N ASN B 105 " --> pdb=" O ASP B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 125 removed outlier: 4.291A pdb=" N LEU B 122 " --> pdb=" O ASN B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 142 Processing helix chain 'B' and resid 168 through 172 Processing helix chain 'B' and resid 176 through 180 Processing helix chain 'C' and resid 3 through 20 Processing helix chain 'C' and resid 21 through 24 removed outlier: 3.557A pdb=" N SER C 24 " --> pdb=" O ARG C 21 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 21 through 24' Processing helix chain 'C' and resid 25 through 41 Processing helix chain 'C' and resid 44 through 61 Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 38 Processing sheet with id=AA2, first strand: chain 'A' and resid 201 through 202 Processing sheet with id=AA3, first strand: chain 'A' and resid 338 through 343 Processing sheet with id=AA4, first strand: chain 'A' and resid 345 through 348 Processing sheet with id=AA5, first strand: chain 'A' and resid 556 through 559 removed outlier: 6.719A pdb=" N LEU A 673 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N VAL A 398 " --> pdb=" O LEU A 388 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N LEU A 388 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ILE B 185 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N VAL B 159 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N THR B 187 " --> pdb=" O GLN B 157 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 414 through 415 Processing sheet with id=AA7, first strand: chain 'A' and resid 753 through 758 removed outlier: 4.780A pdb=" N ALA A 762 " --> pdb=" O TRP A 617 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N TRP A 617 " --> pdb=" O ALA A 762 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 815 through 822 404 hydrogen bonds defined for protein. 1107 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 12 hydrogen bonds 20 hydrogen bond angles 0 basepair planarities 5 basepair parallelities 16 stacking parallelities Total time for adding SS restraints: 0.85 Time building geometry restraints manager: 0.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1332 1.31 - 1.43: 2522 1.43 - 1.56: 4657 1.56 - 1.69: 46 1.69 - 1.81: 86 Bond restraints: 8643 Sorted by residual: bond pdb=" O4' 16B T 9 " pdb=" C1' 16B T 9 " ideal model delta sigma weight residual 1.412 1.625 -0.213 1.50e-02 4.44e+03 2.01e+02 bond pdb=" C2' 16B T 9 " pdb=" C1' 16B T 9 " ideal model delta sigma weight residual 1.529 1.345 0.184 1.50e-02 4.44e+03 1.51e+02 bond pdb=" C4' 16B T 9 " pdb=" O4' 16B T 9 " ideal model delta sigma weight residual 1.451 1.299 0.152 1.50e-02 4.44e+03 1.03e+02 bond pdb=" P 16B T 9 " pdb=" OP1 16B T 9 " ideal model delta sigma weight residual 1.526 1.664 -0.138 2.00e-02 2.50e+03 4.74e+01 bond pdb=" P 16B T 9 " pdb=" OP2 16B T 9 " ideal model delta sigma weight residual 1.522 1.653 -0.131 2.00e-02 2.50e+03 4.26e+01 ... (remaining 8638 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.28: 11679 2.28 - 4.57: 126 4.57 - 6.85: 19 6.85 - 9.13: 1 9.13 - 11.42: 2 Bond angle restraints: 11827 Sorted by residual: angle pdb=" C2' 16B T 9 " pdb=" C1' 16B T 9 " pdb=" N1 16B T 9 " ideal model delta sigma weight residual 112.00 121.73 -9.73 1.50e+00 4.44e-01 4.21e+01 angle pdb=" O4' 16B T 9 " pdb=" C1' 16B T 9 " pdb=" N1 16B T 9 " ideal model delta sigma weight residual 108.50 100.62 7.88 1.50e+00 4.44e-01 2.76e+01 angle pdb=" C4' 16B T 9 " pdb=" O4' 16B T 9 " pdb=" C1' 16B T 9 " ideal model delta sigma weight residual 109.90 105.90 4.00 1.00e+00 1.00e+00 1.60e+01 angle pdb=" OP2 16B T 9 " pdb=" P 16B T 9 " pdb=" O5' 16B T 9 " ideal model delta sigma weight residual 99.96 111.38 -11.42 3.00e+00 1.11e-01 1.45e+01 angle pdb=" N GLU A 658 " pdb=" CA GLU A 658 " pdb=" CB GLU A 658 " ideal model delta sigma weight residual 110.12 115.65 -5.53 1.47e+00 4.63e-01 1.42e+01 ... (remaining 11822 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.15: 4624 18.15 - 36.30: 369 36.30 - 54.46: 66 54.46 - 72.61: 16 72.61 - 90.76: 14 Dihedral angle restraints: 5089 sinusoidal: 2149 harmonic: 2940 Sorted by residual: dihedral pdb=" C4' G P 15 " pdb=" C3' G P 15 " pdb=" C2' G P 15 " pdb=" C1' G P 15 " ideal model delta sinusoidal sigma weight residual 36.34 -36.07 72.41 1 3.10e+00 1.04e-01 6.97e+02 dihedral pdb=" O4' G P 15 " pdb=" C4' G P 15 " pdb=" C3' G P 15 " pdb=" C2' G P 15 " ideal model delta sinusoidal sigma weight residual -35.15 24.59 -59.74 1 4.00e+00 6.25e-02 2.98e+02 dihedral pdb=" O4' G P 15 " pdb=" C2' G P 15 " pdb=" C1' G P 15 " pdb=" C3' G P 15 " ideal model delta sinusoidal sigma weight residual -94.41 -36.04 -58.36 3 3.80e+00 6.93e-02 1.47e+02 ... (remaining 5086 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 1225 0.078 - 0.156: 94 0.156 - 0.235: 13 0.235 - 0.313: 10 0.313 - 0.391: 1 Chirality restraints: 1343 Sorted by residual: chirality pdb=" C2' 16B T 9 " pdb=" C3' 16B T 9 " pdb=" O2' 16B T 9 " pdb=" C1' 16B T 9 " both_signs ideal model delta sigma weight residual False -2.75 -2.36 -0.39 2.00e-01 2.50e+01 3.82e+00 chirality pdb=" C2' G P 15 " pdb=" C3' G P 15 " pdb=" O2' G P 15 " pdb=" C1' G P 15 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" P A T 10 " pdb=" OP1 A T 10 " pdb=" OP2 A T 10 " pdb=" O5' A T 10 " both_signs ideal model delta sigma weight residual True 2.17 -2.44 -0.27 2.00e-01 2.50e+01 1.79e+00 ... (remaining 1340 not shown) Planarity restraints: 1425 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' 16B T 9 " -0.096 2.00e-02 2.50e+03 1.37e-01 4.70e+02 pdb=" N1 16B T 9 " -0.010 2.00e-02 2.50e+03 pdb=" C2 16B T 9 " -0.017 2.00e-02 2.50e+03 pdb=" O2 16B T 9 " -0.078 2.00e-02 2.50e+03 pdb=" N3 16B T 9 " 0.047 2.00e-02 2.50e+03 pdb=" C4 16B T 9 " 0.117 2.00e-02 2.50e+03 pdb=" N4 16B T 9 " 0.184 2.00e-02 2.50e+03 pdb=" C5 16B T 9 " 0.120 2.00e-02 2.50e+03 pdb=" C6 16B T 9 " 0.057 2.00e-02 2.50e+03 pdb=" OAC 16B T 9 " -0.324 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 758 " -0.010 2.00e-02 2.50e+03 2.03e-02 4.10e+00 pdb=" C LEU A 758 " 0.035 2.00e-02 2.50e+03 pdb=" O LEU A 758 " -0.013 2.00e-02 2.50e+03 pdb=" N SER A 759 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE B 120 " -0.027 5.00e-02 4.00e+02 4.15e-02 2.76e+00 pdb=" N PRO B 121 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO B 121 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 121 " -0.024 5.00e-02 4.00e+02 ... (remaining 1422 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 793 2.74 - 3.28: 8369 3.28 - 3.82: 14175 3.82 - 4.36: 17557 4.36 - 4.90: 29619 Nonbonded interactions: 70513 Sorted by model distance: nonbonded pdb=" O TYR A 915 " pdb=" OH TYR A 921 " model vdw 2.202 3.040 nonbonded pdb=" OG1 THR A 710 " pdb=" O GLY A 774 " model vdw 2.210 3.040 nonbonded pdb=" OE2 GLU A 254 " pdb=" OH TYR A 286 " model vdw 2.215 3.040 nonbonded pdb=" OG1 THR A 206 " pdb=" OD1 ASN A 209 " model vdw 2.219 3.040 nonbonded pdb=" OG SER A 318 " pdb=" O ARG A 349 " model vdw 2.236 3.040 ... (remaining 70508 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: 0.380 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: 0.010 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 7.800 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 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 : 0.006 0.213 8651 Z= 0.323 Angle : 0.708 26.345 11833 Z= 0.329 Chirality : 0.052 0.391 1343 Planarity : 0.005 0.137 1425 Dihedral : 14.497 90.760 3191 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.26), residues: 979 helix: 0.20 (0.23), residues: 471 sheet: -0.05 (0.53), residues: 102 loop : -0.40 (0.30), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 197 TYR 0.018 0.002 TYR A 530 PHE 0.019 0.002 PHE A 920 TRP 0.020 0.001 TRP A 916 HIS 0.006 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00576 / 0.32 ( 8643) covalent geometry : angle 0.59751 / 0.31 (11827) hydrogen bonds : bond 0.15295 / 9.68 ( 416) hydrogen bonds : angle 6.40324 / 4.44 ( 1127) metal coordination : bond 0.08401 / 3.40 ( 8) metal coordination : angle 16.84970 / 9.89 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.157 Fit side-chains REVERT: A 729 GLU cc_start: 0.6875 (tp30) cc_final: 0.6637 (mt-10) REVERT: A 825 ASP cc_start: 0.6068 (m-30) cc_final: 0.5741 (m-30) outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.0462 time to fit residues: 8.0220 Evaluate side-chains 87 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: [49, 97, 53, 5, 33, 65, 62, 51, 38, 61, 45] chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 6.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 9.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 105 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.135320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.112378 restraints weight = 9619.785| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 1.30 r_work: 0.3179 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.1055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8651 Z= 0.136 Angle : 0.569 8.755 11833 Z= 0.278 Chirality : 0.043 0.189 1343 Planarity : 0.003 0.032 1425 Dihedral : 10.223 78.080 1353 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.57 % Allowed : 7.19 % Favored : 92.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.27), residues: 979 helix: 0.78 (0.24), residues: 480 sheet: 0.14 (0.57), residues: 89 loop : -0.31 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 197 TYR 0.014 0.001 TYR A 530 PHE 0.014 0.002 PHE A 920 TRP 0.014 0.001 TRP A 916 HIS 0.005 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 ( 8643) covalent geometry : angle 0.56273 / 0.28 (11827) hydrogen bonds : bond 0.04397 / 2.62 ( 416) hydrogen bonds : angle 4.36111 / 3.03 ( 1127) metal coordination : bond 0.01392 / 0.78 ( 8) metal coordination : angle 3.81269 / 2.23 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 95 time to evaluate : 0.239 Fit side-chains REVERT: A 825 ASP cc_start: 0.6482 (m-30) cc_final: 0.6223 (m-30) outliers start: 5 outliers final: 0 residues processed: 99 average time/residue: 0.0740 time to fit residues: 10.8204 Evaluate side-chains 85 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: [72, 46, 30, 3, 10, 71, 13, 84, 39, 54, 49] chunk 72 optimal weight: 4.9990 chunk 46 optimal weight: 4.9990 chunk 30 optimal weight: 6.9990 chunk 3 optimal weight: 6.9990 chunk 10 optimal weight: 9.9990 chunk 71 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 84 optimal weight: 8.9990 chunk 39 optimal weight: 7.9990 chunk 54 optimal weight: 4.9990 chunk 49 optimal weight: 0.7980 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.130305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.107194 restraints weight = 9657.996| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 1.30 r_work: 0.3115 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.1277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 8651 Z= 0.245 Angle : 0.647 8.263 11833 Z= 0.319 Chirality : 0.047 0.189 1343 Planarity : 0.004 0.036 1425 Dihedral : 10.409 83.510 1353 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.60 % Allowed : 9.02 % Favored : 89.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.26), residues: 979 helix: 0.47 (0.24), residues: 481 sheet: -0.27 (0.53), residues: 99 loop : -0.40 (0.30), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 197 TYR 0.014 0.002 TYR A 877 PHE 0.018 0.002 PHE A 652 TRP 0.014 0.002 TRP A 916 HIS 0.007 0.001 HIS A 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00581 / 0.24 ( 8643) covalent geometry : angle 0.64086 / 0.32 (11827) hydrogen bonds : bond 0.05109 / 3.09 ( 416) hydrogen bonds : angle 4.45803 / 3.10 ( 1127) metal coordination : bond 0.02371 / 1.30 ( 8) metal coordination : angle 3.84460 / 2.21 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 90 time to evaluate : 0.320 Fit side-chains REVERT: A 122 TYR cc_start: 0.7963 (m-80) cc_final: 0.7746 (m-80) REVERT: A 280 LEU cc_start: 0.8089 (OUTLIER) cc_final: 0.7862 (mp) REVERT: A 726 ARG cc_start: 0.7709 (mtm110) cc_final: 0.7496 (mtm110) outliers start: 14 outliers final: 9 residues processed: 102 average time/residue: 0.0820 time to fit residues: 12.2055 Evaluate side-chains 97 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 87 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 658 GLU Chi-restraints excluded: chain A residue 681 SER Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain C residue 33 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: [14, 71, 99, 89, 97, 80, 54, 2, 50, 39, 64] chunk 14 optimal weight: 0.6980 chunk 71 optimal weight: 3.9990 chunk 99 optimal weight: 5.9990 chunk 89 optimal weight: 6.9990 chunk 97 optimal weight: 1.9990 chunk 80 optimal weight: 0.0170 chunk 54 optimal weight: 4.9990 chunk 2 optimal weight: 7.9990 chunk 50 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 64 optimal weight: 0.7980 overall best weight: 1.5022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.133338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.110584 restraints weight = 9768.153| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 1.29 r_work: 0.3156 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8651 Z= 0.149 Angle : 0.555 7.935 11833 Z= 0.275 Chirality : 0.043 0.172 1343 Planarity : 0.003 0.032 1425 Dihedral : 10.261 79.167 1353 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.71 % Allowed : 11.64 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.26), residues: 979 helix: 0.75 (0.24), residues: 475 sheet: 0.11 (0.60), residues: 79 loop : -0.32 (0.29), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 197 TYR 0.011 0.001 TYR A 149 PHE 0.014 0.002 PHE A 753 TRP 0.011 0.001 TRP A 916 HIS 0.005 0.001 HIS A 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 ( 8643) covalent geometry : angle 0.55054 / 0.27 (11827) hydrogen bonds : bond 0.04335 / 2.55 ( 416) hydrogen bonds : angle 4.22009 / 2.92 ( 1127) metal coordination : bond 0.01407 / 0.78 ( 8) metal coordination : angle 3.09335 / 1.80 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 0.297 Fit side-chains REVERT: A 280 LEU cc_start: 0.8010 (OUTLIER) cc_final: 0.7805 (mp) outliers start: 15 outliers final: 9 residues processed: 104 average time/residue: 0.0840 time to fit residues: 13.0395 Evaluate side-chains 95 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 85 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 658 GLU Chi-restraints excluded: chain A residue 681 SER Chi-restraints excluded: chain A residue 817 THR Chi-restraints excluded: chain C residue 6 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: [22, 58, 68, 46, 27, 54, 43, 51, 25, 87, 38] chunk 22 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 68 optimal weight: 5.9990 chunk 46 optimal weight: 5.9990 chunk 27 optimal weight: 7.9990 chunk 54 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 87 optimal weight: 9.9990 chunk 38 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.130052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.106953 restraints weight = 9896.641| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 1.31 r_work: 0.3112 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 8651 Z= 0.247 Angle : 0.639 7.716 11833 Z= 0.317 Chirality : 0.046 0.184 1343 Planarity : 0.004 0.036 1425 Dihedral : 10.545 83.669 1353 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.40 % Allowed : 12.10 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.26), residues: 979 helix: 0.47 (0.24), residues: 476 sheet: -0.36 (0.57), residues: 87 loop : -0.50 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 197 TYR 0.012 0.002 TYR A 149 PHE 0.018 0.002 PHE A 652 TRP 0.013 0.002 TRP A 916 HIS 0.007 0.001 HIS A 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00586 / 0.25 ( 8643) covalent geometry : angle 0.63474 / 0.32 (11827) hydrogen bonds : bond 0.04988 / 3.02 ( 416) hydrogen bonds : angle 4.42904 / 3.07 ( 1127) metal coordination : bond 0.02334 / 1.27 ( 8) metal coordination : angle 3.47601 / 1.99 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 89 time to evaluate : 0.316 Fit side-chains REVERT: A 280 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7861 (mp) outliers start: 21 outliers final: 14 residues processed: 108 average time/residue: 0.0753 time to fit residues: 12.1318 Evaluate side-chains 101 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 86 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 ASP Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 658 GLU Chi-restraints excluded: chain A residue 681 SER Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 817 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 33 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: [21, 31, 34, 68, 71, 4, 15, 9, 57, 61, 55] chunk 21 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 34 optimal weight: 8.9990 chunk 68 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 57 optimal weight: 0.4980 chunk 61 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.135992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.111679 restraints weight = 9758.418| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 1.41 r_work: 0.3184 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8651 Z= 0.148 Angle : 0.550 7.799 11833 Z= 0.273 Chirality : 0.042 0.145 1343 Planarity : 0.003 0.032 1425 Dihedral : 10.390 78.813 1353 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.05 % Allowed : 13.24 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.26), residues: 979 helix: 0.68 (0.24), residues: 476 sheet: -0.03 (0.60), residues: 79 loop : -0.34 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 197 TYR 0.011 0.001 TYR A 653 PHE 0.018 0.002 PHE A 652 TRP 0.011 0.001 TRP A 916 HIS 0.005 0.001 HIS A 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 ( 8643) covalent geometry : angle 0.54622 / 0.27 (11827) hydrogen bonds : bond 0.04293 / 2.52 ( 416) hydrogen bonds : angle 4.21547 / 2.91 ( 1127) metal coordination : bond 0.01398 / 0.77 ( 8) metal coordination : angle 2.84047 / 1.65 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 90 time to evaluate : 0.301 Fit side-chains REVERT: A 280 LEU cc_start: 0.8010 (OUTLIER) cc_final: 0.7784 (mp) REVERT: B 177 SER cc_start: 0.7868 (OUTLIER) cc_final: 0.7476 (m) outliers start: 18 outliers final: 12 residues processed: 105 average time/residue: 0.0769 time to fit residues: 11.8232 Evaluate side-chains 101 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 87 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 658 GLU Chi-restraints excluded: chain A residue 681 SER Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 817 THR Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 6 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: [87, 15, 53, 92, 45, 99, 54, 57, 12, 30, 42] chunk 87 optimal weight: 9.9990 chunk 15 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 chunk 45 optimal weight: 4.9990 chunk 99 optimal weight: 6.9990 chunk 54 optimal weight: 5.9990 chunk 57 optimal weight: 4.9990 chunk 12 optimal weight: 10.0000 chunk 30 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.132135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.107912 restraints weight = 9942.952| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 1.40 r_work: 0.3085 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 8651 Z= 0.234 Angle : 0.626 7.730 11833 Z= 0.312 Chirality : 0.046 0.169 1343 Planarity : 0.004 0.036 1425 Dihedral : 10.612 83.197 1353 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.51 % Allowed : 13.58 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.26), residues: 979 helix: 0.47 (0.23), residues: 476 sheet: -0.17 (0.60), residues: 79 loop : -0.48 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 197 TYR 0.018 0.002 TYR A 289 PHE 0.023 0.002 PHE A 652 TRP 0.013 0.001 TRP A 916 HIS 0.007 0.001 HIS A 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00557 / 0.23 ( 8643) covalent geometry : angle 0.62147 / 0.31 (11827) hydrogen bonds : bond 0.04870 / 2.93 ( 416) hydrogen bonds : angle 4.39489 / 3.05 ( 1127) metal coordination : bond 0.02222 / 1.21 ( 8) metal coordination : angle 3.29900 / 1.88 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 90 time to evaluate : 0.288 Fit side-chains REVERT: A 280 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7845 (mp) REVERT: B 177 SER cc_start: 0.7857 (OUTLIER) cc_final: 0.7467 (m) outliers start: 22 outliers final: 14 residues processed: 110 average time/residue: 0.0704 time to fit residues: 11.6525 Evaluate side-chains 100 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 84 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 658 GLU Chi-restraints excluded: chain A residue 681 SER Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 817 THR Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 33 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: [13, 38, 89, 9, 60, 36, 67, 48, 80, 85, 79] chunk 13 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 89 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 48 optimal weight: 5.9990 chunk 80 optimal weight: 0.0670 chunk 85 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 overall best weight: 0.9120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.135808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.111776 restraints weight = 9678.676| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 1.38 r_work: 0.3164 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8651 Z= 0.118 Angle : 0.521 7.834 11833 Z= 0.259 Chirality : 0.041 0.145 1343 Planarity : 0.003 0.031 1425 Dihedral : 10.294 76.218 1353 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.60 % Allowed : 14.84 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.26), residues: 979 helix: 0.70 (0.23), residues: 481 sheet: -0.05 (0.60), residues: 79 loop : -0.32 (0.29), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 197 TYR 0.014 0.001 TYR A 289 PHE 0.014 0.001 PHE A 843 TRP 0.011 0.001 TRP A 916 HIS 0.004 0.001 HIS A 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 ( 8643) covalent geometry : angle 0.51846 / 0.26 (11827) hydrogen bonds : bond 0.04056 / 2.35 ( 416) hydrogen bonds : angle 4.13069 / 2.84 ( 1127) metal coordination : bond 0.00987 / 0.55 ( 8) metal coordination : angle 2.49175 / 1.45 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 91 time to evaluate : 0.322 Fit side-chains REVERT: A 122 TYR cc_start: 0.8010 (m-80) cc_final: 0.7695 (m-80) REVERT: B 177 SER cc_start: 0.7856 (OUTLIER) cc_final: 0.7454 (m) outliers start: 14 outliers final: 10 residues processed: 102 average time/residue: 0.0747 time to fit residues: 11.1385 Evaluate side-chains 95 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 658 GLU Chi-restraints excluded: chain A residue 681 SER Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 817 THR Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 33 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: [5, 53, 60, 86, 36, 72, 61, 2, 75, 37, 8] chunk 5 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 60 optimal weight: 0.7980 chunk 86 optimal weight: 7.9990 chunk 36 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 2 optimal weight: 7.9990 chunk 75 optimal weight: 3.9990 chunk 37 optimal weight: 0.5980 chunk 8 optimal weight: 0.9980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.136092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.111895 restraints weight = 9803.588| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 1.40 r_work: 0.3177 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8651 Z= 0.125 Angle : 0.523 7.836 11833 Z= 0.260 Chirality : 0.041 0.133 1343 Planarity : 0.003 0.030 1425 Dihedral : 10.289 77.412 1353 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.60 % Allowed : 14.95 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.26), residues: 979 helix: 0.78 (0.24), residues: 480 sheet: 0.02 (0.61), residues: 79 loop : -0.30 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 197 TYR 0.011 0.001 TYR A 149 PHE 0.016 0.001 PHE A 652 TRP 0.010 0.001 TRP A 916 HIS 0.005 0.001 HIS A 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.12 ( 8643) covalent geometry : angle 0.52027 / 0.26 (11827) hydrogen bonds : bond 0.04061 / 2.36 ( 416) hydrogen bonds : angle 4.07684 / 2.81 ( 1127) metal coordination : bond 0.01161 / 0.64 ( 8) metal coordination : angle 2.42628 / 1.41 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 86 time to evaluate : 0.221 Fit side-chains REVERT: A 122 TYR cc_start: 0.8012 (m-80) cc_final: 0.7734 (m-80) REVERT: A 280 LEU cc_start: 0.8013 (OUTLIER) cc_final: 0.7809 (mp) REVERT: B 177 SER cc_start: 0.7819 (OUTLIER) cc_final: 0.7413 (m) outliers start: 14 outliers final: 9 residues processed: 99 average time/residue: 0.0768 time to fit residues: 11.0652 Evaluate side-chains 94 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 83 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 658 GLU Chi-restraints excluded: chain A residue 681 SER Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 33 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: [62, 67, 80, 11, 69, 29, 4, 34, 48, 73, 51] chunk 62 optimal weight: 1.9990 chunk 67 optimal weight: 6.9990 chunk 80 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 69 optimal weight: 4.9990 chunk 29 optimal weight: 6.9990 chunk 4 optimal weight: 4.9990 chunk 34 optimal weight: 8.9990 chunk 48 optimal weight: 0.0010 chunk 73 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 overall best weight: 1.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.133614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.109493 restraints weight = 9818.773| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 1.39 r_work: 0.3152 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8651 Z= 0.178 Angle : 0.568 8.140 11833 Z= 0.283 Chirality : 0.043 0.145 1343 Planarity : 0.003 0.031 1425 Dihedral : 10.374 80.072 1353 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.71 % Allowed : 14.84 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.26), residues: 979 helix: 0.66 (0.24), residues: 482 sheet: -0.08 (0.60), residues: 79 loop : -0.36 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 197 TYR 0.011 0.001 TYR A 149 PHE 0.020 0.002 PHE A 652 TRP 0.011 0.001 TRP A 916 HIS 0.007 0.001 HIS A 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.18 ( 8643) covalent geometry : angle 0.56445 / 0.28 (11827) hydrogen bonds : bond 0.04416 / 2.61 ( 416) hydrogen bonds : angle 4.19548 / 2.90 ( 1127) metal coordination : bond 0.01722 / 0.93 ( 8) metal coordination : angle 2.84834 / 1.64 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 88 time to evaluate : 0.267 Fit side-chains REVERT: A 280 LEU cc_start: 0.8032 (OUTLIER) cc_final: 0.7807 (mp) REVERT: B 177 SER cc_start: 0.7843 (OUTLIER) cc_final: 0.7455 (m) outliers start: 15 outliers final: 12 residues processed: 102 average time/residue: 0.0744 time to fit residues: 11.1322 Evaluate side-chains 102 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 658 GLU Chi-restraints excluded: chain A residue 681 SER Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 817 THR Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 33 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: [90, 20, 15, 80, 47, 8, 35, 82, 63, 88, 29] chunk 90 optimal weight: 8.9990 chunk 20 optimal weight: 0.6980 chunk 15 optimal weight: 10.0000 chunk 80 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 82 optimal weight: 8.9990 chunk 63 optimal weight: 2.9990 chunk 88 optimal weight: 7.9990 chunk 29 optimal weight: 2.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.135656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.111985 restraints weight = 9679.511| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 1.35 r_work: 0.3180 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8651 Z= 0.189 Angle : 0.583 7.815 11833 Z= 0.290 Chirality : 0.044 0.153 1343 Planarity : 0.003 0.032 1425 Dihedral : 10.435 80.951 1353 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.60 % Allowed : 15.18 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.26), residues: 979 helix: 0.61 (0.24), residues: 476 sheet: -0.13 (0.60), residues: 79 loop : -0.39 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 197 TYR 0.012 0.001 TYR A 546 PHE 0.020 0.002 PHE A 652 TRP 0.012 0.001 TRP A 916 HIS 0.007 0.001 HIS A 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.19 ( 8643) covalent geometry : angle 0.57937 / 0.29 (11827) hydrogen bonds : bond 0.04533 / 2.69 ( 416) hydrogen bonds : angle 4.26090 / 2.94 ( 1127) metal coordination : bond 0.01800 / 0.98 ( 8) metal coordination : angle 2.94728 / 1.70 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1928.81 seconds wall clock time: 33 minutes 53.10 seconds (2033.10 seconds total)