Starting phenix.real_space_refine on Wed Aug 5 22:54:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vv2_43547/08_2026/8vv2_43547.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vv2_43547/08_2026/8vv2_43547.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8vv2_43547/08_2026/8vv2_43547.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vv2_43547/08_2026/8vv2_43547.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8vv2_43547/08_2026/8vv2_43547.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vv2_43547/08_2026/8vv2_43547.map" } resolution = 2.6 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= 0.002 sd= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 6094 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 23 5.49 5 S 35 5.16 5 C 4365 2.51 5 N 1212 2.21 5 O 1389 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7024 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6519 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 852, 6509 Classifications: {'peptide': 852} Incomplete info: {'truncation_to_alanine': 81} Link IDs: {'PTRANS': 34, 'TRANS': 817} Chain breaks: 2 Unresolved non-hydrogen bonds: 350 Unresolved non-hydrogen angles: 424 Unresolved non-hydrogen dihedrals: 292 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ARG:plan': 10, 'GLU:plan': 22, 'TRP:plan': 1, 'TYR:plan': 1, 'GLN:plan1': 9, 'ASN:plan1': 4, 'ASP:plan': 9, 'PHE:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 245 Conformer: "B" Number of residues, atoms: 852, 6509 Classifications: {'peptide': 852} Incomplete info: {'truncation_to_alanine': 81} Link IDs: {'PTRANS': 34, 'TRANS': 817} Chain breaks: 2 Unresolved non-hydrogen bonds: 350 Unresolved non-hydrogen angles: 424 Unresolved non-hydrogen dihedrals: 292 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ARG:plan': 10, 'GLU:plan': 22, 'TRP:plan': 1, 'TYR:plan': 1, 'GLN:plan1': 9, 'ASN:plan1': 4, 'ASP:plan': 9, 'PHE:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 245 bond proxies already assigned to first conformer: 6619 Chain: "C" Number of atoms: 475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 475 Classifications: {'RNA': 23} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 2, 'rna3p_pur': 6, 'rna3p_pyr': 7} Link IDs: {'rna2p': 9, 'rna3p': 13} Unresolved chain links: 1 Chain breaks: 2 Unresolved chain link angles: 4 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {' U:plan': 1, ' U%rna3p_pyr:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AHIS A 578 " occ=0.63 ... (18 atoms not shown) pdb=" NE2BHIS A 578 " occ=0.37 Time building chain proxies: 2.27, per 1000 atoms: 0.32 Number of scatterers: 7024 At special positions: 0 Unit cell: (74.7, 106.24, 108.73, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 35 16.00 P 23 15.00 O 1389 8.00 N 1212 7.00 C 4365 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: 0.69 Conformation dependent library (CDL) restraints added in 476.8 milliseconds 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1624 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 4 sheets defined 55.2% alpha, 12.9% beta 3 base pairs and 7 stacking pairs defined. Time for finding SS restraints: 0.90 Creating SS restraints... Processing helix chain 'A' and resid 62 through 84 removed outlier: 3.877A pdb=" N TYR A 69 " --> pdb=" O ILE A 65 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N LYS A 72 " --> pdb=" O TRP A 68 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS A 76 " --> pdb=" O LYS A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 107 removed outlier: 3.569A pdb=" N THR A 107 " --> pdb=" O HIS A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 194 removed outlier: 3.639A pdb=" N GLN A 184 " --> pdb=" O ALA A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 207 Processing helix chain 'A' and resid 209 through 214 removed outlier: 4.242A pdb=" N GLY A 213 " --> pdb=" O LEU A 209 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N MET A 214 " --> pdb=" O PRO A 210 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 209 through 214' Processing helix chain 'A' and resid 214 through 225 Processing helix chain 'A' and resid 237 through 253 removed outlier: 4.899A pdb=" N THR A 243 " --> pdb=" O THR A 239 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N GLN A 244 " --> pdb=" O THR A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 258 Processing helix chain 'A' and resid 267 through 282 Processing helix chain 'A' and resid 314 through 324 removed outlier: 3.608A pdb=" N LEU A 318 " --> pdb=" O THR A 314 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLN A 322 " --> pdb=" O LEU A 318 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N SER A 323 " --> pdb=" O GLN A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 356 Processing helix chain 'A' and resid 373 through 380 removed outlier: 3.695A pdb=" N SER A 377 " --> pdb=" O ALA A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 408 Processing helix chain 'A' and resid 433 through 456 removed outlier: 3.574A pdb=" N ALA A 439 " --> pdb=" O GLU A 435 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE A 440 " --> pdb=" O GLU A 436 " (cutoff:3.500A) Proline residue: A 446 - end of helix removed outlier: 3.505A pdb=" N GLN A 454 " --> pdb=" O ARG A 450 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG A 455 " --> pdb=" O GLU A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 467 Processing helix chain 'A' and resid 473 through 488 Processing helix chain 'A' and resid 499 through 512 Processing helix chain 'A' and resid 514 through 518 removed outlier: 3.760A pdb=" N SER A 518 " --> pdb=" O MET A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 559 removed outlier: 3.965A pdb=" N THR A 558 " --> pdb=" O ASN A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 605 removed outlier: 3.891A pdb=" N ALA A 605 " --> pdb=" O ARG A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 624 Processing helix chain 'A' and resid 631 through 635 Processing helix chain 'A' and resid 638 through 648 Processing helix chain 'A' and resid 652 through 659 removed outlier: 3.649A pdb=" N ARG A 659 " --> pdb=" O HIS A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 679 Processing helix chain 'A' and resid 689 through 698 removed outlier: 3.620A pdb=" N HIS A 694 " --> pdb=" O PRO A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 714 Processing helix chain 'A' and resid 716 through 729 Processing helix chain 'A' and resid 740 through 752 Processing helix chain 'A' and resid 758 through 775 Processing helix chain 'A' and resid 775 through 787 Processing helix chain 'A' and resid 789 through 811 Processing helix chain 'A' and resid 820 through 824 Processing helix chain 'A' and resid 829 through 841 Processing helix chain 'A' and resid 908 through 915 Processing helix chain 'A' and resid 941 through 965 removed outlier: 3.690A pdb=" N ILE A 957 " --> pdb=" O LYS A 953 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 989 Processing sheet with id=AA1, first strand: chain 'A' and resid 299 through 301 removed outlier: 6.820A pdb=" N GLY A 293 " --> pdb=" O TYR A 311 " (cutoff:3.500A) removed outlier: 8.872A pdb=" N THR A 313 " --> pdb=" O GLY A 293 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N GLN A 295 " --> pdb=" O THR A 313 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N ARG A 260 " --> pdb=" O HIS A 332 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N VAL A 334 " --> pdb=" O ARG A 260 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N VAL A 262 " --> pdb=" O VAL A 334 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N ASP A 336 " --> pdb=" O VAL A 262 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N THR A 264 " --> pdb=" O ASP A 336 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 395 through 398 removed outlier: 6.102A pdb=" N VAL A 396 " --> pdb=" O CYS A 613 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N HIS A 615 " --> pdb=" O VAL A 396 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N TYR A 398 " --> pdb=" O HIS A 615 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ALA A 492 " --> pdb=" O TYR A 567 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N ILE A 569 " --> pdb=" O ALA A 492 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N LEU A 494 " --> pdb=" O ILE A 569 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ILE A 493 " --> pdb=" O VAL A 550 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N ALA A 552 " --> pdb=" O ILE A 493 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N VAL A 495 " --> pdb=" O ALA A 552 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 573 through 580 removed outlier: 4.057A pdb=" N SER A 586 " --> pdb=" O LYS A 893 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N ILE A 899 " --> pdb=" O VAL A 868 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL A 861 " --> pdb=" O VAL A 869 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N ILE A 871 " --> pdb=" O VAL A 859 " (cutoff:3.500A) removed outlier: 10.627A pdb=" N VAL A 859 " --> pdb=" O ILE A 871 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N MET A 858 " --> pdb=" O ASN A 851 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ASN A 851 " --> pdb=" O MET A 858 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N TRP A 887 " --> pdb=" O VAL A 907 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 919 through 924 366 hydrogen bonds defined for protein. 1068 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 6 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 3 basepair parallelities 7 stacking parallelities Total time for adding SS restraints: 1.30 Time building geometry restraints manager: 0.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1192 1.32 - 1.44: 1850 1.44 - 1.57: 4031 1.57 - 1.69: 42 1.69 - 1.81: 55 Bond restraints: 7170 Sorted by residual: bond pdb=" N TRP A 445 " pdb=" CA TRP A 445 " ideal model delta sigma weight residual 1.462 1.486 -0.024 7.70e-03 1.69e+04 9.75e+00 bond pdb=" C PRO A 446 " pdb=" O PRO A 446 " ideal model delta sigma weight residual 1.237 1.198 0.039 1.29e-02 6.01e+03 9.05e+00 bond pdb=" P U C 19 " pdb=" O5' U C 19 " ideal model delta sigma weight residual 1.593 1.622 -0.029 1.00e-02 1.00e+04 8.40e+00 bond pdb=" CA ALA A 439 " pdb=" CB ALA A 439 " ideal model delta sigma weight residual 1.530 1.487 0.043 1.56e-02 4.11e+03 7.56e+00 bond pdb=" N LYS A 854 " pdb=" CA LYS A 854 " ideal model delta sigma weight residual 1.455 1.489 -0.034 1.33e-02 5.65e+03 6.57e+00 ... (remaining 7165 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.95: 9699 2.95 - 5.90: 120 5.90 - 8.85: 14 8.85 - 11.80: 4 11.80 - 14.75: 3 Bond angle restraints: 9840 Sorted by residual: angle pdb=" C3' G C 17 " pdb=" O3' G C 17 " pdb=" P U C 18 " ideal model delta sigma weight residual 119.70 134.45 -14.75 1.20e+00 6.94e-01 1.51e+02 angle pdb=" C3' U C 19 " pdb=" O3' U C 19 " pdb=" P G C 20 " ideal model delta sigma weight residual 119.70 106.26 13.44 1.20e+00 6.94e-01 1.25e+02 angle pdb=" C3' U C 21 " pdb=" O3' U C 21 " pdb=" P U C 22 " ideal model delta sigma weight residual 119.70 107.07 12.63 1.20e+00 6.94e-01 1.11e+02 angle pdb=" C3' U C 23 " pdb=" O3' U C 23 " pdb=" P U C 24 " ideal model delta sigma weight residual 119.70 108.14 11.56 1.20e+00 6.94e-01 9.29e+01 angle pdb=" C3' U C 22 " pdb=" O3' U C 22 " pdb=" P U C 23 " ideal model delta sigma weight residual 119.70 109.32 10.38 1.20e+00 6.94e-01 7.49e+01 ... (remaining 9835 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.26: 3861 21.26 - 42.52: 384 42.52 - 63.78: 131 63.78 - 85.04: 23 85.04 - 106.30: 3 Dihedral angle restraints: 4402 sinusoidal: 1900 harmonic: 2502 Sorted by residual: dihedral pdb=" CA LYS A 972 " pdb=" C LYS A 972 " pdb=" N ASP A 973 " pdb=" CA ASP A 973 " ideal model delta harmonic sigma weight residual 180.00 159.45 20.55 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" CA TYR A 842 " pdb=" C TYR A 842 " pdb=" N PRO A 843 " pdb=" CA PRO A 843 " ideal model delta harmonic sigma weight residual 180.00 -161.49 -18.51 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CG ARG A 747 " pdb=" CD ARG A 747 " pdb=" NE ARG A 747 " pdb=" CZ ARG A 747 " ideal model delta sinusoidal sigma weight residual -90.00 -39.60 -50.40 2 1.50e+01 4.44e-03 1.27e+01 ... (remaining 4399 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 1098 0.106 - 0.213: 65 0.213 - 0.319: 4 0.319 - 0.425: 3 0.425 - 0.532: 2 Chirality restraints: 1172 Sorted by residual: chirality pdb=" P U C 18 " pdb=" OP1 U C 18 " pdb=" OP2 U C 18 " pdb=" O5' U C 18 " both_signs ideal model delta sigma weight residual True 2.41 -2.94 -0.53 2.00e-01 2.50e+01 7.06e+00 chirality pdb=" P U C 19 " pdb=" OP1 U C 19 " pdb=" OP2 U C 19 " pdb=" O5' U C 19 " both_signs ideal model delta sigma weight residual True 2.41 -2.87 -0.46 2.00e-01 2.50e+01 5.34e+00 chirality pdb=" P U C 27 " pdb=" OP1 U C 27 " pdb=" OP2 U C 27 " pdb=" O5' U C 27 " both_signs ideal model delta sigma weight residual True 2.41 -2.77 -0.36 2.00e-01 2.50e+01 3.22e+00 ... (remaining 1169 not shown) Planarity restraints: 1171 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 450 " 0.322 9.50e-02 1.11e+02 1.44e-01 1.28e+01 pdb=" NE ARG A 450 " -0.019 2.00e-02 2.50e+03 pdb=" CZ ARG A 450 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG A 450 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 450 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 735 " 0.037 5.00e-02 4.00e+02 5.66e-02 5.13e+00 pdb=" N PRO A 736 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO A 736 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 736 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' G C 12 " -0.028 2.00e-02 2.50e+03 1.17e-02 4.14e+00 pdb=" N9 G C 12 " 0.026 2.00e-02 2.50e+03 pdb=" C8 G C 12 " 0.002 2.00e-02 2.50e+03 pdb=" N7 G C 12 " 0.001 2.00e-02 2.50e+03 pdb=" C5 G C 12 " 0.006 2.00e-02 2.50e+03 pdb=" C6 G C 12 " -0.006 2.00e-02 2.50e+03 pdb=" O6 G C 12 " -0.007 2.00e-02 2.50e+03 pdb=" N1 G C 12 " -0.006 2.00e-02 2.50e+03 pdb=" C2 G C 12 " 0.001 2.00e-02 2.50e+03 pdb=" N2 G C 12 " 0.003 2.00e-02 2.50e+03 pdb=" N3 G C 12 " 0.005 2.00e-02 2.50e+03 pdb=" C4 G C 12 " 0.004 2.00e-02 2.50e+03 ... (remaining 1168 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1274 2.77 - 3.30: 6604 3.30 - 3.83: 11976 3.83 - 4.37: 14186 4.37 - 4.90: 23879 Nonbonded interactions: 57919 Sorted by model distance: nonbonded pdb=" N GLU A 374 " pdb=" OE1 GLU A 374 " model vdw 2.231 3.120 nonbonded pdb=" OD1 ASP A 402 " pdb=" OH TYR A 456 " model vdw 2.254 3.040 nonbonded pdb=" OE1 GLU A 576 " pdb=" NE2AHIS A 578 " model vdw 2.286 3.120 nonbonded pdb=" O TYR A 902 " pdb=" O HOH A1101 " model vdw 2.294 3.040 nonbonded pdb=" OD1 ASP A 501 " pdb=" O HOH A1102 " model vdw 2.300 3.040 ... (remaining 57914 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=0.37 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.710 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 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 0.047 7170 Z= 0.247 Angle : 0.816 14.754 9840 Z= 0.538 Chirality : 0.058 0.532 1172 Planarity : 0.007 0.144 1171 Dihedral : 19.065 106.296 2778 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.02 % Favored : 95.86 % Rotamer: Outliers : 3.68 % Allowed : 26.18 % Favored : 70.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.30), residues: 849 helix: 1.74 (0.26), residues: 441 sheet: 1.24 (0.54), residues: 90 loop : -0.45 (0.36), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 93 TYR 0.016 0.001 TYR A 778 PHE 0.010 0.001 PHE A 205 TRP 0.013 0.001 TRP A 445 HIS 0.007 0.001 HIS A 507 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.25 ( 7170) covalent geometry : angle 0.81631 / 0.54 ( 9840) hydrogen bonds : bond 0.15218 / 10.58 ( 372) hydrogen bonds : angle 5.27095 / 3.94 ( 1068) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 65 time to evaluate : 0.276 Fit side-chains revert: symmetry clash outliers start: 25 outliers final: 16 residues processed: 89 average time/residue: 0.5645 time to fit residues: 53.0408 Evaluate side-chains 65 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 49 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 HIS Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 183 ASP Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 713 LEU Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 889 ILE Chi-restraints excluded: chain A residue 907 VAL Chi-restraints excluded: chain A residue 963 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.0570 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 0.3980 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 97 GLN A 203 GLN A 615 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.089996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.062211 restraints weight = 27574.380| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 3.93 r_work: 0.2767 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2767 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2767 r_free = 0.2767 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2767 r_free = 0.2767 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2767 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.1023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7170 Z= 0.131 Angle : 0.580 7.348 9840 Z= 0.312 Chirality : 0.043 0.294 1172 Planarity : 0.005 0.054 1171 Dihedral : 15.264 99.876 1304 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.84 % Favored : 97.04 % Rotamer: Outliers : 3.68 % Allowed : 25.15 % Favored : 71.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.30), residues: 849 helix: 1.93 (0.26), residues: 445 sheet: 1.11 (0.49), residues: 112 loop : -0.31 (0.38), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 93 TYR 0.010 0.001 TYR A 842 PHE 0.016 0.001 PHE A 376 TRP 0.007 0.001 TRP A 935 HIS 0.003 0.001 HIS A 758 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 ( 7170) covalent geometry : angle 0.57994 / 0.31 ( 9840) hydrogen bonds : bond 0.04188 / 2.99 ( 372) hydrogen bonds : angle 4.04721 / 3.00 ( 1068) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 52 time to evaluate : 0.217 Fit side-chains revert: symmetry clash REVERT: A 774 ARG cc_start: 0.9081 (ttm-80) cc_final: 0.8559 (ttp80) REVERT: A 785 GLU cc_start: 0.8583 (tp30) cc_final: 0.8266 (tm-30) outliers start: 25 outliers final: 9 residues processed: 74 average time/residue: 0.4807 time to fit residues: 37.8271 Evaluate side-chains 58 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 49 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 HIS Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 713 LEU Chi-restraints excluded: chain A residue 889 ILE Chi-restraints excluded: chain A residue 988 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 45 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 75 optimal weight: 0.5980 chunk 72 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 56 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 851 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.089575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.061244 restraints weight = 35230.725| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 4.38 r_work: 0.2736 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2738 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2738 r_free = 0.2738 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2738 r_free = 0.2738 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2738 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.1283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 7170 Z= 0.132 Angle : 0.540 7.993 9840 Z= 0.285 Chirality : 0.042 0.238 1172 Planarity : 0.004 0.053 1171 Dihedral : 14.898 104.304 1293 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.07 % Favored : 96.81 % Rotamer: Outliers : 2.94 % Allowed : 24.71 % Favored : 72.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.69 (0.30), residues: 849 helix: 2.04 (0.25), residues: 445 sheet: 0.97 (0.49), residues: 114 loop : -0.23 (0.39), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 93 TYR 0.009 0.001 TYR A 842 PHE 0.011 0.001 PHE A 205 TRP 0.009 0.001 TRP A 935 HIS 0.004 0.001 HIS A 527 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 ( 7170) covalent geometry : angle 0.53960 / 0.29 ( 9840) hydrogen bonds : bond 0.03674 / 2.62 ( 372) hydrogen bonds : angle 3.74718 / 2.76 ( 1068) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 49 time to evaluate : 0.268 Fit side-chains revert: symmetry clash REVERT: A 774 ARG cc_start: 0.9082 (ttm-80) cc_final: 0.8574 (ttp80) outliers start: 20 outliers final: 10 residues processed: 66 average time/residue: 0.5081 time to fit residues: 35.4657 Evaluate side-chains 55 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 45 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 HIS Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 713 LEU Chi-restraints excluded: chain A residue 907 VAL Chi-restraints excluded: chain A residue 963 ILE Chi-restraints excluded: chain A residue 988 LEU Chi-restraints excluded: chain A residue 993 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 48 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 27 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 chunk 73 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 68 optimal weight: 0.5980 chunk 32 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 55 optimal weight: 0.5980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 326 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.088960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.060671 restraints weight = 34141.526| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 4.31 r_work: 0.2728 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2730 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2730 r_free = 0.2730 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2730 r_free = 0.2730 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2730 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 7170 Z= 0.152 Angle : 0.544 10.719 9840 Z= 0.286 Chirality : 0.042 0.155 1172 Planarity : 0.004 0.054 1171 Dihedral : 14.641 102.470 1289 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.72 % Favored : 97.16 % Rotamer: Outliers : 2.94 % Allowed : 25.15 % Favored : 71.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.73 (0.30), residues: 849 helix: 2.13 (0.25), residues: 444 sheet: 0.95 (0.49), residues: 112 loop : -0.27 (0.38), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 93 TYR 0.018 0.001 TYR A 358 PHE 0.011 0.001 PHE A 376 TRP 0.007 0.001 TRP A 935 HIS 0.005 0.001 HIS A 527 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.15 ( 7170) covalent geometry : angle 0.54422 / 0.29 ( 9840) hydrogen bonds : bond 0.03515 / 2.52 ( 372) hydrogen bonds : angle 3.67235 / 2.71 ( 1068) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 48 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 255 LYS cc_start: 0.8421 (OUTLIER) cc_final: 0.8077 (mtmm) outliers start: 20 outliers final: 8 residues processed: 64 average time/residue: 0.5219 time to fit residues: 35.4182 Evaluate side-chains 56 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 HIS Chi-restraints excluded: chain A residue 255 LYS Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 907 VAL Chi-restraints excluded: chain A residue 963 ILE Chi-restraints excluded: chain A residue 988 LEU Chi-restraints excluded: chain A residue 993 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 56 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 61 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 54 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 85 optimal weight: 50.0000 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.3447 r_free = 0.3447 target = 0.089166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.061044 restraints weight = 32668.720| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 4.25 r_work: 0.2728 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2739 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2739 r_free = 0.2739 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2739 r_free = 0.2739 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2739 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7170 Z= 0.127 Angle : 0.526 6.924 9840 Z= 0.278 Chirality : 0.041 0.133 1172 Planarity : 0.004 0.052 1171 Dihedral : 14.461 102.195 1287 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.65 % Allowed : 25.74 % Favored : 71.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.88 (0.30), residues: 849 helix: 2.25 (0.25), residues: 443 sheet: 0.90 (0.49), residues: 114 loop : -0.15 (0.38), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 93 TYR 0.010 0.001 TYR A 842 PHE 0.008 0.001 PHE A 376 TRP 0.008 0.001 TRP A 935 HIS 0.004 0.001 HIS A 527 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 ( 7170) covalent geometry : angle 0.52576 / 0.28 ( 9840) hydrogen bonds : bond 0.03277 / 2.35 ( 372) hydrogen bonds : angle 3.60795 / 2.67 ( 1068) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 47 time to evaluate : 0.286 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 255 LYS cc_start: 0.8389 (OUTLIER) cc_final: 0.8071 (mtmm) outliers start: 18 outliers final: 8 residues processed: 62 average time/residue: 0.6738 time to fit residues: 44.0453 Evaluate side-chains 55 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 46 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 HIS Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 255 LYS Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 988 LEU Chi-restraints excluded: chain A residue 993 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 9 optimal weight: 1.9990 chunk 41 optimal weight: 0.4980 chunk 76 optimal weight: 0.8980 chunk 60 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 45 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 chunk 64 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3451 r_free = 0.3451 target = 0.089366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.061337 restraints weight = 32916.367| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 4.25 r_work: 0.2724 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2747 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2747 r_free = 0.2747 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2747 r_free = 0.2747 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2747 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7170 Z= 0.119 Angle : 0.529 10.956 9840 Z= 0.276 Chirality : 0.041 0.132 1172 Planarity : 0.004 0.053 1171 Dihedral : 14.413 101.515 1287 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.50 % Allowed : 26.03 % Favored : 71.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.90 (0.30), residues: 849 helix: 2.28 (0.25), residues: 445 sheet: 0.90 (0.50), residues: 114 loop : -0.17 (0.38), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 93 TYR 0.009 0.001 TYR A 842 PHE 0.008 0.001 PHE A 376 TRP 0.007 0.001 TRP A 935 HIS 0.004 0.001 HIS A 527 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 ( 7170) covalent geometry : angle 0.52885 / 0.28 ( 9840) hydrogen bonds : bond 0.03168 / 2.28 ( 372) hydrogen bonds : angle 3.58661 / 2.67 ( 1068) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 47 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 GLN cc_start: 0.8490 (tm-30) cc_final: 0.8270 (pp30) REVERT: A 255 LYS cc_start: 0.8359 (OUTLIER) cc_final: 0.8052 (mtmm) outliers start: 17 outliers final: 10 residues processed: 63 average time/residue: 0.5810 time to fit residues: 38.8201 Evaluate side-chains 57 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 46 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 HIS Chi-restraints excluded: chain A residue 255 LYS Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 716 CYS Chi-restraints excluded: chain A residue 907 VAL Chi-restraints excluded: chain A residue 988 LEU Chi-restraints excluded: chain A residue 993 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 51 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 41 optimal weight: 0.0870 chunk 16 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 62 optimal weight: 0.7980 overall best weight: 0.6558 ------------------------------------------------------------------------------- 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 = 0.3460 r_free = 0.3460 target = 0.089737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.061684 restraints weight = 33042.948| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 4.26 r_work: 0.2734 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2750 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2750 r_free = 0.2750 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2750 r_free = 0.2750 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2750 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7170 Z= 0.114 Angle : 0.518 7.938 9840 Z= 0.272 Chirality : 0.041 0.132 1172 Planarity : 0.004 0.050 1171 Dihedral : 14.357 100.846 1287 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.50 % Allowed : 26.18 % Favored : 71.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.99 (0.30), residues: 849 helix: 2.37 (0.25), residues: 444 sheet: 0.91 (0.50), residues: 114 loop : -0.13 (0.39), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 93 TYR 0.010 0.001 TYR A 842 PHE 0.007 0.001 PHE A 376 TRP 0.007 0.001 TRP A 935 HIS 0.004 0.001 HIS A 527 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.11 ( 7170) covalent geometry : angle 0.51829 / 0.27 ( 9840) hydrogen bonds : bond 0.03103 / 2.23 ( 372) hydrogen bonds : angle 3.53337 / 2.61 ( 1068) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 47 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 LYS cc_start: 0.8343 (OUTLIER) cc_final: 0.8051 (mtmm) outliers start: 17 outliers final: 10 residues processed: 61 average time/residue: 0.6083 time to fit residues: 39.2898 Evaluate side-chains 57 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 46 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 HIS Chi-restraints excluded: chain A residue 255 LYS Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 467 MET Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 716 CYS Chi-restraints excluded: chain A residue 907 VAL Chi-restraints excluded: chain A residue 988 LEU Chi-restraints excluded: chain A residue 993 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 68 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 59 optimal weight: 0.5980 chunk 55 optimal weight: 0.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 851 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.089051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.061732 restraints weight = 24153.220| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 3.70 r_work: 0.2762 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2778 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2778 r_free = 0.2778 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2778 r_free = 0.2778 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2778 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 7170 Z= 0.135 Angle : 0.539 12.313 9840 Z= 0.281 Chirality : 0.041 0.132 1172 Planarity : 0.004 0.051 1171 Dihedral : 14.327 100.108 1287 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.62 % Allowed : 26.76 % Favored : 71.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.94 (0.30), residues: 849 helix: 2.32 (0.25), residues: 444 sheet: 0.91 (0.50), residues: 114 loop : -0.16 (0.38), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 93 TYR 0.010 0.001 TYR A 842 PHE 0.008 0.001 PHE A 376 TRP 0.006 0.001 TRP A 935 HIS 0.005 0.001 HIS A 527 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.13 ( 7170) covalent geometry : angle 0.53896 / 0.28 ( 9840) hydrogen bonds : bond 0.03223 / 2.33 ( 372) hydrogen bonds : angle 3.55157 / 2.64 ( 1068) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 48 time to evaluate : 0.264 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 GLN cc_start: 0.8560 (tm-30) cc_final: 0.8327 (pp30) REVERT: A 255 LYS cc_start: 0.8369 (OUTLIER) cc_final: 0.8126 (mtmm) outliers start: 11 outliers final: 9 residues processed: 58 average time/residue: 0.6525 time to fit residues: 39.8767 Evaluate side-chains 57 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 HIS Chi-restraints excluded: chain A residue 255 LYS Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 716 CYS Chi-restraints excluded: chain A residue 907 VAL Chi-restraints excluded: chain A residue 988 LEU Chi-restraints excluded: chain A residue 993 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 59 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 83 optimal weight: 0.1980 chunk 28 optimal weight: 0.1980 chunk 52 optimal weight: 0.0980 chunk 4 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 8 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 19 optimal weight: 0.0980 chunk 15 optimal weight: 6.9990 overall best weight: 0.2580 ------------------------------------------------------------------------------- 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 = 0.3470 r_free = 0.3470 target = 0.090583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.062249 restraints weight = 35376.484| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 4.44 r_work: 0.2720 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2730 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2730 r_free = 0.2730 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2730 r_free = 0.2730 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2730 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 7170 Z= 0.100 Angle : 0.535 8.050 9840 Z= 0.280 Chirality : 0.040 0.134 1172 Planarity : 0.004 0.049 1171 Dihedral : 14.307 99.862 1287 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.91 % Allowed : 26.47 % Favored : 71.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.10 (0.30), residues: 849 helix: 2.46 (0.25), residues: 444 sheet: 0.92 (0.50), residues: 114 loop : -0.08 (0.39), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 93 TYR 0.007 0.001 TYR A 294 PHE 0.006 0.001 PHE A 205 TRP 0.008 0.001 TRP A 935 HIS 0.002 0.000 HIS A 527 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.10 ( 7170) covalent geometry : angle 0.53461 / 0.28 ( 9840) hydrogen bonds : bond 0.02836 / 2.05 ( 372) hydrogen bonds : angle 3.49310 / 2.59 ( 1068) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 49 time to evaluate : 0.294 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 GLN cc_start: 0.8571 (tm-30) cc_final: 0.8337 (pp30) REVERT: A 214 MET cc_start: 0.9022 (mtp) cc_final: 0.8600 (mtm) REVERT: A 255 LYS cc_start: 0.8315 (OUTLIER) cc_final: 0.8034 (mtmm) REVERT: A 785 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.8231 (tm-30) outliers start: 13 outliers final: 8 residues processed: 61 average time/residue: 0.6593 time to fit residues: 42.5832 Evaluate side-chains 59 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 49 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 HIS Chi-restraints excluded: chain A residue 255 LYS Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 716 CYS Chi-restraints excluded: chain A residue 785 GLU Chi-restraints excluded: chain A residue 988 LEU Chi-restraints excluded: chain A residue 993 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 23 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 68 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 41 optimal weight: 0.0670 chunk 30 optimal weight: 0.9990 chunk 26 optimal weight: 7.9990 chunk 37 optimal weight: 0.4980 chunk 13 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 overall best weight: 0.6920 ------------------------------------------------------------------------------- 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 = 0.3433 r_free = 0.3433 target = 0.089291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.060766 restraints weight = 30892.862| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 4.26 r_work: 0.2709 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2719 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2719 r_free = 0.2719 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2719 r_free = 0.2719 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2719 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7170 Z= 0.119 Angle : 0.548 12.810 9840 Z= 0.282 Chirality : 0.040 0.130 1172 Planarity : 0.004 0.049 1171 Dihedral : 14.268 99.321 1287 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.32 % Allowed : 26.91 % Favored : 71.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.09 (0.30), residues: 849 helix: 2.44 (0.25), residues: 444 sheet: 0.95 (0.50), residues: 114 loop : -0.08 (0.39), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 93 TYR 0.009 0.001 TYR A 842 PHE 0.007 0.001 PHE A 376 TRP 0.008 0.001 TRP A 500 HIS 0.004 0.001 HIS A 527 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 ( 7170) covalent geometry : angle 0.54788 / 0.28 ( 9840) hydrogen bonds : bond 0.03007 / 2.18 ( 372) hydrogen bonds : angle 3.50029 / 2.61 ( 1068) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 49 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 GLN cc_start: 0.8569 (tm-30) cc_final: 0.8341 (pp30) REVERT: A 214 MET cc_start: 0.9032 (mtp) cc_final: 0.8744 (mtm) REVERT: A 255 LYS cc_start: 0.8310 (OUTLIER) cc_final: 0.8073 (mtmm) outliers start: 9 outliers final: 8 residues processed: 57 average time/residue: 0.6779 time to fit residues: 40.8265 Evaluate side-chains 56 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 HIS Chi-restraints excluded: chain A residue 255 LYS Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 716 CYS Chi-restraints excluded: chain A residue 988 LEU Chi-restraints excluded: chain A residue 993 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 33 optimal weight: 0.9980 chunk 55 optimal weight: 0.9990 chunk 82 optimal weight: 0.9980 chunk 3 optimal weight: 7.9990 chunk 22 optimal weight: 1.9990 chunk 0 optimal weight: 70.0000 chunk 15 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 85 optimal weight: 50.0000 chunk 19 optimal weight: 0.0010 overall best weight: 0.9990 ------------------------------------------------------------------------------- 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 = 0.3439 r_free = 0.3439 target = 0.088895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.060222 restraints weight = 36943.057| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 4.50 r_work: 0.2674 rms_B_bonded: 4.87 restraints_weight: 0.5000 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2684 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2684 r_free = 0.2684 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2684 r_free = 0.2684 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2684 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7170 Z= 0.141 Angle : 0.562 9.317 9840 Z= 0.291 Chirality : 0.041 0.134 1172 Planarity : 0.004 0.048 1171 Dihedral : 14.229 98.133 1287 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.47 % Allowed : 26.91 % Favored : 71.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.08 (0.30), residues: 849 helix: 2.46 (0.25), residues: 443 sheet: 0.90 (0.50), residues: 114 loop : -0.08 (0.39), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 93 TYR 0.012 0.001 TYR A 842 PHE 0.008 0.001 PHE A 376 TRP 0.006 0.001 TRP A 935 HIS 0.005 0.001 HIS A 527 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.14 ( 7170) covalent geometry : angle 0.56176 / 0.29 ( 9840) hydrogen bonds : bond 0.03256 / 2.35 ( 372) hydrogen bonds : angle 3.52500 / 2.61 ( 1068) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2641.80 seconds wall clock time: 45 minutes 41.48 seconds (2741.48 seconds total)