Starting phenix.real_space_refine on Fri Jul 3 04:48:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vv2_43547/07_2026/8vv2_43547.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vv2_43547/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8vv2_43547/07_2026/8vv2_43547.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vv2_43547/07_2026/8vv2_43547.map" model { file = "/net/cci-nas-00/data/ceres_data/8vv2_43547/07_2026/8vv2_43547.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vv2_43547/07_2026/8vv2_43547.cif" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/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: 2.53, per 1000 atoms: 0.36 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: 0.55 Conformation dependent library (CDL) restraints added in 435.7 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: 0.86 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: 1.24 Time building geometry restraints manager: 0.73 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=" 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 bond pdb=" O5' U C 19 " pdb=" C5' U C 19 " ideal model delta sigma weight residual 1.424 1.458 -0.034 1.50e-02 4.44e+03 5.03e+00 ... (remaining 7165 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.85: 9691 2.85 - 5.70: 126 5.70 - 8.55: 14 8.55 - 11.40: 4 11.40 - 14.25: 5 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 120.20 134.45 -14.25 1.50e+00 4.44e-01 9.03e+01 angle pdb=" C3' U C 19 " pdb=" O3' U C 19 " pdb=" P G C 20 " ideal model delta sigma weight residual 120.20 106.26 13.94 1.50e+00 4.44e-01 8.64e+01 angle pdb=" C3' U C 21 " pdb=" O3' U C 21 " pdb=" P U C 22 " ideal model delta sigma weight residual 120.20 107.07 13.13 1.50e+00 4.44e-01 7.66e+01 angle pdb=" C3' U C 23 " pdb=" O3' U C 23 " pdb=" P U C 24 " ideal model delta sigma weight residual 120.20 108.14 12.06 1.50e+00 4.44e-01 6.47e+01 angle pdb=" C3' U C 22 " pdb=" O3' U C 22 " pdb=" P U C 23 " ideal model delta sigma weight residual 120.20 109.32 10.88 1.50e+00 4.44e-01 5.26e+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: 1103 0.106 - 0.213: 60 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: 2.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 9.490 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.750 ------------------------------------------------------------------------------- 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= 0.238 Angle : 0.811 14.254 9840 Z= 0.502 Chirality : 0.057 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 0.00426 / 0.24 ( 7170) covalent geometry : angle 0.81113 / 0.50 ( 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 : 0.242 Fit side-chains revert: symmetry clash outliers start: 25 outliers final: 16 residues processed: 89 average time/residue: 0.5386 time to fit residues: 50.5100 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 : 0.287 ------------------------------------------------------------------------------- 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 = 0.3457 r_free = 0.3457 target = 0.089881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.062128 restraints weight = 27524.915| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 3.92 r_work: 0.2766 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.2766 ------------------------------------------------------------------------------- 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: 0.8602 moved from start: 0.0997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7170 Z= 0.131 Angle : 0.572 7.401 9840 Z= 0.311 Chirality : 0.043 0.181 1172 Planarity : 0.005 0.055 1171 Dihedral : 15.252 100.469 1304 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.84 % Favored : 97.04 % Rotamer: Outliers : 3.53 % Allowed : 25.00 % 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: 1.61 (0.30), residues: 849 helix: 1.95 (0.26), residues: 445 sheet: 1.15 (0.49), residues: 112 loop : -0.32 (0.38), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 93 TYR 0.009 0.001 TYR A 842 PHE 0.015 0.001 PHE A 376 TRP 0.007 0.001 TRP A 935 HIS 0.003 0.001 HIS A 527 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 ( 7170) covalent geometry : angle 0.57197 / 0.31 ( 9840) hydrogen bonds : bond 0.04272 / 3.05 ( 372) hydrogen bonds : angle 4.06492 / 3.02 ( 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 76 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 52 time to evaluate : 0.259 Fit side-chains revert: symmetry clash REVERT: A 509 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8659 (tt) REVERT: A 774 ARG cc_start: 0.9078 (ttm-80) cc_final: 0.8555 (ttp80) REVERT: A 785 GLU cc_start: 0.8554 (tp30) cc_final: 0.8248 (tm-30) outliers start: 24 outliers final: 10 residues processed: 74 average time/residue: 0.4854 time to fit residues: 37.9540 Evaluate side-chains 60 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 49 time to evaluate : 0.212 ------------------------------------------------------------------------------- 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 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 889 ILE Chi-restraints excluded: chain A residue 963 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: 2.9990 chunk 59 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 56 optimal weight: 0.5980 chunk 44 optimal weight: 0.4980 chunk 77 optimal weight: 0.7980 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.3455 r_free = 0.3455 target = 0.089659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.061643 restraints weight = 35113.945| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 4.31 r_work: 0.2732 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2744 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2744 r_free = 0.2744 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 = 0.2744 r_free = 0.2744 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: 0.2744 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.1288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 7170 Z= 0.127 Angle : 0.532 7.925 9840 Z= 0.283 Chirality : 0.042 0.171 1172 Planarity : 0.004 0.052 1171 Dihedral : 14.881 104.780 1297 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.19 % Favored : 96.69 % Rotamer: Outliers : 2.94 % Allowed : 24.56 % Favored : 72.50 % 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: 1.71 (0.30), residues: 849 helix: 2.06 (0.25), residues: 445 sheet: 0.98 (0.49), residues: 114 loop : -0.22 (0.39), 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 0.012 0.001 PHE A 205 TRP 0.009 0.001 TRP A 935 HIS 0.003 0.001 HIS A 527 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 ( 7170) covalent geometry : angle 0.53167 / 0.28 ( 9840) hydrogen bonds : bond 0.03600 / 2.58 ( 372) hydrogen bonds : angle 3.73657 / 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 : 0.222 Fit side-chains revert: symmetry clash REVERT: A 774 ARG cc_start: 0.9089 (ttm-80) cc_final: 0.8583 (ttp80) outliers start: 20 outliers final: 9 residues processed: 65 average time/residue: 0.5075 time to fit residues: 34.9501 Evaluate side-chains 53 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 44 time to evaluate : 0.159 ------------------------------------------------------------------------------- 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 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: 3.9990 chunk 33 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 73 optimal weight: 0.6980 chunk 13 optimal weight: 3.9990 chunk 68 optimal weight: 0.0870 chunk 32 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 overall best weight: 1.3362 ------------------------------------------------------------------------------- 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 = 0.3434 r_free = 0.3434 target = 0.088381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.060174 restraints weight = 34174.605| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 4.29 r_work: 0.2716 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.2716 ------------------------------------------------------------------------------- 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 = 0.41 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 = 0.41 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: 0.8627 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 7170 Z= 0.173 Angle : 0.550 10.462 9840 Z= 0.291 Chirality : 0.043 0.169 1172 Planarity : 0.004 0.055 1171 Dihedral : 14.569 103.305 1289 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.84 % Favored : 97.04 % Rotamer: Outliers : 3.09 % Allowed : 24.41 % Favored : 72.50 % 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: 1.74 (0.30), residues: 849 helix: 2.12 (0.25), residues: 443 sheet: 0.97 (0.49), residues: 112 loop : -0.24 (0.38), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 93 TYR 0.017 0.001 TYR A 358 PHE 0.011 0.001 PHE A 376 TRP 0.007 0.001 TRP A 935 HIS 0.006 0.001 HIS A 527 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.17 ( 7170) covalent geometry : angle 0.55020 / 0.29 ( 9840) hydrogen bonds : bond 0.03700 / 2.65 ( 372) hydrogen bonds : angle 3.69146 / 2.72 ( 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: 21 poor density : 47 time to evaluate : 0.201 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 10 residues processed: 65 average time/residue: 0.5428 time to fit residues: 37.3177 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 : 0.277 ------------------------------------------------------------------------------- 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 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 737 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 56 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 44 optimal weight: 0.0470 chunk 33 optimal weight: 0.9980 chunk 54 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 85 optimal weight: 40.0000 overall best weight: 0.7278 ------------------------------------------------------------------------------- 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 = 0.3452 r_free = 0.3452 target = 0.089390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.061274 restraints weight = 32687.475| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 4.25 r_work: 0.2731 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2740 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2740 r_free = 0.2740 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 = 0.2740 r_free = 0.2740 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: 0.2740 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7170 Z= 0.119 Angle : 0.519 7.364 9840 Z= 0.276 Chirality : 0.041 0.160 1172 Planarity : 0.004 0.050 1171 Dihedral : 14.423 102.841 1287 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.21 % Allowed : 25.88 % 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: 1.86 (0.30), residues: 849 helix: 2.24 (0.25), residues: 444 sheet: 0.94 (0.49), residues: 112 loop : -0.20 (0.38), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 93 TYR 0.009 0.001 TYR A 842 PHE 0.009 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 0.00272 / 0.12 ( 7170) covalent geometry : angle 0.51879 / 0.28 ( 9840) hydrogen bonds : bond 0.03265 / 2.34 ( 372) hydrogen bonds : angle 3.61193 / 2.66 ( 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 62 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 47 time to evaluate : 0.248 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 255 LYS cc_start: 0.8391 (OUTLIER) cc_final: 0.8069 (mtmm) outliers start: 15 outliers final: 7 residues processed: 61 average time/residue: 0.5335 time to fit residues: 34.3012 Evaluate side-chains 54 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.257 ------------------------------------------------------------------------------- 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 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: 0.7980 chunk 41 optimal weight: 0.6980 chunk 76 optimal weight: 0.9980 chunk 60 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 chunk 22 optimal weight: 0.4980 chunk 64 optimal weight: 0.5980 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 = 0.3454 r_free = 0.3454 target = 0.089547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.061442 restraints weight = 32980.061| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 4.26 r_work: 0.2736 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2749 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2749 r_free = 0.2749 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 = 0.2749 r_free = 0.2749 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: 0.2749 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7170 Z= 0.118 Angle : 0.529 12.244 9840 Z= 0.276 Chirality : 0.041 0.148 1172 Planarity : 0.004 0.051 1171 Dihedral : 14.365 101.850 1287 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.06 % Allowed : 26.32 % 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: 1.95 (0.30), residues: 849 helix: 2.31 (0.25), residues: 444 sheet: 0.93 (0.49), residues: 114 loop : -0.12 (0.38), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 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 0.52888 / 0.28 ( 9840) hydrogen bonds : bond 0.03167 / 2.28 ( 372) hydrogen bonds : angle 3.54526 / 2.62 ( 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 62 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 48 time to evaluate : 0.269 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 GLN cc_start: 0.8455 (tm-30) cc_final: 0.8218 (pp30) REVERT: A 255 LYS cc_start: 0.8358 (OUTLIER) cc_final: 0.8055 (mtmm) outliers start: 14 outliers final: 8 residues processed: 61 average time/residue: 0.5373 time to fit residues: 34.7126 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 : 0.226 ------------------------------------------------------------------------------- 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 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: 0.9990 chunk 20 optimal weight: 0.9980 chunk 30 optimal weight: 0.4980 chunk 41 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 44 optimal weight: 0.0970 chunk 11 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 62 optimal weight: 0.7980 overall best weight: 0.5978 ------------------------------------------------------------------------------- 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 = 0.3425 r_free = 0.3425 target = 0.088741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.060688 restraints weight = 32819.899| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 4.25 r_work: 0.2701 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2708 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2708 r_free = 0.2708 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 = 0.2708 r_free = 0.2708 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: 0.2708 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.1760 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= 0.111 Angle : 0.519 7.958 9840 Z= 0.272 Chirality : 0.040 0.140 1172 Planarity : 0.004 0.051 1171 Dihedral : 14.334 101.267 1287 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.76 % Allowed : 26.91 % 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: 2.02 (0.30), residues: 849 helix: 2.38 (0.25), residues: 444 sheet: 0.91 (0.49), residues: 114 loop : -0.10 (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 0.007 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 0.00256 / 0.11 ( 7170) covalent geometry : angle 0.51867 / 0.27 ( 9840) hydrogen bonds : bond 0.03035 / 2.18 ( 372) hydrogen bonds : angle 3.52125 / 2.60 ( 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 60 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 48 time to evaluate : 0.250 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 255 LYS cc_start: 0.8346 (OUTLIER) cc_final: 0.8044 (mtmm) outliers start: 12 outliers final: 8 residues processed: 59 average time/residue: 0.5654 time to fit residues: 35.2746 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 : 0.256 ------------------------------------------------------------------------------- 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 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: 3.9990 chunk 26 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 chunk 40 optimal weight: 0.7980 chunk 64 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 = 0.3436 r_free = 0.3436 target = 0.088649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.061397 restraints weight = 24201.897| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 3.70 r_work: 0.2755 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2768 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2768 r_free = 0.2768 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2768 r_free = 0.2768 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: 0.2768 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 7170 Z= 0.148 Angle : 0.543 12.281 9840 Z= 0.283 Chirality : 0.041 0.133 1172 Planarity : 0.004 0.048 1171 Dihedral : 14.298 100.257 1287 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.62 % Allowed : 26.91 % 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: 1.92 (0.30), residues: 849 helix: 2.32 (0.25), residues: 444 sheet: 0.93 (0.50), residues: 112 loop : -0.19 (0.38), residues: 293 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 0.007 0.001 TRP A 500 HIS 0.005 0.001 HIS A 527 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 ( 7170) covalent geometry : angle 0.54302 / 0.28 ( 9840) hydrogen bonds : bond 0.03310 / 2.38 ( 372) hydrogen bonds : angle 3.54742 / 2.63 ( 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 58 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 47 time to evaluate : 0.218 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 GLN cc_start: 0.8549 (tm-30) cc_final: 0.8332 (pp30) REVERT: A 255 LYS cc_start: 0.8367 (OUTLIER) cc_final: 0.8122 (mtmm) outliers start: 11 outliers final: 8 residues processed: 57 average time/residue: 0.5946 time to fit residues: 35.8415 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 : 0.276 ------------------------------------------------------------------------------- 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 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: 4.9990 chunk 39 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 28 optimal weight: 0.0270 chunk 52 optimal weight: 0.0050 chunk 4 optimal weight: 0.2980 chunk 78 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 81 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 15 optimal weight: 6.9990 overall best weight: 0.4452 ------------------------------------------------------------------------------- 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 = 0.3436 r_free = 0.3436 target = 0.089347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.060624 restraints weight = 35466.129| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 4.48 r_work: 0.2698 rms_B_bonded: 4.87 restraints_weight: 0.5000 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2709 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2709 r_free = 0.2709 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 = 0.2709 r_free = 0.2709 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: 0.2709 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 7170 Z= 0.103 Angle : 0.519 8.473 9840 Z= 0.273 Chirality : 0.040 0.131 1172 Planarity : 0.004 0.047 1171 Dihedral : 14.278 99.944 1287 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.47 % Allowed : 27.06 % 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: 2.11 (0.30), residues: 849 helix: 2.46 (0.25), residues: 444 sheet: 0.93 (0.50), residues: 114 loop : -0.06 (0.39), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 93 TYR 0.008 0.001 TYR A 842 PHE 0.007 0.001 PHE A 376 TRP 0.008 0.001 TRP A 935 HIS 0.003 0.001 HIS A 527 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.10 ( 7170) covalent geometry : angle 0.51922 / 0.27 ( 9840) hydrogen bonds : bond 0.02961 / 2.14 ( 372) hydrogen bonds : angle 3.49934 / 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 58 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 48 time to evaluate : 0.270 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 GLN cc_start: 0.8576 (tm-30) cc_final: 0.8344 (pp30) outliers start: 10 outliers final: 7 residues processed: 56 average time/residue: 0.5831 time to fit residues: 34.4458 Evaluate side-chains 55 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 48 time to evaluate : 0.280 ------------------------------------------------------------------------------- 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 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: 3.9990 chunk 78 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 68 optimal weight: 0.2980 chunk 75 optimal weight: 2.9990 chunk 41 optimal weight: 0.0470 chunk 30 optimal weight: 0.7980 chunk 26 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 overall best weight: 0.5878 ------------------------------------------------------------------------------- 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 = 0.089734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.061472 restraints weight = 30801.900| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 4.20 r_work: 0.2707 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2720 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2720 r_free = 0.2720 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 = 0.2720 r_free = 0.2720 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: 0.2720 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 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 0.046 7170 Z= 0.113 Angle : 0.545 12.870 9840 Z= 0.283 Chirality : 0.040 0.130 1172 Planarity : 0.004 0.047 1171 Dihedral : 14.237 99.603 1287 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.03 % Allowed : 27.50 % 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: 2.11 (0.30), residues: 849 helix: 2.45 (0.25), residues: 444 sheet: 0.96 (0.50), residues: 114 loop : -0.04 (0.39), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 93 TYR 0.008 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 0.00265 / 0.11 ( 7170) covalent geometry : angle 0.54474 / 0.28 ( 9840) hydrogen bonds : bond 0.02983 / 2.16 ( 372) hydrogen bonds : angle 3.51570 / 2.62 ( 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 54 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 47 time to evaluate : 0.264 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 GLN cc_start: 0.8576 (tm-30) cc_final: 0.8344 (pp30) outliers start: 7 outliers final: 7 residues processed: 53 average time/residue: 0.6395 time to fit residues: 35.7263 Evaluate side-chains 52 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 0.284 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 55 optimal weight: 0.0470 chunk 82 optimal weight: 0.0000 chunk 3 optimal weight: 5.9990 chunk 22 optimal weight: 0.6980 chunk 0 optimal weight: 80.0000 chunk 15 optimal weight: 5.9990 chunk 74 optimal weight: 0.2980 chunk 24 optimal weight: 1.9990 chunk 85 optimal weight: 30.0000 chunk 19 optimal weight: 0.9990 overall best weight: 0.4084 ------------------------------------------------------------------------------- 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 = 0.3462 r_free = 0.3462 target = 0.090259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.061758 restraints weight = 36807.051| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 4.52 r_work: 0.2709 rms_B_bonded: 4.90 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: 0.8588 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 7170 Z= 0.105 Angle : 0.548 10.012 9840 Z= 0.285 Chirality : 0.040 0.133 1172 Planarity : 0.004 0.050 1171 Dihedral : 14.190 99.182 1287 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.32 % Allowed : 27.21 % 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: 2.17 (0.30), residues: 849 helix: 2.50 (0.25), residues: 444 sheet: 0.93 (0.50), residues: 116 loop : -0.02 (0.39), residues: 289 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 0.007 0.001 TRP A 935 HIS 0.003 0.001 HIS A 527 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 ( 7170) covalent geometry : angle 0.54839 / 0.28 ( 9840) hydrogen bonds : bond 0.02853 / 2.07 ( 372) hydrogen bonds : angle 3.48905 / 2.59 ( 1068) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2548.67 seconds wall clock time: 44 minutes 4.00 seconds (2644.00 seconds total)