Starting phenix.real_space_refine on Thu Aug 6 18:47:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gen_51295/08_2026/9gen_51295.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gen_51295/08_2026/9gen_51295.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9gen_51295/08_2026/9gen_51295.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gen_51295/08_2026/9gen_51295.map" model { file = "/net/cci-nas-00/data/ceres_data/9gen_51295/08_2026/9gen_51295.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gen_51295/08_2026/9gen_51295.cif" } resolution = 3.76 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 290 5.49 5 S 44 5.16 5 C 9525 2.51 5 N 3092 2.21 5 O 3639 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.02s 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: 16590 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 807 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "B" Number of atoms: 633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 633 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "C" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 834 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "D" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 735 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 802 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "G" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 825 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "H" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 735 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "I" Number of atoms: 2990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2990 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2955 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "L" Number of atoms: 4619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 577, 4619 Classifications: {'peptide': 577} Link IDs: {'PCIS': 3, 'PTRANS': 43, 'TRANS': 530} Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.94, per 1000 atoms: 0.24 Number of scatterers: 16590 At special positions: 0 Unit cell: (125.84, 116.16, 125.84, 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 44 16.00 P 290 15.00 O 3639 8.00 N 3092 7.00 C 9525 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS L 167 " - pdb=" SG CYS L 180 " distance=2.03 Simple disulfide: pdb=" SG CYS L 281 " - pdb=" SG CYS L 291 " distance=2.03 Simple disulfide: pdb=" SG CYS L 285 " - pdb=" SG CYS L 309 " distance=2.03 Simple disulfide: pdb=" SG CYS L 387 " - pdb=" SG CYS L 398 " distance=2.03 Simple disulfide: pdb=" SG CYS L 606 " - pdb=" SG CYS L 663 " distance=2.03 Simple disulfide: pdb=" SG CYS L 704 " - pdb=" SG CYS L 730 " distance=2.03 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 Links applied NAG-ASN " NAG L 801 " - " ASN L 483 " " NAG L 802 " - " ASN L 391 " Time building additional restraints: 1.23 Conformation dependent library (CDL) restraints added in 458.2 milliseconds 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2502 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 12 sheets defined 59.7% alpha, 2.6% beta 140 base pairs and 243 stacking pairs defined. Time for finding SS restraints: 1.81 Creating SS restraints... Processing helix chain 'A' and resid 45 through 55 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.878A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 24 through 29 removed outlier: 4.042A pdb=" N GLN B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.188A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 removed outlier: 3.523A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 removed outlier: 3.575A pdb=" N ARG C 20 " --> pdb=" O THR C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.309A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.652A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 35 through 46 removed outlier: 3.536A pdb=" N TYR D 39 " --> pdb=" O ALA D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 81 removed outlier: 3.588A pdb=" N ASN D 81 " --> pdb=" O LEU D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 101 through 121 removed outlier: 3.929A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 57 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.880A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 46 through 73 Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 101 through 121 removed outlier: 3.880A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) Processing helix chain 'L' and resid 226 through 234 removed outlier: 3.852A pdb=" N GLU L 233 " --> pdb=" O ALA L 229 " (cutoff:3.500A) Processing helix chain 'L' and resid 238 through 242 removed outlier: 3.629A pdb=" N GLN L 241 " --> pdb=" O PRO L 238 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU L 242 " --> pdb=" O THR L 239 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 238 through 242' Processing helix chain 'L' and resid 250 through 264 removed outlier: 3.703A pdb=" N ASP L 264 " --> pdb=" O ASP L 260 " (cutoff:3.500A) Processing helix chain 'L' and resid 346 through 353 removed outlier: 3.697A pdb=" N ASN L 352 " --> pdb=" O PRO L 348 " (cutoff:3.500A) Processing helix chain 'L' and resid 386 through 390 Processing helix chain 'L' and resid 403 through 408 removed outlier: 4.394A pdb=" N SER L 407 " --> pdb=" O THR L 404 " (cutoff:3.500A) Processing helix chain 'L' and resid 409 through 434 Processing helix chain 'L' and resid 438 through 462 Processing helix chain 'L' and resid 463 through 466 Processing helix chain 'L' and resid 468 through 476 Processing helix chain 'L' and resid 491 through 498 removed outlier: 3.678A pdb=" N THR L 495 " --> pdb=" O ALA L 491 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ASN L 496 " --> pdb=" O ASN L 492 " (cutoff:3.500A) Processing helix chain 'L' and resid 499 through 503 Processing helix chain 'L' and resid 528 through 530 No H-bonds generated for 'chain 'L' and resid 528 through 530' Processing helix chain 'L' and resid 534 through 540 removed outlier: 3.594A pdb=" N VAL L 538 " --> pdb=" O SER L 534 " (cutoff:3.500A) Processing helix chain 'L' and resid 543 through 552 Processing helix chain 'L' and resid 566 through 571 Processing helix chain 'L' and resid 582 through 595 Processing helix chain 'L' and resid 598 through 607 Processing helix chain 'L' and resid 613 through 622 Processing helix chain 'L' and resid 623 through 635 removed outlier: 3.730A pdb=" N GLN L 633 " --> pdb=" O LYS L 629 " (cutoff:3.500A) Processing helix chain 'L' and resid 636 through 640 Processing helix chain 'L' and resid 641 through 649 Processing helix chain 'L' and resid 658 through 675 Processing helix chain 'L' and resid 689 through 695 removed outlier: 4.133A pdb=" N ALA L 693 " --> pdb=" O GLN L 689 " (cutoff:3.500A) Processing helix chain 'L' and resid 698 through 707 Processing helix chain 'L' and resid 738 through 742 removed outlier: 3.576A pdb=" N ARG L 742 " --> pdb=" O ALA L 739 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.106A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 6.952A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.785A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA7, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.379A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'L' and resid 193 through 194 Processing sheet with id=AA9, first strand: chain 'L' and resid 218 through 219 Processing sheet with id=AB1, first strand: chain 'L' and resid 244 through 249 removed outlier: 4.225A pdb=" N ALA L 555 " --> pdb=" O ASP L 245 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 508 through 510 Processing sheet with id=AB3, first strand: chain 'L' and resid 711 through 713 553 hydrogen bonds defined for protein. 1614 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 357 hydrogen bonds 710 hydrogen bond angles 0 basepair planarities 140 basepair parallelities 243 stacking parallelities Total time for adding SS restraints: 4.02 Time building geometry restraints manager: 1.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4243 1.34 - 1.46: 4541 1.46 - 1.58: 8072 1.58 - 1.70: 578 1.70 - 1.82: 72 Bond restraints: 17506 Sorted by residual: bond pdb=" C3' DA I -1 " pdb=" C2' DA I -1 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.22e+01 bond pdb=" C3' DC I 1 " pdb=" C2' DC I 1 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.14e+01 bond pdb=" C3' DC I 53 " pdb=" C2' DC I 53 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.00e+01 bond pdb=" C3' DG I 62 " pdb=" C2' DG I 62 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.93e+00 bond pdb=" C3' DT I 22 " pdb=" C2' DT I 22 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.15e+00 ... (remaining 17501 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 23830 1.60 - 3.19: 1038 3.19 - 4.79: 44 4.79 - 6.39: 6 6.39 - 7.99: 5 Bond angle restraints: 24923 Sorted by residual: angle pdb=" N3 DT I -24 " pdb=" C4 DT I -24 " pdb=" O4 DT I -24 " ideal model delta sigma weight residual 119.90 122.62 -2.72 6.00e-01 2.78e+00 2.05e+01 angle pdb=" N3 DT I 13 " pdb=" C4 DT I 13 " pdb=" O4 DT I 13 " ideal model delta sigma weight residual 119.90 122.52 -2.62 6.00e-01 2.78e+00 1.91e+01 angle pdb=" N3 DT J -26 " pdb=" C4 DT J -26 " pdb=" O4 DT J -26 " ideal model delta sigma weight residual 119.90 122.52 -2.62 6.00e-01 2.78e+00 1.90e+01 angle pdb=" N3 DT I 66 " pdb=" C4 DT I 66 " pdb=" O4 DT I 66 " ideal model delta sigma weight residual 119.90 122.50 -2.60 6.00e-01 2.78e+00 1.88e+01 angle pdb=" N3 DT J 15 " pdb=" C4 DT J 15 " pdb=" O4 DT J 15 " ideal model delta sigma weight residual 119.90 122.48 -2.58 6.00e-01 2.78e+00 1.85e+01 ... (remaining 24918 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.69: 8276 34.69 - 69.38: 1579 69.38 - 104.08: 18 104.08 - 138.77: 2 138.77 - 173.46: 1 Dihedral angle restraints: 9876 sinusoidal: 6005 harmonic: 3871 Sorted by residual: dihedral pdb=" CA HIS H 79 " pdb=" C HIS H 79 " pdb=" N TYR H 80 " pdb=" CA TYR H 80 " ideal model delta harmonic sigma weight residual 180.00 -160.17 -19.83 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" C4' DG I 20 " pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " pdb=" P DG I 21 " ideal model delta sinusoidal sigma weight residual 220.00 46.54 173.46 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DC J 51 " pdb=" C3' DC J 51 " pdb=" O3' DC J 51 " pdb=" P DG J 52 " ideal model delta sinusoidal sigma weight residual 220.00 83.43 136.57 1 3.50e+01 8.16e-04 1.35e+01 ... (remaining 9873 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 2004 0.042 - 0.083: 612 0.083 - 0.125: 178 0.125 - 0.166: 8 0.166 - 0.208: 1 Chirality restraints: 2803 Sorted by residual: chirality pdb=" C1 NAG L 802 " pdb=" ND2 ASN L 391 " pdb=" C2 NAG L 802 " pdb=" O5 NAG L 802 " both_signs ideal model delta sigma weight residual False -2.40 -2.19 -0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA ASN L 280 " pdb=" N ASN L 280 " pdb=" C ASN L 280 " pdb=" CB ASN L 280 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.36e-01 chirality pdb=" C3' DG I 20 " pdb=" C4' DG I 20 " pdb=" O3' DG I 20 " pdb=" C2' DG I 20 " both_signs ideal model delta sigma weight residual False -2.73 -2.60 -0.13 2.00e-01 2.50e+01 4.30e-01 ... (remaining 2800 not shown) Planarity restraints: 2191 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL H 108 " -0.008 2.00e-02 2.50e+03 1.51e-02 2.28e+00 pdb=" C VAL H 108 " 0.026 2.00e-02 2.50e+03 pdb=" O VAL H 108 " -0.010 2.00e-02 2.50e+03 pdb=" N SER H 109 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU D 110 " -0.007 2.00e-02 2.50e+03 1.50e-02 2.24e+00 pdb=" C GLU D 110 " 0.026 2.00e-02 2.50e+03 pdb=" O GLU D 110 " -0.010 2.00e-02 2.50e+03 pdb=" N GLY D 111 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER H 109 " -0.007 2.00e-02 2.50e+03 1.48e-02 2.20e+00 pdb=" C SER H 109 " 0.026 2.00e-02 2.50e+03 pdb=" O SER H 109 " -0.010 2.00e-02 2.50e+03 pdb=" N GLU H 110 " -0.009 2.00e-02 2.50e+03 ... (remaining 2188 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 3131 2.78 - 3.31: 15046 3.31 - 3.84: 31872 3.84 - 4.37: 34900 4.37 - 4.90: 53173 Nonbonded interactions: 138122 Sorted by model distance: nonbonded pdb=" OG SER D 61 " pdb=" O GLY F 101 " model vdw 2.252 3.040 nonbonded pdb=" OE1 GLN L 689 " pdb=" OG SER L 740 " model vdw 2.252 3.040 nonbonded pdb=" O TYR G 39 " pdb=" OG SER H 75 " model vdw 2.262 3.040 nonbonded pdb=" OG SER L 528 " pdb=" OE1 GLU L 567 " model vdw 2.273 3.040 nonbonded pdb=" OH TYR L 343 " pdb=" ND1 HIS L 423 " model vdw 2.288 3.120 ... (remaining 138117 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 Found NCS groups: ncs_group { reference = (chain 'A' and resid 38 through 134) selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 24 through 101) selection = (chain 'F' and resid 24 through 101) } ncs_group { reference = (chain 'C' and resid 11 through 117) selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 17.490 Find NCS groups from input model: 0.150 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:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 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 : 0.005 0.040 17514 Z= 0.434 Angle : 0.675 7.986 24941 Z= 0.571 Chirality : 0.042 0.208 2803 Planarity : 0.004 0.033 2189 Dihedral : 26.167 173.459 7356 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.03 % Allowed : 26.90 % Favored : 71.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % 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: 1.84 (0.24), residues: 1315 helix: 2.15 (0.20), residues: 736 sheet: None (None), residues: 0 loop : 0.05 (0.27), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 515 TYR 0.018 0.001 TYR D 80 PHE 0.009 0.001 PHE L 207 TRP 0.009 0.001 TRP L 602 HIS 0.005 0.001 HIS H 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00485 / 0.43 (17506) covalent geometry : angle 0.67212 / 0.57 (24923) SS BOND : bond 0.00249 / 0.15 ( 6) SS BOND : angle 0.50925 / 0.28 ( 12) hydrogen bonds : bond 0.11277 / 7.79 ( 910) hydrogen bonds : angle 4.68043 / 3.28 ( 2324) link_NAG-ASN : bond 0.00574 / 0.38 ( 2) link_NAG-ASN : angle 3.84597 / 1.98 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 161 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 25 ASN cc_start: 0.8389 (t0) cc_final: 0.8179 (t0) REVERT: D 81 ASN cc_start: 0.9194 (m-40) cc_final: 0.8892 (m110) REVERT: D 83 ARG cc_start: 0.7734 (mmt90) cc_final: 0.7117 (mtm-85) REVERT: E 77 ASP cc_start: 0.8530 (m-30) cc_final: 0.8003 (t0) REVERT: F 77 LYS cc_start: 0.8807 (mttt) cc_final: 0.8422 (mmmm) REVERT: G 95 LYS cc_start: 0.8545 (tttt) cc_final: 0.8325 (tttm) REVERT: L 202 GLU cc_start: 0.7641 (tp30) cc_final: 0.7415 (tp30) REVERT: L 345 SER cc_start: 0.8785 (m) cc_final: 0.8442 (t) REVERT: L 409 MET cc_start: 0.7904 (mtp) cc_final: 0.7610 (mtm) REVERT: L 530 VAL cc_start: 0.8710 (OUTLIER) cc_final: 0.8477 (p) REVERT: L 631 MET cc_start: 0.8792 (mmt) cc_final: 0.8516 (mmt) REVERT: L 689 GLN cc_start: 0.8795 (tm-30) cc_final: 0.8420 (tm-30) outliers start: 23 outliers final: 20 residues processed: 179 average time/residue: 0.1521 time to fit residues: 39.5802 Evaluate side-chains 172 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 151 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 117 LYS Chi-restraints excluded: chain L residue 199 LEU Chi-restraints excluded: chain L residue 235 VAL Chi-restraints excluded: chain L residue 281 CYS Chi-restraints excluded: chain L residue 286 VAL Chi-restraints excluded: chain L residue 299 ASN Chi-restraints excluded: chain L residue 309 CYS Chi-restraints excluded: chain L residue 326 ILE Chi-restraints excluded: chain L residue 438 ASP Chi-restraints excluded: chain L residue 530 VAL Chi-restraints excluded: chain L residue 565 VAL Chi-restraints excluded: chain L residue 588 MET Chi-restraints excluded: chain L residue 596 LEU Chi-restraints excluded: chain L residue 717 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 98 optimal weight: 0.0170 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 9.9990 chunk 149 optimal weight: 0.0170 overall best weight: 0.5056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 113 HIS ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.181294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.138988 restraints weight = 21623.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.142700 restraints weight = 11938.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.145095 restraints weight = 8471.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.146479 restraints weight = 7038.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.147307 restraints weight = 6381.601| |-----------------------------------------------------------------------------| r_work (final): 0.3802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.0639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 17514 Z= 0.132 Angle : 0.559 8.128 24941 Z= 0.326 Chirality : 0.039 0.265 2803 Planarity : 0.004 0.033 2189 Dihedral : 28.446 171.437 4732 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.62 % Allowed : 24.16 % Favored : 72.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % 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 (0.24), residues: 1315 helix: 2.47 (0.19), residues: 741 sheet: None (None), residues: 0 loop : -0.07 (0.27), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 656 TYR 0.029 0.001 TYR D 80 PHE 0.009 0.001 PHE L 252 TRP 0.009 0.001 TRP L 602 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.13 (17506) covalent geometry : angle 0.55530 / 0.33 (24923) SS BOND : bond 0.00306 / 0.16 ( 6) SS BOND : angle 0.75417 / 0.33 ( 12) hydrogen bonds : bond 0.04767 / 3.20 ( 910) hydrogen bonds : angle 3.54309 / 2.53 ( 2324) link_NAG-ASN : bond 0.00602 / 0.41 ( 2) link_NAG-ASN : angle 3.96583 / 2.03 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 155 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.7799 (pt0) cc_final: 0.7303 (pm20) REVERT: B 25 ASN cc_start: 0.8432 (t0) cc_final: 0.8215 (t0) REVERT: B 92 ARG cc_start: 0.8781 (ttp80) cc_final: 0.8422 (ttp80) REVERT: D 79 HIS cc_start: 0.8173 (t-90) cc_final: 0.7746 (t-170) REVERT: D 83 ARG cc_start: 0.7725 (mmt90) cc_final: 0.7344 (mtp-110) REVERT: E 77 ASP cc_start: 0.8406 (m-30) cc_final: 0.7952 (t0) REVERT: G 95 LYS cc_start: 0.8607 (tttt) cc_final: 0.8382 (tttm) REVERT: L 202 GLU cc_start: 0.7823 (tp30) cc_final: 0.7553 (tp30) REVERT: L 345 SER cc_start: 0.8808 (m) cc_final: 0.8427 (t) REVERT: L 409 MET cc_start: 0.7722 (mtp) cc_final: 0.7437 (mtm) REVERT: L 530 VAL cc_start: 0.8589 (OUTLIER) cc_final: 0.8279 (p) REVERT: L 631 MET cc_start: 0.8770 (mmt) cc_final: 0.8502 (mmt) REVERT: L 696 GLN cc_start: 0.8384 (OUTLIER) cc_final: 0.7922 (tp40) REVERT: L 726 ASP cc_start: 0.7991 (p0) cc_final: 0.7415 (p0) outliers start: 41 outliers final: 21 residues processed: 187 average time/residue: 0.1374 time to fit residues: 37.8942 Evaluate side-chains 170 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 147 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain L residue 175 THR Chi-restraints excluded: chain L residue 177 THR Chi-restraints excluded: chain L residue 235 VAL Chi-restraints excluded: chain L residue 240 ASP Chi-restraints excluded: chain L residue 325 THR Chi-restraints excluded: chain L residue 389 LEU Chi-restraints excluded: chain L residue 404 THR Chi-restraints excluded: chain L residue 429 GLU Chi-restraints excluded: chain L residue 465 LEU Chi-restraints excluded: chain L residue 486 VAL Chi-restraints excluded: chain L residue 530 VAL Chi-restraints excluded: chain L residue 696 GLN Chi-restraints excluded: chain L residue 717 ILE Chi-restraints excluded: chain L residue 722 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 129 optimal weight: 6.9990 chunk 122 optimal weight: 3.9990 chunk 81 optimal weight: 20.0000 chunk 114 optimal weight: 7.9990 chunk 138 optimal weight: 5.9990 chunk 147 optimal weight: 5.9990 chunk 115 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 106 optimal weight: 4.9990 chunk 150 optimal weight: 9.9990 chunk 27 optimal weight: 0.8980 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 55 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN L 299 ASN ** L 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 372 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.174546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.131135 restraints weight = 21700.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.134228 restraints weight = 12995.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.136252 restraints weight = 9710.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.137433 restraints weight = 8295.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.137441 restraints weight = 7628.390| |-----------------------------------------------------------------------------| r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.1433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.105 17514 Z= 0.337 Angle : 0.805 10.329 24941 Z= 0.427 Chirality : 0.049 0.287 2803 Planarity : 0.006 0.049 2189 Dihedral : 28.880 170.853 4706 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 6.79 % Allowed : 23.72 % Favored : 69.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % 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: 1.43 (0.24), residues: 1315 helix: 1.90 (0.19), residues: 741 sheet: None (None), residues: 0 loop : -0.29 (0.27), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 603 TYR 0.038 0.003 TYR D 80 PHE 0.018 0.002 PHE L 252 TRP 0.006 0.001 TRP L 643 HIS 0.008 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00774 / 0.34 (17506) covalent geometry : angle 0.80232 / 0.43 (24923) SS BOND : bond 0.00420 / 0.26 ( 6) SS BOND : angle 0.73119 / 0.32 ( 12) hydrogen bonds : bond 0.06092 / 4.13 ( 910) hydrogen bonds : angle 3.93014 / 2.86 ( 2324) link_NAG-ASN : bond 0.00284 / 0.19 ( 2) link_NAG-ASN : angle 4.17547 / 2.12 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 165 time to evaluate : 0.319 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.7952 (pt0) cc_final: 0.7649 (pm20) REVERT: B 25 ASN cc_start: 0.8535 (t0) cc_final: 0.8329 (t0) REVERT: E 71 VAL cc_start: 0.8661 (OUTLIER) cc_final: 0.8397 (t) REVERT: F 43 VAL cc_start: 0.9442 (t) cc_final: 0.9235 (p) REVERT: G 38 ASN cc_start: 0.8465 (m-40) cc_final: 0.8179 (m110) REVERT: G 104 GLN cc_start: 0.8856 (mt0) cc_final: 0.8623 (mt0) REVERT: H 32 GLU cc_start: 0.8075 (mt-10) cc_final: 0.7875 (mt-10) REVERT: L 202 GLU cc_start: 0.7772 (tp30) cc_final: 0.7560 (tp30) REVERT: L 409 MET cc_start: 0.7936 (mtp) cc_final: 0.7607 (mtm) REVERT: L 437 TRP cc_start: 0.7853 (OUTLIER) cc_final: 0.7376 (m-10) REVERT: L 530 VAL cc_start: 0.8770 (OUTLIER) cc_final: 0.8520 (p) REVERT: L 631 MET cc_start: 0.8795 (mmt) cc_final: 0.8590 (mmt) REVERT: L 726 ASP cc_start: 0.8059 (p0) cc_final: 0.7511 (p0) outliers start: 77 outliers final: 55 residues processed: 226 average time/residue: 0.1355 time to fit residues: 45.4645 Evaluate side-chains 220 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 162 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain L residue 177 THR Chi-restraints excluded: chain L residue 199 LEU Chi-restraints excluded: chain L residue 235 VAL Chi-restraints excluded: chain L residue 240 ASP Chi-restraints excluded: chain L residue 281 CYS Chi-restraints excluded: chain L residue 286 VAL Chi-restraints excluded: chain L residue 299 ASN Chi-restraints excluded: chain L residue 303 ILE Chi-restraints excluded: chain L residue 308 ASP Chi-restraints excluded: chain L residue 325 THR Chi-restraints excluded: chain L residue 326 ILE Chi-restraints excluded: chain L residue 357 SER Chi-restraints excluded: chain L residue 389 LEU Chi-restraints excluded: chain L residue 404 THR Chi-restraints excluded: chain L residue 428 THR Chi-restraints excluded: chain L residue 430 LEU Chi-restraints excluded: chain L residue 437 TRP Chi-restraints excluded: chain L residue 458 THR Chi-restraints excluded: chain L residue 463 LEU Chi-restraints excluded: chain L residue 493 VAL Chi-restraints excluded: chain L residue 495 THR Chi-restraints excluded: chain L residue 530 VAL Chi-restraints excluded: chain L residue 565 VAL Chi-restraints excluded: chain L residue 588 MET Chi-restraints excluded: chain L residue 596 LEU Chi-restraints excluded: chain L residue 613 THR Chi-restraints excluded: chain L residue 619 THR Chi-restraints excluded: chain L residue 711 THR Chi-restraints excluded: chain L residue 717 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 16 optimal weight: 10.0000 chunk 112 optimal weight: 5.9990 chunk 49 optimal weight: 0.5980 chunk 74 optimal weight: 20.0000 chunk 102 optimal weight: 3.9990 chunk 103 optimal weight: 8.9990 chunk 131 optimal weight: 0.8980 chunk 114 optimal weight: 0.6980 chunk 75 optimal weight: 10.0000 chunk 73 optimal weight: 10.0000 chunk 141 optimal weight: 0.8980 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.182270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.138532 restraints weight = 22979.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.142225 restraints weight = 12783.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.144666 restraints weight = 9101.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.145940 restraints weight = 7567.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.146843 restraints weight = 6899.743| |-----------------------------------------------------------------------------| r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.1425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17514 Z= 0.160 Angle : 0.599 8.334 24941 Z= 0.338 Chirality : 0.042 0.270 2803 Planarity : 0.004 0.045 2189 Dihedral : 28.687 170.553 4704 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 4.06 % Allowed : 26.90 % Favored : 69.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % 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: 1.85 (0.24), residues: 1315 helix: 2.29 (0.19), residues: 742 sheet: None (None), residues: 0 loop : -0.19 (0.27), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 76 TYR 0.050 0.002 TYR D 80 PHE 0.013 0.001 PHE E 67 TRP 0.011 0.001 TRP L 602 HIS 0.004 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.16 (17506) covalent geometry : angle 0.59614 / 0.34 (24923) SS BOND : bond 0.00295 / 0.17 ( 6) SS BOND : angle 0.57763 / 0.26 ( 12) hydrogen bonds : bond 0.04722 / 3.20 ( 910) hydrogen bonds : angle 3.48614 / 2.51 ( 2324) link_NAG-ASN : bond 0.00451 / 0.30 ( 2) link_NAG-ASN : angle 4.12857 / 2.12 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 158 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.7938 (pt0) cc_final: 0.7602 (pm20) REVERT: B 92 ARG cc_start: 0.8785 (ttp80) cc_final: 0.8453 (ttp80) REVERT: D 79 HIS cc_start: 0.8264 (t-90) cc_final: 0.7849 (t-170) REVERT: E 71 VAL cc_start: 0.8570 (OUTLIER) cc_final: 0.8320 (t) REVERT: G 38 ASN cc_start: 0.8336 (m-40) cc_final: 0.8081 (m110) REVERT: G 104 GLN cc_start: 0.8818 (mt0) cc_final: 0.8582 (mt0) REVERT: H 32 GLU cc_start: 0.8075 (mt-10) cc_final: 0.7847 (mt-10) REVERT: L 202 GLU cc_start: 0.7763 (tp30) cc_final: 0.7551 (tp30) REVERT: L 345 SER cc_start: 0.8779 (m) cc_final: 0.8355 (t) REVERT: L 409 MET cc_start: 0.7822 (mtp) cc_final: 0.7511 (mtm) REVERT: L 422 GLU cc_start: 0.8434 (tm-30) cc_final: 0.8103 (tm-30) REVERT: L 530 VAL cc_start: 0.8683 (OUTLIER) cc_final: 0.8416 (p) REVERT: L 631 MET cc_start: 0.8895 (mmp) cc_final: 0.8694 (mmt) REVERT: L 696 GLN cc_start: 0.8325 (OUTLIER) cc_final: 0.7948 (tp40) REVERT: L 726 ASP cc_start: 0.8061 (p0) cc_final: 0.7522 (p0) outliers start: 46 outliers final: 29 residues processed: 195 average time/residue: 0.1334 time to fit residues: 38.4942 Evaluate side-chains 183 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 151 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain L residue 177 THR Chi-restraints excluded: chain L residue 191 SER Chi-restraints excluded: chain L residue 235 VAL Chi-restraints excluded: chain L residue 240 ASP Chi-restraints excluded: chain L residue 281 CYS Chi-restraints excluded: chain L residue 286 VAL Chi-restraints excluded: chain L residue 308 ASP Chi-restraints excluded: chain L residue 325 THR Chi-restraints excluded: chain L residue 326 ILE Chi-restraints excluded: chain L residue 530 VAL Chi-restraints excluded: chain L residue 596 LEU Chi-restraints excluded: chain L residue 619 THR Chi-restraints excluded: chain L residue 654 LYS Chi-restraints excluded: chain L residue 696 GLN Chi-restraints excluded: chain L residue 711 THR Chi-restraints excluded: chain L residue 717 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 34 optimal weight: 1.9990 chunk 108 optimal weight: 8.9990 chunk 7 optimal weight: 0.7980 chunk 6 optimal weight: 0.5980 chunk 148 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 43 optimal weight: 0.6980 chunk 144 optimal weight: 1.9990 chunk 35 optimal weight: 6.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.183400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.139928 restraints weight = 22812.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.143597 restraints weight = 12714.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.146014 restraints weight = 9078.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.147434 restraints weight = 7567.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.148112 restraints weight = 6871.674| |-----------------------------------------------------------------------------| r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 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 : 0.003 0.051 17514 Z= 0.150 Angle : 0.592 8.173 24941 Z= 0.332 Chirality : 0.041 0.275 2803 Planarity : 0.004 0.043 2189 Dihedral : 28.679 170.309 4704 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 4.32 % Allowed : 26.63 % Favored : 69.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % 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 (0.24), residues: 1315 helix: 2.39 (0.19), residues: 745 sheet: None (None), residues: 0 loop : -0.17 (0.27), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 92 TYR 0.056 0.002 TYR D 80 PHE 0.013 0.001 PHE E 67 TRP 0.009 0.001 TRP L 602 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.15 (17506) covalent geometry : angle 0.58852 / 0.33 (24923) SS BOND : bond 0.00291 / 0.17 ( 6) SS BOND : angle 0.55149 / 0.26 ( 12) hydrogen bonds : bond 0.04540 / 3.09 ( 910) hydrogen bonds : angle 3.40138 / 2.45 ( 2324) link_NAG-ASN : bond 0.00497 / 0.33 ( 2) link_NAG-ASN : angle 4.00509 / 2.06 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 160 time to evaluate : 0.536 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.7855 (pt0) cc_final: 0.7581 (pm20) REVERT: B 25 ASN cc_start: 0.8522 (t0) cc_final: 0.8096 (t0) REVERT: D 79 HIS cc_start: 0.8223 (t-90) cc_final: 0.7760 (t-170) REVERT: D 90 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7353 (mp0) REVERT: E 71 VAL cc_start: 0.8545 (OUTLIER) cc_final: 0.8288 (t) REVERT: G 38 ASN cc_start: 0.8334 (m-40) cc_final: 0.8013 (m110) REVERT: G 104 GLN cc_start: 0.8793 (mt0) cc_final: 0.8551 (mt0) REVERT: L 202 GLU cc_start: 0.7722 (tp30) cc_final: 0.7433 (tp30) REVERT: L 345 SER cc_start: 0.8750 (m) cc_final: 0.8346 (t) REVERT: L 409 MET cc_start: 0.7794 (mtp) cc_final: 0.7570 (mtm) REVERT: L 422 GLU cc_start: 0.8416 (tm-30) cc_final: 0.8078 (tm-30) REVERT: L 437 TRP cc_start: 0.7853 (OUTLIER) cc_final: 0.7440 (m-10) REVERT: L 530 VAL cc_start: 0.8689 (OUTLIER) cc_final: 0.8471 (p) REVERT: L 726 ASP cc_start: 0.7984 (p0) cc_final: 0.7461 (p0) outliers start: 49 outliers final: 37 residues processed: 201 average time/residue: 0.1208 time to fit residues: 36.7692 Evaluate side-chains 192 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 151 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain L residue 177 THR Chi-restraints excluded: chain L residue 191 SER Chi-restraints excluded: chain L residue 199 LEU Chi-restraints excluded: chain L residue 235 VAL Chi-restraints excluded: chain L residue 240 ASP Chi-restraints excluded: chain L residue 261 HIS Chi-restraints excluded: chain L residue 281 CYS Chi-restraints excluded: chain L residue 286 VAL Chi-restraints excluded: chain L residue 303 ILE Chi-restraints excluded: chain L residue 325 THR Chi-restraints excluded: chain L residue 326 ILE Chi-restraints excluded: chain L residue 342 VAL Chi-restraints excluded: chain L residue 389 LEU Chi-restraints excluded: chain L residue 437 TRP Chi-restraints excluded: chain L residue 463 LEU Chi-restraints excluded: chain L residue 530 VAL Chi-restraints excluded: chain L residue 596 LEU Chi-restraints excluded: chain L residue 619 THR Chi-restraints excluded: chain L residue 654 LYS Chi-restraints excluded: chain L residue 711 THR Chi-restraints excluded: chain L residue 717 ILE Chi-restraints excluded: chain L residue 719 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 116 optimal weight: 3.9990 chunk 148 optimal weight: 2.9990 chunk 72 optimal weight: 20.0000 chunk 152 optimal weight: 6.9990 chunk 111 optimal weight: 2.9990 chunk 19 optimal weight: 0.0050 chunk 56 optimal weight: 0.9990 chunk 142 optimal weight: 8.9990 chunk 15 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 overall best weight: 1.1800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.180756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.138165 restraints weight = 21403.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.141583 restraints weight = 12446.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.143775 restraints weight = 9140.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.145025 restraints weight = 7754.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.145630 restraints weight = 7109.803| |-----------------------------------------------------------------------------| r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 17514 Z= 0.148 Angle : 0.584 8.099 24941 Z= 0.328 Chirality : 0.041 0.273 2803 Planarity : 0.004 0.042 2189 Dihedral : 28.674 170.257 4704 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 4.23 % Allowed : 26.90 % Favored : 68.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % 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: 1.97 (0.24), residues: 1315 helix: 2.40 (0.19), residues: 744 sheet: None (None), residues: 0 loop : -0.16 (0.27), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 92 TYR 0.028 0.002 TYR D 37 PHE 0.012 0.001 PHE E 67 TRP 0.009 0.001 TRP L 602 HIS 0.004 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.15 (17506) covalent geometry : angle 0.58072 / 0.33 (24923) SS BOND : bond 0.00286 / 0.16 ( 6) SS BOND : angle 0.55775 / 0.27 ( 12) hydrogen bonds : bond 0.04445 / 3.02 ( 910) hydrogen bonds : angle 3.36003 / 2.41 ( 2324) link_NAG-ASN : bond 0.00502 / 0.34 ( 2) link_NAG-ASN : angle 3.96894 / 2.05 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 154 time to evaluate : 0.514 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.7870 (pt0) cc_final: 0.7529 (pm20) REVERT: B 25 ASN cc_start: 0.8460 (t0) cc_final: 0.8018 (t0) REVERT: D 56 MET cc_start: 0.8455 (tpp) cc_final: 0.8171 (tpp) REVERT: D 79 HIS cc_start: 0.8265 (t-90) cc_final: 0.7968 (t-170) REVERT: E 71 VAL cc_start: 0.8557 (OUTLIER) cc_final: 0.8269 (t) REVERT: E 73 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.8296 (tt0) REVERT: G 38 ASN cc_start: 0.8269 (m-40) cc_final: 0.7966 (m110) REVERT: G 104 GLN cc_start: 0.8744 (mt0) cc_final: 0.8527 (mt0) REVERT: L 202 GLU cc_start: 0.7662 (tp30) cc_final: 0.7427 (tp30) REVERT: L 345 SER cc_start: 0.8762 (m) cc_final: 0.8355 (t) REVERT: L 409 MET cc_start: 0.7778 (mtp) cc_final: 0.7572 (mtm) REVERT: L 422 GLU cc_start: 0.8377 (tm-30) cc_final: 0.8024 (tm-30) REVERT: L 437 TRP cc_start: 0.7890 (OUTLIER) cc_final: 0.7386 (m-10) REVERT: L 530 VAL cc_start: 0.8719 (OUTLIER) cc_final: 0.8504 (p) REVERT: L 726 ASP cc_start: 0.7941 (p0) cc_final: 0.7387 (p0) outliers start: 48 outliers final: 35 residues processed: 193 average time/residue: 0.1371 time to fit residues: 39.8143 Evaluate side-chains 186 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 147 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain L residue 177 THR Chi-restraints excluded: chain L residue 191 SER Chi-restraints excluded: chain L residue 199 LEU Chi-restraints excluded: chain L residue 235 VAL Chi-restraints excluded: chain L residue 261 HIS Chi-restraints excluded: chain L residue 281 CYS Chi-restraints excluded: chain L residue 286 VAL Chi-restraints excluded: chain L residue 309 CYS Chi-restraints excluded: chain L residue 325 THR Chi-restraints excluded: chain L residue 326 ILE Chi-restraints excluded: chain L residue 342 VAL Chi-restraints excluded: chain L residue 429 GLU Chi-restraints excluded: chain L residue 430 LEU Chi-restraints excluded: chain L residue 437 TRP Chi-restraints excluded: chain L residue 530 VAL Chi-restraints excluded: chain L residue 588 MET Chi-restraints excluded: chain L residue 596 LEU Chi-restraints excluded: chain L residue 619 THR Chi-restraints excluded: chain L residue 654 LYS Chi-restraints excluded: chain L residue 711 THR Chi-restraints excluded: chain L residue 717 ILE Chi-restraints excluded: chain L residue 719 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 82 optimal weight: 20.0000 chunk 50 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 134 optimal weight: 5.9990 chunk 99 optimal weight: 0.2980 chunk 90 optimal weight: 10.0000 chunk 74 optimal weight: 20.0000 chunk 26 optimal weight: 0.3980 chunk 86 optimal weight: 20.0000 chunk 125 optimal weight: 8.9990 chunk 100 optimal weight: 8.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 ASN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 299 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.173036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.130360 restraints weight = 21551.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.133913 restraints weight = 12180.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.136195 restraints weight = 8738.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.137395 restraints weight = 7321.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.138111 restraints weight = 6699.302| |-----------------------------------------------------------------------------| r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 17514 Z= 0.175 Angle : 0.609 7.974 24941 Z= 0.338 Chirality : 0.042 0.275 2803 Planarity : 0.004 0.041 2189 Dihedral : 28.736 170.219 4704 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 4.59 % Allowed : 26.72 % Favored : 68.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % 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: 1.93 (0.24), residues: 1315 helix: 2.38 (0.19), residues: 742 sheet: None (None), residues: 0 loop : -0.19 (0.27), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 92 TYR 0.038 0.002 TYR D 37 PHE 0.011 0.001 PHE E 67 TRP 0.007 0.001 TRP L 602 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.17 (17506) covalent geometry : angle 0.60621 / 0.34 (24923) SS BOND : bond 0.00297 / 0.17 ( 6) SS BOND : angle 0.54453 / 0.25 ( 12) hydrogen bonds : bond 0.04560 / 3.11 ( 910) hydrogen bonds : angle 3.39669 / 2.43 ( 2324) link_NAG-ASN : bond 0.00459 / 0.31 ( 2) link_NAG-ASN : angle 3.91836 / 2.01 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 152 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.7883 (pt0) cc_final: 0.7601 (pm20) REVERT: B 25 ASN cc_start: 0.8519 (t0) cc_final: 0.8060 (t0) REVERT: D 79 HIS cc_start: 0.8389 (t-90) cc_final: 0.8180 (t-170) REVERT: E 71 VAL cc_start: 0.8494 (OUTLIER) cc_final: 0.8214 (t) REVERT: E 73 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.8375 (tt0) REVERT: G 104 GLN cc_start: 0.8801 (mt0) cc_final: 0.8574 (mt0) REVERT: H 118 TYR cc_start: 0.8767 (t80) cc_final: 0.8452 (t80) REVERT: L 202 GLU cc_start: 0.7776 (tp30) cc_final: 0.7524 (tp30) REVERT: L 345 SER cc_start: 0.8750 (m) cc_final: 0.8352 (t) REVERT: L 409 MET cc_start: 0.7773 (mtp) cc_final: 0.7554 (mtm) REVERT: L 422 GLU cc_start: 0.8368 (tm-30) cc_final: 0.7976 (tm-30) REVERT: L 437 TRP cc_start: 0.7900 (OUTLIER) cc_final: 0.7394 (m-10) REVERT: L 530 VAL cc_start: 0.8644 (OUTLIER) cc_final: 0.8402 (p) outliers start: 52 outliers final: 40 residues processed: 193 average time/residue: 0.1404 time to fit residues: 40.4370 Evaluate side-chains 191 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 147 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain L residue 177 THR Chi-restraints excluded: chain L residue 191 SER Chi-restraints excluded: chain L residue 199 LEU Chi-restraints excluded: chain L residue 235 VAL Chi-restraints excluded: chain L residue 240 ASP Chi-restraints excluded: chain L residue 281 CYS Chi-restraints excluded: chain L residue 286 VAL Chi-restraints excluded: chain L residue 299 ASN Chi-restraints excluded: chain L residue 303 ILE Chi-restraints excluded: chain L residue 308 ASP Chi-restraints excluded: chain L residue 309 CYS Chi-restraints excluded: chain L residue 325 THR Chi-restraints excluded: chain L residue 326 ILE Chi-restraints excluded: chain L residue 357 SER Chi-restraints excluded: chain L residue 429 GLU Chi-restraints excluded: chain L residue 430 LEU Chi-restraints excluded: chain L residue 437 TRP Chi-restraints excluded: chain L residue 530 VAL Chi-restraints excluded: chain L residue 565 VAL Chi-restraints excluded: chain L residue 588 MET Chi-restraints excluded: chain L residue 596 LEU Chi-restraints excluded: chain L residue 619 THR Chi-restraints excluded: chain L residue 654 LYS Chi-restraints excluded: chain L residue 711 THR Chi-restraints excluded: chain L residue 717 ILE Chi-restraints excluded: chain L residue 719 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 13 optimal weight: 0.7980 chunk 120 optimal weight: 10.0000 chunk 9 optimal weight: 3.9990 chunk 87 optimal weight: 10.0000 chunk 25 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 108 optimal weight: 10.0000 chunk 16 optimal weight: 9.9990 chunk 65 optimal weight: 0.5980 chunk 59 optimal weight: 0.9990 chunk 60 optimal weight: 4.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.174217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.131800 restraints weight = 21588.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.135315 restraints weight = 12162.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.137587 restraints weight = 8752.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.138836 restraints weight = 7338.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.139655 restraints weight = 6696.329| |-----------------------------------------------------------------------------| r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17514 Z= 0.151 Angle : 0.590 8.101 24941 Z= 0.330 Chirality : 0.041 0.273 2803 Planarity : 0.004 0.040 2189 Dihedral : 28.714 170.225 4704 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 4.14 % Allowed : 26.98 % Favored : 68.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % 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: 2.00 (0.24), residues: 1315 helix: 2.47 (0.19), residues: 739 sheet: None (None), residues: 0 loop : -0.19 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 83 TYR 0.035 0.002 TYR D 37 PHE 0.012 0.001 PHE E 67 TRP 0.008 0.001 TRP L 602 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.15 (17506) covalent geometry : angle 0.58701 / 0.33 (24923) SS BOND : bond 0.00287 / 0.16 ( 6) SS BOND : angle 0.55203 / 0.26 ( 12) hydrogen bonds : bond 0.04434 / 3.02 ( 910) hydrogen bonds : angle 3.32945 / 2.38 ( 2324) link_NAG-ASN : bond 0.00516 / 0.35 ( 2) link_NAG-ASN : angle 3.97491 / 2.05 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 149 time to evaluate : 0.499 Fit side-chains REVERT: A 59 GLU cc_start: 0.8018 (pt0) cc_final: 0.7604 (pm20) REVERT: B 25 ASN cc_start: 0.8589 (t0) cc_final: 0.8090 (t0) REVERT: E 71 VAL cc_start: 0.8389 (OUTLIER) cc_final: 0.8118 (t) REVERT: E 73 GLU cc_start: 0.8615 (OUTLIER) cc_final: 0.8295 (tt0) REVERT: G 104 GLN cc_start: 0.8878 (mt0) cc_final: 0.8610 (mt0) REVERT: H 118 TYR cc_start: 0.8670 (t80) cc_final: 0.8451 (t80) REVERT: L 202 GLU cc_start: 0.7893 (tp30) cc_final: 0.7608 (tp30) REVERT: L 345 SER cc_start: 0.8703 (m) cc_final: 0.8294 (t) REVERT: L 409 MET cc_start: 0.7709 (mtp) cc_final: 0.7490 (mtm) REVERT: L 422 GLU cc_start: 0.8287 (tm-30) cc_final: 0.7901 (tm-30) REVERT: L 437 TRP cc_start: 0.7892 (OUTLIER) cc_final: 0.7456 (m-10) REVERT: L 530 VAL cc_start: 0.8589 (OUTLIER) cc_final: 0.8388 (p) REVERT: L 726 ASP cc_start: 0.8262 (p0) cc_final: 0.8005 (p0) outliers start: 47 outliers final: 40 residues processed: 185 average time/residue: 0.1388 time to fit residues: 38.5229 Evaluate side-chains 189 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 145 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain L residue 177 THR Chi-restraints excluded: chain L residue 191 SER Chi-restraints excluded: chain L residue 199 LEU Chi-restraints excluded: chain L residue 235 VAL Chi-restraints excluded: chain L residue 286 VAL Chi-restraints excluded: chain L residue 303 ILE Chi-restraints excluded: chain L residue 308 ASP Chi-restraints excluded: chain L residue 309 CYS Chi-restraints excluded: chain L residue 325 THR Chi-restraints excluded: chain L residue 326 ILE Chi-restraints excluded: chain L residue 357 SER Chi-restraints excluded: chain L residue 404 THR Chi-restraints excluded: chain L residue 429 GLU Chi-restraints excluded: chain L residue 430 LEU Chi-restraints excluded: chain L residue 437 TRP Chi-restraints excluded: chain L residue 530 VAL Chi-restraints excluded: chain L residue 565 VAL Chi-restraints excluded: chain L residue 588 MET Chi-restraints excluded: chain L residue 596 LEU Chi-restraints excluded: chain L residue 619 THR Chi-restraints excluded: chain L residue 654 LYS Chi-restraints excluded: chain L residue 711 THR Chi-restraints excluded: chain L residue 717 ILE Chi-restraints excluded: chain L residue 722 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 44 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 49 optimal weight: 0.0870 chunk 110 optimal weight: 0.3980 chunk 103 optimal weight: 0.0270 chunk 139 optimal weight: 10.0000 chunk 101 optimal weight: 6.9990 chunk 80 optimal weight: 20.0000 chunk 53 optimal weight: 0.0870 chunk 147 optimal weight: 3.9990 overall best weight: 0.3194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 79 HIS ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.173895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.134812 restraints weight = 21453.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.138144 restraints weight = 12261.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.140325 restraints weight = 8922.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.141568 restraints weight = 7525.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.142182 restraints weight = 6883.128| |-----------------------------------------------------------------------------| r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 17514 Z= 0.123 Angle : 0.561 11.308 24941 Z= 0.319 Chirality : 0.039 0.272 2803 Planarity : 0.004 0.037 2189 Dihedral : 28.622 170.070 4704 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.65 % Allowed : 28.31 % Favored : 69.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % 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 (0.24), residues: 1315 helix: 2.63 (0.19), residues: 733 sheet: -1.25 (1.59), residues: 12 loop : -0.22 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 83 TYR 0.030 0.001 TYR D 37 PHE 0.013 0.001 PHE E 67 TRP 0.011 0.001 TRP L 602 HIS 0.004 0.001 HIS D 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.12 (17506) covalent geometry : angle 0.55731 / 0.32 (24923) SS BOND : bond 0.00292 / 0.16 ( 6) SS BOND : angle 0.56169 / 0.29 ( 12) hydrogen bonds : bond 0.04198 / 2.86 ( 910) hydrogen bonds : angle 3.20477 / 2.28 ( 2324) link_NAG-ASN : bond 0.00577 / 0.39 ( 2) link_NAG-ASN : angle 3.89569 / 2.03 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 151 time to evaluate : 0.503 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.7881 (pt0) cc_final: 0.7412 (pm20) REVERT: B 25 ASN cc_start: 0.8520 (t0) cc_final: 0.8064 (t0) REVERT: D 56 MET cc_start: 0.8467 (tpp) cc_final: 0.8082 (tpp) REVERT: D 79 HIS cc_start: 0.8256 (OUTLIER) cc_final: 0.7961 (t-90) REVERT: E 71 VAL cc_start: 0.8412 (OUTLIER) cc_final: 0.8145 (t) REVERT: E 73 GLU cc_start: 0.8607 (OUTLIER) cc_final: 0.8280 (tt0) REVERT: F 77 LYS cc_start: 0.9076 (mttm) cc_final: 0.8830 (tppp) REVERT: F 92 ARG cc_start: 0.8456 (ttp80) cc_final: 0.7953 (tmm160) REVERT: L 202 GLU cc_start: 0.7726 (tp30) cc_final: 0.7477 (tp30) REVERT: L 345 SER cc_start: 0.8670 (m) cc_final: 0.8277 (t) REVERT: L 422 GLU cc_start: 0.8279 (tm-30) cc_final: 0.7782 (tm-30) REVERT: L 437 TRP cc_start: 0.7840 (OUTLIER) cc_final: 0.7397 (m-10) REVERT: L 631 MET cc_start: 0.8305 (mmp) cc_final: 0.7919 (mmt) REVERT: L 726 ASP cc_start: 0.8099 (p0) cc_final: 0.7816 (p0) outliers start: 30 outliers final: 23 residues processed: 175 average time/residue: 0.1368 time to fit residues: 36.4395 Evaluate side-chains 171 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 144 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 79 HIS Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain L residue 191 SER Chi-restraints excluded: chain L residue 235 VAL Chi-restraints excluded: chain L residue 281 CYS Chi-restraints excluded: chain L residue 286 VAL Chi-restraints excluded: chain L residue 309 CYS Chi-restraints excluded: chain L residue 326 ILE Chi-restraints excluded: chain L residue 357 SER Chi-restraints excluded: chain L residue 429 GLU Chi-restraints excluded: chain L residue 437 TRP Chi-restraints excluded: chain L residue 486 VAL Chi-restraints excluded: chain L residue 654 LYS Chi-restraints excluded: chain L residue 717 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 86 optimal weight: 20.0000 chunk 54 optimal weight: 0.0270 chunk 121 optimal weight: 0.7980 chunk 40 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 111 optimal weight: 7.9990 chunk 26 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 132 optimal weight: 0.0870 chunk 44 optimal weight: 0.1980 chunk 138 optimal weight: 1.9990 overall best weight: 0.3616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 79 HIS L 257 GLN L 517 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.178154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.136299 restraints weight = 21563.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.139912 restraints weight = 12001.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.142204 restraints weight = 8612.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.143516 restraints weight = 7200.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.144341 restraints weight = 6554.555| |-----------------------------------------------------------------------------| r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 17514 Z= 0.125 Angle : 0.568 11.440 24941 Z= 0.322 Chirality : 0.040 0.294 2803 Planarity : 0.004 0.037 2189 Dihedral : 28.627 169.957 4703 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.73 % Allowed : 28.66 % Favored : 68.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % 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 (0.24), residues: 1315 helix: 2.65 (0.19), residues: 732 sheet: -1.19 (1.59), residues: 12 loop : -0.25 (0.26), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 83 TYR 0.039 0.002 TYR D 80 PHE 0.013 0.001 PHE E 67 TRP 0.010 0.001 TRP L 602 HIS 0.016 0.001 HIS D 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.12 (17506) covalent geometry : angle 0.56496 / 0.32 (24923) SS BOND : bond 0.00298 / 0.17 ( 6) SS BOND : angle 0.58101 / 0.32 ( 12) hydrogen bonds : bond 0.04168 / 2.84 ( 910) hydrogen bonds : angle 3.23205 / 2.29 ( 2324) link_NAG-ASN : bond 0.00628 / 0.42 ( 2) link_NAG-ASN : angle 3.78377 / 1.95 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 145 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.7848 (pt0) cc_final: 0.7420 (pm20) REVERT: B 25 ASN cc_start: 0.8503 (t0) cc_final: 0.8078 (t0) REVERT: D 56 MET cc_start: 0.8490 (tpp) cc_final: 0.8212 (tpp) REVERT: E 71 VAL cc_start: 0.8479 (OUTLIER) cc_final: 0.8192 (t) REVERT: E 73 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.8233 (tt0) REVERT: E 77 ASP cc_start: 0.8317 (t0) cc_final: 0.7800 (t0) REVERT: F 77 LYS cc_start: 0.9060 (mttm) cc_final: 0.8823 (tppp) REVERT: L 202 GLU cc_start: 0.7721 (tp30) cc_final: 0.7476 (tp30) REVERT: L 345 SER cc_start: 0.8674 (m) cc_final: 0.8272 (t) REVERT: L 422 GLU cc_start: 0.8098 (tm-30) cc_final: 0.7821 (tm-30) REVERT: L 437 TRP cc_start: 0.7842 (OUTLIER) cc_final: 0.7443 (m-10) REVERT: L 631 MET cc_start: 0.8294 (mmp) cc_final: 0.7894 (mmt) REVERT: L 726 ASP cc_start: 0.8066 (p0) cc_final: 0.7787 (p0) outliers start: 31 outliers final: 26 residues processed: 170 average time/residue: 0.1356 time to fit residues: 34.9291 Evaluate side-chains 172 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 143 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain L residue 175 THR Chi-restraints excluded: chain L residue 191 SER Chi-restraints excluded: chain L residue 235 VAL Chi-restraints excluded: chain L residue 257 GLN Chi-restraints excluded: chain L residue 281 CYS Chi-restraints excluded: chain L residue 286 VAL Chi-restraints excluded: chain L residue 309 CYS Chi-restraints excluded: chain L residue 326 ILE Chi-restraints excluded: chain L residue 429 GLU Chi-restraints excluded: chain L residue 430 LEU Chi-restraints excluded: chain L residue 437 TRP Chi-restraints excluded: chain L residue 486 VAL Chi-restraints excluded: chain L residue 588 MET Chi-restraints excluded: chain L residue 654 LYS Chi-restraints excluded: chain L residue 717 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 19 optimal weight: 0.6980 chunk 145 optimal weight: 7.9990 chunk 30 optimal weight: 1.9990 chunk 16 optimal weight: 10.0000 chunk 75 optimal weight: 20.0000 chunk 99 optimal weight: 0.0870 chunk 5 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 chunk 137 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 overall best weight: 1.1562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 517 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.177920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.135996 restraints weight = 21567.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.139587 restraints weight = 12008.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.141901 restraints weight = 8620.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.143222 restraints weight = 7213.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.143876 restraints weight = 6577.502| |-----------------------------------------------------------------------------| r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.224 17514 Z= 0.179 Angle : 0.737 59.191 24941 Z= 0.439 Chirality : 0.048 1.450 2803 Planarity : 0.004 0.036 2189 Dihedral : 28.627 169.979 4703 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.73 % Allowed : 28.57 % Favored : 68.69 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 4.41 % 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: 2.04 (0.24), residues: 1315 helix: 2.59 (0.19), residues: 732 sheet: -1.18 (1.59), residues: 12 loop : -0.25 (0.26), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 92 TYR 0.032 0.002 TYR D 80 PHE 0.012 0.001 PHE E 67 TRP 0.009 0.001 TRP L 602 HIS 0.011 0.001 HIS D 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.18 (17506) covalent geometry : angle 0.73469 / 0.44 (24923) SS BOND : bond 0.00282 / 0.16 ( 6) SS BOND : angle 0.58524 / 0.32 ( 12) hydrogen bonds : bond 0.04179 / 2.85 ( 910) hydrogen bonds : angle 3.23316 / 2.29 ( 2324) link_NAG-ASN : bond 0.00622 / 0.42 ( 2) link_NAG-ASN : angle 3.78155 / 1.95 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2309.48 seconds wall clock time: 40 minutes 42.30 seconds (2442.30 seconds total)